Affiliations

Professor, Molecular, Cell, and Developmental Biology

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

Our lab is interested in the development of computational approaches to interpret genomic data. These methodologies allow us to develop large-scale models of transcriptional and epigenetic regulation as well as signal transduction. Our approach is to build models that integrate varied data that sheds light on these phenomena. This data is produced using the latest generation of high throughput sequencers, tiling and expression arrays along with mass spectrometry. Our research focuses on the development of both low and high-level analyses. For instance we are developing suites of tools for the analysis of high throughput sequencing data, as well as tools that combine multiple data types to infer transcriptional regulatory mechanisms.

Massoud Amir Hossein, Charbonnier Louis-Marie, Lopez David, Pellegrini Matteo, Phipatanakul Wanda, Chatila Talal A An asthma-associated IL4R variant exacerbates airway inflammation by promoting conversion of regulatory T cells to TH17-like cells. Nature medicine. 2016; 7(8): . Escuin-Ordinas Helena, Li Shuoran, Xie Michael W, Sun Lu, Hugo Willy, Huang Rong Rong, Jiao Jing, de-Faria Felipe Meira, Realegeno Susan, Krystofinski Paige, Azhdam Ariel, Komenan Sara Marie D, Atefi Mohammad, Comin-Anduix Begoña, Pellegrini Matteo, Cochran Alistair J, Modlin Robert L, Herschman Harvey R, Lo Roger S, McBride William H, Segura Tatiana, Ribas Antoni Cutaneous wound healing through paradoxical MAPK activation by BRAF inhibitors. Nature communications. 2016; 7(8): 12348. Vega-Vaquero Alejandro, Bonora Giancarlo, Morselli Marco, Vaquero-Sedas María I, Rubbi Liudmilla, Pellegrini Matteo, Vega-Palas Miguel A Novel features of telomere biology revealed by the absence of telomeric DNA methylation. Genome research. 2016; 26(8): 1047-56. Brumm Andrew J, Nunez Stefanie, Doroudchi Mehdi M, Kawaguchi Riki, Duan Jinhzu, Pellegrini Matteo, Lam Larry, Carmichael S Thomas, Deb Arjun, Hinman Jason D Astrocytes Can Adopt Endothelial Cell Fates in a p53-Dependent Manner. Molecular neurobiology. 2016; 7(8): . Schokrpur Shiruyeh, Hu Junhui, Moughon Diana L, Liu Peijun, Lin Lucia C, Hermann Kip, Mangul Serghei, Guan Wei, Pellegrini Matteo, Xu Hua, Wu Lily CRISPR-Mediated VHL Knockout Generates an Improved Model for Metastatic Renal Cell Carcinoma. Scientific reports. 2016; 6(1): 29032. Hoban Megan D, Lumaquin Dianne, Kuo Caroline Y, Romero Zulema, Long Joseph, Ho Michelle, Young Courtney S, Mojadidi Michelle, Fitz-Gibbon Sorel, Cooper Aaron R, Lill Georgia R, Urbinati Fabrizia, Campo-Fernandez Beatriz, Bjurstrom Carmen F, Pellegrini Matteo, Hollis Roger P, Kohn Donald B CRISPR/Cas9-mediated correction of the sickle mutation in human CD34+ cells. Molecular therapy : the journal of the American Society of Gene Therapy. 2016; 7(8): . Lam Larry, Chin Lydia, Halder Ramesh C, Sagong Bien, Famenini Sam, Sayre James, Montoya Dennis, Rubbi Liudmilla, Pellegrini Matteo, Fiala Milan 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; 132(1): . Rocchi Anna, Milioto Carmelo, Parodi Sara, Armirotti Andrea, Borgia Doriana, Pellegrini Matteo, Urciuolo Anna, Molon Sibilla, Morbidoni Valeria, Marabita Manuela, Romanello Vanina, Gatto Pamela, Blaauw Bert, Bonaldo Paolo, Sambataro Fabio, Robins Diane M, Lieberman Andrew P, Sorarù Gianni, Vergani Lodovica, Sandri Marco, Pennuto Maria 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; 132(1): 127-44. Hamaji Takashi, Lopez David, Pellegrini Matteo, Umen James Identification and Characterization of a cis-Regulatory Element for Zygotic Gene Expression in Chlamydomonas reinhardtii. G3 (Bethesda, Md.). 2016; 6(6): 1541-8. Steiger Julia, Stephan Alexander, Inkeles Megan S, Realegeno Susan, Bruns Heiko, Kröll Philipp, de Castro Kroner Juliana, Sommer Andrea, Batinica Marina, Pitzler Lena, Kalscheuer Rainer, Hartmann Pia, Plum Georg, Stenger Steffen, Pellegrini Matteo, Brachvogel Bent, Modlin Robert L, Fabri Mario 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; 197(1): 222-32. Douglass Stephen, Hsu Ssu-Wei, Cokus Shawn, Goldberg Robert B, Harada John J, Pellegrini Matteo A naïve Bayesian classifier for identifying plant microRNAs. The Plant journal : for cell and molecular biology. 