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Eddy Rubin, MD, Ph.D.

Principal Scientist (visiting)

Laboratory for Research in Complex Systems


  • MD, University of Rochester Medical Center, Rochester, NY

  • Ph.D. (Physics), University of Rochester Medical Center, Rochester, NY

Other appointments

Research Interests

Eddy joins the organization after spending nearly 14 years as Director of the Joint Genome Institute of the US Dept. of Energy in Walnut Creek. Eddy provides scientific leadership and guidance to the many ongoing projects at Global Viral. In 2002 he assumed the directorship of the DOE Joint Genome Institute (JGI) to lead the JGI’s involvement in the Human Genome Project (HGP). Under his leadership, the JGI completed the sequencing and analysis of human chromosomes 5, 16 and 19 (~13% of the human genome). After completion of the HGP, Dr. Rubin has led the reorientation of the JGI as a next-generation genome science center, applying genomics to studies related to bioenergy and the environment, sequencing and analyzing the genetic code of thousands of plants, fungi and microbes. In March 2016, Dr. Rubin stepped down as JGI Director. Dr. Rubin’s research has involved the development and application of computational and biological approaches for studying genomes. His early work focused on decoding the human genome. He then championed its functional exploration, harnessing sequence comparisons between species for the discovery of genes and non-coding sequences of pivotal evolutionary and biomedical importance. Other related work included sequencing and analysis of regions of the genomes of extinct cave bears and Neanderthals. More recently, he has expanded the frontiers of the new science of metagenomics, deriving important insights from his investigations of microbial communities inhabiting environments ranging from gutless ocean-dwelling worms to cow rumen. Dr. Rubin has published over 250 peer-reviewed manuscripts with more than 35 of them appearing in the journals Science and Nature.


Eddy has a BA in Physics from University of California, San Diego, a MD from University of Rochester Medical Center, Rochester, NY, and a PhD in Biophysics from the University of Rochester, Rochester, NY. He received an Honorary Doctorate of Science Degree from Middlebury College, University of Rochester Dean’s Award, Netherlands Heart Association Declaration of Esteem, American Heart Association Established Investigator Award and has been inducted into the American Society of Clinical Investigation. He is a member of the Jackson Laboratory Board of Trustees, Genome Canada Board of Directors, Chair of the Scientific Advisory Board for the Genome Institute of Singapore, and serves on the scientific advisory boards of several additional biotechnology and research institutions. He has served as a member of the Board of Reviewing Editors for the Journal Science and the editorial boards of several other journals.

Key Publications

1-Rubin EM, Wilson G, Young FE. Expression of thymidylate synthetase activity in B. subtilis upon integration of cloned gene from E. coli. Gene  10:227-235 (1980).


2-Rubin EM, Rowley P. Sickle trait/HPFH trait: Misdiagnosis of sickle cell anemia by newborn screenings. American Journal of Diseases in Childhood  133:1248-1250 (1980).


3-Rubin EM. Cloning of the Bacillus subtilis thymidylate synthetase gene and its structure. PhD Thesis (1980).


4-Rubin EM, Kan YW.  A simple sensitive prenatal test for hydrops fetalis caused by a-thalassemia. Lancet  1:75-77 (1985).


5-Beaudry MA, Yanofsky RA, Rubin EM, Kan YW. Survival of a hydropic infant with homozygous a-thalassemia-1. Journal of Pediatrics  108:713-716 (1986).


6-Chehab F, Doherty M, Cai S, Kan YW, Cooper S, Rubin EM. Detection of sickle cell anemia and thalassemia mutations. Nature  329:293-294 (1987).


7-Rubin EM, Kan  YW. The Geneticist’s Grail. Western Journal of Clinical Medicine  147:462-463 (1987).


8-Rubin EM, Ronghua L, Cooper S, Mohandas N, Kan YW. Introduction and expression of a human bs-globin gene in transgenic mice. American Journal of Human Genetics  42:585-591 (1988).


9-Rubin EM, Kan YW, Mohandas N. Effect of human bs-globin chains on cellular properties of red cells from b-thalassemic mice. Journal of Clinical Investigation  82:1129-1133 (1988).


10-Couto L, Spangler E, Rubin EM. A method for the preparative isolation and concentration of intact yeast artificial chromosomes. Nucleic Acid Research  17:8010 (1989).


11-Rubin EM, Andrews K, Kan YW. Newborn screening by DNA analysis of dried blood spots. Human Genetics  82:134-136 (1989).


12-Sorenson S, Rubin EM, Pollster H, Mohandas N, Schrier S. The role of membrane skeletal associated alpha-globin chain in the pathophysiology of b-thalassemia. Blood  75:1333-1336 (1990).


13-Spangler E, Andrews K, Rubin EM. Developmental regulation of the human z-globin gene in transgenic mice. Nucleic Acid Research  18:7093-7097 (1990).


14-La Belle M, Rubin EM, Austin M, Krauss RM. Linkage analysis of low-density lipoprotein subclass phenotypes and the apolipoprotein B gene. Genetic Epidemiology  8:269-275 (1991).


15-Rubin EM, Krauss RM, Spangler E, Verstuyft JG, Clift SM. Inhibition of early atherogenesis in transgenic mice by human apolipoprotein AI. Nature  353:265-267 (1991).


16-Rubin EM, Ishida BY, Clift SM, Krauss RM. Expression of human apolipoprotein A-I in transgenic mice results in reduced plasma levels of murine apolipoprotein A-I and the appearance of two new high density lipoprotein size subclasses. Proceedings of the National Academy of Science, USA  88:434-438 (1991).


