Matteo Pellegrini*

Publications:

Pianka ST, Li T, Prins TJ, Eldred BSC, Kevan BM, Liang H, Zapanta Rinonos S, Kornblum HI, Nathanson DA, Pellegrini M, Liau LM, Nghiemphu PL, Cloughesy TF, Lai A. D-2-HG Inhibits IDH1mut Glioma Growth via FTO Inhibition and Resultant m6A Hypermethylation. Cancer Res Commun. 2024 Mar 22; 4(3):876-894. view on PubMed

Veena MS, Gahng JJ, Alani M, Ko AY, Basak SK, Liu IY, Hwang KJ, Chatoff JR, Venkatesan N, Morselli M, Yan W, Ali I, Kaczor-Urbanowicz KE, Gowda BS, Frost P, Pellegrini M, Moatamed NA, Wilczynski SP, Bomont P, Wang MB, Shin DS, Srivatsan ES. Gigaxonin Suppresses Epithelial-to-Mesenchymal Transition of Human Cancer Through Downregulation of Snail. Cancer Res Commun. 2024 03 08; 4(3):706-722. view on PubMed

van Straalen KR, Ma F, Tsou PS, Plazyo O, Gharaee-Kermani M, Calbet M, Xing X, Sarkar MK, Uppala R, Harms PW, Wasikowski R, Nahlawi L, Nakamura M, Eshaq M, Wang C, Dobry C, Kozlow JH, Cherry-Bukowiec J, Brodie WD, Wolk K, Uluçkan Ö, Mattichak MN, Pellegrini M, Modlin RL, Maverakis E, Sabat R, Kahlenberg JM, Billi AC, Tsoi LC, Gudjonsson JE. Single-cell sequencing reveals Hippo signaling as a driver of fibrosis in hidradenitis suppurativa. J Clin Invest. 2024 Feb 01; 134(3). view on PubMed

Fu H, Pickering H, Rubbi L, Ross TM, Reed EF, Pellegrini M. Longitudinal analysis of influenza vaccination implicates regulation of RIG-I signaling by DNA methylation. Sci Rep. 2024 01 17; 14(1):1455. view on PubMed

Farrell C, Hu C, Lapborisuth K, Pu K, Snir S, Pellegrini M. Identifying epigenetic aging moderators using the epigenetic pacemaker. Front Bioinform. 2023; 3:1308680. view on PubMed

Ma F, Tsou PS, Gharaee-Kermani M, Plazyo O, Xing X, Kirma J, Wasikowski R, Hile GA, Harms PW, Jiang Y, Xing E, Nakamura M, Ochocki D, Brodie WD, Pillai S, Maverakis E, Pellegrini M, Modlin RL, Varga J, Tsoi LC, Lafyatis R, Kahlenberg JM, Billi AC, Khanna D, Gudjonsson JE. Systems-based identification of the Hippo pathway for promoting fibrotic mesenchymal differentiation in systemic sclerosis. Nat Commun. 2024 Jan 03; 15(1):210. view on PubMed

Morselli M, Holton TR, Pellegrini M, Yeates TO, Arbing MA. Design and Construction of a Designed Ankyrin Repeat Protein (DARPin) Display Library. Curr Protoc. 2024 Jan; 4(1):e960. view on PubMed

Dufek G, Katriel G, Snir S, Pellegrini M. Exponential dynamics of DNA methylation with age. J Theor Biol. 2024 02 21; 579:111697. view on PubMed

Buono R, Tucci J, Cutri R, Guidi N, Mangul S, Raucci F, Pellegrini M, Mittelman SD, Longo VD. Fasting-Mimicking Diet Inhibits Autophagy and Synergizes with Chemotherapy to Promote T-Cell-Dependent Leukemia-Free Survival. Cancers (Basel). 2023 Dec 16; 15(24). view on PubMed

Yang JO, Zinter MS, Pellegrini M, Wong MY, Gala K, Markovic D, Nadel B, Peng K, Do N, Mangul S, Nadkarni VM, Karlsberg A, Deshpande D, Butte MJ, Asaro L, Agus M, Sapru A, Study Site Investigators for CAF-PINT. Whole blood transcriptomics identifies subclasses of pediatric septic shock. Crit Care. 2023 12 08; 27(1):486. view on PubMed

Morselli M, Bennett R, Shaidani NI, Horb M, Peshkin L, Pellegrini M. Age-associated DNA methylation changes in Xenopus frogs. Epigenetics. 2023 12; 18(1):2201517. view on PubMed

Ratan P, Rubbi L, Thompson M, Naresh K, Waddell J, Jones B, Pellegrini M. Epigenetic aging in cows is accelerated by milk production. Epigenetics. 2023 12; 18(1):2240188. view on PubMed

Lee D, Dunn ZS, Guo W, Rosenthal CJ, Penn NE, Yu Y, Zhou K, Li Z, Ma F, Li M, Song TC, Cen X, Li YR, Zhou JJ, Pellegrini M, Wang P, Yang L. Unlocking the potential of allogeneic Vδ2 T cells for ovarian cancer therapy through CD16 biomarker selection and CAR/IL-15 engineering. Nat Commun. 2023 11 08; 14(1):6942. view on PubMed

Palermo A, Li S, Ten Hoeve J, Chellappa A, Morris A, Dillon B, Ma F, Wang Y, Cao E, Shabane B, Acín-Perez R, Petcherski A, Lusis AJ, Hazen S, Shirihai OS, Pellegrini M, Arumugaswami V, Graeber TG, Deb A. A ketogenic diet can mitigate SARS-CoV-2 induced systemic reprogramming and inflammation. Commun Biol. 2023 11 03; 6(1):1115. view on PubMed

Cheng J, Swarup N, Li F, Kordi M, Lin CC, Yang SC, Huang WL, Aziz M, Kim Y, Chia D, Yeh YM, Wei F, Zheng D, Zhang L, Pellegrini M, Su WC, Wong DTW. Distinct Features of Plasma Ultrashort Single-Stranded Cell-Free DNA as Biomarkers for Lung Cancer Detection. Clin Chem. 2023 11 02; 69(11):1270-1282. view on PubMed

Langenbacher AD, Lu F, Tsang L, Huang ZYS, Keer B, Tian Z, Eide A, Pellegrini M, Nakano H, Nakano A, Chen JN. Rtf1-dependent transcriptional pausing regulates cardiogenesis. bioRxiv. 2023 Oct 15. view on PubMed

Presicce P, Cappelletti M, Morselli M, Ma F, Senthamaraikannan P, Protti G, Nadel BB, Aryan L, Eghbali M, Salwinski L, Pithia N, De Franco E, Miller LA, Pellegrini M, Jobe AH, Chougnet CA, Kallapur SG. Amnion responses to intrauterine inflammation and effects of inhibition of TNF signaling in preterm Rhesus macaque. iScience. 2023 Nov 17; 26(11):108118. view on PubMed

Protti G, Rubbi L, Gören T, Sabirli R, Civlan S, Kurt Ö, Türkçüer I, Köseler A, Pellegrini M. The methylome of buccal epithelial cells is influenced by age, sex, and physiological properties. Physiol Genomics. 2023 Dec 01; 55(12):618-633. view on PubMed

Adema V, Ganan-Gomez I, Ma F, Rodriguez-Sevilla JJ, Chien K, Yang H, Thongon N, Kanagal-Shamanna R, Loghavi S, Montalban-Bravo G, Hammond D, Gu Y, Tan R, Tan L, Lorenzi P, Al-Atrash G, Clise-Dwyer K, Bejar R, Pellegrini M, Garcia-Manero G, Colla S. IL-1β-mediated inflammatory signaling drives ineffective erythropoiesis in early-stage myelodysplastic syndromes. bioRxiv. 2023 Sep 30. view on PubMed

Wang Y, Li Q, Tao B, Angelini M, Ramadoss S, Sun B, Wang P, Krokhaleva Y, Ma F, Gu Y, Espinoza A, Yamauchi K, Pellegrini M, Novitch B, Olcese R, Qu Z, Song Z, Deb A. Fibroblasts in heart scar tissue directly regulate cardiac excitability and arrhythmogenesis. Science. 2023 09 29; 381(6665):1480-1487. view on PubMed

Yang JO, Zinter MS, Pellegrini M, Wong MY, Gala K, Markovic D, Nadel B, Peng K, Do N, Mangul S, Nadkarni VM, Karlsberg A, Deshpande D, Butte MJ, Asaro L, Agus M, Sapru A. Whole Blood Transcriptomics Identifies Subclasses of Pediatric Septic Shock. Res Sq. 2023 Aug 28. view on PubMed

Haghani A, Li CZ, Robeck TR, Zhang J, Lu AT, Ablaeva J, Acosta-Rodríguez VA, Adams DM, Alagaili AN, Almunia J, Aloysius A, Amor NMS, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter G, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chavez AS, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke S, Cook JA, Cooper LN, Cossette ML, Day J, DeYoung J, Dirocco S, Dold C, Dunnum JL, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Fei Z, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Goya RG, Grant MJ, Green CB, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaître JF, Levine AJ, Li X, Li C, Lim AR, Lin DTS, Lindemann DM, Liphardt SW, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Murphy WJ, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, Nyamsuren B, O'Brien JK, Ginn PO, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pedersen AB, Pellegrini M, Peters KJ, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Shafer ABA, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmohammadi E, Spangler ML, Spriggs M, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Vu H, Wallingford MC, Wang N, Wilkinson GS, Williams RW, Yan Q, Yao M, Young BG, Zhang B, Zhang Z, Zhao Y, Zhao P, Zhou W, Zoller JA, Ernst J, Seluanov A, Gorbunova V, Yang XW, Raj K, Horvath S. DNA methylation networks underlying mammalian traits. Science. 2023 08 11; 381(6658):eabq5693. view on PubMed

Horvath S, Haghani A, Zoller JA, Lu AT, Ernst J, Pellegrini M, Jasinska AJ, Mattison JA, Salmon AB, Raj K, Horvath M, Paul KC, Ritz BR, Robeck TR, Spriggs M, Ehmke EE, Jenkins S, Li C, Nathanielsz PW. Pan-primate studies of age and sex. Geroscience. 2023 Dec; 45(6):3187-3209. view on PubMed

Emami MR, Espinoza A, Young CS, Ma F, Farahat PK, Felgner PL, Chamberlain JS, Xu X, Pyle AD, Pellegrini M, Villalta SA, Spencer MJ. Innate and adaptive AAV-mediated immune responses in a mouse model of Duchenne muscular dystrophy. Mol Ther Methods Clin Dev. 2023 Sep 14; 30:90-102. view on PubMed

Ma F, Plazyo O, Billi AC, Tsoi LC, Xing X, Wasikowski R, Gharaee-Kermani M, Hile G, Jiang Y, Harms PW, Xing E, Kirma J, Xi J, Hsu JE, Sarkar MK, Chung Y, Di Domizio J, Gilliet M, Ward NL, Maverakis E, Klechevsky E, Voorhees JJ, Elder JT, Lee JH, Kahlenberg JM, Pellegrini M, Modlin RL, Gudjonsson JE. Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis. Nat Commun. 2023 06 12; 14(1):3455. view on PubMed

Chella Krishnan K, El Hachem EJ, Keller MP, Patel SG, Carroll L, Vegas AD, Gerdes Gyuricza I, Light C, Cao Y, Pan C, Kaczor-Urbanowicz KE, Shravah V, Anum D, Pellegrini M, Lee CF, Seldin MM, Rosenthal NA, Churchill GA, Attie AD, Parker B, James DE, Lusis AJ. Genetic architecture of heart mitochondrial proteome influencing cardiac hypertrophy. Elife. 2023 06 05; 12. view on PubMed

Moore TM, Lee S, Olsen T, Morselli M, Strumwasser AR, Lin AJ, Zhou Z, Abrishami A, Garcia SM, Bribiesca J, Cory K, Whitney K, Ho T, Ho T, Lee JL, Rucker DH, Nguyen CQA, Anand ATS, Yackly A, Mendoza LQ, Leyva BK, Aliman C, Artiga DJ, Meng Y, Charugundla S, Pan C, Jedian V, Seldin MM, Ahn IS, Diamante G, Blencowe M, Yang X, Mouisel E, Pellegrini M, Turcotte LP, Birkeland KI, Norheim F, Drevon CA, Lusis AJ, Hevener AL. Conserved multi-tissue transcriptomic adaptations to exercise training in humans and mice. Cell Rep. 2023 05 30; 42(5):112499. view on PubMed

Afshar Y, Ma F, Quach A, Jeong A, Sunshine HL, Freitas V, Jami-Alahmadi Y, Helaers R, Li X, Pellegrini M, Wohlschlegel JA, Romanoski CE, Vikkula M, Iruela-Arispe ML. Transcriptional drifts associated with environmental changes in endothelial cells. Elife. 2023 03 27; 12. view on PubMed

Cheng MI, Li JH, Riggan L, Chen B, Tafti RY, Chin S, Ma F, Pellegrini M, Hrncir H, Arnold AP, O'Sullivan TE, Su MA. The X-linked epigenetic regulator UTX controls NK cell-intrinsic sex differences. Nat Immunol. 2023 05; 24(5):780-791. view on PubMed

Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H. Genetic variants of glucose metabolism and exposure to smoking in African American breast cancer. Endocr Relat Cancer. 2023 04 01; 30(4). view on PubMed

He M, Roussak K, Ma F, Borcherding N, Garin V, White M, Schutt C, Jensen TI, Zhao Y, Iberg CA, Shah K, Bhatia H, Korenfeld D, Dinkel S, Gray J, Ulezko Antonova A, Ferris S, Donermeyer D, Lindestam Arlehamn C, Gubin MM, Luo J, Gorvel L, Pellegrini M, Sette A, Tung T, Bak R, Modlin RL, Fields RC, Schreiber RD, Allen PM, Klechevsky E. CD5 expression by dendritic cells directs T cell immunity and sustains immunotherapy responses. Science. 2023 02 17; 379(6633):eabg2752. view on PubMed

Jung SY, Bhatti P, Pellegrini M. DNA methylation in peripheral blood leukocytes for the association with glucose metabolism and invasive breast cancer. Clin Epigenetics. 2023 02 13; 15(1):23. view on PubMed

Li T, Morselli M, Su T, Million M, Larauche M, Pellegrini M, Taché Y, Yuan PQ. Comparative transcriptomics reveals highly conserved regional programs between porcine and human colonic enteric nervous system. Commun Biol. 2023 01 24; 6(1):98. view on PubMed

Dover M, Moseley T, Biskaduros A, Paulchakrabarti M, Hwang SH, Hammock B, Choudhury B, Kaczor-Urbanowicz KE, Urbanowicz A, Morselli M, Dang J, Pellegrini M, Paul K, Bentolila LA, Fiala M. Polyunsaturated Fatty Acids Mend Macrophage Transcriptome, Glycome, and Phenotype in the Patients with Neurodegenerative Diseases, Including Alzheimer's Disease. J Alzheimers Dis. 2023; 91(1):245-261. view on PubMed

Krämer B, Nalin AP, Ma F, Eickhoff S, Lutz P, Leonardelli S, Goeser F, Finnemann C, Hack G, Raabe J, ToVinh M, Ahmad S, Hoffmeister C, Kaiser KM, Manekeller S, Branchi V, Bald T, Hölzel M, Hüneburg R, Nischalke HD, Semaan A, Langhans B, Kaczmarek DJ, Benner B, Lordo MR, Kowalski J, Gerhardt A, Timm J, Toma M, Mohr R, Türler A, Charpentier A, van Bremen T, Feldmann G, Sattler A, Kotsch K, Abdallah AT, Strassburg CP, Spengler U, Carson WE, Mundy-Bosse BL, Pellegrini M, O'Sullivan TE, Freud AG, Nattermann J. Single-cell RNA sequencing identifies a population of human liver-type ILC1s. Cell Rep. 2023 01 31; 42(1):111937. view on PubMed

Fischer MA, Chapski DJ, Soehalim E, Montoya DJ, Grogan T, Pellegrini M, Cai H, Shemin RJ, Vondriska TM. Longitudinal profiling in patients undergoing cardiac surgery reveals postoperative changes in DNA methylation. Clin Epigenetics. 2022 12 30; 14(1):195. view on PubMed