2016; 86(6): 481-92. Realegeno Susan, Kelly-Scumpia Kindra M, Dang Angeline Tilly, Lu Jing, Teles Rosane, Liu Philip T, Schenk Mirjam, Lee Ernest Y, Schmidt Nathan W, Wong Gerard C L, Sarno Euzenir N, Rea Thomas H, Ochoa Maria T, Pellegrini Matteo, Modlin Robert L S100A12 Is Part of the Antimicrobial Network against Mycobacterium leprae in Human Macrophages. PLoS pathogens. 2016; 12(6): e1005705. Zhang Hanwei, Prado Kris, Zhang Kelvin X, Peek Elizabeth M, Lee Jane, Wang Xiaoyan, Huang Jiaoti, Li Gang, Pellegrini Matteo, Chin Arnold I 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; 12(6): . Flinders Colin, Lam Larry, Rubbi Liudmilla, Ferrari Roberto, Fitz-Gibbon Sorel, Chen Pao-Yang, Thompson Michael, Christofk Heather, B Agus David, Ruderman Daniel, Mallick Parag, Pellegrini Matteo Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma. Genome medicine. 2016; 8(1): 54. Chin Chee Jia, Cooper Aaron R, Lill Georgia R, Evseenko Denis, Zhu Yuhua, He Chong Bin, Casero David, Pellegrini Matteo, Kohn Donald B, Crooks Gay M Genetic Tagging During Human Mesoderm Differentiation Reveals Tripotent Lateral Plate Mesodermal Progenitors. Stem cells (Dayton, Ohio). 2016; 34(5): 1239-50. Meng Qingying, Ying Zhe, Noble Emily, Zhao Yuqi, Agrawal Rahul, Mikhail Andrew, Zhuang Yumei, Tyagi Ethika, Zhang Qing, Lee Jae-Hyung, Morselli Marco, Orozco Luz, Guo Weilong, Kilts Tina M, Zhu Jun, Zhang Bin, Pellegrini Matteo, Xiao Xinshu, Young Marian F, Gomez-Pinilla Fernando, Yang Xia Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders. EBioMedicine. 2016; 7(1): 157-66. Sack Lawren, Ball Marilyn C, Brodersen Craig, Davis Stephen D, Des Marais David L, Donovan Lisa A, Givnish Thomas J, Hacke Uwe G, Huxman Travis, Jansen Steven, Jacobsen Anna L, Johnson Daniel M, Koch George W, Maurel Christophe, McCulloh Katherine A, McDowell Nate G, McElrone Andrew, Meinzer Frederick C, Melcher Peter J, North Gretchen, Pellegrini Matteo, Pockman William T, Pratt R Brandon, Sala Anna, Santiago Louis S, Savage Jessica A, Scoffoni Christine, Sevanto Sanna, Sperry John, Tyerman Stephen D, Way Danielle, Holbrook N Michele 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; 34(5): . Gugger Paul F, Fitz-Gibbon Sorel, PellEgrini Matteo, Sork Victoria L Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients. Molecular ecology. 2016; 25(8): 1665-80. Janowitz Koch Ilana, Clark Michelle M, Thompson Michael J, Deere-Machemer Kerry A, Wang Jun, Duarte Lionel, Gnanadesikan Gitanjali E, McCoy Eskender L, Rubbi Liudmilla, Stahler Daniel R, Pellegrini Matteo, Ostrander Elaine A, Wayne Robert K, Sinsheimer Janet S, vonHoldt Bridgett M The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Molecular ecology. 2016; 25(8): 1838-55. Chen Haodong, Orozco Luz D, Wang Jessica, Rau Christoph D, Rubbi Liudmilla, Ren Shuxun, Wang Yibin, Pellegrini Matteo, Lusis Aldons J, Vondriska Thomas M DNA Methylation Indicates Susceptibility to Isoproterenol-Induced Cardiac Pathology and Is Associated With Chromatin States. Circulation research. 2016; 118(5): 786-97. Liu Wei, Jiang Xingpeng, Pellegrini Matteo, Wang Xiaofan Discovering communities in complex networks by edge label propagation. Scientific reports. 2016; 6(5): 22470. Zhang Kelvin Xi, Tan Liming, Pellegrini Matteo, Zipursky S Lawrence, McEwen Jason M Rapid Changes in the Translatome during the Conversion of Growth Cones to Synaptic Terminals. Cell reports. 2016; 14(5): 1258-71. Soragni Alice, Janzen Deanna M, Johnson Lisa M, Lindgren Anne G, Thai-Quynh Nguyen Anh, Tiourin Ekaterina, Soriaga Angela B, Lu Jing, Jiang Lin, Faull Kym F, Pellegrini Matteo, Memarzadeh Sanaz, Eisenberg David S A Designed Inhibitor of p53 Aggregation Rescues p53 Tumor Suppression in Ovarian Carcinomas. Cancer cell. 2016; 29(1): 90-103. Lopez David, Hamaji Takashi, Kropat Janette, De Hoff Peter, Morselli Marco, Rubbi Liudmilla, Fitz-Gibbon Sorel, Gallaher Sean D, Merchant Sabeeha S, Umen James, Pellegrini Matteo Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle. Plant physiology. 2015; 169(4): 2730-43. Liu Wei, Wu Aiping, Pellegrini Matteo, Wang Xiaofan Integrative analysis of human protein, function and disease networks. Scientific reports. 2015; 5(4): 14344. Gallaher Sean D, Fitz-Gibbon Sorel T, Glaesener Anne G, Pellegrini Matteo, Merchant Sabeeha S 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; 27(9): 2335-52. Clark Rebecca I, Salazar Anna, Yamada Ryuichi, Fitz-Gibbon Sorel, Morselli Marco, Alcaraz Jeanette, Rana Anil, Rera Michael, Pellegrini Matteo, Ja William W, Walker David W Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality. Cell reports. 