Publications

1. Morselli M, Bennett R, Shaidani NI, Horb M, Peshkin L, Pellegrini M. Age-associated DNA methylation changes in Xenopus frogs.. Epigenetics, 2023.
2. 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.
3. 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.. Nature communications, 2023.
4. 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.
5. 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 reports, 2023.
6. 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.
7. 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.. Nature immunology, 2023.
8. Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H. Genetic variants of glucose metabolism and exposure to smoking in African American breast cancer.. Endocrine-related cancer, 2023.
9. 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 (New York, N.Y.), 2023.
10. Jung SY, Bhatti P, Pellegrini M. DNA methylation in peripheral blood leukocytes for the association with glucose metabolism and invasive breast cancer.. Clinical epigenetics, 2023.
11. 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.. Communications biology, 2023.
12. 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.. Journal of Alzheimer's disease : JAD, 2023.
13. 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 reports, 2023.
14. 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.. Clinical epigenetics, 2022.
15. Sanders AR, Bhongir N, vonHoldt B, Pellegrini M. Association of DNA methylation with energy and fear-related behaviors in canines.. Frontiers in psychology, 2022.
16. 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 discovery, 2022.
17. 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).. Journal of phycology, 2022.
18. 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 (Dayton, Ohio), 2022.
19. 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.
20. 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 reports, 2022.
21. 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.. The Plant journal : for cell and molecular biology, 2022.
22. 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.. The New phytologist, 2022.
23. 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.. Science immunology, 2022.
24. 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.
25. 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.
26. 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.. Scientific reports, 2022.
27. 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.. Frontiers in cardiovascular medicine, 2022.
28. 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.. Frontiers in oncology, 2022.
29. 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.
30. 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.. Nature medicine, 2022.
31. 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.. Science translational medicine, 2022.
32. 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.. Arteriosclerosis, thrombosis, and vascular biology, 2022.
33. 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.. Nature communications, 2022.
34. 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.
35. 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.. Communications biology, 2022.
36. 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.
37. 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.
38. 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.. Nature immunology, 2022.
39. 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.. Nature ecology & evolution, 2022.
40. 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.. Nature medicine, 2022.
41. 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 research, 2022.
42. Lapborisuth K, Farrell C, Pellegrini M. Pseudotime Analysis Reveals Exponential Trends in DNA Methylation Aging with Mortality Associated Timescales.. Cells, 2022.
43. 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 (Cambridge, England), 2022.
44. 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.. Nature communications, 2022.
45. 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.
46. 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.. The Journal of clinical investigation, 2022.
47. 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.. Nature cardiovascular research, 2022.
48. 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 research, 2022.
49. 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.. Communications biology, 2021.
50. 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.. Nature communications, 2021.
51. 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, 2021.
52. 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 reports. Medicine, 2021.
53. 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.. Briefings in bioinformatics, 2021.
54. 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.. Nature metabolism, 2021.
55. 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.. Frontiers in oncology, 2021.
56. 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.
57. 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 biology, 2021.
58. 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.. Frontiers in immunology, 2021.
59. 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.. Scientific reports, 2021.
60. 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.. Journal of molecular and cellular cardiology, 2021.
61. 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.. Nature immunology, 2021.
62. 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.. Nature communications, 2021.
63. Ma F, Salomé PA, Merchant SS, Pellegrini M. Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase.. The Plant cell, 2021.
64. 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.. Science immunology, 2021.
65. 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.. Frontiers in cell and developmental biology, 2021.
66. Farrell C, Thompson M, Tosevska A, Oyetunde A, Pellegrini M. BiSulfite Bolt: A bisulfite sequencing analysis platform.. GigaScience, 2021.
67. 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.. Nature immunology, 2021.
68. 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.. Scientific reports, 2021.
69. 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.. American journal of cancer research, 2021.
70. 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.. The Journal of investigative dermatology, 2021.
71. 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.
72. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2021.
73. 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.
74. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2021.
75. 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.. Frontiers in oncology, 2021.