17-Rubin EM, Witowska E, Spangler E, Curtin P, Lubin B, Mohandas N, Clift S. Hypoxia-induced in vivo sickling of transgenic mouse red cells. Journal of Clinical Investigation  87:639-647 (1991).


18-Advani R, Rubin EM, Mohandas N, Schrier S. Oxidative red cell membrane injury in the pathophysiology of severe b-thalassemia. Blood 79:1064-1067 (1992).


19-Golder-Novoselsky E, Forte T, Nichols A, Rubin EM. Apolipoprotein AI expression and HDL distribution in transgenic mice during development. Journal of Biological Chemistry  267:20787-20790 (1992).


20-Lawn RM, Wade DP, Hammer RE, Verstuyft JG, Chiesa G, Rubin EM. Atherogenesis in transgenic mice expressing human apolipoprotein(a). Nature  360:670-672 (1992) (Accompanying News and Views).


21-Plump AS, Smith J, Hayek T, Aalto-Setala K, Walsh A, Verstuyft JG, Rubin EM, Breslow J. Severe hypercholesterolemia and atherosclerosis in apolipoprotein E deficient mice created by homologous recombination in ES cells. Cell  71:343-353 (1992) (Accompanying News and Views).


22-Robinson M, McCall M, Rubin EM, Lauer S, LaBelle M, Forte T. Apolipoprotein B genetic polymorphisms in several human hepatoma derived cell lines. Biochemical and Biophysical Research Communications 183:1224-1229 (1992).


23-Schultz JR, Gong E, McCall M, Nichols A, Clift SM, Rubin EM. Expression of human apolipoprotein A-II and its effects on high density lipoproteins in transgenic mice. Journal of Biological Chemistry  267:21630-21636 (1992).


24-Bethel C, Muragesh D, Harrison M, Mohandas N, Rubin EM. Selective erythroid replacement in murine b-thalassemia using fetal hematopoietic stem cells. Proceedings of the National Academy of Science, USA 90:10120-10124 (1993).


25-Bethel CA, Muragesh D, Harrison MR, Mohandas N, Rubin EM.  Fetal hematopoietic stem cell transplantation into beta-thalassemic  mice. Journal of Pediatric Surgery 28:1232-7 (1993).


26-Sabath D, Spangler E, Rubin EM, Stamatoyannopoulos G.  Analysis of the human z-globin promoter in transgenic mice. Blood 82:2899-2905 (1993).


27-Schultz JR, Verstuyft JG, Gong EL, Nichols A, Rubin EM. Protein composition determines the anti-atherogenic properties of high density lipoproteins in transgenic mice. Nature  365:762-764 (1993).


28-Stoltzfus LJ, Rubin EM. Atherogenesis: Insights from transgenic and gene-targeted mice. Trends in Cardiovascular  Medicine 3:130-134 (1993).


29-Callow MJ, Stoltzfus LJ, Lawn RM, Rubin EM. Expression of human apolipoprotein B and assembly of lipoprotein(a) in transgenic mice. Proceedings of the National Academy of Science, USA 91:2130-2134 (1994).


30-Callow MJ, Ferrin LJ, Rubin EM.  Single base, site-directed mutagenesis of a 90-kilobase-pair P1 clone. Nucleic Acid Research  22:4348-4349 (1994).


31-Gong EL, Tan CS, Shoukry MI, Rubin EM Nichols AV.  Structural and functional properties of human and mouse apolipoprotein A-I. Biochimica et Biophysica Acta 1213:335-342 (1994).


32-Liu AC, Lawn RM, Verstuyft JG, Rubin EM. Human apolipoprotein A-I prevents atherosclerosis associated with apolipoprotein(a) in transgenic mice. Journal of Lipid Research  35:2263-2267 (1994).


33-Mortimer B-C, Redgrave TG, Spangler EA, Verstuyft JG, Rubin EM. Effects of human apoE4 on the clearance of chylomicron-like lipid emulsions and atherogenesis in transgenic mice. Arteriosclerosis and Thrombosis in Vascular Biology  14:1542-1552 (1994).


34-Paigen B, Plump AS, Rubin EM. The mouse as a model for human cardiovascular disease and hyperlipidemia. Current Opinions in Lipidology 5:258-264 (1994).


35-Pászty C, Maeda N, Verstuyft JG, Rubin EM. Apolipoprotein A-I transgene corrects apolipoprotein E deficiency-induced atherosclerosis in mice. Journal of Clinical Investigation  94:899-903 (1994).


36-Rubin EM, Smith DJ. Atheroslerosis in mice: Getting to the heart of a polygenic disorder. Trends in Genetics  10:199-203 (1994).


37-Rubin, EM. Studies of lipoprotein(a) and high density lipoproteins in transgenic mice. Atherosclerosis  110:77-81 (1994).


38-Schultz J, Rubin EM. The properties of HDL in genetically engineered mice. Current Opinions in Lipidology 5:126-137 (1994).


39-Yuan J, Rubin E, Aljurf M, Ma L, Schrier SL. Defective assembly of membrane proteins in erythroid precursors of beta-thalassemic mice. Blood  84:632-7 (1994).