Sanders AR, Bhongir N, vonHoldt B, Pellegrini M. Association of DNA methylation with energy and fear-related behaviors in canines. Front Psychol. 2022; 13:1025494. view on PubMed

Adema V, Ma F, Kanagal-Shamanna R, Thongon N, Montalban-Bravo G, Yang H, Peslak SA, Wang F, Acha P, Sole F, Lockyer P, Cassari M, Maciejewski JP, Visconte V, Gañán-Gómez I, Song Y, Bueso-Ramos C, Pellegrini M, Tan TM, Bejar R, Carew JS, Halene S, Santini V, Al-Atrash G, Clise-Dwyer K, Garcia-Manero G, Blobel GA, Colla S. Targeting the EIF2AK1 Signaling Pathway Rescues Red Blood Cell Production in SF3B1-Mutant Myelodysplastic Syndromes With Ringed Sideroblasts. Blood Cancer Discov. 2022 11 02; 3(6):554-567. view on PubMed

Poulsen N, Hennig H, Geyer VF, Diez S, Wetherbee R, Fitz-Gibbon S, Pellegrini M, Kröger N. On the role of cell surface associated, mucin-like glycoproteins in the pennate diatom Craspedostauros australis (Bacillariophyceae). J Phycol. 2023 02; 59(1):54-69. view on PubMed

Yao J, Ma F, Zhang L, Zhu C, Jumabay M, Yao Z, Wang L, Cai X, Zhang D, Qiao X, Shivkumar K, Pellegrini M, Yao Y, Wu X, Boström KI. Single-Cell RNA-Seq Identifies Dynamic Cardiac Transition Program from ADCs Induced by Leukemia Inhibitory Factor. Stem Cells. 2022 10 21; 40(10):932-948. view on PubMed

Civlan S, Harvey C, Herek D, Türkçüer I, Sabirli R, Pellegrini M, Koseler A. A Hypertrophic Spinal Pachymeningitis Patient With Factor V Leiden (G1691A), MTHFR C677T, MTHFR A1298C, PAI-1 4G-5G, Glycoprotein IIIa L33P Gene Mutations. Cureus. 2022 Oct; 14(10):e29937. view on PubMed

Rangan P, Lobo F, Parrella E, Rochette N, Morselli M, Stephen TL, Cremonini AL, Tagliafico L, Persia A, Caffa I, Monacelli F, Odetti P, Bonfiglio T, Nencioni A, Pigliautile M, Boccardi V, Mecocci P, Pike CJ, Cohen P, LaDu MJ, Pellegrini M, Xia K, Tran K, Ann B, Chowdhury D, Longo VD. Fasting-mimicking diet cycles reduce neuroinflammation to attenuate cognitive decline in Alzheimer's models. Cell Rep. 2022 09 27; 40(13):111417. view on PubMed

Strenkert D, Yildirim A, Yan J, Yoshinaga Y, Pellegrini M, O'Malley RC, Merchant SS, Umen JG. The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle. Plant J. 2022 10; 112(2):352-368. view on PubMed

Fletcher LR, Scoffoni C, Farrell C, Buckley TN, Pellegrini M, Sack L. Testing the association of relative growth rate and adaptation to climate across natural ecotypes of Arabidopsis. New Phytol. 2022 10; 236(2):413-432. view on PubMed

Do TH, Ma F, Andrade PR, Teles R, de Andrade Silva BJ, Hu C, Espinoza A, Hsu JE, Cho CS, Kim M, Xi J, Xing X, Plazyo O, Tsoi LC, Cheng C, Kim J, Bryson BD, O'Neill AM, Colonna M, Gudjonsson JE, Klechevsky E, Lee JH, Gallo RL, Bloom BR, Pellegrini M, Modlin RL. TREM2 macrophages induced by human lipids drive inflammation in acne lesions. Sci Immunol. 2022 07 22; 7(73):eabo2787. view on PubMed

Di Lena P, Nardini C, Pellegrini M. Editorial: Computational Methods for Analysis of DNA Methylation Data. Front Bioinform. 2022; 2:926066. view on PubMed

Cheng J, Morselli M, Huang WL, Heo YJ, Pinheiro-Ferreira T, Li F, Wei F, Chia D, Kim Y, He HJ, Cole KD, Su WC, Pellegrini M, Wong DTW. Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA. iScience. 2022 Jul 15; 25(7):104554. view on PubMed

Coller HA, Beggs S, Andrews S, Maloy J, Chiu A, Sankararaman S, Pellegrini M, Freimer N, Johnson T, Papp J, Eskin E, Hoffmann A. Bruins-in-Genomics: Evaluation of the impact of a UCLA undergraduate summer program in computational biology on participating students. PLoS One. 2022; 17(5):e0268861. view on PubMed

Tosevska A, Ghosh S, Ganguly A, Cappelletti M, Kallapur SG, Pellegrini M, Devaskar SU. Integrated analysis of an in vivo model of intra-nasal exposure to instilled air pollutants reveals cell-type specific responses in the placenta. Sci Rep. 2022 05 19; 12(1):8438. view on PubMed

Fischer MA, Mahajan A, Cabaj M, Kimball TH, Morselli M, Soehalim E, Chapski DJ, Montoya D, Farrell CP, Scovotti J, Bueno CT, Mimila NA, Shemin RJ, Elashoff D, Pellegrini M, Monte E, Vondriska TM. DNA Methylation-Based Prediction of Post-operative Atrial Fibrillation. Front Cardiovasc Med. 2022; 9:837725. view on PubMed

Tosevska A, Morselli M, Basak SK, Avila L, Mehta P, Wang MB, Srivatsan ES, Pellegrini M. Cell-Free RNA as a Novel Biomarker for Response to Therapy in Head & Neck Cancer. Front Oncol. 2022; 12:869108. view on PubMed

Rubbi L, Zhang H, Feng J, He C, Kurnia P, Ratan P, Tammana A, House S, Thompson M, Farrell C, Snir S, Stahler D, Ostrander EA, vonHoldt BM, Pellegrini M. The effects of age, sex, weight, and breed on canid methylomes. Epigenetics. 2022 11; 17(11):1497-1512. view on PubMed

Ganan-Gomez I, Yang H, Ma F, Montalban-Bravo G, Thongon N, Marchica V, Richard-Carpentier G, Chien K, Manyam G, Wang F, Alfonso A, Chen S, Class C, Kanagal-Shamanna R, Ingram JP, Ogoti Y, Rose A, Loghavi S, Lockyer P, Cambo B, Muftuoglu M, Schneider S, Adema V, McLellan M, Garza J, Marchesini M, Giuliani N, Pellegrini M, Wang J, Walker J, Li Z, Takahashi K, Leverson JD, Bueso-Ramos C, Andreeff M, Clise-Dwyer K, Garcia-Manero G, Colla S. Author Correction: Stem cell architecture drives myelodysplastic syndrome progression and predicts response to venetoclax-based therapy. Nat Med. 2022 May; 28(5):1097. view on PubMed

Billi AC, Ma F, Plazyo O, Gharaee-Kermani M, Wasikowski R, Hile GA, Xing X, Yee CM, Rizvi SM, Maz MP, Berthier CC, Wen F, Tsoi LC, Pellegrini M, Modlin RL, Gudjonsson JE, Kahlenberg JM. Nonlesional lupus skin contributes to inflammatory education of myeloid cells and primes for cutaneous inflammation. Sci Transl Med. 2022 04 27; 14(642):eabn2263. view on PubMed

Salvador J, Hernandez GE, Ma F, Abrahamson CW, Pellegrini M, Goldman R, Ridge KM, Iruela-Arispe ML. Transcriptional Evaluation of the Ductus Arteriosus at the Single-Cell Level Uncovers a Requirement for Vim (Vimentin) for Complete Closure. Arterioscler Thromb Vasc Biol. 2022 06; 42(6):732-742. view on PubMed

Sork VL, Cokus SJ, Fitz-Gibbon ST, Zimin AV, Puiu D, Garcia JA, Gugger PF, Henriquez CL, Zhen Y, Lohmueller KE, Pellegrini M, Salzberg SL. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks. Nat Commun. 2022 04 19; 13(1):2047. view on PubMed

Calvanese V, Capellera-Garcia S, Ma F, Fares I, Liebscher S, Ng ES, Ekstrand S, Aguadé-Gorgorió J, Vavilina A, Lefaudeux D, Nadel B, Li JY, Wang Y, Lee LK, Ardehali R, Iruela-Arispe ML, Pellegrini M, Stanley EG, Elefanty AG, Schenke-Layland K, Mikkola HKA. Mapping human haematopoietic stem cells from haemogenic endothelium to birth. Nature. 2022 04; 604(7906):534-540. view on PubMed

Min J, Ma F, Seyran B, Pellegrini M, Greeff O, Moncada S, Tudzarova S. β-cell-specific deletion of PFKFB3 restores cell fitness competition and physiological replication under diabetogenic stress. Commun Biol. 2022 03 22; 5(1):248. view on PubMed

Morselli M, Farrell C, Montoya D, Gören T, Sabirli R, Türkçüer I, Kurt Ö, Köseler A, Pellegrini M. DNA methylation profiles in pneumonia patients reflect changes in cell types and pneumonia severity. Epigenetics. 2022 12; 17(12):1646-1660. view on PubMed

Tejeda-Muñoz N, Morselli M, Moriyama Y, Sheladiya P, Pellegrini M, De Robertis EM. Canonical Wnt signaling induces focal adhesion and Integrin beta-1 endocytosis. iScience. 2022 Apr 15; 25(4):104123. view on PubMed

Riggan L, Ma F, Li JH, Fernandez E, Nathanson DA, Pellegrini M, O'Sullivan TE. The transcription factor Fli1 restricts the formation of memory precursor NK cells during viral infection. Nat Immunol. 2022 04; 23(4):556-567. view on PubMed

Pinho GM, Martin JGA, Farrell C, Haghani A, Zoller JA, Zhang J, Snir S, Pellegrini M, Wayne RK, Blumstein DT, Horvath S. Hibernation slows epigenetic ageing in yellow-bellied marmots. Nat Ecol Evol. 2022 04; 6(4):418-426. view on PubMed

Ganan-Gomez I, Yang H, Ma F, Montalban-Bravo G, Thongon N, Marchica V, Richard-Carpentier G, Chien K, Manyam G, Wang F, Alfonso A, Chen S, Class C, Kanagal-Shamanna R, Ingram JP, Ogoti Y, Rose A, Loghavi S, Lockyer P, Cambo B, Muftuoglu M, Schneider S, Adema V, McLellan M, Garza J, Marchesini M, Giuliani N, Pellegrini M, Wang J, Walker J, Li Z, Takahashi K, Leverson JD, Bueso-Ramos C, Andreeff M, Clise-Dwyer K, Garcia-Manero G, Colla S. Stem cell architecture drives myelodysplastic syndrome progression and predicts response to venetoclax-based therapy. Nat Med. 2022 03; 28(3):557-567. view on PubMed

Farrell C, Vaquero-Sedas MI, Cubiles MD, Thompson M, Vega-Vaquero A, Pellegrini M, Vega-Palas MA. A complex network of interactions governs DNA methylation at telomeric regions. Nucleic Acids Res. 2022 02 22; 50(3):1449-1464. view on PubMed

Lapborisuth K, Farrell C, Pellegrini M. Pseudotime Analysis Reveals Exponential Trends in DNA Methylation Aging with Mortality Associated Timescales. Cells. 2022 02 22; 11(5). view on PubMed

Kapuria S, Bai H, Fierros J, Huang Y, Ma F, Yoshida T, Aguayo A, Kok F, Wiens KM, Yip JK, McCain ML, Pellegrini M, Nagashima M, Hitchcock PF, Mochizuki N, Lawson ND, Harrison MMR, Lien CL. Heterogeneous pdgfrb+ cells regulate coronary vessel development and revascularization during heart regeneration. Development. 2022 02 15; 149(4). view on PubMed

Arneson A, Haghani A, Thompson MJ, Pellegrini M, Kwon SB, Vu H, Maciejewski E, Yao M, Li CZ, Lu AT, Morselli M, Rubbi L, Barnes B, Hansen KD, Zhou W, Breeze CE, Ernst J, Horvath S. A mammalian methylation array for profiling methylation levels at conserved sequences. Nat Commun. 2022 02 10; 13(1):783. view on PubMed

Minteer C, Morselli M, Meer M, Cao J, Higgins-Chen A, Lang SM, Pellegrini M, Yan Q, Levine ME. Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock. Aging Cell. 2022 02; 21(2):e13553. view on PubMed

Li S, Yokota T, Wang P, Ten Hoeve J, Ma F, Le TM, Abt ER, Zhou Y, Wu R, Nanthavongdouangsy M, Rodriguez A, Wang Y, Lin YJ, Muranaka H, Sharpley M, Braddock DT, MacRae VE, Banerjee U, Chiou PY, Seldin M, Huang D, Teitell M, Gertsman I, Jung M, Bensinger SJ, Damoiseaux R, Faull K, Pellegrini M, Lusis AJ, Graeber TG, Radu CG, Deb A. Cardiomyocytes disrupt pyrimidine biosynthesis in nonmyocytes to regulate heart repair. J Clin Invest. 2022 01 18; 132(2). view on PubMed

Hernandez GE, Ma F, Martinez G, Firozabadi NB, Salvador J, Juang LJ, Leung J, Zhao P, López DA, Ardehali R, Beaudin AE, Kastrup CJ, Pellegrini M, Flick MJ, Iruela-Arispe ML. Aortic intimal resident macrophages are essential for maintenance of the non-thrombogenic intravascular state. Nat Cardiovasc Res. 2022 Jan; 1(1):67-84. view on PubMed

Del Toro N, Shrivastava A, Ragueneau E, Meldal B, Combe C, Barrera E, Perfetto L, How K, Ratan P, Shirodkar G, Lu O, Mészáros B, Watkins X, Pundir S, Licata L, Iannuccelli M, Pellegrini M, Martin MJ, Panni S, Duesbury M, Vallet SD, Rappsilber J, Ricard-Blum S, Cesareni G, Salwinski L, Orchard S, Porras P, Panneerselvam K, Hermjakob H. The IntAct database: efficient access to fine-grained molecular interaction data. Nucleic Acids Res. 2022 01 07; 50(D1):D648-D653. view on PubMed

Larison B, Pinho GM, Haghani A, Zoller JA, Li CZ, Finno CJ, Farrell C, Kaelin CB, Barsh GS, Wooding B, Robeck TR, Maddox D, Pellegrini M, Horvath S. Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids. Commun Biol. 2021 12 17; 4(1):1412. view on PubMed

Thongon N, Ma F, Santoni A, Marchesini M, Fiorini E, Rose A, Adema V, Ganan-Gomez I, Groarke EM, Gutierrez-Rodrigues F, Chen S, Lockyer P, Schneider S, Bueso-Ramos C, Montalban-Bravo G, Class CA, Soltysiak KA, Pellegrini M, Sahin E, Bertuch AA, DiNardo CD, Garcia-Manero G, Young NS, Dwyer K, Colla S. Hematopoiesis under telomere attrition at the single-cell resolution. Nat Commun. 2021 11 25; 12(1):6850. view on PubMed

Neal A, Lai T, Singh T, Rahseparian N, Grogan T, Elashoff D, Scott P, Pellegrini M, Memarzadeh S. Combining ReACp53 with Carboplatin to Target High-Grade Serous Ovarian Cancers. Cancers (Basel). 2021 Nov 24; 13(23). view on PubMed

Li YR, Zhou Y, Kim YJ, Zhu Y, Ma F, Yu J, Wang YC, Chen X, Li Z, Zeng S, Wang X, Lee D, Ku J, Tsao T, Hardoy C, Huang J, Cheng D, Montel-Hagen A, Seet CS, Crooks GM, Larson SM, Sasine JP, Wang X, Pellegrini M, Ribas A, Kohn DB, Witte O, Wang P, Yang L. Development of allogeneic HSC-engineered iNKT cells for off-the-shelf cancer immunotherapy. Cell Rep Med. 2021 11 16; 2(11):100449. view on PubMed