76. 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 molecular biology, 2021.
77. 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.
78. 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.. The Journal of clinical investigation, 2021.
79. 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.. Scientific reports, 2021.
80. 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.. Scientific reports, 2021.
81. 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.
82. 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.. Nature communications, 2020.
83. 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.. Clinical epigenetics, 2020.
84. 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 research, 2020.
85. 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.
86. 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, 2020.
87. 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.. The Journal of clinical investigation, 2020.
88. Farrell C, Snir S, Pellegrini M. The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework.. Bioinformatics (Oxford, England), 2020.
89. 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, 2020.
90. 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.. The Journal of biological chemistry, 2020.
91. 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.. Frontiers in immunology, 2020.
92. 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 prevention research (Philadelphia, Pa.), 2020.
93. 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.
94. 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.. American journal of cancer research, 2020.
95. Morselli M, Farrell C, Rubbi L, Fehling HL, Henkhaus R, Pellegrini M. Targeted bisulfite sequencing for biomarker discovery.. Methods (San Diego, Calif.), 2020.
96. 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 discovery, 2020.
97. 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.
98. 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 journal : official publication of the Federation of American Societies for Experimental Biology, 2020.
99. 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.. Mutation research. Genetic toxicology and environmental mutagenesis, 2020.
100. 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.. Molecular cancer therapeutics, 2020.
101. 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.. Scientific reports, 2020.
102. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2020.
103. 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.
104. Wang Y, Rhee KD, Pellegrini M, Yang XJ. Impacts of ciliary neurotrophic factor on the retinal transcriptome in a mouse model of photoreceptor degeneration.. Scientific reports, 2020.
105. 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.. Molecular therapy. Methods & clinical development, 2020.
106. 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.
107. 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.. Frontiers in immunology, 2020.
108. 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.. Reproductive sciences (Thousand Oaks, Calif.), 2020.
109. 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.. The Journal of investigative dermatology, 2020.
110. 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.
111. Ma F, Pellegrini M. ACTINN: automated identification of cell types in single cell RNA sequencing.. Bioinformatics (Oxford, England), 2020.
112. 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 (Athens, Greece), 2020.
113. 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.. Journal of Alzheimer's disease : JAD, 2020.
114. 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.
115. 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.. Frontiers in endocrinology, 2019.
116. 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 and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 2019.
117. 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, 2019.
118. 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 neglected tropical diseases, 2019.
119. 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.. Precision clinical medicine, 2019.
120. 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.. The New phytologist, 2019.
121. 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, 2019.
122. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2019.
123. 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.. Nature immunology, 2019.
124. 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 neglected tropical diseases, 2019.
125. 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.
126. 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.. International journal of molecular sciences, 2019.
127. 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 reports, 2019.
128. 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.. Journal of immunology (Baltimore, Md. : 1950), 2019.
129. 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.
130. Snir S, Farrell C, Pellegrini M. Human epigenetic ageing is logarithmic with time across the entire lifespan.. Epigenetics, 2019.
131. 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.. Journal of immunology (Baltimore, Md. : 1950), 2019.
132. 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.
133. 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 reports, 2019.
134. 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.. Developmental cell, 2019.
135. 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.
136. 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.
137. 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, 2018.
138. 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.
139. 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, 2018.
140. 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.
141. 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.. Nature chemical biology, 2018.
142. 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.. Nature neuroscience, 2018.
143. 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 research : an international journal for rapid publication of reports on genes and genomes, 2018.
144. 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.. Science immunology, 2018.
145. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2018.
146. 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.. Metabolic engineering, 2018.
147. 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.
148. 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.. Human molecular genetics, 2018.
149. 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.. Journal of immunology (Baltimore, Md. : 1950), 2018.
150. 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.. Nature neuroscience, 2018.
151. Snir S, Pellegrini M. An epigenetic pacemaker is detected via a fast conditional expectation maximization algorithm.. Epigenomics, 2018.
152. 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.. The Journal of cell biology, 2018.
153. 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 reports, 2018.
