Publications

 

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Publications from 2013 and earlier

2013

Widman N, Feng S, Jacobsen SE, Pellegrini M. Epigenetic differences between shoots and roots in Arabidopsis reveals tissue-specific regulation. Epigenetics. 2013 Oct 29;9(2). [Epub ahead of print] PubMed PMID: 24169618.

Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M. BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics. 2013 Nov 10;14(1):774. [Epub ahead of print] PubMed PMID: 24206606; PubMed Central PMCID: PMC3840619.

Blaby IK, Glaesener AG, Mettler T, Fitz-Gibbon ST, Gallaher SD, Liu B, Boyle NR, Kropat J, Stitt M, Johnson S, Benning C, Pellegrini M, Casero D, Merchant SS. Systems-Level Analysis of Nitrogen Starvation-Induced Modifications of Carbon Metabolism in a Chlamydomonas reinhardtii Starchless Mutant. Plant Cell. 2013 Nov 26. [Epub ahead of print] PubMed PMID: 24280389.

Guo W, Chung WY, Qian M, Pellegrini M, Zhang MQ. Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. Nucleic Acids Res. 2013 Dec 16. [Epub ahead of print] PubMed PMID: 24343027.

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 Sep 11. doi:pii: S1934-5909(13)00376-7. 10.1016/j.stem.2013.08.013. [Epub ahead of print] PubMed PMID: 24035354.

Hemschemeier A, Casero D, Liu B, Benning C, Pellegrini M, Happe T, Merchant SS. COPPER RESPONSE REGULATOR1-Dependent and -Independent Responses of the Chlamydomonas reinhardtii Transcriptome to Dark Anoxia. Plant Cell. 2013 Sep 6. [Epub ahead of print] PubMed PMID: 24014546.

Urzica EI, Vieler A, Hong-Hermesdorf A, Page MD, Casero D, Gallaher SD, Kropat J, Pellegrini M, Benning C, Merchant SS. Remodeling of Membrane Lipids in Iron Starved Chlamydomonas. J Biol Chem. 2013 Aug 27. [Epub ahead of print] PubMed PMID: 23983122.

Tatarinova T, Elhaik E, Pellegrini M. Cross-species analysis of genic GC3 content and DNA methylation patterns. Genome Biol Evol. 2013 Jul 5. [Epub ahead of print] PubMed PMID: 23833164.

Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH. Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa. BMC Plant Biol. 2013 Jun 25;13(1):92.[Epub ahead of print] PubMed PMID: 23799904.

Sridharan R, Gonzales-Cope M, Chronis C, Bonora G, McKee R, Huang C, Patel S, Lopez D, Mishra N, Pellegrini M, Carey M, Garcia BA, Plath K. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency. Nat Cell Biol. 2013 Jul;15(7):872-82. doi: 10.1038/ncb2768. Epub 2013 Jun 9. PubMed PMID: 23748610.

Walker SI, Callahan BJ, Arya G, Barry JD, Bhattacharya T, Grigoryev S, Pellegrini M, Rippe K, Rosenberg SM. Evolutionary dynamics and information hierarchies in biological systems. Ann N Y Acad Sci. 2013 May 20. doi:10.1111/nyas.12140. [Epub ahead of print] PubMed PMID: 23691975.

Chen PY, Ganguly A, Rubbi L, Orozco LD, Morselli M, Ashraf D, Jaroszewicz A, Feng S, Jacobsen SE, Nakano A, Devaskar SU, Pellegrini M. Intra-Uterine Calorie Restriction Affects Placental DNA Methylation and Gene Expression. Physiol Genomics. 2013 May 21. [Epub ahead of print] PubMed PMID: 23695884.

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;2:e00354. doi: 10.7554/eLife.00354. Epub 2013 Mar 19. PubMed PMID: 23539454; PubMed Central PMCID: PMC3601819.

Malasarn D, Kropat J, Hsieh SI, Finazzi G, Casero D, Loo JA, Pellegrini M, Wollman FA, Merchant SS. Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii. J Biol Chem. 2013 Feb 25. [Epub ahead of print] PubMed PMID: 23439652.

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 Feb 13. doi:pii: S1934-5909(13)00019-2. 10.1016/j.stem.2013.01.016. [Epub ahead of print] PubMed PMID: 23415914.