Nadel BB, Oliva M, Shou BL, Mitchell K, Ma F, Montoya DJ, Mouton A, Kim-Hellmuth S, Stranger BE, Pellegrini M, Mangul S. Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples. Brief Bioinform. 2021 11 05; 22(6). view on PubMed

Mishra A, Mirzaei H, Guidi N, Vinciguerra M, Mouton A, Linardic M, Rappa F, Barone R, Navarrete G, Wei M, Brandhorst S, Di Biase S, Morgan TE, Ram Kumar S, Conti PS, Pellegrini M, Bernier M, de Cabo R, Longo VD. Fasting-mimicking diet prevents high-fat diet effect on cardiometabolic risk and lifespan. Nat Metab. 2021 10; 3(10):1342-1356. view on PubMed

Jung SY, Sobel EM, Pellegrini M, Yu H, Papp JC. Synergistic Effects of Genetic Variants of Glucose Homeostasis and Lifelong Exposures to Cigarette Smoking, Female Hormones, and Dietary Fat Intake on Primary Colorectal Cancer Development in African and Hispanic/Latino American Women. Front Oncol. 2021; 11:760243. view on PubMed

Jung SY, Papp JC, Pellegrini M, Yu H, Sobel EM. Molecular Biology Networks and Key Gene Regulators for Inflammatory Biomarkers Shared by Breast Cancer Development: Multi-Omics Systems Analysis. Biomolecules. 2021 09 18; 11(9). view on PubMed

Cappelletti M, Presicce P, Feiyang M, Senthamaraikannan P, Miller LA, Pellegrini M, Sim MS, Jobe AH, Divanovic S, Way SS, Chougnet CA, Kallapur SG. The induction of preterm labor in rhesus macaques is determined by the  strength of immune response to intrauterine infection. PLoS Biol. 2021 09; 19(9):e3001385. view on PubMed

Oulee A, Ma F, Teles RMB, de Andrade Silva BJ, Pellegrini M, Klechevsky E, Harman AN, Rhodes JW, Modlin RL. Identification of Genes Encoding Antimicrobial Proteins in Langerhans Cells. Front Immunol. 2021; 12:695373. view on PubMed

Guo F, Seldin M, Péterfy M, Charugundla S, Zhou Z, Lee SD, Mouton A, Rajbhandari P, Zhang W, Pellegrini M, Tontonoz P, Lusis AJ, Shih DM. NOTUM promotes thermogenic capacity and protects against diet-induced obesity in male mice. Sci Rep. 2021 08 12; 11(1):16409. view on PubMed

Chapski DJ, Cabaj M, Morselli M, Mason RJ, Soehalim E, Ren S, Pellegrini M, Wang Y, Vondriska TM, Rosa-Garrido M. Early adaptive chromatin remodeling events precede pathologic phenotypes and are reinforced in the failing heart. J Mol Cell Cardiol. 2021 11; 160:73-86. view on PubMed

Ma F, Hughes TK, Teles RMB, Andrade PR, de Andrade Silva BJ, Plazyo O, Tsoi LC, Do T, Wadsworth MH, Oulee A, Ochoa MT, Sarno EN, Iruela-Arispe ML, Klechevsky E, Bryson B, Shalek AK, Bloom BR, Gudjonsson JE, Pellegrini M, Modlin RL. The cellular architecture of the antimicrobial response network in human leprosy granulomas. Nat Immunol. 2021 07; 22(7):839-850. view on PubMed

Wang YC, Wang X, Yu J, Ma F, Li Z, Zhou Y, Zeng S, Ma X, Li YR, Neal A, Huang J, To A, Clarke N, Memarzadeh S, Pellegrini M, Yang L. Targeting monoamine oxidase A-regulated tumor-associated macrophage polarization for cancer immunotherapy. Nat Commun. 2021 06 10; 12(1):3530. view on PubMed

Ma F, Salomé PA, Merchant SS, Pellegrini M. Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase. Plant Cell. 2021 05 31; 33(4):1042-1057. view on PubMed

Wang X, Li B, Kim YJ, Wang YC, Li Z, Yu J, Zeng S, Ma X, Choi IY, Di Biase S, Smith DJ, Zhou Y, Li YR, Ma F, Huang J, Clarke N, To A, Gong L, Pham AT, Moon H, Pellegrini M, Yang L. Targeting monoamine oxidase A for T cell-based cancer immunotherapy. Sci Immunol. 2021 05 14; 6(59). view on PubMed

Zhang X, Mandric I, Nguyen KH, Nguyen TTT, Pellegrini M, Grove JCR, Barnes S, Yang XJ. Single Cell Transcriptomic Analyses Reveal the Impact of bHLH Factors on Human Retinal Organoid Development. Front Cell Dev Biol. 2021; 9:653305. view on PubMed

Farrell C, Thompson M, Tosevska A, Oyetunde A, Pellegrini M. BiSulfite Bolt: A bisulfite sequencing analysis platform. Gigascience. 2021 05 08; 10(5). view on PubMed

Hildreth AD, Ma F, Wong YY, Sun R, Pellegrini M, O'Sullivan TE. Single-cell sequencing of human white adipose tissue identifies new cell states in health and obesity. Nat Immunol. 2021 05; 22(5):639-653. view on PubMed

Fajardo VM, Feng I, Chen BY, Perez-Ramirez CA, Shi B, Clark P, Tian R, Lien CL, Pellegrini M, Christofk H, Nakano H, Nakano A. GLUT1 overexpression enhances glucose metabolism and promotes neonatal heart regeneration. Sci Rep. 2021 04 21; 11(1):8669. view on PubMed

Jung SY, Yu H, Pellegrini M, Papp JC, Sobel EM, Zhang ZF. Genetically determined elevated C-reactive protein associated with primary colorectal cancer risk: Mendelian randomization with lifestyle interactions. Am J Cancer Res. 2021; 11(4):1733-1753. view on PubMed

Shao S, Tsoi LC, Swindell WR, Chen J, Uppala R, Billi AC, Xing X, Zeng C, Sarkar MK, Wasikowski R, Jiang Y, Kirma J, Sun J, Plazyo O, Wang G, Harms PW, Voorhees JJ, Ward NL, Ma F, Pellegrini M, Merleev A, Perez White BE, Modlin RL, Andersen B, Maverakis E, Weidinger S, Kahlenberg JM, Gudjonsson JE. IRAK2 Has a Critical Role in Promoting Feed-Forward Amplification of Epidermal Inflammatory Responses. J Invest Dermatol. 2021 10; 141(10):2436-2448. view on PubMed

Langerman J, Lopez D, Pellegrini M, Smale ST. Species-Specific Relationships between DNA and Chromatin Properties of CpG Islands in Embryonic Stem Cells and Differentiated Cells. Stem Cell Reports. 2021 04 13; 16(4):899-912. view on PubMed

Chang YL, Rossetti M, Gjertson DW, Rubbi L, Thompson M, Montoya DJ, Morselli M, Ruffin F, Hoffmann A, Pellegrini M, Fowler VG, Yeaman MR, Reed EF, with the MRSA Systems Immunology Group. Human DNA methylation signatures differentiate persistent from resolving MRSA bacteremia. Proc Natl Acad Sci U S A. 2021 03 09; 118(10). view on PubMed

Nadel BB, Lopez D, Montoya DJ, Ma F, Waddel H, Khan MM, Mangul S, Pellegrini M. The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data. Gigascience. 2021 02 16; 10(2). view on PubMed

Chen M, Lin JY, Wu X, Apuya NR, Henry KF, Le BH, Bui AQ, Pelletier JM, Cokus S, Pellegrini M, Harada JJ, Goldberg RB. Comparative analysis of embryo proper and suspensor transcriptomes in plant embryos with different morphologies. Proc Natl Acad Sci U S A. 2021 02 09; 118(6). view on PubMed

Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H, Zhang ZF. Genetically Predicted C-Reactive Protein Associated With Postmenopausal Breast Cancer Risk: Interrelation With Estrogen and Cancer Molecular Subtypes Using Mendelian Randomization. Front Oncol. 2020; 10:630994. view on PubMed

Teng L, Han W, Fan X, Zhang X, Xu D, Wang Y, Rahman S, Pellegrini M, Mock T, Ye N. Integrative analysis of chloroplast DNA methylation in a marine alga-Saccharina japonica. Plant Mol Biol. 2021 Apr; 105(6):611-623. view on PubMed

Li S, Ma F, Yokota T, Garcia G, Palermo A, Wang Y, Farrell C, Wang YC, Wu R, Zhou Z, Pan C, Morselli M, Teitell MA, Ryazantsev S, Fishbein GA, Hoeve JT, Arboleda VA, Bloom J, Dillon B, Pellegrini M, Lusis AJ, Graeber TG, Arumugaswami V, Deb A. Metabolic reprogramming and epigenetic changes of vital organs in SARS-CoV-2-induced systemic toxicity. JCI Insight. 2021 01 25; 6(2). view on PubMed

Agak GW, Mouton A, Teles RM, Weston T, Morselli M, Andrade PR, Pellegrini M, Modlin RL. Extracellular traps released by antimicrobial TH17 cells contribute to host defense. J Clin Invest. 2021 01 19; 131(2). view on PubMed

Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H, Zhang ZF. Pro-inflammatory cytokine polymorphisms and interactions with dietary alcohol and estrogen, risk factors for invasive breast cancer using a post genome-wide analysis for gene-gene and gene-lifestyle interaction. Sci Rep. 2021 01 13; 11(1):1058. view on PubMed

Zhang W, Miikeda A, Zuckerman J, Jia X, Charugundla S, Zhou Z, Kaczor-Urbanowicz KE, Magyar C, Guo F, Wang Z, Pellegrini M, Hazen SL, Nicholas SB, Lusis AJ, Shih DM. Inhibition of microbiota-dependent TMAO production attenuates chronic kidney disease in mice. Sci Rep. 2021 01 12; 11(1):518. view on PubMed

Wu R, Ma F, Tosevska A, Farrell C, Pellegrini M, Deb A. Cardiac fibroblast proliferation rates and collagen expression mature early and are unaltered with advancing age. JCI Insight. 2020 12 17; 5(24). view on PubMed

Porras P, Barrera E, Bridge A, Del-Toro N, Cesareni G, Duesbury M, Hermjakob H, Iannuccelli M, Jurisica I, Kotlyar M, Licata L, Lovering RC, Lynn DJ, Meldal B, Nanduri B, Paneerselvam K, Panni S, Pastrello C, Pellegrini M, Perfetto L, Rahimzadeh N, Ratan P, Ricard-Blum S, Salwinski L, Shirodkar G, Shrivastava A, Orchard S. Towards a unified open access dataset of molecular interactions. Nat Commun. 2020 12 01; 11(1):6144. view on PubMed

Leung KL, Sanchita S, Pham CT, Davis BA, Okhovat M, Ding X, Dumesic P, Grogan TR, Williams KJ, Morselli M, Ma F, Carbone L, Li X, Pellegrini M, Dumesic DA, Chazenbalk GD. Dynamic changes in chromatin accessibility, altered adipogenic gene expression, and total versus de novo fatty acid synthesis in subcutaneous adipose stem cells of normal-weight polycystic ovary syndrome (PCOS) women during adipogenesis: evidence of cellular programming. Clin Epigenetics. 2020 11 23; 12(1):181. view on PubMed

Hilfenhaus G, Mompeón A, Freshman J, Prajapati DP, Hernandez G, Freitas VM, Ma F, Langenbacher AD, Mirkov S, Song D, Cho BK, Goo YA, Pellegrini M, Chen JN, Damoiseaux R, Iruela-Arispe ML. A High-Content Screen Identifies Drugs That Restrict Tumor Cell Extravasation across the Endothelial Barrier. Cancer Res. 2021 02 01; 81(3):619-633. view on PubMed

Levine M, McDevitt RA, Meer M, Perdue K, Di Francesco A, Meade T, Farrell C, Thrush K, Wang M, Dunn C, Pellegrini M, de Cabo R, Ferrucci L. A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin. Elife. 2020 11 12; 9. view on PubMed

Han J, Tam K, Ma F, Tam C, Aleshe B, Wang X, Quintos JP, Morselli M, Pellegrini M, Hollis RP, Kohn DB. β-Globin Lentiviral Vectors Have Reduced Titers due to Incomplete Vector RNA Genomes and Lowered Virion Production. Stem Cell Reports. 2021 01 12; 16(1):198-211. view on PubMed

Link JC, Wiese CB, Chen X, Avetisyan R, Ronquillo E, Ma F, Guo X, Yao J, Allison M, Chen YI, Rotter JI, El-Sayed Moustafa JS, Small KS, Iwase S, Pellegrini M, Vergnes L, Arnold AP, Reue K. X chromosome dosage of histone demethylase KDM5C determines sex differences in adiposity. J Clin Invest. 2020 11 02; 130(11):5688-5702. view on PubMed

Farrell C, Snir S, Pellegrini M. The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework. Bioinformatics. 2020 11 01; 36(17):4662-4663. view on PubMed

Del Vecchio G, Li Q, Li W, Thamotharan S, Tosevska A, Morselli M, Sung K, Janzen C, Zhou X, Pellegrini M, Devaskar SU. Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes. Epigenetics. 2021 06; 16(6):642-661. view on PubMed

Veena MS, Raychaudhuri S, Basak SK, Venkatesan N, Kumar P, Biswas R, Chakrabarti R, Lu J, Su T, Gallagher-Jones M, Morselli M, Fu H, Pellegrini M, Goldstein T, Aladjem MI, Rettig MB, Wilczynski SP, Shin DS, Srivatsan ES. Dysregulation of hsa-miR-34a and hsa-miR-449a leads to overexpression of PACS-1 and loss of DNA damage response (DDR) in cervical cancer. J Biol Chem. 2020 12 11; 295(50):17169-17186. view on PubMed

Covino DA, Kaczor-Urbanowicz KE, Lu J, Chiantore MV, Fiorucci G, Vescio MF, Catapano L, Purificato C, Galluzzo CM, Amici R, Andreotti M, Gauzzi MC, Pellegrini M, Fantuzzi L. Transcriptome Profiling of Human Monocyte-Derived Macrophages Upon CCL2 Neutralization Reveals an Association Between Activation of Innate Immune Pathways and Restriction of HIV-1 Gene Expression. Front Immunol. 2020; 11:2129. view on PubMed

Jung SY, Scott PA, Papp JC, Sobel EM, Pellegrini M, Yu H, Han S, Zhang ZF. Genome-wide Association Analysis of Proinflammatory Cytokines and Gene-lifestyle Interaction for Invasive Breast Cancer Risk: The WHI dbGaP Study. Cancer Prev Res (Phila). 2021 01; 14(1):41-54. view on PubMed

Sharma NK, Comeau ME, Montoya D, Pellegrini M, Howard TD, Langefeld CD, Das SK. Integrative Analysis of Glucometabolic Traits, Adipose Tissue DNA Methylation, and Gene Expression Identifies Epigenetic Regulatory Mechanisms of Insulin Resistance and Obesity in African Americans. Diabetes. 2020 12; 69(12):2779-2793. view on PubMed

Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H, Zhang ZF. Pro-inflammatory cytokine polymorphisms in ONECUT2 and HNF4A and primary colorectal carcinoma: a post genome-wide gene-lifestyle interaction study. Am J Cancer Res. 2020; 10(9):2955-2976. view on PubMed

Morselli M, Farrell C, Rubbi L, Fehling HL, Henkhaus R, Pellegrini M. Targeted bisulfite sequencing for biomarker discovery. Methods. 2021 03; 187:13-27. view on PubMed

Nowicki TS, Farrell C, Morselli M, Rubbi L, Campbell KM, Macabali MH, Berent-Maoz B, Comin-Anduix B, Pellegrini M, Ribas A. Epigenetic Suppression of Transgenic T-cell Receptor Expression via Gamma-Retroviral Vector Methylation in Adoptive Cell Transfer Therapy. Cancer Discov. 2020 11; 10(11):1645-1653. view on PubMed