2015; 12(10): 1656-67. Brusslan Judy A, Bonora Giancarlo, Rus-Canterbury Ana M, Tariq Fayha, Jaroszewicz Artur, Pellegrini Matteo A Genome-Wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence. Plant physiology. 2015; 168(4): 1246-61. Sabbatucci Michela, Covino Daniela Angela, Purificato Cristina, Mallano Alessandra, Federico Maurizio, Lu Jing, Rinaldi Arturo Ottavio, Pellegrini Matteo, Bona Roberta, Michelini Zuleika, Cara Andrea, Vella Stefano, Gessani Sandra, Andreotti Mauro, Fantuzzi Laura Erratum to: Endogenous CCL2 neutralization restricts HIV-1 replication in primary human macrophages by inhibiting viral DNA accumulation. Retrovirology. 2015; 12(4): 47. Platt Alexander, Gugger Paul F, Pellegrini Matteo, Sork Victoria L Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations. Molecular ecology. 2015; 24(15): 3823-30. Orozco Luz D, Morselli Marco, Rubbi Liudmilla, Guo Weilong, Go James, Shi Huwenbo, Lopez David, Furlotte Nicholas A, Bennett Brian J, Farber Charles R, Ghazalpour Anatole, Zhang Michael Q, Bahous Renata, Rozen Rima, Lusis Aldons J, Pellegrini Matteo Epigenome-wide association of liver methylation patterns and complex metabolic traits in mice. Cell metabolism. 2015; 21(6): 905-17. Morselli Marco, Pastor William A, Montanini Barbara, Nee Kevin, Ferrari Roberto, Fu Kai, Bonora Giancarlo, Rubbi Liudmilla, Clark Amander T, Ottonello Simone, Jacobsen Steven E, Pellegrini Matteo In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse. eLife. 2015; 4(3): e06205. Soufi Abdenour, Garcia Meilin Fernandez, Jaroszewicz Artur, Osman Nebiyu, Pellegrini Matteo, Zaret Kenneth S Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming. Cell. 2015; 161(3): 555-68. Minkovsky Alissa, Sahakyan Anna, Bonora Giancarlo, Damoiseaux Robert, Dimitrova Elizabeth, Rubbi Liudmilla, Pellegrini Matteo, Radu Caius G, Plath Kathrin A high-throughput screen of inactive X chromosome reactivation identifies the enhancement of DNA demethylation by 5-aza-2'-dC upon inhibition of ribonucleotide reductase. Epigenetics & chromatin. 2015; 8(2): 42. Lam Larry, Halder Ramesh C, Montoya Dennis J, Rubbi Liudmilla, Rinaldi Arturo, Sagong Bien, Weitzman Sarah, Rubattino Rachel, Singh Ram Raj, Pellegrini Matteo, Fiala Milan Anti-inflammatory therapies of amyotrophic lateral sclerosis guided by immune pathways. American journal of neurodegenerative disease. 2015; 4(2): 28-39. Fiala Milan, Pellegrini Matteo Development of effective therapy for sporadic ALS. Expert opinion on biological therapy. 2015; 15(8): 1249. Sabbatucci Michela, Covino Daniela Angela, Purificato Cristina, Mallano Alessandra, Federico Maurizio, Lu Jing, Rinaldi Arturo Ottavio, Pellegrini Matteo, Bona Roberta, Michelini Zuleika, Cara Andrea, Vella Stefano, Gessani Sandra, Andreotti Mauro, Fantuzzi Laura Endogenous CCL2 neutralization restricts HIV-1 replication in primary human macrophages by inhibiting viral DNA accumulation. Retrovirology. 2015; 12(6): 4. Org Tõnis, Duan Dan, Ferrari Roberto, Montel-Hagen Amelie, Van Handel Ben, Kerényi Marc A, Sasidharan Rajkumar, Rubbi Liudmilla, Fujiwara Yuko, Pellegrini Matteo, Orkin Stuart H, Kurdistani Siavash K, Mikkola Hanna Ka Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence. The EMBO journal. 2015; 34(6): 759-77. Inkeles Megan S, Scumpia Philip O, Swindell William R, Lopez David, Teles Rosane M B, Graeber Thomas G, Meller Stephan, Homey Bernhard, Elder James T, Gilliet Michel, Modlin Robert L, Pellegrini Matteo Comparison of molecular signatures from multiple skin diseases identifies mechanisms of immunopathogenesis. The Journal of investigative dermatology. 2015; 135(1): 151-9. Simpson Larry, Douglass Stephen M, Lake James A, Pellegrini Matteo, Li Feng Comparison of the Mitochondrial Genomes and Steady State Transcriptomes of Two Strains of the Trypanosomatid Parasite, Leishmania tarentolae. PLoS neglected tropical diseases. 2015; 9(7): e0003841. Conti Anastasia, Carnevali Davide, Bollati Valentina, Fustinoni Silvia, Pellegrini Matteo, Dieci Giorgio Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data. Nucleic acids research. 