154. 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.. Human molecular genetics, 2018.
155. 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.
156. 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.. Circulation research, 2018.
157. 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.. Journal of immunology (Baltimore, Md. : 1950), 2018.
158. 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 discovery, 2018.
159. 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 microbiology, 2018.
160. 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 (Oxford, England), 2018.
161. 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.. The Plant journal : for cell and molecular biology, 2018.
162. 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?. Journal of Alzheimer's disease : JAD, 2018.
163. 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.
164. 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.
165. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2017.
166. Gang SS, Castelletto ML, Bryant AS, Yang E, Mancuso N, Lopez JB, Pellegrini M, Hallem EA. Targeted mutagenesis in a human-parasitic nematode.. PLoS pathogens, 2017.
167. 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.
168. 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.
169. Mangul S, Martin LS, Hoffmann A, Pellegrini M, Eskin E. Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX.. Trends in biotechnology, 2017.
170. 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.. Reproductive sciences (Thousand Oaks, Calif.), 2017.
171. Prado K, Zhang KX, Pellegrini M, Chin AI. Sequencing of cancer cell subpopulations identifies micrometastases in a bladder cancer patient.. Oncotarget, 2017.
172. 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 journal : official publication of the Federation of American Societies for Experimental Biology, 2017.
173. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2017.
174. 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 research, 2017.
175. 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 journal : official publication of the Federation of American Societies for Experimental Biology, 2017.
176. Thompson MJ, vonHoldt B, Horvath S, Pellegrini M. An epigenetic aging clock for dogs and wolves.. Aging, 2017.
177. 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.
178. 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 journal : official publication of the Federation of American Societies for Experimental Biology, 2017.
179. 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.
180. 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.. Frontiers in immunology, 2017.
181. 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 plasticity, 2016.
182. 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 reports, 2016.
183. 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.. Biotechnology for biofuels, 2016.
184. 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, 2016.
185. Snir S, vonHoldt BM, Pellegrini M. A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging.. PLoS computational biology, 2016.
186. 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, Md.), 2016.
187. 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.
188. 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 journal : official publication of the Federation of American Societies for Experimental Biology, 2016.
189. 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 reports, 2016.
190. 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.
191. 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.
192. 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.. Nutrition research (New York, N.Y.), 2016.
193. 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.. Nature medicine, 2016.
194. 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.. Nature communications, 2016.
195. 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.. Molecular therapy : the journal of the American Society of Gene Therapy, 2016.
196. 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 & environment, 2016.
197. 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 research, 2016.
198. 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.. Molecular neurobiology, 2016.
199. 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 journal : official publication of the Federation of American Societies for Experimental Biology, 2016.
200. 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.. Scientific reports, 2016.
201. 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 pathogens, 2016.
202. Douglass S, Hsu SW, Cokus S, Goldberg RB, Harada JJ, Pellegrini M. A naïve Bayesian classifier for identifying plant microRNAs.. The Plant journal : for cell and molecular biology, 2016.
203. 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, Md.), 2016.
204. 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.. Journal of immunology (Baltimore, Md. : 1950), 2016.
205. 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.. Clinical cancer research : an official journal of the American Association for Cancer Research, 2016.
206. 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 medicine, 2016.
207. 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.
208. 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 (Dayton, Ohio), 2016.
209. 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.. Molecular ecology, 2016.
210. 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 neuropathologica, 2016.
211. Liu W, Jiang X, Pellegrini M, Wang X. Discovering communities in complex networks by edge label propagation.. Scientific reports, 2016.
212. 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 reports, 2016.
213. 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.. Molecular ecology, 2016.
214. 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.. Circulation research, 2016.
215. 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, 2015.
216. 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.. American journal of neurodegenerative disease, 2015.
217. 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.
218. 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 physiology, 2015.
219. Liu W, Wu A, Pellegrini M, Wang X. Integrative analysis of human protein, function and disease networks.. Scientific reports, 2015.
220. 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 reports, 2015.