40-Zhong S, Goldberg IJ, Bruce C, Rubin EM, Breslow J, Tall A. Human apoA-II inhibits the hydrolysis of HDL triglyceride and the decrease of HDL size induced by hypertriglyceridemia and cholesteryl ester transfer protein in transgenic mice. Journal of Clinical Investigation  94:2457-2467 (1994.)


41-Callow MJ, Rubin EM. Site-specific mutagenesis demonstrates that cysteine 4326 of apolipoprotein B is required for covalent linkage with apolipoprotein(a) in vivo. Journal of Biological Chemistry  41:23914-23917 (1995).


42-Callow MJ, Verstuyft JG, Tangirala R, Palinski W, Rubin EM. Atherogenesis in transgenic mice with human apolipoprotein B and lipoprotein(a). Journal of Clinical Investigation  96(3):1639-1646 (1995).


43-Denefle P, Hughes S, Desurmont C, Vigne E, Bassinet L, Verstuyft J, Perricaudet M, Benoit P, Rubin EM. Towards gene therapy targeting HDL. Atherosclerosis  10:501-505 (1995).


44-Khoo J-C, Pittman R, Rubin EM. Selective uptake of HDL cholesteryl esters is active in transgenic mice expressing human apolipoprotein A-I. Journal of Lipid Research  36:593-600 (1995).


45-Fabry ME, Sengupta A, Suzuka SM, Costantini F, Rubin EM, Hofrichter J, Christoph G, Mancie E, Culberson D, Factor SM, Nagel RL. A second generation transgenic mouse model expressing both hemoglobin S(HbS) and HbS-Antilles results in increased phenotypic severity. Blood 86:2419-2428 (1995).


46-Francone OL, Gong EL, Ng DS, Fielding CJ, Rubin EM. Expression of human lecithin:cholesterol acyltransferase: Effect of human apolipoprotein AI and human apolipoprotein AII on plasma lipoprotein cholesterol metabobism. Journal of Clinical Investigation  96:1440-1448 (1995).


47-Frazer KA, Narla G, Zhang J, Rubin EM. The apolipoprotein(a) gene is regulated by sex hormones and acute phase inducers in YAC transgenic mice. Nature Genetics 9:424-431 (1995).


48-Golder-Novoselsky E, Nichols AV, Rubin EM, Forte TM. Human apo A-I in transgenic mice is more efficient in activating lecithin: cholesterol acyltransferase than mouse apo A-I. Biochimica et Biophysica Acta 1254:217-220 (1995).


49-Hayek T, Masucci-Magoulas L, Jiang X, Walsh A, Rubin EM, Breslow JL, Tall AR. Decreased early atherosclerotic lesions in hypertriglyceridemic mice expressing cholesteryl ester transfer protein transgene. Journal of Clinical Investigation  96:2071-2080 (1995).


50-Kaul DK, Fabry ME, Costantini F, Rubin EM, Nagel RL. In vivo demonstration of red cell-endothelial interaction, sickling, and altered microvascular response to oxygen in the sickle transgenic mouse. Journal of Clinical Investigation  96:2845-2853 (1995).


51-Pászty C, Mohandas N, Stevens ME, Liebhaber SA, Loring JF, Brion CM, Rubin EM. Lethal a-thalassemia created by gene targeting in mice and its genetic rescue. Nature Genetics  11:33-39 (1995).

52-Smith DJ, Zhu Y, Zhang J-L, Cheng J-F, Rubin EM. Construction of a contiguous 2 Mb YAC/P1 library of human chromosome 21q22.2 in transgenic mice. Genomics  27:425-434 (1995).


53-Tangirala RK, Rubin EM, Palinski, W. Quantitation of atherosclerosis in murine models: Correlation between lesions in the aortic region and in the entire aorta, and differences in the extent of lesions between sexes in LDL receptor-deficient and apolipoprotein E-deficient mice. Journal of Lipid Research  36:2320-2328 (1995).


54-Berthou L, Duverger N, Emmanuel F, Langouët S, Auwerx J, Guillouzo A, Fruchart J-C, Rubin EM, Denéfle P, Staels B, Branellec D. Opposite regulation of human versus mouse apolipoprotein AI by fibrates in human apolipoprotein AI transgenic mice. Journal of Clinical Investigation  97:1-9 (1996).


55-Gong EL, Stoltzfus LJ, Brion CM, Murugesh D, Rubin EM. Contrasting in vivo effects of murine and human apolipoprotein A-II: Role of monomer vs dimer. Journal of Biological Chemistry  271:5984-5987 (1996).


56-Rubin EM, Barsh G. Biological insights through genomics: Mouse to man. Journal of Clinical Investigation  97:275-280 (1996).


57-Hughes SD, Rouy D, Navaratnam N, Scott J, Rubin EM. Gene Transfer of cystine deaminase apobec-1 lowers lipoprotein(a) in transgenic mice and induces apolipoprotein B editing in rabbits. Human Gene Therapy  7:39-49 (1996).


58-Morrison JR, Paszty C, Stevens ME, Hughes SD, Forte T, Scott J, Rubin EM. Apolipoprotein B RNA editing enzyme-deficient mice are viable despite significant alterations to lipoprotein metabolism. Proceedings of the National Academy of Science, USA 93:7154-7159 (1996).


59-Huang LS, Voyiaziakis E, Chen HL, Rubin EM, Gordon JW. A novel functional role for apolipoprotein B in male infertility in heterozygous apolipoprotein B knockout mice. Proceedings of the National Academy of Science, USA 93:10903-10907 (1996).