2015; 43(2): 817-35. Averna Monica, De Tullio Roberta, Pedrazzi Marco, Bavestrello Margherita, Pellegrini Matteo, Salamino Franca, Pontremoli Sandro, Melloni Edon Interaction between calpain-1 and HSP90: new insights into the regulation of localization and activity of the protease. PloS one. 2015; 10(1): e0116738. Thompson Michael J, Rubbi Liudmilla, Dawson David W, Donahue Timothy R, Pellegrini Matteo Pancreatic cancer patient survival correlates with DNA methylation of pancreas development genes. PloS one. 2015; 10(6): e0128814. Averna Monica, Pellegrini Matteo, Cervetto Chiara, Pedrazzi Marco, Bavestrello Margherita, De Tullio Roberta, Salamino Franca, Pontremoli Sandro, Melloni Edon Physiological Roles of Calpain 1 Associated to Multiprotein NMDA Receptor Complex. PloS one. 2015; 10(10): e0139750. Briot Anaïs, Jaroszewicz Artur, Warren Carmen M, Lu Jing, Touma Marlin, Rudat Carsten, Hofmann Jennifer J, Airik Rannar, Weinmaster Gerry, Lyons Karen, Wang Yibin, Kispert Andreas, Pellegrini Matteo, Iruela-Arispe M Luisa Repression of Sox9 by Jag1 is continuously required to suppress the default chondrogenic fate of vascular smooth muscle cells. Developmental cell. 2014; 31(6): 707-21. Huang Kevin, Wu Zhourui, Liu Zhenshan, Hu Ganlu, Yu Juehua, Chang Kai H, Kim Kee-Pyo, Le Thuc, Faull Kym F, Rao Nagesh, Gennery Andrew, Xue Zhigang, Wang Cun-Yu, Pellegrini Matteo, Fan Guoping 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; 23(24): 6448-57. Ferrari Roberto, Gou Dawei, Jawdekar Gauri, Johnson Sarah A, Nava Miguel, Su Trent, Yousef Ahmed F, Zemke Nathan R, Pellegrini Matteo, Kurdistani Siavash K, Berk Arnold J 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; 16(5): 663-76. Feng Suhua, Cokus Shawn J, Schubert Veit, Zhai Jixian, Pellegrini Matteo, Jacobsen Steven E Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Molecular cell. 2014; 55(5): 694-707. Liu Wei, Pellegrini Matteo, Wang Xiaofan Detecting communities based on network topology. Scientific reports. 2014; 4(7): 5739. Montoya Dennis, Inkeles Megan S, Liu Phillip T, Realegeno Susan, Teles Rosane M B, Vaidya Poorva, Munoz Marcos A, Schenk Mirjam, Swindell William R, Chun Rene, Zavala Kathryn, Hewison Martin, Adams John S, Horvath Steve, Pellegrini Matteo, Bloom Barry R, Modlin Robert L IL-32 is a molecular marker of a host defense network in human tuberculosis. Science translational medicine. 2014; 6(250): 250ra114. Montanini Barbara, Chen Pao-Yang, Morselli Marco, Jaroszewicz Artur, Lopez David, Martin Francis, Ottonello Simone, Pellegrini Matteo Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content. Genome biology. 2014; 15(7): 411. Ramundo Silvia, Casero David, Mühlhaus Timo, Hemme Dorothea, Sommer Frederik, Crèvecoeur Michèle, Rahire Michèle, Schroda Michael, Rusch Jannette, Goodenough Ursula, Pellegrini Matteo, Perez-Perez Maria Esther, Crespo José Luis, Schaad Olivier, Civic Natacha, Rochaix Jean David Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control. The Plant cell. 2014; 26(5): 2201-2222. Orozco Luz D, Rubbi Liudmilla, Martin Lisa J, Fang Fang, Hormozdiari Farhad, Che Nam, Smith Andrew D, Lusis Aldons J, Pellegrini Matteo Intergenerational genomic DNA methylation patterns in mouse hybrid strains. Genome biology. 2014; 15(5): R68. Ooi Aik T, Gower Adam C, Zhang Kelvin X, Vick Jessica L, Hong Longsheng, Nagao Brian, Wallace W Dean, Elashoff David A, Walser Tonya C, Dubinett Steven M, Pellegrini Matteo, Lenburg Marc E, Spira Avrum, Gomperts Brigitte N Molecular profiling of premalignant lesions in lung squamous cell carcinomas identifies mechanisms involved in stepwise carcinogenesis. Cancer prevention research (Philadelphia, Pa.). 2014; 7(5): 487-95. Wakao Setsuko, Chin Brian L, Ledford Heidi K, Dent Rachel M, Casero David, Pellegrini Matteo, Merchant Sabeeha S, Niyogi Krishna K Phosphoprotein SAK1 is a regulator of acclimation to singlet oxygen in Chlamydomonas reinhardtii. eLife. 2014; 3(5): e02286. Goodenough Ursula, Blaby Ian, Casero David, Gallaher Sean D, Goodson Carrie, Johnson Shannon, Lee Jae-Hyeok, Merchant Sabeeha S, Pellegrini Matteo, Roth Robyn, Rusch Jannette, Singh Manmilan, Umen James G, Weiss Taylor L, Wulan Tuya The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii. Eukaryotic cell. 2014; 13(5): 591-613. Schmollinger Stefan, Mühlhaus Timo, Boyle Nanette R, Blaby Ian K, Casero David, Mettler Tabea, Moseley Jeffrey L, Kropat Janette, Sommer Frederik, Strenkert Daniela, Hemme Dorothea, Pellegrini Matteo, Grossman Arthur R, Stitt Mark, Schroda Michael, Merchant Sabeeha S Nitrogen-Sparing Mechanisms in Chlamydomonas Affect the Transcriptome, the Proteome, and Photosynthetic Metabolism. The Plant cell. 2014; 26(4): 1410-1435. Kawashima Tadashi, Douglass Stephen, Gabunilas Jason, Pellegrini Matteo, Chanfreau Guillaume F Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae. PLoS genetics. 