Yokota T, McCourt J, Ma F, Ren S, Li S, Kim TH, Kurmangaliyev YZ, Nasiri R, Ahadian S, Nguyen T, Tan XHM, Zhou Y, Wu R, Rodriguez A, Cohn W, Wang Y, Whitelegge J, Ryazantsev S, Khademhosseini A, Teitell MA, Chiou PY, Birk DE, Rowat AC, Crosbie RH, Pellegrini M, Seldin M, Lusis AJ, Deb A. Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury. Cell. 2020 08 06; 182(3):545-562.e23. view on PubMed

Lau YCC, Ding JA, Simental A, Mirzoyan H, Lee W, Diamante G, Cely I, Tran M, Morselli M, Dang J, Kaczor-Urbanowicz KE, Sayre J, Stiles L, Yang X, Pellegrini M, Fiala M. Omega-3 fatty acids increase OXPHOS energy for immune therapy of Alzheimer disease patients. FASEB J. 2020 08; 34(8):9982-9994. view on PubMed

Santos PW, Machado ART, De Grandis R, Ribeiro DL, Tuttis K, Morselli M, Aissa AF, Pellegrini M, Antunes LMG. Effects of sulforaphane on the oxidative response, apoptosis, and the transcriptional profile of human stomach mucosa cells in vitro. Mutat Res Genet Toxicol Environ Mutagen. 2020 Jun - Jul; 854-855:503201. view on PubMed

Dillard C, Kiyohara M, Mah V, McDermott SP, Bazzoun D, Tsui J, Chan AM, Haddad G, Pellegrini M, Chang YL, Elshimali Y, Wu Y, Vadgama JV, Kim SR, Goodglick L, Law SM, Patel DD, Dhawan P, O'Brien NA, Gordon LK, Braun J, Lazar G, Wicha MS, Wadehra M. EMP2 Is a Novel Regulator of Stemness in Breast Cancer Cells. Mol Cancer Ther. 2020 08; 19(8):1682-1695. view on PubMed

Frausto RF, Swamy VS, Peh GSL, Boere PM, Hanser EM, Chung DD, George BL, Morselli M, Kao L, Azimov R, Wu J, Pellegrini M, Kurtz I, Mehta JS, Aldave AJ. Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion. Sci Rep. 2020 05 04; 10(1):7402. view on PubMed

Bhat K, Saki M, Vlashi E, Cheng F, Duhachek-Muggy S, Alli C, Yu G, Medina P, He L, Damoiseaux R, Pellegrini M, Zemke NR, Nghiemphu PL, Cloughesy TF, Liau LM, Kornblum HI, Pajonk F. The dopamine receptor antagonist trifluoperazine prevents phenotype conversion and improves survival in mouse models of glioblastoma. Proc Natl Acad Sci U S A. 2020 05 19; 117(20):11085-11096. view on PubMed

So AR, Si JM, Lopez D, Pellegrini M. Molecular signatures for inflammation vary across cancer types and correlate significantly with tumor stage, sex and vital status of patients. PLoS One. 2020; 15(4):e0221545. view on PubMed

Wang Y, Rhee KD, Pellegrini M, Yang XJ. Impacts of ciliary neurotrophic factor on the retinal transcriptome in a mouse model of photoreceptor degeneration. Sci Rep. 2020 04 20; 10(1):6593. view on PubMed

Morgan RA, Ma F, Unti MJ, Brown D, Ayoub PG, Tam C, Lathrop L, Aleshe B, Kurita R, Nakamura Y, Senadheera S, Wong RL, Hollis RP, Pellegrini M, Kohn DB. Creating New β-Globin-Expressing Lentiviral Vectors by High-Resolution Mapping of Locus Control Region Enhancer Sequences. Mol Ther Methods Clin Dev. 2020 Jun 12; 17:999-1013. view on PubMed

Kelly-Scumpia KM, Choi A, Shirazi R, Bersabe H, Park E, Scumpia PO, Ochoa MT, Yu J, Ma F, Pellegrini M, Modlin RL. ER Stress Regulates Immunosuppressive Function of Myeloid Derived Suppressor Cells in Leprosy that Can Be Overcome in the Presence of IFN-γ. iScience. 2020 May 22; 23(5):101050. view on PubMed

Presicce P, Cappelletti M, Senthamaraikannan P, Ma F, Morselli M, Jackson CM, Mukherjee S, Miller LA, Pellegrini M, Jobe AH, Chougnet CA, Kallapur SG. TNF-Signaling Modulates Neutrophil-Mediated Immunity at the Feto-Maternal Interface During LPS-Induced Intrauterine Inflammation. Front Immunol. 2020; 11:558. view on PubMed

Neal AS, Nunez M, Lai T, Tosevska A, Morselli M, Amneus M, Zakhour M, Moatamed NA, Pellegrini M, Memarzadeh S. Expression of Stromal Progesterone Receptor and Differential Methylation Patterns in the Endometrium May Correlate with Response to Progesterone Therapy in Endometrial Complex Atypical Hyperplasia. Reprod Sci. 2020 09; 27(9):1778-1790. view on PubMed

Wang H, Jiang H, Teles RMB, Chen Y, Wu A, Lu J, Chen Z, Ma F, Pellegrini M, Modlin RL. Cellular, Molecular, and Immunological Characteristics of Langhans Multinucleated Giant Cells Programmed by IL-15. J Invest Dermatol. 2020 09; 140(9):1824-1836.e7. view on PubMed

Basak SK, Bera A, Yoon AJ, Morselli M, Jeong C, Tosevska A, Dong TS, Eklund M, Russ E, Nasser H, Lagishetty V, Guo R, Sajed D, Mudgal S, Mehta P, Avila L, Srivastava M, Faull K, Jacobs J, Pellegrini M, Shin DS, Srivatsan ES, Wang MB. A randomized, phase 1, placebo-controlled trial of APG-157 in oral cancer demonstrates systemic absorption and an inhibitory effect on cytokines and tumor-associated microbes. Cancer. 2020 04 15; 126(8):1668-1682. view on PubMed

Ma F, Pellegrini M. ACTINN: automated identification of cell types in single cell RNA sequencing. Bioinformatics. 2020 01 15; 36(2):533-538. view on PubMed

Koseler A, Ma F, Kilic ID, Morselli M, Kilic O, Pellegrini M. Genome-wide DNA Methylation Profiling of Blood from Monozygotic Twins Discordant for Myocardial Infarction. In Vivo. 2020 Jan-Feb; 34(1):361-367. view on PubMed

Fiala M, Lau YCC, Aghajani A, Bhargava S, Aminpour E, Kaczor-Urbanowicz KE, Mirzoyan H, Nichols I, Ko MW, Morselli M, Santana J, Dang J, Sayre J, Paul K, Pellegrini M. Omega-3 Fatty Acids Increase Amyloid-β Immunity, Energy, and Circadian Rhythm for Cognitive Protection of Alzheimer's Disease Patients Beyond Cholinesterase Inhibitors. J Alzheimers Dis. 2020; 75(3):993-1002. view on PubMed

Brito JJ, Mosqueiro T, Rotman J, Xue V, Chapski DJ, la Hoz J, Matias P, Martin LS, Zelikovsky A, Pellegrini M, Mangul S. Telescope: an interactive tool for managing large-scale analysis from mobile devices. Gigascience. 2020 01 01; 9(1). view on PubMed

Edillor CR, Parks BW, Mehrabian M, Lusis AJ, Pellegrini M. DNA Methylation Changes More Slowly Than Physiological States in Response to Weight Loss in Genetically Diverse Mouse Strains. Front Endocrinol (Lausanne). 2019; 10:882. view on PubMed

Dos Santos PWDS, Machado ART, De Grandis RA, Ribeiro DL, Tuttis K, Morselli M, Aissa AF, Pellegrini M, Antunes LMG. Transcriptome and DNA methylation changes modulated by sulforaphane induce cell cycle arrest, apoptosis, DNA damage, and suppression of proliferation in human liver cancer cells. Food Chem Toxicol. 2020 Feb; 136:111047. view on PubMed

Nomoto H, Pei L, Montemurro C, Rosenberger M, Furterer A, Coppola G, Nadel B, Pellegrini M, Gurlo T, Butler PC, Tudzarova S. Activation of the HIF1α/PFKFB3 stress response pathway in beta cells in type 1 diabetes. Diabetologia. 2020 01; 63(1):149-161. view on PubMed

Teles RMB, Lu J, Tió-Coma M, Goulart IMB, Banu S, Hagge D, Bobosha K, Ottenhoff THM, Pellegrini M, Geluk A, Modlin RL. Identification of a systemic interferon-γ inducible antimicrobial gene signature in leprosy patients undergoing reversal reaction. PLoS Negl Trop Dis. 2019 10; 13(10):e0007764. view on PubMed

An Q, Hu Y, Li Q, Chen X, Huang J, Pellegrini M, Zhou XJ, Rettig M, Fan G. The size of cell-free mitochondrial DNA in blood is inversely correlated with tumor burden in cancer patients. Precis Clin Med. 2019 Sep; 2(3):131-139. view on PubMed

Fan X, Han W, Teng L, Jiang P, Zhang X, Xu D, Li C, Pellegrini M, Wu C, Wang Y, Kaczurowski MJS, Lin X, Tirichine L, Mock T, Ye N. Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants. New Phytol. 2020 Jan; 225(1):234-249. view on PubMed

Fu K, Bonora G, Pellegrini M. Interactions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissues. Epigenetics. 2020 03; 15(3):272-282. view on PubMed

Bulterys PL, Toesca IJ, Norris MH, Maloy JP, Fitz-Gibbon ST, France B, Toffig B, Morselli M, Somprasong N, Pellegrini M, Schweizer HP, Tuanyok A, Damoiseaux R, French CT, Miller JF. An in situ high-throughput screen identifies inhibitors of intracellular Burkholderia pseudomallei with therapeutic efficacy. Proc Natl Acad Sci U S A. 2019 09 10; 116(37):18597-18606. view on PubMed

Charbonnier LM, Cui Y, Stephen-Victor E, Harb H, Lopez D, Bleesing JJ, Garcia-Lloret MI, Chen K, Ozen A, Carmeliet P, Li MO, Pellegrini M, Chatila TA. Functional reprogramming of regulatory T cells in the absence of Foxp3. Nat Immunol. 2019 09; 20(9):1208-1219. view on PubMed

R Andrade P, Mehta M, Lu J, M B Teles R, Montoya D, O Scumpia P, Nunes Sarno E, Ochoa MT, Ma F, Pellegrini M, Modlin RL. The cell fate regulator NUPR1 is induced by Mycobacterium leprae via type I interferon in human leprosy. PLoS Negl Trop Dis. 2019 07; 13(7):e0007589. view on PubMed

Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi P, Talbot NJ, Veneault-Fourrey C, Xavier BB. The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics. 2019 Jul 23; 20(1):605. view on PubMed

Cantarella S, Carnevali D, Morselli M, Conti A, Pellegrini M, Montanini B, Dieci G. Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts. Int J Mol Sci. 2019 Jul 05; 20(13). view on PubMed

Leung CS, Douglass SM, Morselli M, Obusan MB, Pavlyukov MS, Pellegrini M, Johnson TL. H3K36 Methylation and the Chromodomain Protein Eaf3 Are Required for Proper Cotranscriptional Spliceosome Assembly. Cell Rep. 2019 06 25; 27(13):3760-3769.e4. view on PubMed

Weiss DI, Ma F, Merleev AA, Maverakis E, Gilliet M, Balin SJ, Bryson BD, Ochoa MT, Pellegrini M, Bloom BR, Modlin RL. IL-1β Induces the Rapid Secretion of the Antimicrobial Protein IL-26 from Th17 Cells. J Immunol. 2019 08 15; 203(4):911-921. view on PubMed

Frausto RF, Chung DD, Boere PM, Swamy VS, Duong HNV, Kao L, Azimov R, Zhang W, Carrigan L, Wong D, Morselli M, Zakharevich M, Hanser EM, Kassels AC, Kurtz I, Pellegrini M, Aldave AJ. ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing. PLoS One. 2019; 14(6):e0218279. view on PubMed

Snir S, Farrell C, Pellegrini M. Human epigenetic ageing is logarithmic with time across the entire lifespan. Epigenetics. 2019 09; 14(9):912-926. view on PubMed

Woo JS, Srikanth S, Kim KD, Elsaesser H, Lu J, Pellegrini M, Brooks DG, Sun Z, Gwack Y. Correction: CRACR2A-Mediated TCR Signaling Promotes Local Effector Th1 and Th17 Responses. J Immunol. 2019 Jul 01; 203(1):293. view on PubMed

Bonora G, Rubbi L, Morselli M, Ma F, Chronis C, Plath K, Pellegrini M. DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS). PLoS One. 2019; 14(4):e0214368. view on PubMed

Montoya DJ, Andrade P, Silva BJA, Teles RMB, Ma F, Bryson B, Sadanand S, Noel T, Lu J, Sarno E, Arnvig KB, Young D, Lahiri R, Williams DL, Fortune S, Bloom BR, Pellegrini M, Modlin RL. Dual RNA-Seq of Human Leprosy Lesions Identifies Bacterial Determinants Linked to Host Immune Response. Cell Rep. 2019 03 26; 26(13):3574-3585.e3. view on PubMed

Shigeta A, Huang V, Zuo J, Besada R, Nakashima Y, Lu Y, Ding Y, Pellegrini M, Kulkarni RP, Hsiai T, Deb A, Zhou B, Nakano H, Nakano A. Endocardially Derived Macrophages Are Essential for Valvular Remodeling. Dev Cell. 2019 03 11; 48(5):617-630.e3. view on PubMed

Ma F, Fuqua BK, Hasin Y, Yukhtman C, Vulpe CD, Lusis AJ, Pellegrini M. A comparison between whole transcript and 3' RNA sequencing methods using Kapa and Lexogen library preparation methods. BMC Genomics. 2019 Jan 07; 20(1):9. view on PubMed

Fu K, Chronis C, Soufi A, Bonora G, Edwards M, Smale ST, Zaret KS, Plath K, Pellegrini M. Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPSC reprogramming. BMC Genomics. 2018 Dec 22; 19(1):956. view on PubMed

Montoya D, Mehta M, Ferguson BG, Teles RMB, Krutzik SR, Cruz D, Pellegrini M, Modlin RL. Plasticity of antimicrobial and phagocytic programs in human macrophages. Immunology. 2019 02; 156(2):164-173. view on PubMed

Avni E, Montoya D, Lopez D, Modlin R, Pellegrini M, Snir S. A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes-The Mycobacterium leprae case. PLoS One. 2018; 13(11):e0204322. view on PubMed

Thompson MJ, Chwialkowska K, Rubbi L, Lusis AJ, Davis RC, Srivastava A, Korstanje R, Churchill GA, Horvath S, Pellegrini M. A multi-tissue full lifespan epigenetic clock for mice. Aging (Albany NY). 2018 10 21; 10(10):2832-2854. view on PubMed

Fu K, Nakano H, Morselli M, Chen T, Pappoe H, Nakano A, Pellegrini M. A temporal transcriptome and methylome in human embryonic stem cell-derived cardiomyocytes identifies novel regulators of early cardiac development. Epigenetics. 2018; 13(10-11):1013-1026. view on PubMed

Pontrelli S, Fricke RCB, Teoh ST, Laviña WA, Putri SP, Fitz-Gibbon S, Chung M, Pellegrini M, Fukusaki E, Liao JC. Metabolic repair through emergence of new pathways in Escherichia coli. Nat Chem Biol. 2018 11; 14(11):1005-1009. view on PubMed

Merkurjev D, Hong WT, Iida K, Oomoto I, Goldie BJ, Yamaguti H, Ohara T, Kawaguchi SY, Hirano T, Martin KC, Pellegrini M, Wang DO. Author Correction: Synaptic N6-methyladenosine (m6A) epitranscriptome reveals functional partitioning of localized transcripts. Nat Neurosci. 2018 Oct; 21(10):1493. view on PubMed

Borgognone A, Castanera R, Morselli M, López-Varas L, Rubbi L, Pisabarro AG, Pellegrini M, Ramírez L. Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle. DNA Res. 2018 Oct 01; 25(5):451-464. view on PubMed