60-Lawn RM, Pearle AD, Kunz LL, Rubin EM, Reckless J, Metcalfe JC, Grainger DJ. Feedback mechanism of focal vascular lesion formation in transgenic apolipoprotein(a) mice. Journal of Biological Chemistry 271:31367-31371 (1996).


61-Fabry ME, Kennan RP, Paszty C, Costantini F, Rubin EM, Gore JC, Nagel RL. Magnetic resonance evidence of hypoxia in a homozygous alpha-knockout of a transgenic mouse model for sickle cell disease. Journal of Clinical Investigation 98:2450-2455 (1996).


62-Séguret-Macé S, Latta-Mahieu M, Castro G, Luc G, Fruchart JC, Rubin EM, Denèfle P, Duverger N. Potential gene therapy for lecithin:cholesterol acyltransferase (LCAT)-deficient and hypoalphalipoproteinemic patients with adenovirus-mediated transfer of human LCAT gene. Circulation 94:2177-84 (1996).


63-Borén J, Lee I, Callow MJ, Rubin EM, Innerarity TL. A simple and efficient method for making site-directed mutants, deletions and fusions of large DNA such as P1 and BAC clones. Genome Research 6:1123-1130 (1996).


64-Hodgson JG, Smith DJ, Stevens, ME, Cutcheon, KM, Koide B, Nishiyama K, Dinulos MB, Bissada N, Nasir J, Kanazawa I, Disteche C, Rubin EM, Hayden MR. Human Huntington derived from YAC transgenes compensates for loss of murine Huntington by rescue of the embryonic lethal phenotype. Human Molecular Genetics 5:1875-1885 (1996).


65-Hamilton BA, Smith DJ, Mueller KL, Kerrebrock AW, Bronson RT, vanBerkel V, Daly MJ, Reeve-Daly MP, Nemhauser JL, Hawkins TL, Rubin EM, Lander ES. The neurodegenerative vibrator mutation causes reduced expression of phosphatidylinositol transfer proten a: cloning by positional complementation invivo and mapping of an extragenic suppressor. Neuron.18:711-722 (1997).


66-Smith DJ, Stevens ME, Sudanagunta SP, Bronson RT, Makhinson M, Watabe AM, O’Dell TJ, Fung J, Weier HG, Cheng J-F, Rubin EM.  Functional screening of 2 Mb of human 21q22.2 in transgenic mice implicates minibrain in learning defects and down syndrome. Nature Genetics 16:28-36 (1997) (Accompanying News and Views).


67-Frazer KA, Ueda Y, Zhu Y, Gifford VR, Garafolo M, Mohandas N, Martin CH, Palazzolo MJ, Cheng J-F, Rubin EM. Computational and biological analysis of 680 kilobases of DNA sequence from the human 5q31 cytokine gene cluster region. Genome Res  7:495-512 (1997).


68-Castro G, Nihoul LP, Dengremont C, de Geitere C, Delfly B, Tailleux A, Fievet C, Duverger N, Denefle P, Fruchart J-C, Rubin EM. Cholesterol efflux, LCAT activity, and pre-b particle formation by serum from human apolipoprotein A-I and apolipoprotein A-I: Apolipoprotein A-II transgenic mice consistent with the latter being less effective for diverse cholesterol transport. Biochemistry 36:2243-2249 (1997)


69-Ng DS, Francone OL, Forte TM, Zhang JL, Haghpassand M, Rubin EM. Disruption of the murine lecithin:cholesterol acyltransferase gene causes impairment of adrenal lipid delivery and up-regulation of scavenger receptor BI. Journal of Biological Chemistry. 272: 15777-15781 (1997).


70-Pászty C, Brion CM, Manci E, Witkowska E, Stevens ME, Mohandas N, Rubin EM.  Transgenic/knockout mice with exclusively human sickle hemoglobin and sickle cell disease. Science 278:876-878 (1997) (Accompanying News and Views).


71-Popp RA, Popp DM, Shinpock SG, Yang MY, Mural JG, Aguinaga MdP, Kopsombut P, Roa PD, Turner EA, Rubin EM.  A transgenic mouse model of hemoglobin S Antilles disease. Blood 89:4204-4212 (1997).


72-Boonmark NW, Lou XJ, Yang ZJ, Schwartz K, Zhang J-L, Rubin EM, Lawn RM. Modification of apolipoprotein(a) lysine binding site reduces atherosclerosis in transgenic mice. Journal of Clinical Investigation. 100:558-564 (1997).


73-Hughes S, Verstuyft J, Rubin EM. HDL deficiency in genetically engineered mice requires elevated LDL to accelerate atherogenesis. Artiosclerosis and Thrombosis in Vascular Biology  17:1725-1729 (1997).


74-Hughes SD, Ighani S, Verstuyft JG, Grainger DJ, Lou XJ, Lawn RM, Rubin EM. Lipoprotein(a) vascular accumulation in mice: In vivo analysis of the role of lysine binding sites using recombinant adenovirus. Journal of Clinical Investigation 100:1493-1500 (1997).


75-Rubin EM, Smith DJ. Optimizing the mouse to sift sequence for function, Trends in Genetics. 13:423-426 (1997).


76-Smith DJ, Rubin EM.Functional screening and complex traits: human 21q22.2 sequences affecting learning in mice. Human Molecular Genetics 6:1729-1733 (1997).