221. 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.. The Plant cell, 2015.
222. 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 neglected tropical diseases, 2015.
223. 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.
224. Platt A, Gugger PF, Pellegrini M, Sork VL. Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations.. Molecular ecology, 2015.
225. 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.
226. 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 metabolism, 2015.
227. 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.
228. 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.
229. 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 physiology, 2015.
230. 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.
231. House CH, Pellegrini M, Fitz-Gibbon ST. Genome-wide gene order distances support clustering the gram-positive bacteria.. Frontiers in microbiology, 2015.
232. 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.. The EMBO journal, 2015.
233. Fiala M, Pellegrini M. Development of effective therapy for sporadic ALS.. Expert opinion on biological therapy, 2015.
234. 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 research, 2014.
235. 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.. Developmental cell, 2014.
236. 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.
237. 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.
238. 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.. Science translational medicine, 2014.
239. 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.. Molecular cell, 2014.
240. 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.. The Journal of investigative dermatology, 2014.
241. 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 biology, 2014.
242. Liu W, Pellegrini M, Wang X. Detecting communities based on network topology.. Scientific reports, 2014.
243. 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.. Human molecular genetics, 2014.
244. 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.. Biology of sex differences, 2014.
245. 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.. The Plant cell, 2014.
246. 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.
247. 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 biology, 2014.
248. 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.. The Plant cell, 2014.
249. Kawashima T, Douglass S, Gabunilas J, Pellegrini M, Chanfreau GF. Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae.. PLoS genetics, 2014.
250. 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 prevention research (Philadelphia, Pa.), 2014.
251. 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 genetics, 2014.
252. 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.. Eukaryotic cell, 2014.
253. 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.. Circulation research, 2014.
254. 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.. Journal of immunology (Baltimore, Md. : 1950), 2014.
255. 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.
256. Elhaik E, Pellegrini M, Tatarinova TV. Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa.. BMC bioinformatics, 2014.
257. 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.
258. 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 (Oxford, England), 2014.
259. 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, 2013.
260. 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 research, 2013.
261. 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.. The Plant cell, 2013.
262. 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.
263. Widman N, Feng S, Jacobsen SE, Pellegrini M. Epigenetic differences between shoots and roots in Arabidopsis reveals tissue-specific regulation.. Epigenetics, 2013.
264. 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.
265. 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.. The Plant cell, 2013.
266. 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 biology, 2013.
267. 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.. Nature cell biology, 2013.
268. 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.. Physiological genomics, 2013.
269. 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.. Annals of the New York Academy of Sciences, 2013.
270. 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 (Dayton, Ohio), 2013.
271. 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.
272. 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.. The Journal of biological chemistry, 2013.
273. 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.
274. 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 research, 2013.
275. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2013.
276. Tatarinova T, Elhaik E, Pellegrini M. Cross-species analysis of genic GC3 content and DNA methylation patterns.. Genome biology and evolution, 2013.
277. 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.. Nature cell biology, 2012.
278. 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.
279. 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.
280. 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.. Toxicology in vitro : an international journal published in association with BIBRA, 2012.
281. 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.. Molecular & cellular proteomics : MCP, 2012.
282. 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.. The Plant cell, 2012.
283. 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.. Developmental neurobiology, 2012.
284. 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.
285. 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.. Mammalian genome : official journal of the International Mammalian Genome Society, 2012.
286. 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.. The New phytologist, 2012.
287. 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.
288. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2012.
289. 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.. The Plant cell, 2012.
290. 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 (New York, N.Y.), 2012.
291. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2012.
292. 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 research, 2012.
293. 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.. American journal of translational research, 2012.
294. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2012.
295. 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.
296. 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.. The Journal of biological chemistry, 2012.
297. 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.. The Journal of biological chemistry, 2012.
298. 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.. The Plant cell, 2012.
299. 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.
300. Pellegrini M, Ferrari R. Epigenetic analysis: ChIP-chip and ChIP-seq.. Methods in molecular biology (Clifton, N.J.), 2012.