Varshney GK, Lu J, Gildea D, Huang H, Pei W, Yang Z, Huang SC, Schoenfeld DS, Pho N, Casero D, Hirase T, Mosbrook-Davis DM, Zhang S, Jao LE, Zhang B, Woods IG, Zimmerman S, Schier AF, Wolfsberg T, Pellegrini M, Burgess SM, Lin S. A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Genome Res. 2013 Feb 4. [Epub ahead of print] PubMed PMID: 23382537.

Janzen DM, Cheng D, Schafenacker AM, Paik DY, Goldstein AS, Witte ON, Jaroszewicz A, Pellegrini M, Memarzadeh S. Estrogen and Progesterone Together Expand Murine Endometrial Epithelial Progenitor Cells. Stem Cells. 2013 Jan 22. doi: 10.1002/stem.1337. [Epub ahead of print] PubMed PMID: 23341289.

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 bilinsignaling enables Chlamydomonas greening and phototrophic survival. Proc Natl Acad Sci U S A. 2013 Jan 23. [Epub ahead of print] PubMed PMID: 23345435.

Hsieh SI, Castruita M, Malasarn D, Urzica E, Erde J, Page MD, Yamasaki H, Casero D, Pellegrini M, Merchant SS, Loo JA. The Proteome of Copper, Iron, Zinc, and Manganese Micronutrient Deficiency in Chlamydomonas reinhardtii. Mol Cell Proteomics. 2013 Jan;12(1):65-86. doi: 10.1074/mcp.M112.021840. Epub 2012 Oct 13. PubMed PMID: 23065468; PubMed Central PMCID: PMC3536910.

2012

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 Biol. 2012 Dec 16;15(1):113-22. doi: 10.1038/ncb2638. Epub 2012 Dec 16. PubMed PMID: 23242216.

Molnar I, Lopez D, Wisecaver JH, Devarenne TP, Weiss TL, Pellegrini M, Hackett JD. Bio-crude transcriptomics: Gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa)*. BMC Genomics. 2012 Oct 30;13(1):576. [Epub ahead of print] PubMed PMID: 23110428.

Orozco LD, Bennett BJ, Farber CR, Ghazalpour A, Pan C, Che N, Wen P, Qi HX, Mutukulu A, Siemers N, Neuhaus I, Yordanova R, Gargalovic P, Pellegrini M, Kirchgessner T, Lusis AJ. Unraveling Inflammatory Responses using Systems Genetics and Gene-Environment Interactions in Macrophages. Cell. 2012 Oct 26;151(3):658-70. doi: 10.1016/j.cell.2012.08.043. PubMed PMID: 23101632.

Daniels-Wells TR, Helguera G, Rodríguez JA, Leoh LS, Erb MA, Diamante G, Casero D, Matteo P, Martínez-Maza O, Penichet ML. Insights into the mechanism of  cell death induced by saporin delivered into cancer cells by an antibody fusion protein targeting the transferrin receptor 1. Toxicol In Vitro. 2012 Oct 17. doi:pii: S0887-2333(12)00282-2. 10.1016/j.tiv.2012.10.006. [Epub ahead of print]  PubMed PMID: 23085102.

Urzica EI, Casero D, Yamasaki H, Hsieh SI, Adler LN, Karpowicz SJ, Blaby-Haas CE, Clarke SG, Loo JA, Pellegrini M, Merchant SS. Systems and Trans-System Level Analysis Identifies Conserved Iron Deficiency Responses in the Plant Lineage. Plant Cell. 2012 Oct 5. [Epub ahead of print] PubMed PMID: 23043051.

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 Sep 25;3(5). pii: e00279-12. doi: 10.1128/mBio.00279-12. Print 2012. PubMed PMID: 23015740;

PubMed Central PMCID: PMC3448167. Ghazalpour A, Rau CD, Farber CR, Bennett BJ, Orozco LD, van Nas A, Pan C, Allayee H, Beaven SW, Civelek M, Davis RC, Drake TA, Friedman RA, Furlotte N, Hui ST, Jentsch JD, Kostem E, Kang HM, Kang EY, Joo JW, Korshunov VA, Laughlin RE, Martin LJ, Ohmen JD, Parks BW, Pellegrini M, Reue K, Smith DJ, Tetradis S, Wang J, Wang Y, Weiss JN, Kirchgessner T, Gargalovic PS, Eskin E, Lusis AJ, Leboeuf RC. Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits. Mamm Genome. 2012 Aug 15. [Epub ahead of print] PubMed PMID: 22892838.