77-Wilhide CC, Jin Y, Guo Q, Li L, Li S-X, Rubin EM, Bray PF.The human integrin b3 gene is 63 kb and contains a 5’-UTR sequence regulating expression. Blood 90:3951-3961 (1997).


78-Bielicki JK, McCall MR, Stoltzfus LJ, Rubin EM, Forte TM. Evidence that Apolipoprotein A-IMilano has decreased capacity, compared to wild-type apolipoprotein A-I to recruit membrane cholesterol. Arteriosclerosis and Thrombosis in Vascular Biology. 17:1637-1643 (1997).


79-Bielicki JK, Forte TM, McCall MR, Stoltzfus LJ, Chiesa G, Sirtori CR, Franceschini G, Rubin EM. High density lipoprotein particle size restriction in apolipoproteinA-IMilano transgenic mice. Journal of Lipid Research 38:2314-2321 (1997).


80-Rubin EM, Smith DJ.  Increasing the throughput of mouse studies to search DNA sequence for function.  Atherosclerosis XI (1997).


81-Rubin EM.  Using the mouse to sift sequence for function.  Genomics, 30 June-2 July, (1997).


82-Hughes SD, Rubin, EM.  Vascular accumulation of Lp(a):  in vivo analysis of the role of lysine-binding sites using recombinant adenovirus.  Clinical Genetics 52:361-366 (1997).


83-Reckless J, Rubin EM, Verstuyft JG, Metcalfe JC, Grainger DJ. A common pathway associated with atherogenesis in diverse mouse models of vascular lipid lesions. Journal of Biological Chemistry  (1997 in press).


84-Chiesa, G, Stoltzfus, LJ, Michelagnoli, S, Bielicki, JK, Santi, M, Forte, TM, Sirtori, CR, Franceschini, G and Rubin, EM. Elevated triglycerides and low HDL cholesterol in transgenic mice expressing human apolipoprotein A-IMilano. Atherosclerosis 136:139-146 (1998).


85-Rouy D, Duverger N, Lin SD, Emmanuel F, Houdebine L-M, Denefle P, Viglietta C, Gong E, Rubin EM, and Hughes SD. Apolipoprotein (a) Yeast Artificial Chromosome transgenic rabbits:  Lipoprotein (a) assembly with human and rabbit apolipoproteins B. Journal of Biological Chemistry 273:1247-1251 (1998).


86-Whitney JB III, Leder A, Lewis J, Popp RA, Paszty C, Rubin EM, Shehee WR, Townes TM, Smithies O.  Rapid genotyping of mice with hemoglobinopathies and globin transgenes.  Biochemical Genetics 36:65-77 (1998)


87-Lindholm EM, Bielicki, JK, Curtiss LK, Rubin EM, Forte EM. Deletion of amino acids Glu146ŠArg160 in human apolipoprotein A-I (apoA-ISeattle) alters lecithin:  cholesterol acyltransferase activity and recruitment of cell phospholipid.  Biochemistry 37:4863-4868 (1998).


88-Voyiaziakis E, Goldberg IJ, Plump AS, Rubin EM, Breslow JL, and Huang LS.  ApoA-I deficiency causes both hypertriglyceridemia and increased atherosclerosis in human apoB transgenic mice.  Journal of Lipid Research 39:313-321 (1998).


89-Rubin EM, Mockrin S.  Giving Genomics a Heart.  Trends in Genetics 14:260 (1998).


90-Sago H, Carlson EJ, Smith DJ, Kilbridge J, Rubin EM, Mobley WC, Epstein CJ, Huang T-T. Ts108Cje, a new partial trisomy 16 mouse model for Down syndrome, exhibits learning and behavioral abnormalities. Proceedings of the National Academy of Science, USA 95:6256-6261 (1998).


91-Walensky LD, Shi ZT, Blackshaw S, DeVries AC, Demas GE, Gascard P, Nelson RJ, Conboy JG, Rubin EM, Snyder SH, Mohandas N.  Neurobehavioral deficits in mice lacking the erythrocyte membrane cytoskeletal protein 4.1.  Current Biology 8:1269-1272 (1998).


92-Zhu Y, Paszty C, Turetsky T, Mohandas N, Tsai S, Kuypers FA, Lee G, Gallagher P, Stevens M, Rubin E, Mentzer WC. Stomatocytosis is absent in “stomatin” deficient mouse red cells.  Blood 93: 2404-2410 (1999).


93-Forte TM, Oda MN, Knoff L, Frei B, Suh J, Harmony JAK, Stuart WD, Rubin EM and Ng DS.  Targeted disruption of the murine lecithin:  cholesterol acyltransferase gene is associated with reductions in plasma paraoxonase and platelet-activating factor acetylhydrolase activities but not in apolipoprotein J concentration.  Journal of Lipid Research 40: 1276-1281 (1999).


94-Reckless J, Rubin EM, Verstuyft J, Metcalfe JC, Grainger DJ.  Monocyte chemoattractant protein-1 but not tumor necrosis factor-alpha is correlated with macrophage infiltration in mouse lipid lesions.  Circulation 99(17): 2310-6 (1999).

95-Shi ZT, Afzal V, Coller B, Chasis JA, Parra M, Paszty C, Stevens M, Walensky LD, Mohandas N, Rubin EM, Conboy JG.  Protein 4.1R-deficient mice are viable but have erythroid membrane skeleton abnormalities. Journal of Clinical Investigation 103: 331-340 (1999).