Balin SJ, Pellegrini M, Klechevsky E, Won ST, Weiss DI, Choi AW, Hakimian J, Lu J, Ochoa MT, Bloom BR, Lanier LL, Stenger S, Modlin RL. Human antimicrobial cytotoxic T lymphocytes, defined by NK receptors and antimicrobial proteins, kill intracellular bacteria. Sci Immunol. 2018 08 31; 3(26). view on PubMed

Chen M, Lin JY, Hur J, Pelletier JM, Baden R, Pellegrini M, Harada JJ, Goldberg RB. Seed genome hypomethylated regions are enriched in transcription factor genes. Proc Natl Acad Sci U S A. 2018 08 28; 115(35):E8315-E8322. view on PubMed

Pontrelli S, Fricke RCB, Sakurai SSM, Putri SP, Fitz-Gibbon S, Chung M, Wu HY, Chen YJ, Pellegrini M, Fukusaki E, Liao JC. Directed strain evolution restructures metabolism for 1-butanol production in minimal media. Metab Eng. 2018 09; 49:153-163. view on PubMed

Khalid AB, Slayden AV, Kumpati J, Perry CD, Berryhill SB, Crawford JA, Fatima I, Morselli M, Pellegrini M, Miranda-Carboni GA, Krum SA. GATA4 represses RANKL in osteoblasts via multiple long-range enhancers to regulate osteoclast differentiation. Bone. 2018 11; 116:78-86. view on PubMed

Orozco LD, Farrell C, Hale C, Rubbi L, Rinaldi A, Civelek M, Pan C, Lam L, Montoya D, Edillor C, Seldin M, Boehnke M, Mohlke KL, Jacobsen S, Kuusisto J, Laakso M, Lusis AJ, Pellegrini M. Epigenome-wide association in adipose tissue from the METSIM cohort. Hum Mol Genet. 2018 07 15; 27(14):2586. view on PubMed

Woo JS, Srikanth S, Kim KD, Elsaesser H, Lu J, Pellegrini M, Brooks DG, Sun Z, Gwack Y. CRACR2A-Mediated TCR Signaling Promotes Local Effector Th1 and Th17 Responses. J Immunol. 2018 08 15; 201(4):1174-1185. view on PubMed

Merkurjev D, Hong WT, Iida K, Oomoto I, Goldie BJ, Yamaguti H, Ohara T, Kawaguchi SY, Hirano T, Martin KC, Pellegrini M, Wang DO. Synaptic N6-methyladenosine (m6A) epitranscriptome reveals functional partitioning of localized transcripts. Nat Neurosci. 2018 07; 21(7):1004-1014. view on PubMed

Snir S, Pellegrini M. An epigenetic pacemaker is detected via a fast conditional expectation maximization algorithm. Epigenomics. 2018 06; 10(6):695-706. view on PubMed

Hilfenhaus G, Nguyen DP, Freshman J, Prajapati D, Ma F, Song D, Ziyad S, Cuadrado M, Pellegrini M, Bustelo XR, Iruela-Arispe ML. Vav3-induced cytoskeletal dynamics contribute to heterotypic properties of endothelial barriers. J Cell Biol. 2018 08 06; 217(8):2813-2830. view on PubMed

Camacho J, Truong L, Kurt Z, Chen YW, Morselli M, Gutierrez G, Pellegrini M, Yang X, Allard P. The Memory of Environmental Chemical Exposure in C. elegans Is Dependent on the Jumonji Demethylases jmjd-2 and jmjd-3/utx-1. Cell Rep. 2018 05 22; 23(8):2392-2404. view on PubMed

Orozco LD, Farrell C, Hale C, Rubbi L, Rinaldi A, Civelek M, Pan C, Lam L, Montoya D, Edillor C, Seldin M, Boehnke M, Mohlke KL, Jacobsen S, Kuusisto J, Laakso M, Lusis AJ, Pellegrini M. Epigenome-wide association in adipose tissue from the METSIM cohort. Hum Mol Genet. 2018 05 15; 27(10):1830-1846. view on PubMed

Ohashi M, Korsakova E, Allen D, Lee P, Fu K, Vargas BS, Cinkornpumin J, Salas C, Park JC, Germanguz I, Langerman J, Chronis C, Kuoy E, Tran S, Xiao X, Pellegrini M, Plath K, Lowry WE. Loss of MECP2 Leads to Activation of P53 and Neuronal Senescence. Stem Cell Reports. 2018 05 08; 10(5):1453-1463. view on PubMed

Yu J, Seldin MM, Fu K, Li S, Lam L, Wang P, Wang Y, Huang D, Nguyen TL, Wei B, Kulkarni RP, Di Carlo D, Teitell M, Pellegrini M, Lusis AJ, Deb A. Topological Arrangement of Cardiac Fibroblasts Regulates Cellular Plasticity. Circ Res. 2018 06 22; 123(1):73-85. view on PubMed

Keegan C, Krutzik S, Schenk M, Scumpia PO, Lu J, Pang YLJ, Russell BS, Lim KS, Shell S, Prestwich E, Su D, Elashoff D, Hershberg RM, Bloom BR, Belisle JT, Fortune S, Dedon PC, Pellegrini M, Modlin RL. Mycobacterium tuberculosis Transfer RNA Induces IL-12p70 via Synergistic Activation of Pattern Recognition Receptors within a Cell Network. J Immunol. 2018 05 01; 200(9):3244-3258. view on PubMed

Grasso CS, Giannakis M, Wells DK, Hamada T, Mu XJ, Quist M, Nowak JA, Nishihara R, Qian ZR, Inamura K, Morikawa T, Nosho K, Abril-Rodriguez G, Connolly C, Escuin-Ordinas H, Geybels MS, Grady WM, Hsu L, Hu-Lieskovan S, Huyghe JR, Kim YJ, Krystofinski P, Leiserson MDM, Montoya DJ, Nadel BB, Pellegrini M, Pritchard CC, Puig-Saus C, Quist EH, Raphael BJ, Salipante SJ, Shin DS, Shinbrot E, Shirts B, Shukla S, Stanford JL, Sun W, Tsoi J, Upfill-Brown A, Wheeler DA, Wu CJ, Yu M, Zaidi SH, Zaretsky JM, Gabriel SB, Lander ES, Garraway LA, Hudson TJ, Fuchs CS, Ribas A, Ogino S, Peters U. Genetic Mechanisms of Immune Evasion in Colorectal Cancer. Cancer Discov. 2018 06; 8(6):730-749. view on PubMed

Cheng L, Marinelli LJ, Grosset N, Fitz-Gibbon ST, Bowman CA, Dang BQ, Russell DA, Jacobs-Sera D, Shi B, Pellegrini M, Miller JF, Gautier M, Hatfull GF, Modlin RL. Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages. BMC Microbiol. 2018 03 01; 18(1):19. view on PubMed

Guo W, Zhu P, Pellegrini M, Zhang MQ, Wang X, Ni Z. CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. Bioinformatics. 2018 02 01; 34(3):381-387. view on PubMed

Gallaher SD, Fitz-Gibbon ST, Strenkert D, Purvine SO, Pellegrini M, Merchant SS. High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates. Plant J. 2018 02; 93(3):545-565. view on PubMed

Fiala M, Restrepo L, Pellegrini M. Immunotherapy of Mild Cognitive Impairment by ω-3 Supplementation: Why Are Amyloid-β Antibodies and ω-3 Not Working in Clinical Trials? J Alzheimers Dis. 2018; 62(3):1013-1022. view on PubMed

Nakano H, Minami I, Braas D, Pappoe H, Wu X, Sagadevan A, Vergnes L, Fu K, Morselli M, Dunham C, Ding X, Stieg AZ, Gimzewski JK, Pellegrini M, Clark PM, Reue K, Lusis AJ, Ribalet B, Kurdistani SK, Christofk H, Nakatsuji N, Nakano A. Glucose inhibits cardiac muscle maturation through nucleotide biosynthesis. Elife. 2017 12 12; 6. view on PubMed

Lopez D, Montoya D, Ambrose M, Lam L, Briscoe L, Adams C, Modlin RL, Pellegrini M. SaVanT: a web-based tool for the sample-level visualization of molecular signatures in gene expression profiles. BMC Genomics. 2017 Oct 25; 18(1):824. view on PubMed

Lin JY, Le BH, Chen M, Henry KF, Hur J, Hsieh TF, Chen PY, Pelletier JM, Pellegrini M, Fischer RL, Harada JJ, Goldberg RB. Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development. Proc Natl Acad Sci U S A. 2017 11 07; 114(45):E9730-E9739. view on PubMed

Gang SS, Castelletto ML, Bryant AS, Yang E, Mancuso N, Lopez JB, Pellegrini M, Hallem EA. Targeted mutagenesis in a human-parasitic nematode. PLoS Pathog. 2017 Oct; 13(10):e1006675. view on PubMed

Morselli M, Pastor WA, Montanini B, Nee K, Ferrari R, Fu K, Bonora G, Rubbi L, Clark AT, Ottonello S, Jacobsen SE, Pellegrini M. Correction: In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse. Elife. 2017 08 31; 6. view on PubMed

Rosa-Garrido M, Chapski DJ, Schmitt AD, Kimball TH, Karbassi E, Monte E, Balderas E, Pellegrini M, Shih TT, Soehalim E, Liem D, Ping P, Galjart NJ, Ren S, Wang Y, Ren B, Vondriska TM. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure. Circulation. 2017 Oct 24; 136(17):1613-1625. view on PubMed

Mangul S, Martin LS, Hoffmann A, Pellegrini M, Eskin E. Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX. Trends Biotechnol. 2017 10; 35(10):901-903. view on PubMed

Chen PY, Chu A, Liao WW, Rubbi L, Janzen C, Hsu FM, Thamotharan S, Ganguly A, Lam L, Montoya D, Pellegrini M, Devaskar SU. Prenatal Growth Patterns and Birthweight Are Associated With Differential DNA Methylation and Gene Expression of Cardiometabolic Risk Genes in Human Placentas: A Discovery-Based Approach. Reprod Sci. 2018 04; 25(4):523-539. view on PubMed

Prado K, Zhang KX, Pellegrini M, Chin AI. Sequencing of cancer cell subpopulations identifies micrometastases in a bladder cancer patient. Oncotarget. 2017 Jul 11; 8(28):45619-45625. view on PubMed

Olivera-Perez HM, Lam L, Dang J, Jiang W, Rodriguez F, Rigali E, Weitzman S, Porter V, Rubbi L, Morselli M, Pellegrini M, Fiala M. Omega-3 fatty acids increase the unfolded protein response and improve amyloid-β phagocytosis by macrophages of patients with mild cognitive impairment. FASEB J. 2017 10; 31(10):4359-4369. view on PubMed

Roth MS, Cokus SJ, Gallaher SD, Walter A, Lopez D, Erickson E, Endelman B, Westcott D, Larabell CA, Merchant SS, Pellegrini M, Niyogi KK. Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production. Proc Natl Acad Sci U S A. 2017 05 23; 114(21):E4296-E4305. view on PubMed

Bosio MC, Fermi B, Spagnoli G, Levati E, Rubbi L, Ferrari R, Pellegrini M, Dieci G. Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast. Nucleic Acids Res. 2017 05 05; 45(8):4493-4506. view on PubMed

Fiala M, Kooij G, Wagner K, Hammock B, Pellegrini M. Modulation of innate immunity of patients with Alzheimer's disease by omega-3 fatty acids. FASEB J. 2017 08; 31(8):3229-3239. view on PubMed

Thompson MJ, vonHoldt B, Horvath S, Pellegrini M. An epigenetic aging clock for dogs and wolves. Aging (Albany NY). 2017 03 28; 9(3):1055-1068. view on PubMed

Cooper AR, Lill GR, Shaw K, Carbonaro-Sarracino DA, Davila A, Sokolic R, Candotti F, Pellegrini M, Kohn DB. Cytoreductive conditioning intensity predicts clonal diversity in ADA-SCID retroviral gene therapy patients. Blood. 2017 05 11; 129(19):2624-2635. view on PubMed

Lupu DS, Orozco LD, Wang Y, Cullen JM, Pellegrini M, Zeisel SH. Altered methylation of specific DNA loci in the liver of Bhmt-null mice results in repression of Iqgap2 and F2rl2 and is associated with development of preneoplastic foci. FASEB J. 2017 05; 31(5):2090-2103. view on PubMed

Johnson LM, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK, Zhong X, Marson G, Pellegrini M, Segal DJ, Patel DJ, Jacobsen SE. Corrigendum: SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature. 2017 03 02; 543(7643):136. view on PubMed

King JK, Ung NM, Paing MH, Contreras JR, Alberti MO, Fernando TR, Zhang K, Pellegrini M, Rao DS. Regulation of Marginal Zone B-Cell Differentiation by MicroRNA-146a. Front Immunol. 2016; 7:670. view on PubMed

Holmes B, Jung SH, Lu J, Wagner JA, Rubbi L, Pellegrini M, Jankord R. Transcriptomic Modification in the Cerebral Cortex following Noninvasive Brain Stimulation: RNA-Sequencing Approach. Neural Plast. 2016; 2016:5942980. view on PubMed

Patel S, Bonora G, Sahakyan A, Kim R, Chronis C, Langerman J, Fitz-Gibbon S, Rubbi L, Skelton RJP, Ardehali R, Pellegrini M, Lowry WE, Clark AT, Plath K. Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during Differentiation. Cell Rep. 2017 01 03; 18(1):54-67. view on PubMed

Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O, Morselli M, Jaroszewicz A, Allen EE, Allen AE, Merchant SS, Pellegrini M, Hildebrand M. Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnol Biofuels. 2016; 9:258. view on PubMed

Pillai ICL, Li S, Romay M, Lam L, Lu Y, Huang J, Dillard N, Zemanova M, Rubbi L, Wang Y, Lee J, Xia M, Liang O, Xie YH, Pellegrini M, Lusis AJ, Deb A. Cardiac Fibroblasts Adopt Osteogenic Fates and Can Be Targeted to Attenuate Pathological Heart Calcification. Cell Stem Cell. 2017 02 02; 20(2):218-232.e5. view on PubMed

Snir S, vonHoldt BM, Pellegrini M. A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLoS Comput Biol. 2016 Nov; 12(11):e1005183. view on PubMed

Sork VL, Fitz-Gibbon ST, Puiu D, Crepeau M, Gugger PF, Sherman R, Stevens K, Langley CH, Pellegrini M, Salzberg SL. First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae). G3 (Bethesda). 2016 Nov 08; 6(11):3485-3495. view on PubMed

Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD, Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Mäkinen VP, Yang X. Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. BMC Genomics. 2016 11 04; 17(1):874. view on PubMed

Famenini S, Rigali EA, Olivera-Perez HM, Dang J, Chang MT, Halder R, Rao RV, Pellegrini M, Porter V, Bredesen D, Fiala M. Increased intermediate M1-M2 macrophage polarization and improved cognition in mild cognitive impairment patients on ω-3 supplementation. FASEB J. 2017 01; 31(1):148-160. view on PubMed

King AD, Huang K, Rubbi L, Liu S, Wang CY, Wang Y, Pellegrini M, Fan G. Reversible Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Mouse Embryonic Stem Cells. Cell Rep. 2016 09 27; 17(1):289-302. view on PubMed

Inkeles MS, Teles RM, Pouldar D, Andrade PR, Madigan CA, Lopez D, Ambrose M, Noursadeghi M, Sarno EN, Rea TH, Ochoa MT, Iruela-Arispe ML, Swindell WR, Ottenhoff TH, Geluk A, Bloom BR, Pellegrini M, Modlin RL. Cell-type deconvolution with immune pathways identifies gene networks of host defense and immunopathology in leprosy. JCI Insight. 2016 09 22; 1(15):e88843. view on PubMed

Hasin-Brumshtein Y, Khan AH, Hormozdiari F, Pan C, Parks BW, Petyuk VA, Piehowski PD, Brümmer A, Pellegrini M, Xiao X, Eskin E, Smith RD, Lusis AJ, Smith DJ. Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes. Elife. 2016 09 13; 5. view on PubMed