Palanca AM, Lee SL, Yee LE, Joe-Wong C, Trinh LA, Hiroyasu E, Husain M, Fraser SE, Pellegrini M, Sagasti A. New transgenic reporters identify somatosensory neuron subtypes in larval zebrafish. Dev Neurobiol. 2012 Aug 2. doi: 10.1002/dneu.22049. [Epub ahead of print] PubMed PMID: 22865660.

Van Handel B, Montel-Hagen A, Sasidharan R, Nakano H, Ferrari R, Boogerd CJ, Schredelseker J, Wang Y, Hunter S, Org T, Zhou J, Li X, Pellegrini M, Chen JN, Orkin SH, Kurdistani SK, Evans SM, Nakano A, Mikkola HK. Scl represses cardiomyogenesis in prospective hemogenic endothelium and endocardium. Cell. 2012 Aug 3;150(3):590-605. PubMed PMID: 22863011.

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 QC, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA. Genome resequencing reveals multiscale geographic structure and
extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol. 2012 Aug 3. doi: 10.1111/j.1469-8137.2012.04258.x. [Epub ahead of print] PubMed PMID: 22861491.

PY Chen, M Pellegrini. Methylomes, Encyclopedia of Molecular Cell Biology and Molecular Medicine, 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. Proc Natl Acad Sci U S A. 2012 Jul 9. [Epub ahead of print] PubMed PMID: 22778444.

This Week in PNAS Fang W, Si Y, Douglass S, Casero D, Merchant SS, Pellegrini M, Ladunga I, Liu P, Spalding MH. Transcriptome-Wide Changes in Chlamydomonas reinhardtii Gene Expression Regulated by Carbon Dioxide and the CO2-Concentrating Mechanism Regulator CIA5/CCM1. Plant Cell. 2012 May;24(5):1876-93. Epub 2012 May 25. PubMed PMID: 22634760.

Aik T Ooi, Sonal Ram, Alan Kuo, Jennifer L Gilbert, Weihong Yan, Matteo Pellegrini, Derek W Nickerson, Talal A Chatila, and Brigitte N Gomperts Identification of an interleukin 13-induced epigenetic signature in allergic airway inflammation Am J Transl Res. 2012; 4(2): 219–228.

Boyle NR, Page MD, Liu B, Blaby IK, Casero D, Kropat J, Cokus SJ, Hong-Hermesdorf A, Shaw J, Karpowicz SJ, Gallaher SD, Johnson S, Benning C, Pellegrini M, Grossman A, Merchant SS. Three Acyltransferases and Nitrogen-responsive Regulator Are Implicated in Nitrogen Starvation-induced Triacylglycerol Accumulation in Chlamydomonas. J Biol Chem. 2012 May 4;287(19):15811-25. Epub 2012 Mar 8. PubMed PMID: 22403401; PubMed Central PMCID: PMC3346115.

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 S. MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing. Science. 2012 May 3. [Epub ahead of print] PubMed PMID: 22555433.

Fischer BB, Ledford HK, Wakao S, Huang SG, Casero D, Pellegrini M, Merchant SS, Koller A, Eggen RI, Niyogi KK. SINGLET OXYGEN RESISTANT 1 links reactive electrophile signaling to singlet oxygen acclimation in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A. 2012 Apr 23. [Epub ahead of print] PubMed PMID: 22529359.

Ferrari R, Su T, Li B, Bonora G, Oberai A, Sasidharan R, Chan Y, Berk AJ, Pellegrini M, Kurdistani SK. Reorganization of the host epigenome by a viral oncogene. Genome Res. 2012 Apr 12. [Epub ahead of print] PubMed PMID: 22499665.

Brusslan JA, Rus Alvarez-Canterbury AM, Nair NU, Rice JC, Hitchler MJ, Pellegrini M. Genome-wide evaluation of histone methylation changes associated with leaf senescence in Arabidopsis. PLoS One. 2012;7(3):e33151. Epub 2012 Mar 12. PubMed PMID: 22427974; PubMed Central PMCID: PMC3299739.

Foret S, Kucharski R, Pellegrini M, Feng S, Jacobsen SE, Robinson GE, Maleszka R. DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Proc Natl Acad Sci U S A. 2012 Mar 13. [Epub ahead of print] PubMed PMID: 22416128.