96-Ueda Y, Royer L, Gong E, Zhang J, Cooper PN, Francone O, Rubin EM.  Lower plasma levels and accelerated clearance of HDL and non-HDL cholesterol in SR-BI transgenic mice. Journal of Biological Chemistry 274: 7165-7171 (1999).


97-Hodgson JG, Agopyan N, Gutekunst C-A, Leavitt BR, LePiane F, Singaraja R, Smith DJ, Bissada N, McCutcheon K, Nasir J, Jamot L, Li XJ, Rosemond E, Roder JC, Phillips AG, Rubin EM, Hersch SM, Hayden, MR.  A YAC mouse model for Huntington’s Disease with full-length mutant huntingtin, cytoplasmic toxicity, and selective striatal neurodegeneration.  Neuron 22: 1-20 (1999).


98-Tall A, Breslow J, Rubin EM. High density lipoprotein metabolism. In The Metabolic and Molecular Basis of Inherited Disease. (Scriver CR, Beaudet AL, Sly WS, Valle D, eds.), 8th edition, vol II, Chapter 110, McGraw-Hill, Montreal, (1999).


99-Symula DJ, Frazer KA, Ueda Y, Denefle P, Stevens ME, Wang Z-E, Locksley R, Rubin EM.  Functional screening of an asthma QTL in YAC transgenic mice.  Nature Genetics, 23:241-244 (1999).


100-Zhu Y, Jong MC, Frazer KA, Gong E, Krauss RM, Cheng J-F, Boffelli D, Rubin EM.  Genomic interval engineering of mice identifies a novel modulator of triglyceride production. Proceedings of the National Academy of Science USA 97: 1137-1142, (2000)


101-Loots GG, Locksley RM, Blankespoor CM, Wang Z-E, Miller W, Rubin EM and Frazer KA.  Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons.  Science, 288:136-140 (2000).


102-Lin SD, Cooper P, Fung J, Weier H-U, Rubin EM.  Genome scan identifies a locus affecting gamma-globin expression in human beta-cluster YAC transgenic mice.  Mammalian Genome 11, 1024-1029 (2000).


103-Ueda Y, Gong E, Royer L, Cooper PN, Francone OL, Rubin EM. SR-BI Transgenics:  Relationship between Expression Levels and Atherogenesis, Journal of Biological Chemistry 275: 20368-20373 (2000).


104-Dubchak I, Meyers C, Pachtor L, Brudno M, Rubin EM, Frazer KA. Active conservation of noncoding sequences revealed by 3-way species comparisons. Genome Research, 10:1304-1306,(2000).


105-Friddle C, Koga T, Rubin EM, Bristow J.  Expression profiling reveals distinct sets of genes altered during induction and regression of cardiac hypertrophy. Proceedings of the National Academy of Science USA 97:6745-6750, (2000).


106-Lacy DA, Wang Z-E, Symula DJ, McArthur CJ, Rubin EM, Frazer KA, Locksley RM.  Faithful expression of the human 5q31 cytokine cluster in transgenic mice.  The Journal of Immunology, 9:4569-74 (2000).


107-Callow MJ, Dudoit S, Gong EL, Speed TP, Rubin EM.  Microarray expression profiling identifies genes with altered expression in HDL deficient mice.  Genome Research 10: 2022-2029 (2000).


108-Rubin EM, Tall A.  Perspectives for vascular genomics.  Nature, 407: 267-269 (2000).


109-Santamarina-Fojo S, Peterson K, Knapper C, Qiu, Freeman L, Cheng J-F, Osorio J, Remaley A,  et al.  Complete genomic sequence of the human ABCA1 gene:  Analysis of the human and mouse ATP-binding cassette A promoter. Proceedings of the National Academy of Science USA 97:7987-7992, (2000).


110-Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS and Dubchak I.  VISTA: visualizing global DNA sequence alignments of arbitrary length.  Bioinformatics, 16:1046-1047 (2000).


111-Pennacchio L, Rubin E.  Genomic strategies to identify mammalian regulatory sequences.  Nature Reviews, 2:100-109 (2001).


112-Cavelier L, Qiu Y, Bielicki JK, Afzal V, Cheng J-F, Rubin EM.  Regulation and activity of the human ABCA1 gene in transgenic mice. Journal of Biological Chemistry 276: 18046-18051 (2001).


113-Qiu Y, Cavelier L, Chiu S, Rubin E, Cheng J-F.  Human  and mouse ABCA1 comparative sequencing and transgenesis studies identify a conserved proximal promoter sequence and other potential regulatory sequences. Genomics, 73: 66-76 (2001)


114-Mohrs M, Blankespoor CM, Wang Z-E, Loots GG, Hadeiba H, Shinkai K, Rubin EM, Locksley RM.  Deletion of a coordinate regulator of type 2 cytokine expression in mice.  Nature Immunology, 2:826-828, (2001).


115-Reckless J, Rubin EM, Verstuyft JB, Metcalfe JC, Grainger DJ.  A common phenotype associated with atherogenesis in diverse mouse models of vascular lipid lesions.  Journal of Vascular Research, 38(3):256-65 (2001).


116-Pennacchio LA, Olivier M, Hubacek JA, Cohen J, Cox D, Fruchart JC, Krauss R, Rubin EM.  An apolipoprotein identified through comparative sequence analysis influences triglyceride levels in humans and mice.  Science 294: 169-173 (2001) (Accompanying News and Views).