2014; 10(4): e1004249. Wheelwright Matthew, Kim Elliot W, Inkeles Megan S, De Leon Avelino, Pellegrini Matteo, Krutzik Stephan R, Liu Philip T All-trans retinoic acid-triggered antimicrobial activity against Mycobacterium tuberculosis is dependent on NPC2. Journal of immunology (Baltimore, Md. : 1950). 2014; 192(5): 2280-90. Li Yun, Chen Jason A, Sears Renee L, Gao Fuying, Klein Eric D, Karydas Anna, Geschwind Michael D, Rosen Howard J, Boxer Adam L, Guo Weilong, Pellegrini Matteo, Horvath Steve, Miller Bruce L, Geschwind Daniel H, Coppola Giovanni An epigenetic signature in peripheral blood associated with the haplotype on 17q21.31, a risk factor for neurodegenerative tauopathy. PLoS genetics. 2014; 10(3): e1004211. Guo Weilong, Chung Wen-Yu, Qian Minping, Pellegrini Matteo, Zhang Michael Q Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. Nucleic acids research. 2014; 42(5): 3009-16. Nakashima Yasuhiro, Yanez Diana A, Touma Marlin, Nakano Haruko, Jaroszewicz Artur, Jordan Maria C, Pellegrini Matteo, Roos Kenneth P, Nakano Atsushi Nkx2-5 suppresses the proliferation of atrial myocytes and conduction system. Circulation research. 2014; 114(7): 1103-13. Johnson Lianna M, Du Jiamu, Hale Christopher J, Bischof Sylvain, Feng Suhua, Chodavarapu Ramakrishna K, Zhong Xuehua, Marson Giuseppe, Pellegrini Matteo, Segal David J, Patel Dinshaw J, Jacobsen Steven E SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature. 2014; 507(7490): 124-8. Widman Nicolas, Feng Suhua, Jacobsen Steven E, Pellegrini Matteo Epigenetic differences between shoots and roots in Arabidopsis reveals tissue-specific regulation. Epigenetics. 2014; 9(2): 236-42. Elhaik Eran, Pellegrini Matteo, Tatarinova Tatiana V Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa. BMC bioinformatics. 2014; 15(2): 23. Chen Pao-Yang, Montanini Barbara, Liao Wen-Wei, Morselli Marco, Jaroszewicz Artur, Lopez David, Ottonello Simone, Pellegrini Matteo A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum. GigaScience. 2014; 3(1): 25. Huang Kevin, Shen Yin, Xue Zhigang, Bibikova Marina, April Craig, Liu Zhenshan, Cheng Linzhao, Nagy Andras, Pellegrini Matteo, Fan Jian-Bing, Fan Guoping A panel of CpG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells. Stem cell reports. 2014; 2(1): 36-43. Yao Jianchao, Zhang Kelvin Xi, Kramer Melissa, Pellegrini Matteo, McCombie W Richard FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies. Bioinformatics (Oxford, England). 2014; 2(1): . House Christopher H, Pellegrini Matteo, Fitz-Gibbon Sorel T Genome-wide gene order distances support clustering the gram-positive bacteria. Frontiers in microbiology. 2014; 5(1): 785. Lei Nan Ye, Jabaji Ziyad, Wang Jiafang, Joshi Vaidehi S, Brinkley Garrett J, Khalil Hassan, Wang Fengchao, Jaroszewicz Artur, Pellegrini Matteo, Li Linheng, Lewis Michael, Stelzner Matthias, Dunn James C Y, Martín Martín G Intestinal subepithelial myofibroblasts support the growth of intestinal epithelial stem cells. PloS one. 2014; 9(1): e84651. Ghahramani Negar M, Ngun Tuck C, Chen Pao-Yang, Tian Yuan, Krishnan Sangitha, Muir Stephanie, Rubbi Liudmilla, Arnold Arthur P, de Vries Geert J, Forger Nancy G, Pellegrini Matteo, Vilain Eric The effects of perinatal testosterone exposure on the DNA methylome of the mouse brain are late-emerging. Biology of sex differences. 2014; 5(1): 8. Guo Weilong, Fiziev Petko, Yan Weihong, Cokus Shawn, Sun Xueguang, Zhang Michael Q, Chen Pao-Yang, Pellegrini Matteo BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC genomics. 2013; 14(1): 774. Walker Sara Imari, Callahan Benjamin J, Arya Gaurav, Barry J David, Bhattacharya Tanmoy, Grigoryev Sergei, Pellegrini Matteo, Rippe Karsten, Rosenberg Susan M Evolutionary dynamics and information hierarchies in biological systems. Annals of the New York Academy of Sciences. 2013; 1305(1): 1-17. Denholtz Matthew, Bonora Giancarlo, Chronis Constantinos, Splinter Erik, de Laat Wouter, Ernst Jason, Pellegrini Matteo, Plath Kathrin Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell stem cell. 2013; 13(5): 602-16. Blaby Ian K, Glaesener Anne G, Mettler Tabea, Fitz-Gibbon Sorel T, Gallaher Sean D, Liu Bensheng, Boyle Nanette R, Kropat Janette, Stitt Mark, Johnson Shannon, Benning Christoph, Pellegrini Matteo, Casero David, Merchant Sabeeha S Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant. The Plant cell. 2013; 25(11): 4305-23. Urzica Eugen I, Vieler Astrid, Hong-Hermesdorf Anne, Page M Dudley, Casero David, Gallaher Sean D, Kropat Janette, Pellegrini Matteo, Benning Christoph, Merchant Sabeeha S Remodeling of membrane lipids in iron-starved Chlamydomonas. The Journal of biological chemistry. 