Urzica EI, Adler LN, Page MD, Linster CL, Arbing MA, Casero D, Pellegrini M, Merchant SS, Clarke SG. Impact of oxidative stress on ascorbate biosynthesis in Chlamydomonas via regulation of the VTC2 gene encoding a GDP-L-galactose phosphorylase. J Biol Chem. 2012 Mar 5. [Epub ahead of print] PubMed PMID: 22393048.

Bernal M, Casero D, Singh V, Wilson GT, Grande A, Yang H, Dodani SC, Pellegrini M, Huijser P, Connolly EL, Merchant SS, Krämer U. Transcriptome Sequencing Identifies SPL7-Regulated Copper Acquisition Genes FRO4/FRO5 and the Copper Dependence of Iron Homeostasis in Arabidopsis. Plant Cell. 2012 Feb 28. [Epub ahead of print] PubMed PMID: 22374396.

Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler TC, Freitag M, Strauss S. Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression. BMC Genomics. 2012 Jan 17;13(1):27. [Epub ahead of print] PubMed PMID: 22251412.

Pellegrini M. Using phylogenetic profiles to predict functional relationships.  Methods Mol Biol. 2012;804:167-77. PubMed PMID: 22144153.

Pellegrini M, Ferrari R. Epigenetic Analysis: ChIP-chip and ChIP-seq. Methods Mol Biol. 2012;802:377-87. PubMed PMID: 22130894.

2011

Marban C, Su T, Ferrari R, Li B, Vatakis D, Pellegrini M, Zack JA, Rohr O, Kurdistani SK. Genome-Wide Binding Map of the HIV-1 Tat Protein to the Human Genome. PLoS One. 2011;6(11):e26894. Epub 2011 Nov 4. PubMed PMID: 22073215; PubMed Central PMCID: PMC3208564.

Rao AR, Pellegrini M. Regulation of the yeast metabolic cycle by transcription factors with periodic activities. BMC Syst Biol. 2011 Oct 12;5(1):160. [Epub ahead of print] PubMed PMID: 21992532.

Rodríguez JA, Luria-Pérez R, López-Valdés HE, Casero D, Daniels TR, Patel S, Avila D, Leuchter R, So S, Ortiz-Sánchez E, Bonavida B, Martínez-Maza O, Charles AC, Pellegrini M, Helguera G, Penichet ML. Lethal iron deprivation induced by non-neutralizing antibodies targeting transferrin receptor 1 in malignant B cells. Leuk Lymphoma. 2011 Aug 28. [Epub ahead of print] PubMed PMID: 21870996.

Hegab AE, Ha VL, Gilbert JL, Zhang KX, Malkoski SP, Chon AT, Darmawan DO, Bisht B, Ooi AT, Pellegrini M, Nickerson DW, Gomperts BN. A Novel Stem/Progenitor Cell Population from Murine Tracheal Submucosal Gland Ducts with Multipotent Regenerative Potential. Stem Cells. 2011 Jun 24. doi: 10.1002/stem.680. [Epub ahead of print] PubMed PMID: 21710468.

Chen PY, Feng S, Joo JW, Jacobsen SE, Pellegrini M. A comparative analysis of DNA methylation across human embryonic stem cell lines. Genome Biol. 2011 Jul 6;12(7):R62. [Epub ahead of print] PubMed PMID: 21733148.

Lopez D, Casero D, Cokus SJ, Merchant SS, Pellegrini M. Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. BMC Bioinformatics. 2011 Jul 12;12(1):282. [Epub ahead of print] PubMed PMID: 21749710.

Hamidi H, Gustafason D, Pellegrini M, Gasson J. Identification of Novel Targets of CSL-Dependent Notch Signaling in Hematopoiesis. PLoS One. 2011;6(5):e20022. Epub 2011 May 26. PubMed PMID: 21637838; PubMed Central PMCID: PMC3102675.

Castruita M, Casero D, Karpowicz SJ, Kropat J, Vieler A, Hsieh SI, Yan W, Cokus S, Loo JA, Benning C, Pellegrini M, Merchant SS. Systems Biology Approach in Chlamydomonas Reveals Connections between Copper Nutrition and Multiple Metabolic Steps. Plant Cell. 2011 Apr 15. [Epub ahead of print] PubMed PMID: 21498682.