117-Mao JR, Dean WB, Taylor G, Afzal V, Rubin EM, Bristow J.  Tenascin-X deficiency mimics the Ehlers-Danlos syndrome in mice through regulation of collagen deposition.  Nature Genetics 30:421-25 (2001)


118-Oda MN, Bielicki JK, Ho TT, Berger T, Rubin EM and Forte TM.  Paraoxonase 1 over-expression in mice and its effect on high density lipoproteins.  Biochemical and Biophysical Research Communications 290:921-927 (2002).


119-LootsG G, Ovcharenko I, Pachter L, Dubchak I and Rubin EM.  rVISTA for comparative sequence-based discovery of functional transcription factor binding sites.  Genome Research 2255-0 (2002).


120-Banerjee P, Bahlo M, Schwartz JR, Loots GR, Houston KA, Dubchak I, Speed TP, Rubin EM, SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data. Mammalian Genome, Oct 13 (10) 554-7 (2002).


121-Callow M and Rubin EM.  Expression profiling and comparative sequence derived insights into lipid metabolism.  Current Opinion in Lipidology, 13:173-179 (2002).


122-Pennacchio LA, Olivier M, Hubacek J, Krauss RM, Rubin EM, and Cohen JC.  Two independent apolipoprotein A5 haplotypes influence human plasma triglyceride levels.  Human Molecular Genetics,11(24): 3031-38. (2002).


123-Talmud P J, Martin S, Hawe E, Nicaud V, Oliver M, Miller GJ, Rubin E M, Pennacchio LA, and Humphries SE.  Relative contribution of variation within the APOC3-A4-A5 gene cluster in determining plasma triglycerides. Human Molecular Genetics, 11(24):3039-46. (2002)


124-Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D, Rubin E, Dubchak I.  Strategies and tools for whole genome alignments.  Genome Research, Jan;13(1):73-80 (2003).


125-Pennacchio LA, Rubin EM.  Apolipoprotein A5:  A newly identified gene impacting plasma triglyceride levels in humans and mice.  Arteriosclerosis, Thrombosis, and Vascular Biology.  23(4): 529-34 (2003).


126-Waterston et al.. Initial sequencing and comparative analysis of the mouse genome. Nature, Dec 5; 420 (6915):520-62. (2003)


127-Parolini et al.  Targeted replacement of mouse apolipoprotein A-I with the human apo-I or the mutant apoa-Imilano: Evidence of apoa-IM impaired hepatic secretion.  Journal of Biological Chemistry.  278(7):4740-6 (2003).


128-Vu-Dac, N., Gervois, P., Jakel, H., Nowak, M., Bauge, E., Dehondt, H., Staels, B., Pennacchio, L. A., Rubin, E.M.,Fruchart-Najib, J. and Fruchart, J.-C. Apolipoprotein A5, a Crucial Determinant of Plasma Triglyceride Levels, isHighly Responsive to PPARa Activators, Journal of Biological Chemistry, 278(20): 17982-85 (2003).


129-Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, and Rubin EM.  Phylogenetic shadowing of primate sequences to find functional regions of the human genome.  Science Feb 28 (299): 1391-1394 (2003).


130-Pennacchio, L. A. and Rubin, E. M.   Comparative sequence tools and databases providing insights into the human genome, Journal of Clinical Investigation, 111(8): 1099-1106.  (2003)


131-Olivier, M., Wang, X., Cole, R., Gau, B., Kim, J., Rubin, E. M., and Pennacchio, L. A. Haplotype analysis of the apolipoprotein gene cluster on human chromosome 11, Genomics, submitted.


132-Ishida T, Choi, S, Kundu, R. K, Hirata, K, Rubin, E. M, Cooper, A. D, Quertermous, T.  Endothelial lipase is a major determinant of HDL level, Journal of Clinical Investigation, 111(3): 347-55.  (2003).


133-Huby , T, Afzal, V, Doucer, C, Lawn, D, Gong, E, Chapman, MJ, Thillet, J, Rubin, E  “Regulation of the expression of the apolipoprotein(a) gene : Evidence for a regulatory role of the 5' distal ACR enhancer in YAC transgenic mice”. Arteriosclerosis, Thrombosis and Vascular Biology, Sept 1, 23(9):1633-9(2003).


134-Nobrega, M.A., Ovcharenko, I., Afzal, V., Rubin, E.M. Scanning Human Gene Deserts for Long-Range Enhancers. Science 302:413 (2003)


135-Zeng, P., Pennacchio, L. A., Rubin, E. M., and Smith, J. D.  A novel enhancer for brain expression near the human apoE gene locus, Biochimica et Biophysica Acta, in press.(2003)


136-Grogan JL, Wang ZE, Stanley S, Harmon B, Loots GG, Rubin EM, Locksley RM., Basal chromatin modification at the IL-4 gene in helper T cells. J Immunol. Dec 15; 171(12): 6672-9, (2003).


137-Pennacchio, L. A., Baroukh, N., and Rubin, E. M.  “Human-Mouse Comparative Genomics: Successes and Failures to Reveal Functional Regions of the Human Genome.” Symposia on Quantitative Biology: The Genome of Homo sapiens, 68:303-9, Cold Spring Harbor Press. (2003)


138-Ahituv N, Rubin EM, Nobrega MA. “Exploiting human--fish genome comparisons for deciphering gene regulation.” Hum Mol Genet. 13 Spec No 2:R261-6. (2004)


139-Symula DJ, Zhu Y, Schimenti JC, Rubin EM.  Functional annotation of mouse mutations in embryonic stem cells by use of expression profiling.  Mammalian Genome, Jan 15(1):1-13 (2004).