2013; 288(42): 30246-58. Hemschemeier Anja, Casero David, Liu Bensheng, Benning Christoph, Pellegrini Matteo, Happe Thomas, Merchant Sabeeha S Copper response regulator1-dependent and -independent responses of the Chlamydomonas reinhardtii transcriptome to dark anoxia. The Plant cell. 2013; 25(9): 3186-211. Chen Pao-Yang, Ganguly Amit, Rubbi Liudmilla, Orozco Luz D, Morselli Marco, Ashraf Davin, Jaroszewicz Artur, Feng Suhua, Jacobsen Steve E, Nakano Atsushi, Devaskar Sherin U, Pellegrini Matteo Intrauterine calorie restriction affects placental DNA methylation and gene expression. Physiological genomics. 2013; 45(14): 565-76. Vining Kelly, Pomraning Kyle R, Wilhelm Larry J, Ma Cathleen, Pellegrini Matteo, Di Yanming, Mockler Todd C, Freitag Michael, Strauss Steven H Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa. BMC plant biology. 2013; 13(7): 92. Sridharan Rupa, Gonzales-Cope Michelle, Chronis Constantinos, Bonora Giancarlo, McKee Robin, Huang Chengyang, Patel Sanjeet, Lopez David, Mishra Nilamadhab, Pellegrini Matteo, Carey Michael, Garcia Benjamin A, Plath Kathrin Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency. Nature cell biology. 2013; 15(7): 872-82. Varshney Gaurav K, Lu Jing, Gildea Derek E, Huang Haigen, Pei Wuhong, Yang Zhongan, Huang Sunny C, Schoenfeld David, Pho Nam H, Casero David, Hirase Takashi, Mosbrook-Davis Deborah, Zhang Suiyuan, Jao Li-En, Zhang Bo, Woods Ian G, Zimmerman Steven, Schier Alexander F, Wolfsberg Tyra G, Pellegrini Matteo, Burgess Shawn M, Lin Shuo A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Genome research. 2013; 23(4): 727-35. Janzen Deanna M, Cheng Donghui, Schafenacker Amanda M, Paik Daniel Y, Goldstein Andrew S, Witte Owen N, Jaroszewicz Artur, Pellegrini Matteo, Memarzadeh Sanaz Estrogen and progesterone together expand murine endometrial epithelial progenitor cells. Stem cells (Dayton, Ohio). 2013; 31(4): 808-22. Stroud Hume, Ding Bo, Simon Stacey A, Feng Suhua, Bellizzi Maria, Pellegrini Matteo, Wang Guo-Liang, Meyers Blake C, Jacobsen Steven E Plants regenerated from tissue culture contain stable epigenome changes in rice. eLife. 2013; 2(4): e00354. Vincent John J, Huang Yun, Chen Pao-Yang, Feng Suhua, Calvopiña Joseph H, Nee Kevin, Lee Serena A, Le Thuc, Yoon Alexander J, Faull Kym, Fan Guoping, Rao Anjana, Jacobsen Steven E, Pellegrini Matteo, Clark Amander T Stage-specific roles for tet1 and tet2 in DNA demethylation in primordial germ cells. Cell stem cell. 2013; 12(4): 470-8. Malasarn Davin, Kropat Janette, Hsieh Scott I, Finazzi Giovanni, Casero David, Loo Joseph A, Pellegrini Matteo, Wollman Francis-André, Merchant Sabeeha S Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii. The Journal of biological chemistry. 2013; 288(15): 10672-83. Tatarinova Tatiana, Elhaik Eran, Pellegrini Matteo Cross-species analysis of genic GC3 content and DNA methylation patterns. Genome biology and evolution. 2013; 5(8): 1443-56. Daniels-Wells Tracy R, Helguera Gustavo, Rodríguez José A, Leoh Lai Sum, Erb Michael A, Diamante Graciel, Casero David, Pellegrini Matteo, Martínez-Maza Otoniel, Penichet Manuel L 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. 2013; 27(1): 220-31. Palanca Ana Marie S, Lee Sung-Ling, Yee Laura E, Joe-Wong Carlee, Trinh Le A, Hiroyasu Elizabeth, Husain Majid, Fraser Scott E, Pellegrini Matteo, Sagasti Alvaro New transgenic reporters identify somatosensory neuron subtypes in larval zebrafish. Developmental neurobiology. 2013; 73(2): 152-67. Duanmu Deqiang, Casero David, Dent Rachel M, Gallaher Sean, Yang Wenqiang, Rockwell Nathan C, Martin Shelley S, Pellegrini Matteo, Niyogi Krishna K, Merchant Sabeeha S, Grossman Arthur R, Lagarias J Clark Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival. Proceedings of the National Academy of Sciences of the United States of America. 2013; 110(9): 3621-6. Gkountela Sofia, Li Ziwei, Vincent John J, Zhang Kelvin X, Chen Angela, Pellegrini Matteo, Clark Amander T 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. 