Author Profile

In brief

Rubbi L, Titz B, Brown L, Galvan E, Komisopoulou E, Chen SS, Low T, Tahmasian M, Skaggs B, Müschen M, Pellegrini M, Graeber TG. Global phosphoproteomics reveals crosstalk between bcr-abl and negative feedback mechanisms controlling SRC signaling. Sci Signal. 2011 Mar 29;4(166):ra18. PubMed PMID: 21447799.

Feng S, Rubbi L, Jacobsen SE, Pellegrini M. Determining DNA Methylation Profiles Using Sequencing. Methods Mol Biol. 2011;733:223-238. PubMed PMID:21431774.

Kropat J, Hong-Hermesdorf A, Casero D, Ent P, Castruita M, Pellegrini M, Merchant SS, Malasarn D. A revised mineral nutrient supplement increases biomass  and growth rate in Chlamydomonas reinhardtii. Plant J. 2011 Feb 11. doi:10.1111/j.1365-313X.2011.04537.x. [Epub ahead of print] PubMed PMID: 21309872.

Greenberg MV, Ausin I, Chan SW, Cokus SJ, Cuperus JT, Feng S, Law JA, Chu C, Pellegrini M, Carrington JC, Jacobsen SE. Identification of genes required for de novo DNA methylation in Arabidopsis. Epigenetics. 2011 Mar 1;6(3). [Epub ahead of print] PubMed PMID: 21150311.

2010

Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, Pellegrini M, Liao JC.  Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol Syst Biol. 2010 Dec 21;6:449. PubMed PMID: 21179021.

AID-Induced Genotoxic Stress Promotes B Cell Differentiation in the Germinal Center via ATM and LKB1 Signaling Sherman MH, Kuraishy AI, Deshpande C, Hong JS, Cacalano NA, Gatti RA, Manis JP, Damore MA, Pellegrini M, Teitell MA. Mol Cell. 2010 Sep 24;39(6):873-85.

Chin MH, Pellegrini M, Plath K, Lowry WE. Molecular Analyses of Human Induced Pluripotent Stem Cells and Embryonic Stem Cells. Cell Stem Cell. 2010 Aug 6;7(2):263-269. PubMed PMID: 20682452.

Gonzalez-Ballester D, Casero D, Cokus S, Pellegrini M, Merchant SS, Grossman AR. RNA-Seq Analysis of Sulfur-Deprived Chlamydomonas Cells Reveals Aspects of Acclimation Critical for Cell Survival. Plant Cell. 2010 Jun 29. [Epub ahead of print] PubMed PMID: 20587772.

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, Kr√§mer U, Merchant SS, Zhang X, Jacobsen SE, Pellegrini M. Relationship between nucleosome positioning and DNA methylation. Nature. 2010 May 30. [Epub ahead of print] PubMed PMID: 20512117. Supplemental file

Chen PY, Cokus SJ, Pellegrini M. BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics. 2010 Apr 23;11(1):203. [Epub ahead of print] PubMed PMID: 20416082.

Ferris P, Olson BJ, De Hoff PL, Douglass S, Casero D, Prochnik S, Geng S, Rai R, Grimwood J, Schmutz J, Nishii I, Hamaji T, Nozaki H, Pellegrini M, Umen JG. Evolution of an expanded sex-determining locus in volvox. Science. 2010 Apr 16;328(5976):351-4. PubMed PMID: 20395508.

Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A. 2010 Apr 15. [Epub ahead of print] PubMed PMID: 20395551.

Commentary of paper in PNAS

Commentary of paper in Science

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 Jan 22. [Epub ahead of print] PubMed PMID: 20098412.

2009

Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M. Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression. BMC Syst Biol. ;3(1):115. [Epub ahead of print] PubMed PMID: 20003439.

Kawashima T, Pellegrini M, Chanfreau GF. Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations. RNA. 2009 Oct 22. PubMed PMID: 19850912.

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 geneexpression and metabolic traits in mice. Hum Mol Genet. 2009 Jul 31. [Epub ahead of print] PubMed PMID: 19648292.

Chin MH, Mason MJ, Xie W, Volinia S, Singer M, Peterson C, Ambartsumyan G, Aimiuwu O, Richter L, Zhang J, Khvorostov I, Ott V, Grunstein M, Lavon N, Benvenisty N, Croce CM, Clark AT, Baxter T, Pyle AD, Teitell MA, Pelegrini M, Plath K, Lowry WE. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell. 2009 Jul 2;5(1):111-23.

Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 2009 Jun 9;10(6):R62.