Chu A, Thamotharan S, Ganguly A, Wadehra M, Pellegrini M, Devaskar SU. Gestational food restriction decreases placental interleukin-10 expression and markers of autophagy and endoplasmic reticulum stress in murine intrauterine growth restriction. Nutr Res. 2016 10; 36(10):1055-1067. view on PubMed

Massoud AH, Charbonnier LM, Lopez D, Pellegrini M, Phipatanakul W, Chatila TA. An asthma-associated IL4R variant exacerbates airway inflammation by promoting conversion of regulatory T cells to TH17-like cells. Nat Med. 2016 09; 22(9):1013-22. view on PubMed

Escuin-Ordinas H, Li S, Xie MW, Sun L, Hugo W, Huang RR, Jiao J, de-Faria FM, Realegeno S, Krystofinski P, Azhdam A, Komenan SM, Atefi M, Comin-Anduix B, Pellegrini M, Cochran AJ, Modlin RL, Herschman HR, Lo RS, McBride WH, Segura T, Ribas A. Cutaneous wound healing through paradoxical MAPK activation by BRAF inhibitors. Nat Commun. 2016 08 01; 7:12348. view on PubMed

Hoban MD, Lumaquin D, Kuo CY, Romero Z, Long J, Ho M, Young CS, Mojadidi M, Fitz-Gibbon S, Cooper AR, Lill GR, Urbinati F, Campo-Fernandez B, Bjurstrom CF, Pellegrini M, Hollis RP, Kohn DB. CRISPR/Cas9-Mediated Correction of the Sickle Mutation in Human CD34+ cells. Mol Ther. 2016 Sep; 24(9):1561-9. view on PubMed

Sack L, Ball MC, Brodersen C, Davis SD, Des Marais DL, Donovan LA, Givnish TJ, Hacke UG, Huxman T, Jansen S, Jacobsen AL, Johnson DM, Koch GW, Maurel C, McCulloh KA, McDowell NG, McElrone A, Meinzer FC, Melcher PJ, North G, Pellegrini M, Pockman WT, Pratt RB, Sala A, Santiago LS, Savage JA, Scoffoni C, Sevanto S, Sperry J, Tyerman SD, Way D, Holbrook NM. Plant hydraulics as a central hub integrating plant and ecosystem function: meeting report for 'Emerging Frontiers in Plant Hydraulics' (Washington, DC, May 2015). Plant Cell Environ. 2016 09; 39(9):2085-94. view on PubMed

Vega-Vaquero A, Bonora G, Morselli M, Vaquero-Sedas MI, Rubbi L, Pellegrini M, Vega-Palas MA. Novel features of telomere biology revealed by the absence of telomeric DNA methylation. Genome Res. 2016 08; 26(8):1047-56. view on PubMed

Brumm AJ, Nunez S, Doroudchi MM, Kawaguchi R, Duan J, Pellegrini M, Lam L, Carmichael ST, Deb A, Hinman JD. Astrocytes Can Adopt Endothelial Cell Fates in a p53-Dependent Manner. Mol Neurobiol. 2017 08; 54(6):4584-4596. view on PubMed

Lam L, Chin L, Halder RC, Sagong B, Famenini S, Sayre J, Montoya D, Rubbi L, Pellegrini M, Fiala M. Epigenetic changes in T-cell and monocyte signatures and production of neurotoxic cytokines in ALS patients. FASEB J. 2016 10; 30(10):3461-3473. view on PubMed

Schokrpur S, Hu J, Moughon DL, Liu P, Lin LC, Hermann K, Mangul S, Guan W, Pellegrini M, Xu H, Wu L. CRISPR-Mediated VHL Knockout Generates an Improved Model for Metastatic Renal Cell Carcinoma. Sci Rep. 2016 Jun 30; 6:29032. view on PubMed

Realegeno S, Kelly-Scumpia KM, Dang AT, Lu J, Teles R, Liu PT, Schenk M, Lee EY, Schmidt NW, Wong GC, Sarno EN, Rea TH, Ochoa MT, Pellegrini M, Modlin RL. S100A12 Is Part of the Antimicrobial Network against Mycobacterium leprae in Human Macrophages. PLoS Pathog. 2016 06; 12(6):e1005705. view on PubMed

Douglass S, Hsu SW, Cokus S, Goldberg RB, Harada JJ, Pellegrini M. A naïve Bayesian classifier for identifying plant microRNAs. Plant J. 2016 06; 86(6):481-92. view on PubMed

Hamaji T, Lopez D, Pellegrini M, Umen J. Identification and Characterization of a cis-Regulatory Element for Zygotic Gene Expression in Chlamydomonas reinhardtii. G3 (Bethesda). 2016 06 01; 6(6):1541-8. view on PubMed

Steiger J, Stephan A, Inkeles MS, Realegeno S, Bruns H, Kröll P, de Castro Kroner J, Sommer A, Batinica M, Pitzler L, Kalscheuer R, Hartmann P, Plum G, Stenger S, Pellegrini M, Brachvogel B, Modlin RL, Fabri M. Imatinib Triggers Phagolysosome Acidification and Antimicrobial Activity against Mycobacterium bovis Bacille Calmette-Guérin in Glucocorticoid-Treated Human Macrophages. J Immunol. 2016 07 01; 197(1):222-32. view on PubMed

Zhang H, Prado K, Zhang KX, Peek EM, Lee J, Wang X, Huang J, Li G, Pellegrini M, Chin AI. Biased Expression of the FOXP3Δ3 Isoform in Aggressive Bladder Cancer Mediates Differentiation and Cisplatin Chemotherapy Resistance. Clin Cancer Res. 2016 Nov 01; 22(21):5349-5361. view on PubMed

Flinders C, Lam L, Rubbi L, Ferrari R, Fitz-Gibbon S, Chen PY, Thompson M, Christofk H, B Agus D, Ruderman D, Mallick P, Pellegrini M. Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma. Genome Med. 2016 05 04; 8(1):54. view on PubMed

Meng Q, Ying Z, Noble E, Zhao Y, Agrawal R, Mikhail A, Zhuang Y, Tyagi E, Zhang Q, Lee JH, Morselli M, Orozco L, Guo W, Kilts TM, Zhu J, Zhang B, Pellegrini M, Xiao X, Young MF, Gomez-Pinilla F, Yang X. Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders. EBioMedicine. 2016 May; 7:157-66. view on PubMed

Chin CJ, Cooper AR, Lill GR, Evseenko D, Zhu Y, He CB, Casero D, Pellegrini M, Kohn DB, Crooks GM. Genetic Tagging During Human Mesoderm Differentiation Reveals Tripotent Lateral Plate Mesodermal Progenitors. Stem Cells. 2016 05; 34(5):1239-50. view on PubMed

Gugger PF, Fitz-Gibbon S, PellEgrini M, Sork VL. Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients. Mol Ecol. 2016 Apr; 25(8):1665-80. view on PubMed

Rocchi A, Milioto C, Parodi S, Armirotti A, Borgia D, Pellegrini M, Urciuolo A, Molon S, Morbidoni V, Marabita M, Romanello V, Gatto P, Blaauw B, Bonaldo P, Sambataro F, Robins DM, Lieberman AP, Sorarù G, Vergani L, Sandri M, Pennuto M. Glycolytic-to-oxidative fiber-type switch and mTOR signaling activation are early-onset features of SBMA muscle modified by high-fat diet. Acta Neuropathol. 2016 07; 132(1):127-44. view on PubMed

Liu W, Jiang X, Pellegrini M, Wang X. Discovering communities in complex networks by edge label propagation. Sci Rep. 2016 Mar 01; 6:22470. view on PubMed

Zhang KX, Tan L, Pellegrini M, Zipursky SL, McEwen JM. Rapid Changes in the Translatome during the Conversion of Growth Cones to Synaptic Terminals. Cell Rep. 2016 Feb 09; 14(5):1258-1271. view on PubMed

Janowitz Koch I, Clark MM, Thompson MJ, Deere-Machemer KA, Wang J, Duarte L, Gnanadesikan GE, McCoy EL, Rubbi L, Stahler DR, Pellegrini M, Ostrander EA, Wayne RK, Sinsheimer JS, vonHoldt BM. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol. 2016 Apr; 25(8):1838-55. view on PubMed

Chen H, Orozco LD, Wang J, Rau CD, Rubbi L, Ren S, Wang Y, Pellegrini M, Lusis AJ, Vondriska TM. DNA Methylation Indicates Susceptibility to Isoproterenol-Induced Cardiac Pathology and Is Associated With Chromatin States. Circ Res. 2016 Mar 04; 118(5):786-97. view on PubMed

Soragni A, Janzen DM, Johnson LM, Lindgren AG, Thai-Quynh Nguyen A, Tiourin E, Soriaga AB, Lu J, Jiang L, Faull KF, Pellegrini M, Memarzadeh S, Eisenberg DS. A Designed Inhibitor of p53 Aggregation Rescues p53 Tumor Suppression in Ovarian Carcinomas. Cancer Cell. 2016 Jan 11; 29(1):90-103. view on PubMed

Lam L, Halder RC, Montoya DJ, Rubbi L, Rinaldi A, Sagong B, Weitzman S, Rubattino R, Singh RR, Pellegrini M, Fiala M. Anti-inflammatory therapies of amyotrophic lateral sclerosis guided by immune pathways. Am J Neurodegener Dis. 2015; 4(2):28-39. view on PubMed

Minkovsky A, Sahakyan A, Bonora G, Damoiseaux R, Dimitrova E, Rubbi L, Pellegrini M, Radu CG, Plath K. A high-throughput screen of inactive X chromosome reactivation identifies the enhancement of DNA demethylation by 5-aza-2'-dC upon inhibition of ribonucleotide reductase. Epigenetics Chromatin. 2015; 8:42. view on PubMed

Lopez D, Hamaji T, Kropat J, De Hoff P, Morselli M, Rubbi L, Fitz-Gibbon S, Gallaher SD, Merchant SS, Umen J, Pellegrini M. Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle. Plant Physiol. 2015 Dec; 169(4):2730-43. view on PubMed

Liu W, Wu A, Pellegrini M, Wang X. Integrative analysis of human protein, function and disease networks. Sci Rep. 2015 Sep 24; 5:14344. view on PubMed

Clark RI, Salazar A, Yamada R, Fitz-Gibbon S, Morselli M, Alcaraz J, Rana A, Rera M, Pellegrini M, Ja WW, Walker DW. Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality. Cell Rep. 2015 Sep 08; 12(10):1656-67. view on PubMed

Gallaher SD, Fitz-Gibbon ST, Glaesener AG, Pellegrini M, Merchant SS. Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies. Plant Cell. 2015 Sep; 27(9):2335-52. view on PubMed

Simpson L, Douglass SM, Lake JA, Pellegrini M, Li F. Comparison of the Mitochondrial Genomes and Steady State Transcriptomes of Two Strains of the Trypanosomatid Parasite, Leishmania tarentolae. PLoS Negl Trop Dis. 2015; 9(7):e0003841. view on PubMed

Sabbatucci M, Covino DA, Purificato C, Mallano A, Federico M, Lu J, Rinaldi AO, Pellegrini M, Bona R, Michelini Z, Cara A, Vella S, Gessani S, Andreotti M, Fantuzzi L. Erratum to: Endogenous CCL2 neutralization restricts HIV-1 replication in primary human macrophages by inhibiting viral DNA accumulation. Retrovirology. 2015 Jun 09; 12:47. view on PubMed

Platt A, Gugger PF, Pellegrini M, Sork VL. Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations. Mol Ecol. 2015 Aug; 24(15):3823-30. view on PubMed

Thompson MJ, Rubbi L, Dawson DW, Donahue TR, Pellegrini M. Pancreatic cancer patient survival correlates with DNA methylation of pancreas development genes. PLoS One. 2015; 10(6):e0128814. view on PubMed

Orozco LD, Morselli M, Rubbi L, Guo W, Go J, Shi H, Lopez D, Furlotte NA, Bennett BJ, Farber CR, Ghazalpour A, Zhang MQ, Bahous R, Rozen R, Lusis AJ, Pellegrini M. Epigenome-wide association of liver methylation patterns and complex metabolic traits in mice. Cell Metab. 2015 Jun 02; 21(6):905-17. view on PubMed

Soufi A, Garcia MF, Jaroszewicz A, Osman N, Pellegrini M, Zaret KS. Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming. Cell. 2015 Apr 23; 161(3):555-568. view on PubMed

Morselli M, Pastor WA, Montanini B, Nee K, Ferrari R, Fu K, Bonora G, Rubbi L, Clark AT, Ottonello S, Jacobsen SE, Pellegrini M. In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse. Elife. 2015 Apr 07; 4:e06205. view on PubMed

Brusslan JA, Bonora G, Rus-Canterbury AM, Tariq F, Jaroszewicz A, Pellegrini M. A Genome-Wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence. Plant Physiol. 2015 Aug; 168(4):1246-61. view on PubMed

Sabbatucci M, Covino DA, Purificato C, Mallano A, Federico M, Lu J, Rinaldi AO, Pellegrini M, Bona R, Michelini Z, Cara A, Vella S, Gessani S, Andreotti M, Fantuzzi L. Endogenous CCL2 neutralization restricts HIV-1 replication in primary human macrophages by inhibiting viral DNA accumulation. Retrovirology. 2015 Jan 22; 12:4. view on PubMed

House CH, Pellegrini M, Fitz-Gibbon ST. Genome-wide gene order distances support clustering the gram-positive bacteria. Front Microbiol. 2014; 5:785. view on PubMed

Org T, Duan D, Ferrari R, Montel-Hagen A, Van Handel B, Kerényi MA, Sasidharan R, Rubbi L, Fujiwara Y, Pellegrini M, Orkin SH, Kurdistani SK, Mikkola HK. Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence. EMBO J. 2015 Mar 12; 34(6):759-77. view on PubMed

Fiala M, Pellegrini M. Development of effective therapy for sporadic ALS. Expert Opin Biol Ther. 2015; 15(8):1249. view on PubMed

Conti A, Carnevali D, Bollati V, Fustinoni S, Pellegrini M, Dieci G. Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data. Nucleic Acids Res. 2015 Jan; 43(2):817-35. view on PubMed

Briot A, Jaroszewicz A, Warren CM, Lu J, Touma M, Rudat C, Hofmann JJ, Airik R, Weinmaster G, Lyons K, Wang Y, Kispert A, Pellegrini M, Iruela-Arispe ML. Repression of Sox9 by Jag1 is continuously required to suppress the default chondrogenic fate of vascular smooth muscle cells. Dev Cell. 2014 Dec 22; 31(6):707-21. view on PubMed

Ferrari R, Gou D, Jawdekar G, Johnson SA, Nava M, Su T, Yousef AF, Zemke NR, Pellegrini M, Kurdistani SK, Berk AJ. Adenovirus small E1A employs the lysine acetylases p300/CBP and tumor suppressor Rb to repress select host genes and promote productive virus infection. Cell Host Microbe. 2014 Nov 12; 16(5):663-76. view on PubMed

Chen PY, Montanini B, Liao WW, Morselli M, Jaroszewicz A, Lopez D, Ottonello S, Pellegrini M. A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum. Gigascience. 2014; 3:25. view on PubMed

Montoya D, Inkeles MS, Liu PT, Realegeno S, Teles RM, Vaidya P, Munoz MA, Schenk M, Swindell WR, Chun R, Zavala K, Hewison M, Adams JS, Horvath S, Pellegrini M, Bloom BR, Modlin RL. IL-32 is a molecular marker of a host defense network in human tuberculosis. Sci Transl Med. 2014 Aug 20; 6(250):250ra114. view on PubMed

Feng S, Cokus SJ, Schubert V, Zhai J, Pellegrini M, Jacobsen SE. Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Mol Cell. 2014 Sep 04; 55(5):694-707. view on PubMed

Inkeles MS, Scumpia PO, Swindell WR, Lopez D, Teles RMB, Graeber TG, Meller S, Homey B, Elder JT, Gilliet M, Modlin RL, Pellegrini M. Comparison of molecular signatures from multiple skin diseases identifies mechanisms of immunopathogenesis. J Invest Dermatol. 2015 Jan; 135(1):151-159. view on PubMed

Montanini B, Chen PY, Morselli M, Jaroszewicz A, Lopez D, Martin F, Ottonello S, Pellegrini M. Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content. Genome Biol. 2014 Jul 31; 15(7):411. view on PubMed