2013; 15(1): 113-22. Hsieh Scott I, Castruita Madeli, Malasarn Davin, Urzica Eugen, Erde Jonathan, Page M Dudley, Yamasaki Hiroaki, Casero David, Pellegrini Matteo, Merchant Sabeeha S, Loo Joseph A The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii. Molecular & cellular proteomics : MCP. 2013; 12(1): 65-86. Molnár István, Lopez David, Wisecaver Jennifer H, Devarenne Timothy P, Weiss Taylor L, Pellegrini Matteo, Hackett Jeremiah D 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; 13(3): 576. Slavov Gancho T, DiFazio Stephen P, Martin Joel, Schackwitz Wendy, Muchero Wellington, Rodgers-Melnick Eli, Lipphardt Mindie F, Pennacchio Christa P, Hellsten Uffe, Pennacchio Len A, Gunter Lee E, Ranjan Priya, Vining Kelly, Pomraning Kyle R, Wilhelm Larry J, Pellegrini Matteo, Mockler Todd C, Freitag Michael, Geraldes Armando, El-Kassaby Yousry A, Mansfield Shawn D, Cronk Quentin C B, Douglas Carl J, Strauss Steven H, Rokhsar Dan, Tuskan Gerald A Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. The New phytologist. 2012; 196(3): 713-25. Ghazalpour Anatole, Rau Christoph D, Farber Charles R, Bennett Brian J, Orozco Luz D, van Nas Atila, Pan Calvin, Allayee Hooman, Beaven Simon W, Civelek Mete, Davis Richard C, Drake Thomas A, Friedman Rick A, Furlotte Nick, Hui Simon T, Jentsch J David, Kostem Emrah, Kang Hyun Min, Kang Eun Yong, Joo Jong Wha, Korshunov Vyacheslav A, Laughlin Rick E, Martin Lisa J, Ohmen Jeffrey D, Parks Brian W, Pellegrini Matteo, Reue Karen, Smith Desmond J, Tetradis Sotirios, Wang Jessica, Wang Yibin, Weiss James N, Kirchgessner Todd, Gargalovic Peter S, Eskin Eleazar, Lusis Aldons J, LeBoeuf Renée C 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; 23(9-10): 680-92. Marinelli Laura J, Fitz-Gibbon Sorel, Hayes Clarmyra, Bowman Charles, Inkeles Megan, Loncaric Anya, Russell Daniel A, Jacobs-Sera Deborah, Cokus Shawn, Pellegrini Matteo, Kim Jenny, Miller Jeff F, Hatfull Graham F, Modlin Robert L Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates. mBio. 2012; 3(5): . Urzica Eugen I, Casero David, Yamasaki Hiroaki, Hsieh Scott I, Adler Lital N, Karpowicz Steven J, Blaby-Haas Crysten E, Clarke Steven G, Loo Joseph A, Pellegrini Matteo, Merchant Sabeeha S Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage. The Plant cell. 2012; 24(10): 3921-48. Orozco Luz D, Bennett Brian J, Farber Charles R, Ghazalpour Anatole, Pan Calvin, Che Nam, Wen Pingzi, Qi Hong Xiu, Mutukulu Adonisa, Siemers Nathan, Neuhaus Isaac, Yordanova Roumyana, Gargalovic Peter, Pellegrini Matteo, Kirchgessner Todd, Lusis Aldons J Unraveling inflammatory responses using systems genetics and gene-environment interactions in macrophages. Cell. 2012; 151(3): 658-70. Van Handel Ben, Montel-Hagen Amélie, Sasidharan Rajkumar, Nakano Haruko, Ferrari Roberto, Boogerd Cornelis J, Schredelseker Johann, Wang Yanling, Hunter Sean, Org Tõnis, Zhou Jian, Li Xinmin, Pellegrini Matteo, Chen Jau-Nian, Orkin Stuart H, Kurdistani Siavash K, Evans Sylvia M, Nakano Atsushi, Mikkola Hanna K A Scl represses cardiomyogenesis in prospective hemogenic endothelium and endocardium. Cell. 2012; 150(3): 590-605. Ferrari Roberto, Su Trent, Li Bing, Bonora Giancarlo, Oberai Amit, Chan Yvonne, Sasidharan Rajkumar, Berk Arnold J, Pellegrini Matteo, Kurdistani Siavash K Reorganization of the host epigenome by a viral oncogene. Genome research. 2012; 22(7): 1212-21. Chodavarapu Ramakrishna K, Feng Suhua, Ding Bo, Simon Stacey A, Lopez David, Jia Yulin, Wang Guo-Liang, Meyers Blake C, Jacobsen Steven E, Pellegrini Matteo Transcriptome and methylome interactions in rice hybrids. Proceedings of the National Academy of Sciences of the United States of America. 2012; 109(30): 12040-5. 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; Epub ahead of print: . 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; 6(3): . Mara H. Sherman, Ali I. Kuraishy, Chetan Deshpande, Jason S. Hong, Nicholas A. Cacalano, Richard A. Gatti, John P. Manis, Michael A. Damore, Matteo Pellegrini, Michael A. Teitell AID-Induced Genotoxic Stress Promotes B Cell Differentiation in the Germinal Center via ATM and LKB1 Signaling. Molecular Cell. 2010; 39(6): 873-885. Chen PY, Cokus SJ, Pellegrini M BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics. 2010; 11: 203. 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; 107(19): 8689-94. 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; 328(5976): 351-4. 