Jacob Y, Feng S, Leblanc CA, Bernatavichute YV, Stroud H, Cokus S, Johnson LM, Pellegrini M, Jacobsen SE, Michaels SD. ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol. 2009 Jun 7.

Nicolas Widman, Steve Jacobsen E. and Matteo Pellegrini Determining the conservation of DNA methylation in Arabidopsis.  Epigenetics 2009 Feb 16 4(2)

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 Feb 11.

Das D, Pellegrini M, Gray JW. A primer on regression methods for decoding cis-regulatory logic. PLoS Comput Biol. 2009 Jan;5(1):e1000269. Epub 2009 Jan 30. 

2008

Conway AE, Lindgren A, Galic Z, Pyle AD, Wu H, Zack JA, Pelligrini M, Teitell MA, Clark A. A Pluripotency and Self-Renewal Program Controls the Expansion of Genetically Unstable Cancer Stem Cells in Pluripotent Stem Cell-Derived Tumors. Stem Cells. 2008 Oct 2.

Pellegrini M, Cheng JC, Voutila J, Judelson D, Taylor J, Nelson SF, Sakamoto KM. Expression Profile of CREB knockdown in Myeloid Leukemia Cells. BMC Cancer. 2008 Sep 18;8(1):264.

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

Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE. Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana. PLoS ONE. 2008 Sep 8;3(9):e3156.

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

Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell. 2008 Feb 7;2(2):160-9.

Shen Y, Matsuno Y, Fouse SD, Rao N, Root S, Xu R, Pellegrini M, Riggs AD, Fan G. X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4709-14. Epub 2008 Mar 13.

Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S,Nelson SF, Pellegrini M, Jacobsen SE.Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. Epub 2008 Feb 17.

2007

Pham H, Ferrari R, Cokus SJ, Kurdistani SK, Pellegrini M. Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae. Mol Syst Biol. 2007;3:153. Epub 2007 Dec 18.

Call GB, Olson JM, Chen J, Villarasa N, Ngo KT, Yabroff AM, Cokus S, Pellegrini M, …, Banerjee U. Genomewide clonal analysis of lethal mutations in the Drosophila melanogaster eye: comparison of the X chromosome and autosomes. Genetics. 2007 Oct;177(2):689-97. Epub 2007 Aug 24.

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

Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J,Jacobsen SE. Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis. PLoS Biol. 2007 Apr 17;5(5):e129

2006

Levine DM, Haynor DR, Castle J, Stepaniants S, Pellegrini M, Mao M, Johnson JM. Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways. Genome Biol. 2006 Oct 17;7(10):R93

Xiaoyu Zhang, Junshi Yazaki, Ambika Sundaresan, Shawn Cokus, Simon W. L. Chan, Huaming Chen, Ian R. Henderson, Paul Shinn, Matteo Pellegrini, Steve E. Jacobsen and Joseph R. Ecker. (2006) Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis. Cell, 2006.08.003

Cokus SJ, Rose S, Haynor D, Gronbech-Jensen N, Pellegrini M. Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae. BMC Bioinformatics. 2006 Aug 16;7(1):381

Before 2006

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

Barbiellini B, Portnova A, Chetoukhina A, Lu CH, Pellegrini M. Position Dependent and Independent Evolutionary Models Based on Empirical Amino Acid Substitution Matrices. http://arxiv.org/abs/q-bio.PE/0405016.

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;5(5):R35. Epub 2004 Apr 16.

Strong M, Graeber TG, Beeby M, Pelligrini M, Thompson MJ, Yeates TO, Eisenberg D. Inference and Visualization of Protein Networks in Mycobacterium tuberculosis Based on Hierarchical Clustering of Whole Genome Functional Linkage Maps. Nucleic Acids Research, 2003, 31(24):7099-109.

Jason Gertz, Georgiy Elfond, Anna Shustrova, Matt Weisinger, Matteo Pellegrini, Shawn Cokus, and Bruce Rothschild, Inferring protein interactions from phylogenetic distance matrices Bioinformatics 2003, 19: 2039-2045

Strong M, Mallick P, Pellegrini M, Thompson MJ, and Eisenberg D, Inference of protein function and protein-protein interactions in M. tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biology, 4R:59, 2003.