Liu W, Pellegrini M, Wang X. Detecting communities based on network topology. Sci Rep. 2014 Jul 18; 4:5739. view on PubMed

Huang K, Wu Z, Liu Z, Hu G, Yu J, Chang KH, Kim KP, Le T, Faull KF, Rao N, Gennery A, Xue Z, Wang CY, Pellegrini M, Fan G. Selective demethylation and altered gene expression are associated with ICF syndrome in human-induced pluripotent stem cells and mesenchymal stem cells. Hum Mol Genet. 2014 Dec 15; 23(24):6448-57. view on PubMed

Ghahramani NM, Ngun TC, Chen PY, Tian Y, Krishnan S, Muir S, Rubbi L, Arnold AP, de Vries GJ, Forger NG, Pellegrini M, Vilain E. The effects of perinatal testosterone exposure on the DNA methylome of the mouse brain are late-emerging. Biol Sex Differ. 2014; 5:8. view on PubMed

Ramundo S, Casero D, Mühlhaus T, Hemme D, Sommer F, Crèvecoeur M, Rahire M, Schroda M, Rusch J, Goodenough U, Pellegrini M, Perez-Perez ME, Crespo JL, Schaad O, Civic N, Rochaix JD. Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control. Plant Cell. 2014 May; 26(5):2201-2222. view on PubMed

Wakao S, Chin BL, Ledford HK, Dent RM, Casero D, Pellegrini M, Merchant SS, Niyogi KK. Phosphoprotein SAK1 is a regulator of acclimation to singlet oxygen in Chlamydomonas reinhardtii. Elife. 2014 May 23; 3:e02286. view on PubMed

Orozco LD, Rubbi L, Martin LJ, Fang F, Hormozdiari F, Che N, Smith AD, Lusis AJ, Pellegrini M. Intergenerational genomic DNA methylation patterns in mouse hybrid strains. Genome Biol. 2014 Apr 30; 15(5):R68. view on PubMed

Schmollinger S, Mühlhaus T, Boyle NR, Blaby IK, Casero D, Mettler T, Moseley JL, Kropat J, Sommer F, Strenkert D, Hemme D, Pellegrini M, Grossman AR, Stitt M, Schroda M, Merchant SS. Nitrogen-Sparing Mechanisms in Chlamydomonas Affect the Transcriptome, the Proteome, and Photosynthetic Metabolism. Plant Cell. 2014 Apr; 26(4):1410-1435. view on PubMed

Kawashima T, Douglass S, Gabunilas J, Pellegrini M, Chanfreau GF. Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae. PLoS Genet. 2014 Apr; 10(4):e1004249. view on PubMed

Ooi AT, Gower AC, Zhang KX, Vick JL, Hong L, Nagao B, Wallace WD, Elashoff DA, Walser TC, Dubinett SM, Pellegrini M, Lenburg ME, Spira A, Gomperts BN. Molecular profiling of premalignant lesions in lung squamous cell carcinomas identifies mechanisms involved in stepwise carcinogenesis. Cancer Prev Res (Phila). 2014 May; 7(5):487-95. view on PubMed

Li Y, Chen JA, Sears RL, Gao F, Klein ED, Karydas A, Geschwind MD, Rosen HJ, Boxer AL, Guo W, Pellegrini M, Horvath S, Miller BL, Geschwind DH, Coppola G. An epigenetic signature in peripheral blood associated with the haplotype on 17q21.31, a risk factor for neurodegenerative tauopathy. PLoS Genet. 2014 Mar; 10(3):e1004211. view on PubMed

Goodenough U, Blaby I, Casero D, Gallaher SD, Goodson C, Johnson S, Lee JH, Merchant SS, Pellegrini M, Roth R, Rusch J, Singh M, Umen JG, Weiss TL, Wulan T. The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii. Eukaryot Cell. 2014 May; 13(5):591-613. view on PubMed

Nakashima Y, Yanez DA, Touma M, Nakano H, Jaroszewicz A, Jordan MC, Pellegrini M, Roos KP, Nakano A. Nkx2-5 suppresses the proliferation of atrial myocytes and conduction system. Circ Res. 2014 Mar 28; 114(7):1103-13. view on PubMed

Wheelwright M, Kim EW, Inkeles MS, De Leon A, Pellegrini M, Krutzik SR, Liu PT. All-trans retinoic acid-triggered antimicrobial activity against Mycobacterium tuberculosis is dependent on NPC2. J Immunol. 2014 Mar 01; 192(5):2280-2290. view on PubMed

Johnson LM, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK, Zhong X, Marson G, Pellegrini M, Segal DJ, Patel DJ, Jacobsen SE. SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature. 2014 03 06; 507(7490):124-128. view on PubMed

Elhaik E, Pellegrini M, Tatarinova TV. Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa. BMC Bioinformatics. 2014 Jan 21; 15:23. view on PubMed

Lei NY, Jabaji Z, Wang J, Joshi VS, Brinkley GJ, Khalil H, Wang F, Jaroszewicz A, Pellegrini M, Li L, Lewis M, Stelzner M, Dunn JC, Martín MG. Intestinal subepithelial myofibroblasts support the growth of intestinal epithelial stem cells. PLoS One. 2014; 9(1):e84651. view on PubMed

Yao J, Zhang KX, Kramer M, Pellegrini M, McCombie WR. FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies. Bioinformatics. 2014 04 15; 30(8):1175-1176. view on PubMed

Huang K, Shen Y, Xue Z, Bibikova M, April C, Liu Z, Cheng L, Nagy A, Pellegrini M, Fan JB, Fan G. A panel of CpG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells. Stem Cell Reports. 2014 Jan 14; 2(1):36-43. view on PubMed

Guo W, Chung WY, Qian M, Pellegrini M, Zhang MQ. Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. Nucleic Acids Res. 2014 Mar; 42(5):3009-16. view on PubMed

Blaby IK, Glaesener AG, Mettler T, Fitz-Gibbon ST, Gallaher SD, Liu B, Boyle NR, Kropat J, Stitt M, Johnson S, Benning C, Pellegrini M, Casero D, Merchant SS. Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant. Plant Cell. 2013 Nov; 25(11):4305-23. view on PubMed

Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M. BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics. 2013 Nov 10; 14:774. view on PubMed

Widman N, Feng S, Jacobsen SE, Pellegrini M. Epigenetic differences between shoots and roots in Arabidopsis reveals tissue-specific regulation. Epigenetics. 2014 Feb; 9(2):236-42. view on PubMed

Denholtz M, Bonora G, Chronis C, Splinter E, de Laat W, Ernst J, Pellegrini M, Plath K. Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell Stem Cell. 2013 Nov 07; 13(5):602-16. view on PubMed

Hemschemeier A, Casero D, Liu B, Benning C, Pellegrini M, Happe T, Merchant SS. Copper response regulator1-dependent and -independent responses of the Chlamydomonas reinhardtii transcriptome to dark anoxia. Plant Cell. 2013 Sep; 25(9):3186-211. view on PubMed

Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH. Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa. BMC Plant Biol. 2013 Jun 25; 13:92. view on PubMed

Sridharan R, Gonzales-Cope M, Chronis C, Bonora G, McKee R, Huang C, Patel S, Lopez D, Mishra N, Pellegrini M, Carey M, Garcia BA, Plath K. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency. Nat Cell Biol. 2013 Jul; 15(7):872-82. view on PubMed

Chen PY, Ganguly A, Rubbi L, Orozco LD, Morselli M, Ashraf D, Jaroszewicz A, Feng S, Jacobsen SE, Nakano A, Devaskar SU, Pellegrini M. Intrauterine calorie restriction affects placental DNA methylation and gene expression. Physiol Genomics. 2013 Jul 15; 45(14):565-76. view on PubMed

Walker SI, Callahan BJ, Arya G, Barry JD, Bhattacharya T, Grigoryev S, Pellegrini M, Rippe K, Rosenberg SM. Evolutionary dynamics and information hierarchies in biological systems. Ann N Y Acad Sci. 2013 Dec; 1305:1-17. view on PubMed

Janzen DM, Cheng D, Schafenacker AM, Paik DY, Goldstein AS, Witte ON, Jaroszewicz A, Pellegrini M, Memarzadeh S. Estrogen and progesterone together expand murine endometrial epithelial progenitor cells. Stem Cells. 2013 Apr; 31(4):808-22. view on PubMed

Stroud H, Ding B, Simon SA, Feng S, Bellizzi M, Pellegrini M, Wang GL, Meyers BC, Jacobsen SE. Plants regenerated from tissue culture contain stable epigenome changes in rice. Elife. 2013 Mar 19; 2:e00354. view on PubMed

Malasarn D, Kropat J, Hsieh SI, Finazzi G, Casero D, Loo JA, Pellegrini M, Wollman FA, Merchant SS. Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii. J Biol Chem. 2013 Apr 12; 288(15):10672-83. view on PubMed

Vincent JJ, Huang Y, Chen PY, Feng S, Calvopiña JH, Nee K, Lee SA, Le T, Yoon AJ, Faull K, Fan G, Rao A, Jacobsen SE, Pellegrini M, Clark AT. Stage-specific roles for tet1 and tet2 in DNA demethylation in primordial germ cells. Cell Stem Cell. 2013 Apr 04; 12(4):470-8. view on PubMed

Varshney GK, Lu J, Gildea DE, Huang H, Pei W, Yang Z, Huang SC, Schoenfeld D, Pho NH, Casero D, Hirase T, Mosbrook-Davis D, Zhang S, Jao LE, Zhang B, Woods IG, Zimmerman S, Schier AF, Wolfsberg TG, Pellegrini M, Burgess SM, Lin S. A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Genome Res. 2013 Apr; 23(4):727-35. view on PubMed

Duanmu D, Casero D, Dent RM, Gallaher S, Yang W, Rockwell NC, Martin SS, Pellegrini M, Niyogi KK, Merchant SS, Grossman AR, Lagarias JC. Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival. Proc Natl Acad Sci U S A. 2013 Feb 26; 110(9):3621-6. view on PubMed

Tatarinova T, Elhaik E, Pellegrini M. Cross-species analysis of genic GC3 content and DNA methylation patterns. Genome Biol Evol. 2013; 5(8):1443-56. view on PubMed

Gkountela S, Li Z, Vincent JJ, Zhang KX, Chen A, Pellegrini M, Clark AT. The ontogeny of cKIT+ human primordial germ cells proves to be a resource for human germ line reprogramming, imprint erasure and in vitro differentiation. Nat Cell Biol. 2013 Jan; 15(1):113-22. view on PubMed

Molnár I, Lopez D, Wisecaver JH, Devarenne TP, Weiss TL, Pellegrini M, Hackett JD. Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa). BMC Genomics. 2012 Oct 30; 13:576. view on PubMed

Orozco LD, Bennett BJ, Farber CR, Ghazalpour A, Pan C, Che N, Wen P, Qi HX, Mutukulu A, Siemers N, Neuhaus I, Yordanova R, Gargalovic P, Pellegrini M, Kirchgessner T, Lusis AJ. Unraveling inflammatory responses using systems genetics and gene-environment interactions in macrophages. Cell. 2012 Oct 26; 151(3):658-70. view on PubMed

Daniels-Wells TR, Helguera G, Rodríguez JA, Leoh LS, Erb MA, Diamante G, Casero D, Pellegrini M, Martínez-Maza O, Penichet ML. Insights into the mechanism of cell death induced by saporin delivered into cancer cells by an antibody fusion protein targeting the transferrin receptor 1. Toxicol In Vitro. 2013 Feb; 27(1):220-31. view on PubMed

Hsieh SI, Castruita M, Malasarn D, Urzica E, Erde J, Page MD, Yamasaki H, Casero D, Pellegrini M, Merchant SS, Loo JA. The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii. Mol Cell Proteomics. 2013 Jan; 12(1):65-86. view on PubMed

Urzica EI, Casero D, Yamasaki H, Hsieh SI, Adler LN, Karpowicz SJ, Blaby-Haas CE, Clarke SG, Loo JA, Pellegrini M, Merchant SS. Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage. Plant Cell. 2012 Oct; 24(10):3921-48. view on PubMed

Palanca AM, Lee SL, Yee LE, Joe-Wong C, Trinh le A, Hiroyasu E, Husain M, Fraser SE, Pellegrini M, Sagasti A. New transgenic reporters identify somatosensory neuron subtypes in larval zebrafish. Dev Neurobiol. 2013 Feb; 73(2):152-67. view on PubMed

Marinelli LJ, Fitz-Gibbon S, Hayes C, Bowman C, Inkeles M, Loncaric A, Russell DA, Jacobs-Sera D, Cokus S, Pellegrini M, Kim J, Miller JF, Hatfull GF, Modlin RL. Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates. mBio. 2012; 3(5). view on PubMed

Ghazalpour A, Rau CD, Farber CR, Bennett BJ, Orozco LD, van Nas A, Pan C, Allayee H, Beaven SW, Civelek M, Davis RC, Drake TA, Friedman RA, Furlotte N, Hui ST, Jentsch JD, Kostem E, Kang HM, Kang EY, Joo JW, Korshunov VA, Laughlin RE, Martin LJ, Ohmen JD, Parks BW, Pellegrini M, Reue K, Smith DJ, Tetradis S, Wang J, Wang Y, Weiss JN, Kirchgessner T, Gargalovic PS, Eskin E, Lusis AJ, LeBoeuf RC. Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits. Mamm Genome. 2012 Oct; 23(9-10):680-92. view on PubMed

Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QCB, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol. 2012 Nov; 196(3):713-725. view on PubMed

Van Handel B, Montel-Hagen A, Sasidharan R, Nakano H, Ferrari R, Boogerd CJ, Schredelseker J, Wang Y, Hunter S, Org T, Zhou J, Li X, Pellegrini M, Chen JN, Orkin SH, Kurdistani SK, Evans SM, Nakano A, Mikkola HK. Scl represses cardiomyogenesis in prospective hemogenic endothelium and endocardium. Cell. 2012 Aug 03; 150(3):590-605. view on PubMed

Chodavarapu RK, Feng S, Ding B, Simon SA, Lopez D, Jia Y, Wang GL, Meyers BC, Jacobsen SE, Pellegrini M. Transcriptome and methylome interactions in rice hybrids. Proc Natl Acad Sci U S A. 2012 Jul 24; 109(30):12040-5. view on PubMed

Fang W, Si Y, Douglass S, Casero D, Merchant SS, Pellegrini M, Ladunga I, Liu P, Spalding MH. Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1. Plant Cell. 2012 May; 24(5):1876-93. view on PubMed

Moissiard G, Cokus SJ, Cary J, Feng S, Billi AC, Stroud H, Husmann D, Zhan Y, Lajoie BR, McCord RP, Hale CJ, Feng W, Michaels SD, Frand AR, Pellegrini M, Dekker J, Kim JK, Jacobsen SE. MORC family ATPases required for heterochromatin condensation and gene silencing. Science. 2012 Jun 15; 336(6087):1448-51. view on PubMed

Fischer BB, Ledford HK, Wakao S, Huang SG, Casero D, Pellegrini M, Merchant SS, Koller A, Eggen RI, Niyogi KK. SINGLET OXYGEN RESISTANT 1 links reactive electrophile signaling to singlet oxygen acclimation in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A. 2012 May 15; 109(20):E1302-11. view on PubMed

Ferrari R, Su T, Li B, Bonora G, Oberai A, Chan Y, Sasidharan R, Berk AJ, Pellegrini M, Kurdistani SK. Reorganization of the host epigenome by a viral oncogene. Genome Res. 2012 Jul; 22(7):1212-21. view on PubMed

Ooi AT, Ram S, Kuo A, Gilbert JL, Yan W, Pellegrini M, Nickerson DW, Chatila TA, Gomperts BN. Identification of an interleukin 13-induced epigenetic signature in allergic airway inflammation. Am J Transl Res. 2012; 4(2):219-28. view on PubMed

Foret S, Kucharski R, Pellegrini M, Feng S, Jacobsen SE, Robinson GE, Maleszka R. DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Proc Natl Acad Sci U S A. 2012 Mar 27; 109(13):4968-73. view on PubMed