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; 6: 449. 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; 463(7284): 1101-5. Chin MH, Pellegrini M, Plath K, Lowry WE Molecular analyses of human induced pluripotent stem cells and embryonic stem cells. Cell Stem Cell. 2010; 7(2): 263-9. González-Ballester D, Casero D, Cokus S, Pellegrini M, Merchant SS, Grossman AR RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. Plant Cell. 2010; 22(6): 2058-84. 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; 466(7304): 388-92. Das D, Pellegrini M, Gray JW A primer on regression methods for decoding cis-regulatory logic. PLoS Comput Biol. 2009; 5(1): e100026. Orozco LD, Cokus SJ, Ghazalpour A, Ingram-Drake L, Wang S, van Nas A, Che N, Araujo JA, Pellegrini M, Lusis AJ Copy number variation influences gene expression and metabolic traits in mice. Hum Mol Genet. 2009; 18(21): 4118-29. Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression. BMC Syst Biol. 2009; 3(115): . Widman, N. Jacobsen, S. E. Pellegrini, M. Determining the conservation of DNA methylation in Arabidopsis. Epigenetics. 2009; 4(2): 119-24. Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 2009; 10(6): R62. Kawashima T, Pellegrini M, Chanfreau GF Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations. RNA. 2009; 15(12): 2236-47. 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; 16(7): 763-8. Gekas, C. Rhodes, K. E. 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An improved method for identifying functionally linked proteins using phylogenetic profiles. BMC Bioinformatics. 2007; 8 Suppl 4: S7. Pham, H. Ferrari, R. Cokus, S. J. Kurdistani, S. K. Pellegrini, M. Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae. Mol Syst Biol. 2007; 3: 153. Zhang, X., Clarenz, O., Cokus, S., Bernatavichute, Y. V., Pellegrini, M., Goodrich, J., Jacobsen, S. E. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 2007; 5(5): e129. Levine, D. M. Haynor, D. R. Castle, J. C. Stepaniants, S. B. Pellegrini, M. Mao, M. Johnson, J. M. Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways. Genome Biol. 2006; 7(10): R93. Zhang, X. Yazaki, J. Sundaresan, A. Cokus, S. Chan, S. W. Chen, H. Henderson, I. R. Shinn, P. Pellegrini, M. Jacobsen, S. E. Ecker, J. R. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell. 2006; 126(6): 1189-201. Cokus, S. 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; 7: 381. Eisenberg, D. Marcotte, E. McLachlan, A. D. Pellegrini, M. Bioinformatic challenges for the next decade(s). Philos Trans R Soc Lond B Biol Sci. 2006; 361(1467): 525-7. Li, H. Pellegrini, M. Eisenberg, D. Detection of parallel functional modules by comparative analysis of genome sequences. Nat Biotechnol. 2005; 23(2): 253-60. M Pellegrini, ST Fitz-Gibbon, TO Yeates, D Eisenberg Phylogenetic Profiling. Encyclopedia of Genetics, Genomics, Proteomics and Bioinfomatics. 2005; Eds: Lynn Jorde , Peter Little , Mike Dunn and Shankar Subramaniam: 4.4. Pellegrini, M. Computational Biology Methods in Protein Research: Identifying Chemokine-Receptor Pairs. Molecular Endocrinology: Methods and Protocols. 2004; . Pellegrini, M., Graeber, TG Computational Methods For Protein Function Analysis. Focus on Protein Research. 2004; Chapter VIII(Ed: John W. Robinson ): 167-191. Bowers, P. M. Pellegrini, M. Thompson, M. J. Fierro, J. Yeates, T. O. Eisenberg, D. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol. 2004; 5(5): R35. Pellegrini, M. Haynor, D. Johnson, J. M. Protein interaction networks. Expert Rev Proteomics. 2004; 1(2): 239-49. Strong, M. Graeber, T. G. Beeby, M. Pellegrini, M. Thompson, M. J. Yeates, T. O. Eisenberg, D. Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res. 2003; 31(24): 7099-109. Gertz, J. Elfond, G. Shustrova, A. Weisinger, M. Pellegrini, M. Cokus, S. Rothschild, B. Inferring protein interactions from phylogenetic distance matrices. Bioinformatics. 2003; 19(16): 2039-45. Pellegrini, M. Defining interacting partners for drug discovery. Expert Opinion on Therapeutic Targets. 2003; 7(2): 287-297. Strong, M. Mallick, P. Pellegrini, M. Thompson, M. J. Eisenberg, D. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol. 2003; 4(9): R59. Barbiellini, B. Portnova, A. Chetoukhina, A. Lu, C. H. Pellegrini, M. Position Dependent and Independent Evolutionary Models Based on Empirical Amino Acid Substitution Matrices. Paper presented at the Biological Language Conference. 2003; .