Pellegrini M, Thompson MJ, Fierro J, Bowers P, A Computational Method to Assign Microbial Genes to Pathways. Journal of Cellular Biochemistry Suppl 37:106-9, 2001

Eastman P, Pellegrini M, Doniach S., Protein flexibility in solution and crystals. Journal of Chemical Physics 110:10141-10152, 1999

Pellegrini M, Yeates TO, Searching for frameshift evolutionary relationships between protein sequence families. Proteins: Structure function and genetics 37(2):278-83, 1999

Marcotte EM*, Pellegrini M*, Thompson MJ, Yeates TO, Eisenberg D, A combined algorithm for genome-wide prediction of protein function. Nature 402(6757):83-6,1999

Marcotte EM*, Pellegrini M*, Yeates TO, Eisenberg D, A census of protein repeats. Journal of Molecular Bioloy. 293(1):151-60, 1999

Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D, Detecting protein function and protein-protein interactions from genome sequences. Science 285(5428):751-3, 1999

Pellegrini M*, Marcotte EM*, Thompson MJ, Eisenberg D, Yeates TO, Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A. 96(8):4285-8,. 1999

Pellegrini M*, Marcotte EM*, Yeates TO, A fast algorithm for genome-wide analysis of proteins with repeated sequences. Proteins: Structure function and genetics 35(4):440-6, 1999

Pellegrini M, Larsen N, Yeates TO, Gronbech-Jensen N, A new constrained langevin method: application to protein crystallographic refinement. Physica A 261: 224, 1998

Hart PJ, Liu H, Pellegrini M, Nersissian AM, Gralla EB, Valentine JS, Eisenberg D, Subunit asymmetry in the three-dimensional structure of a human CuZnSOD mutant found in familial amyotrophic lateral sclerosis. Protein Science 7(3):545-55, 1998

Pellegrini M, Gronbech-Jensen N, Kelly JA, Yeates TO, Highly constrained multiple-copy refinement of protein crystal structures. Proteins: Structure function and genetics 29: 426, 1997

Pellegrini M, Wukowitz SW, Yeates TO, Simulations of protein crystal nucleation. Proteins: Structure function and genetics. 28: 515, 1997

Pellegrini M, Gronbech-Jensen N, Doniach S, Simulations of the thermodynamic properties of a short polyalanine peptide using potentials of mean force. Physica A 239: 244, 1997

Pellegrini M, Gronbech-Jensen N, Doniach S., Potentials of mean force for biomolecular simulations: theory and test on alanine dipeptide. Journal of Chemical Physics 104: 8639, 1996 

Lescar J, Pellegrini M, Souchon H, Tello D, Poljak RJ, Peterson N, Greene M, Alzari PM, Crystal structure of a cross-reaction complex between Fab F9.13.7 and guinea fowl lysozyme. Journal of Biological Chemistry. 270(30):18067-76, 1995

Pellegrini M & Doniach S, Modeling solvation contributions to conformational free energy changes of biomolecules using potential of mean force expansion. Journal of Chemical Physics 103:2696, 1995

Pellegrini M & Doniach S, Computer simulation of antibody binding specificity. Proteins: Structure function and genetics, 15(4):436-44, 1993

Books and Reviews

Pellegrini M, Cokus S. Pathway Analysis of Microarray Data. DNA MICROARRAYS: CURRENT APPLICATIONS Edited by E. DeRinaldis, Norfolk: Horizon Bioscience; 2007

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

Pellegrini M, Fitz-Gibbon ST, Yeates TO, Eisenberg D. Phylogenetic Profiling. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons, Ltd. , UK, 2005.

Matteo Pellegrini, David Haynor, Jason M Johnson. Protein Interaction Networks Expert Review of Proteomics Aug 2004, Vol. 1, No. 2, Pages 239-249.

Pellegrini M, Graeber TG, Computational Methods for protein function analysis. Progress in Protein Research. FOCUS ON PROTEIN RESEARCH Edited by John W. Robinson, Nova Science Publishers, Hauppauge NY. 2004. ISBN: 1-59033-968-1.

Pellegrini M, Computational Biology Methods in Protein Research: Identifying Chemokine-Receptor Pairs. Molecular Endocrinology: Methods and Protocols. Edited by T. Rajendra Kumar, Humana Press, Totowa, NJ, January 2004

Pellegrini, M, Defining interacting partners for drug discovery. Expert Opinion in Therapeutic Targets, 7(2):287-297, 2003.

Pellegrini M, Computational methods for protein function analysis. Current Opinions in Chemical Biology 5(1):46-50, 2000