
Matteo Pellegrini
Professor, Molecular, Cell and Developmental Biology, University of California Los Angeles
Professor, Human Genetics, University of California Los Angeles
Professor, CA NanoSystems, University of California Los Angeles
Professor, Medicine, University of California Los Angeles
Laboratory Address:
3000 Terasaki Life Sciences Building
Lab Number:
310-825-0012
Mailing Address:
UCLA Mol, Cell & Dvlmt Bio
BOX 951606
621 Charles E. Young Dr.
Los Angeles, CA 90095
Fax Number:
(310) 206-3987
Work Address:
3000C TSLB
Affiliations
Member, Bioinformatics GPB Home Area, California NanoSystems Institute, Cell & Developmental Biology GPB Home Area, Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, Genetics & Genomics GPB Home Area, JCCC Gene Regulation Program Area, Medical Informatics GPB Home Area
Research Interests
Biography
Matteo Pellegrini is a biophysicist who has served on the UCLA Life Sciences Division faculty since he joined the Department of Molecular, Cell and Developmental Biology in 2005. Dr. Pellegrini earned his B.A. in Physics at Columbia University and his Ph.D. in Physics at Stanford. He was a postdoctoral fellow at UCLA, where he worked on computational biology. Following his postdoctoral studies Dr. Pellegrini co-founded a start-up company and later worked for the pharmaceutical company Merck before returning to UCLA. His laboratory research centers on the development of novel computational approaches to reverse engineer biomolecular networks. Professor Pellegrini is also a member of the California NanoSystems Institute (CNSI).
Publications
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Lapborisuth K, Farrell C, Pellegrini M. Pseudotime Analysis Reveals Exponential Trends in DNA Methylation Aging with Mortality Associated Timescales.. Cells, 2022.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Farrell C, Thompson M, Tosevska A, Oyetunde A, Pellegrini M. BiSulfite Bolt: A bisulfite sequencing analysis platform.. GigaScience, 2021.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Farrell C, Snir S, Pellegrini M. The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework.. Bioinformatics (Oxford, England), 2020.
- Morselli M, Farrell C, Rubbi L, Fehling HL, Henkhaus R, Pellegrini M. Targeted bisulfite sequencing for biomarker discovery.. Methods (San Diego, Calif.), 2020.
- 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.
- 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.
- 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.
- 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.
- 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.
- Ma F, Pellegrini M. ACTINN: automated identification of cell types in single cell RNA sequencing.. Bioinformatics (Oxford, England), 2020.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Thompson MJ, vonHoldt B, Horvath S, Pellegrini M. An epigenetic aging clock for dogs and wolves.. Aging, 2017.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Liu W, Pellegrini M, Wang X. Detecting communities based on network topology.. Scientific reports, 2014.
- 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.
- Kawashima T, Douglass S, Gabunilas J, Pellegrini M, Chanfreau GF. Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae.. PLoS genetics, 2014.
- 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.
- 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.
- 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.
- 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.
- 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.
- Widman N, Feng S, Jacobsen SE, Pellegrini M. Epigenetic differences between shoots and roots in Arabidopsis reveals tissue-specific regulation.. Epigenetics, 2013.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Pellegrini M, Ferrari R. Epigenetic analysis: ChIP-chip and ChIP-seq.. Methods in molecular biology (Clifton, N.J.), 2012.
- Pellegrini M. Using phylogenetic profiles to predict functional relationships.. Methods in molecular biology (Clifton, N.J.), 2012.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Feng S, Rubbi L, Jacobsen SE, Pellegrini M. Determining DNA methylation profiles using sequencing.. Methods in molecular biology (Clifton, N.J.), 2011.
- 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.
- 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.
- Chin MH, Pellegrini M, Plath K, Lowry WE. Molecular analyses of human induced pluripotent stem cells and embryonic stem cells.. Cell stem cell, 2010.
- 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.
- Chen PY, Cokus SJ, Pellegrini M. BS Seeker: precise mapping for bisulfite sequencing.. BMC bioinformatics, 2010.
- 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.
- 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.
- Kawashima T, Pellegrini M, Chanfreau GF. Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations.. RNA (New York, N.Y.), 2009.
- Widman N, Jacobsen SE, Pellegrini M. Determining the conservation of DNA methylation in Arabidopsis.. Epigenetics, 2009.
- 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.
- 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.
- 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.
- Ferrari R, Pellegrini M, Horwitz GA, Xie W, Berk AJ, Kurdistani SK. Epigenetic reprogramming by adenovirus e1a.. Science (New York, N.Y.), 2008.
- 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.
- 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.
- 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.
- Pham H, Ferrari R, Cokus SJ, Kurdistani SK, Pellegrini M. Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae.. Molecular systems biology, 2007.
- 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.
- Cokus S, Mizutani S, Pellegrini M. An improved method for identifying functionally linked proteins using phylogenetic profiles.. BMC bioinformatics, 2007.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.