Brusslan JA, Rus Alvarez-Canterbury AM, Nair NU, Rice JC, Hitchler MJ, Pellegrini M. Genome-wide evaluation of histone methylation changes associated with leaf senescence in Arabidopsis. PLoS One. 2012; 7(3):e33151. view on PubMed

Boyle NR, Page MD, Liu B, Blaby IK, Casero D, Kropat J, Cokus SJ, Hong-Hermesdorf A, Shaw J, Karpowicz SJ, Gallaher SD, Johnson S, Benning C, Pellegrini M, Grossman A, Merchant SS. Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. J Biol Chem. 2012 May 04; 287(19):15811-25. view on PubMed

Urzica EI, Adler LN, Page MD, Linster CL, Arbing MA, Casero D, Pellegrini M, Merchant SS, Clarke SG. Impact of oxidative stress on ascorbate biosynthesis in Chlamydomonas via regulation of the VTC2 gene encoding a GDP-L-galactose phosphorylase. J Biol Chem. 2012 Apr 20; 287(17):14234-45. view on PubMed

Bernal M, Casero D, Singh V, Wilson GT, Grande A, Yang H, Dodani SC, Pellegrini M, Huijser P, Connolly EL, Merchant SS, Krämer U. Transcriptome sequencing identifies SPL7-regulated copper acquisition genes FRO4/FRO5 and the copper dependence of iron homeostasis in Arabidopsis. Plant Cell. 2012 Feb; 24(2):738-61. view on PubMed

Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler TC, Freitag M, Strauss SH. Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression. BMC Genomics. 2012 Jan 17; 13:27. view on PubMed

Pellegrini M, Ferrari R. Epigenetic analysis: ChIP-chip and ChIP-seq. Methods Mol Biol. 2012; 802:377-87. view on PubMed

Pellegrini M. Using phylogenetic profiles to predict functional relationships. Methods Mol Biol. 2012; 804:167-77. view on PubMed

Marban C, Su T, Ferrari R, Li B, Vatakis D, Pellegrini M, Zack JA, Rohr O, Kurdistani SK. Genome-wide binding map of the HIV-1 Tat protein to the human genome. PLoS One. 2011; 6(11):e26894. view on PubMed

Rao AR, Pellegrini M. Regulation of the yeast metabolic cycle by transcription factors with periodic activities. BMC Syst Biol. 2011 Oct 12; 5:160. view on PubMed

Rodríguez JA, Luria-Pérez R, López-Valdés HE, Casero D, Daniels TR, Patel S, Avila D, Leuchter R, So S, Ortiz-Sánchez E, Bonavida B, Martínez-Maza O, Charles AC, Pellegrini M, Helguera G, Penichet ML. Lethal iron deprivation induced by non-neutralizing antibodies targeting transferrin receptor 1 in malignant B cells. Leuk Lymphoma. 2011 Nov; 52(11):2169-78. view on PubMed

Hegab AE, Ha VL, Gilbert JL, Zhang KX, Malkoski SP, Chon AT, Darmawan DO, Bisht B, Ooi AT, Pellegrini M, Nickerson DW, Gomperts BN. Novel stem/progenitor cell population from murine tracheal submucosal gland ducts with multipotent regenerative potential. Stem Cells. 2011 Aug; 29(8):1283-93. view on PubMed

Lopez D, Casero D, Cokus SJ, Merchant SS, Pellegrini M. Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. BMC Bioinformatics. 2011 Jul 12; 12:282. view on PubMed

Chen PY, Feng S, Joo JW, Jacobsen SE, Pellegrini M. A comparative analysis of DNA methylation across human embryonic stem cell lines. Genome Biol. 2011 Jul 06; 12(7):R62. view on PubMed

Hamidi H, Gustafason D, Pellegrini M, Gasson J. Identification of novel targets of CSL-dependent Notch signaling in hematopoiesis. PLoS One. 2011; 6(5):e20022. view on PubMed

Castruita M, Casero D, Karpowicz SJ, Kropat J, Vieler A, Hsieh SI, Yan W, Cokus S, Loo JA, Benning C, Pellegrini M, Merchant SS. Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps. Plant Cell. 2011 Apr; 23(4):1273-92. view on PubMed

Rubbi L, Titz B, Brown L, Galvan E, Komisopoulou E, Chen SS, Low T, Tahmasian M, Skaggs B, Müschen M, Pellegrini M, Graeber TG. Global phosphoproteomics reveals crosstalk between Bcr-Abl and negative feedback mechanisms controlling Src signaling. Sci Signal. 2011 Mar 29; 4(166):ra18. view on PubMed

Kropat J, Hong-Hermesdorf A, Casero D, Ent P, Castruita M, Pellegrini M, Merchant SS, Malasarn D. A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii. Plant J. 2011 Jun; 66(5):770-80. view on PubMed

Greenberg MV, Ausin I, Chan SW, Cokus SJ, Cuperus JT, Feng S, Law JA, Chu C, Pellegrini M, Carrington JC, Jacobsen SE. Identification of genes required for de novo DNA methylation in Arabidopsis. Epigenetics. 2011 Mar; 6(3):344-54. view on PubMed

Feng S, Rubbi L, Jacobsen SE, Pellegrini M. Determining DNA methylation profiles using sequencing. Methods Mol Biol. 2011; 733:223-38. view on PubMed

Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, Pellegrini M, Liao JC. Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol Syst Biol. 2010 Dec 21; 6:449. view on PubMed

Sherman MH, Kuraishy AI, Deshpande C, Hong JS, Cacalano NA, Gatti RA, Manis JP, Damore MA, Pellegrini M, Teitell MA. AID-induced genotoxic stress promotes B cell differentiation in the germinal center via ATM and LKB1 signaling. Mol Cell. 2010 Sep 24; 39(6):873-85. view on PubMed

Chin MH, Pellegrini M, Plath K, Lowry WE. Molecular analyses of human induced pluripotent stem cells and embryonic stem cells. Cell Stem Cell. 2010 Aug 06; 7(2):263-9. view on PubMed

González-Ballester D, Casero D, Cokus S, Pellegrini M, Merchant SS, Grossman AR. RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. Plant Cell. 2010 Jun; 22(6):2058-84. view on PubMed

Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, Casero D, Bernal M, Huijser P, Clark AT, Krämer U, Merchant SS, Zhang X, Jacobsen SE, Pellegrini M. Relationship between nucleosome positioning and DNA methylation. Nature. 2010 Jul 15; 466(7304):388-92. view on PubMed

Chen PY, Cokus SJ, Pellegrini M. BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics. 2010 Apr 23; 11:203. view on PubMed

Ferris P, Olson BJ, De Hoff PL, Douglass S, Casero D, Prochnik S, Geng S, Rai R, Grimwood J, Schmutz J, Nishii I, Hamaji T, Nozaki H, Pellegrini M, Umen JG. Evolution of an expanded sex-determining locus in Volvox. Science. 2010 Apr 16; 328(5976):351-4. view on PubMed

Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A. 2010 May 11; 107(19):8689-94. view on PubMed

Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature. 2010 Feb 25; 463(7284):1101-5. view on PubMed

Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M. Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression. BMC Syst Biol. 2009 Dec 14; 3:115. view on PubMed

Kawashima T, Pellegrini M, Chanfreau GF. Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations. RNA. 2009 Dec; 15(12):2236-47. view on PubMed

Orozco LD, Cokus SJ, Ghazalpour A, Ingram-Drake L, Wang S, van Nas A, Che N, Araujo JA, Pellegrini M, Lusis AJ. Copy number variation influences gene expression and metabolic traits in mice. Hum Mol Genet. 2009 Nov 01; 18(21):4118-29. view on PubMed

Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 2009; 10(6):R62. view on PubMed

Jacob Y, Feng S, LeBlanc CA, Bernatavichute YV, Stroud H, Cokus S, Johnson LM, Pellegrini M, Jacobsen SE, Michaels SD. ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol. 2009 Jul; 16(7):763-8. view on PubMed

Widman N, Jacobsen SE, Pellegrini M. Determining the conservation of DNA methylation in Arabidopsis. Epigenetics. 2009 Feb 16; 4(2):119-24. view on PubMed

Gekas C, Rhodes KE, Gereige LM, Helgadottir H, Ferrari R, Kurdistani SK, Montecino-Rodriguez E, Bassel-Duby R, Olson E, Krivtsov AV, Armstrong S, Orkin SH, Pellegrini M, Mikkola HK. Mef2C is a lineage-restricted target of Scl/Tal1 and regulates megakaryopoiesis and B-cell homeostasis. Blood. 2009 Apr 09; 113(15):3461-71. view on PubMed

Das D, Pellegrini M, Gray JW. A primer on regression methods for decoding cis-regulatory logic. PLoS Comput Biol. 2009 Jan; 5(1):e1000269. view on PubMed

Pellegrini M, Cheng JC, Voutila J, Judelson D, Taylor J, Nelson SF, Sakamoto KM. Expression profile of CREB knockdown in myeloid leukemia cells. BMC Cancer. 2008 Sep 18; 8:264. view on PubMed

Riley R, Pellegrini M, Eisenberg D. Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis. PLoS Comput Biol. 2008 Sep 12; 4(9):e1000174. view on PubMed

Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE. Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One. 2008 Sep 08; 3(9):e3156. view on PubMed

Ferrari R, Pellegrini M, Horwitz GA, Xie W, Berk AJ, Kurdistani SK. Epigenetic reprogramming by adenovirus e1a. Science. 2008 Aug 22; 321(5892):1086-8. view on PubMed

Shen Y, Matsuno Y, Fouse SD, Rao N, Root S, Xu R, Pellegrini M, Riggs AD, Fan G. X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. Proc Natl Acad Sci U S A. 2008 Mar 25; 105(12):4709-14. view on PubMed

Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13; 452(7184):215-9. view on PubMed

Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell. 2008 Feb 07; 2(2):160-9. view on PubMed

Pham H, Ferrari R, Cokus SJ, Kurdistani SK, Pellegrini M. Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae. Mol Syst Biol. 2007; 3:153. view on PubMed

Call GB, Olson JM, Chen J, Villarasa N, Ngo KT, Yabroff AM, Cokus S, Pellegrini M, Bibikova E, Bui C, Cespedes A, Chan C, Chan S, Cheema AK, Chhabra A, Chitsazzadeh V, Do MT, Fang QA, Folick A, Goodstein GL, Huang CR, Hung T, Kim E, Kim W, Kim Y, Kohan E, Kuoy E, Kwak R, Lee E, Lee J, Lin H, Liu HC, Moroz T, Prasad T, Prashad SL, Patananan AN, Rangel A, Rosselli D, Sidhu S, Sitz D, Taber CE, Tan J, Topp K, Tran P, Tran QM, Unkovic M, Wells M, Wickland J, Yackle K, Yavari A, Zaretsky JM, Allen CM, Alli L, An J, Anwar A, Arevalo S, Ayoub D, Badal SS, Baghdanian A, Baghdanian AH, Baumann SA, Becerra VN, Chan HJ, Chang AE, Cheng XA, Chin M, Chong F, Crisostomo C, Datta S, Delosreyes A, Diep F, Ekanayake P, Engeln M, Evers E, Farshidi F, Fischer K, Formanes AJ, Gong J, Gupta R, Haas BE, Hahm V, Hsieh M, Hui JZ, Iao ML, Jin SD, Kim AY, Kim LS, King M, Knudsen-Robbins C, Kohanchi D, Kovshilovskaya B, Ku A, Kung RW, Landig ME, Latterman SS, Lauw SS, Lee DS, Lee JS, Lei KC, Leung LL, Lerner R, Lin JY, Lin K, Lim BC, Lui CP, Liu TQ, Luong V, Makshanoff J, Mei AC, Meza M, Mikhaeil YA, Moarefi M, Nguyen LH, Pai SS, Pandya M, Patel AR, Picard PD, Safaee MM, Salame C, Sanchez C, Sanchez N, Seifert CC, Shah A, Shilgevorkyan OH, Singh I, Soma V, Song JJ, Srivastava N, StaAna JL, Sun C, Tan D, Teruya AS, Tikia R, Tran T, Travis EG, Trinh JD, Vo D, Walsh T, Wong RS, Wu K, Wu YW, Yang NX, Yeranosian M, Yu JS, Zhou JJ, Zhu RX, Abrams A, Abramson A, Amado L, Anderson J, Bashour K, Beyer E, Bookatz A, Brewer S, Buu N, Calvillo S, Cao J, Chan A, Chan J, Chang A, Chang D, Chang Y, Chen Y, Choi J, Chou J, Dang P, Datta S, Davarifar A, Deravanesian A, Desai P, Fabrikant J, Farnad S, Fu K, Garcia E, Garrone N, Gasparyan S, Gayda P, Go S, Goffstein C, Gonzalez C, Guirguis M, Hassid R, Hermogeno B, Hong J, Hong A, Hovestreydt L, Hu C, Huff D, Jamshidian F, Jen J, Kahen K, Kao L, Kelley M, Kho T, Kim Y, Kim S, Kirkpatrick B, Langenbacher A, Laxamana S, Lee J, Lee C, Lee SY, Lee TS, Lee T, Lewis G, Lezcano S, Lin P, Luu T, Luu J, Marrs W, Marsh E, Marshall J, Min S, Minasian T, Minye H, Misra A, Morimoto M, Moshfegh Y, Murray J, Nguyen K, Nguyen C, Nodado E, O'Donahue A, Onugha N, Orjiakor N, Padhiar B, Paul E, Pavel-Dinu M, Pavlenko A, Paz E, Phaklides S, Pham L, Poulose P, Powell R, Pusic A, Ramola D, Regalia K, Ribbens M, Rifai B, Saakyan M, Saarikoski P, Segura M, Shadpour F, Shemmassian A, Singh R, Singh V, Skinner E, Solomin D, Soneji K, Spivey K, Stageberg E, Stavchanskiy M, Tekchandani L, Thai L, Thiyanaratnam J, Tong M, Toor A, Tovar S, Trangsrud K, Tsang WY, Uemura M, Vollmer E, Weiss E, Wood D, Wu J, Wu S, Wu W, Xu Q, Yamauchi Y, Yarosh W, Yee L, Yen G, Banerjee U. Genomewide clonal analysis of lethal mutations in the Drosophila melanogaster eye: comparison of the X chromosome and autosomes. Genetics. 2007 Oct; 177(2):689-97. view on PubMed

Cokus S, Mizutani S, Pellegrini M. An improved method for identifying functionally linked proteins using phylogenetic profiles. BMC Bioinformatics. 2007 May 22; 8 Suppl 4:S7. view on PubMed

Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 2007 May; 5(5):e129. view on PubMed

Levine DM, Haynor DR, Castle JC, Stepaniants SB, Pellegrini M, Mao M, Johnson JM. Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways. Genome Biol. 2006; 7(10):R93. view on PubMed

Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell. 2006 Sep 22; 126(6):1189-201. view on PubMed

Cokus S, Rose S, Haynor D, Grønbech-Jensen N, Pellegrini M. Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae. BMC Bioinformatics. 2006 Aug 16; 7:381. view on PubMed

Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M. Bioinformatic challenges for the next decade(s). Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29; 361(1467):525-7. view on PubMed

Li H, Pellegrini M, Eisenberg D. Detection of parallel functional modules by comparative analysis of genome sequences. Nat Biotechnol. 2005 Feb; 23(2):253-60. view on PubMed

Pellegrini M, Haynor D, Johnson JM. Protein interaction networks. Expert Rev Proteomics. 2004 Aug; 1(2):239-49. view on PubMed

Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol. 2004; 5(5):R35. view on PubMed

Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res. 2003 Dec 15; 31(24):7099-109. view on PubMed

Gertz J, Elfond G, Shustrova A, Weisinger M, Pellegrini M, Cokus S, Rothschild B. Inferring protein interactions from phylogenetic distance matrices. Bioinformatics. 2003 Nov 01; 19(16):2039-45. view on PubMed

Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol. 2003; 4(9):R59. view on PubMed

Pellegrini M. Defining interacting partners for drug discovery. Expert Opin Ther Targets. 2003 Apr; 7(2):287-97. view on PubMed