301. Pellegrini M. Using phylogenetic profiles to predict functional relationships.. Methods in molecular biology (Clifton, N.J.), 2012.
302. 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.
303. Rao AR, Pellegrini M. Regulation of the yeast metabolic cycle by transcription factors with periodic activities.. BMC systems biology, 2011.
304. 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.. Leukemia & lymphoma, 2011.
305. 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 (Dayton, Ohio), 2011.
306. 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.
307. Chen PY, Feng S, Joo JW, Jacobsen SE, Pellegrini M. A comparative analysis of DNA methylation across human embryonic stem cell lines.. Genome biology, 2011.
308. Hamidi H, Gustafason D, Pellegrini M, Gasson J. Identification of novel targets of CSL-dependent Notch signaling in hematopoiesis.. PloS one, 2011.
309. 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.. The Plant cell, 2011.
310. 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.. Science signaling, 2011.
311. 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.. The Plant journal : for cell and molecular biology, 2011.
312. 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.
313. Feng S, Rubbi L, Jacobsen SE, Pellegrini M. Determining DNA methylation profiles using sequencing.. Methods in molecular biology (Clifton, N.J.), 2011.
314. 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.. Molecular systems biology, 2010.
315. 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.. Molecular cell, 2010.
316. Chin MH, Pellegrini M, Plath K, Lowry WE. Molecular analyses of human induced pluripotent stem cells and embryonic stem cells.. Cell stem cell, 2010.
317. 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.. The Plant cell, 2010.
318. 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.
319. Chen PY, Cokus SJ, Pellegrini M. BS Seeker: precise mapping for bisulfite sequencing.. BMC bioinformatics, 2010.
320. 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 (New York, N.Y.), 2010.
321. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2010.
322. 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.
323. Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M. Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression.. BMC systems biology, 2009.
324. Kawashima T, Pellegrini M, Chanfreau GF. Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations.. RNA (New York, N.Y.), 2009.
325. 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.. Human molecular genetics, 2009.
326. 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 biology, 2009.
327. 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.. Nature structural & molecular biology, 2009.
328. Widman N, Jacobsen SE, Pellegrini M. Determining the conservation of DNA methylation in Arabidopsis.. Epigenetics, 2009.
329. 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.
330. Das D, Pellegrini M, Gray JW. A primer on regression methods for decoding cis-regulatory logic.. PLoS computational biology, 2009.
331. 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.
332. 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 computational biology, 2008.
333. 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.
334. Ferrari R, Pellegrini M, Horwitz GA, Xie W, Berk AJ, Kurdistani SK. Epigenetic reprogramming by adenovirus e1a.. Science (New York, N.Y.), 2008.
335. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2008.
336. 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.
337. 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.
338. Pham H, Ferrari R, Cokus SJ, Kurdistani SK, Pellegrini M. Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae.. Molecular systems biology, 2007.
339. 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.
340. Cokus S, Mizutani S, Pellegrini M. An improved method for identifying functionally linked proteins using phylogenetic profiles.. BMC bioinformatics, 2007.
341. 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 biology, 2007.
342. 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 biology, 2006.
343. 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.
344. 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.
345. Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M. Bioinformatic challenges for the next decade(s).. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2006.
346. Li H, Pellegrini M, Eisenberg D. Detection of parallel functional modules by comparative analysis of genome sequences.. Nature biotechnology, 2005.
347. Pellegrini M, Haynor D, Johnson JM. Protein interaction networks.. Expert review of proteomics, 2004.
348. Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D. Prolinks: a database of protein functional linkages derived from coevolution.. Genome biology, 2004.
349. 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 research, 2003.
350. Gertz J, Elfond G, Shustrova A, Weisinger M, Pellegrini M, Cokus S, Rothschild B. Inferring protein interactions from phylogenetic distance matrices.. Bioinformatics (Oxford, England), 2003.
351. 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 biology, 2003.
352. Pellegrini M. Defining interacting partners for drug discovery.. Expert opinion on therapeutic targets, 2003.