140-Boffelli D, Cheng JF, Rubin EM., Convergent evolution in primates and an insectivore.
Genomics. Jan; 83(1): 19-23 (2004).

141-Li TT, Larrucea S, Souza S, Leal SM, López JA, Rubin EM, Nieswandt B, Bray PF. Genetic variation responsible for mouse strain differences in integrin a2 expression is associated with altered platelet responses to collagen. Blood, in Press (2004)


142-Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield J.  Community structure and metabolism through reconstruction of microbial genomes from the environment.  Nature Mar 4; 428 (6978):37-43 (2004).


143-Grimwood et al.  The DNA sequence and biology of human chromosome 19. Nature. Apr 1;428(6982):529-35 (2004)


144-Gibbs et al.  Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Nature. Apr 1;428(6982):493-521 (2004).


145-Eichenbaum-Voline, S., Olivier, M., Jones, E. L., Naoumova, R. P., Jones, B., Gau, B., Seed, M., Betteridge, D.J., Galton, D. J., Rubin, E. M., Scott, J., Shoulders, C. C., and Pennacchio, L. A.  Linkage and Association of Haplotypes at the APOA1/C3/A4/A5 Gene Cluster to Familial Combined Hyperlipidemia. Arteriosclerosis, Thrombosis, and Vascular Biology, 24(1):167-74 (2004).

146-Olivier, M., Wang, X., Cole, R., Gau, B., Kim, J., Rubin, E. M., and Pennacchio, L. A.   Haplotype analysis of the apolipoprotein gene cluster on human chromosome 11.  Genomics, 83(5): 912-23 (2004).

147-Baroukh N, Akiyama J, Chang J, Rubin EM, Fruchart J, Pennacchio LA.  Analysis of apolipoprotein A5, C3 and plasma triglyceride concentrations in genetically engineered mice.  Arteriosclerosis, Thrombosis and Vascular Biology.  In press. (2004)


148-Brudno M, Poliakov A, Salamov A, Cooper GM, Sidow A, Rubin EM, Solovyev V, Batzoglou S, Dubchak I.  “Automated whole-genome multiple alignment of rat, mouse, and human.” Genome Res. (4):685-92 (2004)


149-Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. “VISTA: computational tools for  comparative genomics.” Nucleic Acids Res. 32 (Web Server issue):W273-9. (2004)


150-Fruchart-Najib J, Bauge E, Niculescu LS, Pham T, Thomas B, Rommens C, Majd Z, Brewer B, Pennacchio LA, Fruchart JC.  “Mechanism of triglyceride lowering in mice expressing human apolipoprotein A5.” Biochem Biophys Res Commun.319(2):397-404 (2004)

151-Shan N, Couronne O, Pennacchio LA, Brudno M, Batzoglou S, Joy K, Bethel W, Rubin EM, Hamman B, and Dubchak I.  Plylo-VISTA:  Interactive visualization of multiple DNA sequence alignments.  Bioinformatics, 20 (5): 636-43. (2004)


152-Wang Q-F, Liu X, O’Connell J, Peng Z, Krauss R, Rubin EM, Cheng J-F, and Pennacchio LA.  Haplotypes in the ApoA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons.  Human Molecular Genetics, 13 (10): 1049-56. (2004). 

153-Boffelli D, Nobrega MA, Rubin EM.  Comparative genomics at the vertebrate extremes.  Nature Review Genetics, June 5 (6):456-65 (2004).


154-Boffelli D, C.V.Weer, L.Weng, K.D.Lewis, M.I.Shoukry, L.Pachter, D.N.Keys and E.M.Rubin. “Intra-species sequence comparisons for annotating genomes.” GenomeResearch.14:2406-2411. (2004)


155-Schmutz, J., Martin, J….. Myers, R.M. and Rubin, E.M.* The complete sequence of human chromosome 5. Nature, in press.(2004) (*Corresponding author)


156-Nobrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM. Megabase deletions of gene deserts result in viable mice.Nature. Oct 21;431(7011):988-93(2004).


157-Martin, J….. Myers, R.M. Rubin, E.M.* Pennacchio.L.,  The complete sequence of human chromosome 16. Nature, 432; 998-994 (2004) (*Corresponding author)


158-Kerns JA, Newton J, Berryere TG, Rubin EM, Cheng JF, Schmutz SM, Barsh GS.  Characterization of the dog Agouti gene and a nonagoutimutation in German Shepherd Dogs.  Mammalian Genome. Oct;15(10):798-808 (2004)


159-Ahituv N, Rubin EM, Nobrega MA.  Exploiting human--fish genome comparisons for deciphering gene regulation. Human Molecular Genetics. Oct 1;13 Spec No 2:R261-6 (2004)


160-Branchi I, Bichler Z, Minghetti L, Delabar JM, Malchiodi-Albedi F, Gonzalez MC, Chettouh Z, Nicolini A, Chabert C, Smith DJ, Rubin EM, Migliore-Samour D, Alleva E.  Transgenic mouse in vivo library of human Down syndrome critical region 1: association between DYRK1A overexpression, brain development abnormalities, and cell cycle protein alteration.J Neuropathol Exp Neurol. May;63(5):429-40 (2004)


161-Teivainen PA, Eliassen KA, Rubin EM, Djurovic S, Berg K.  Human apoB contributes to increased serum total apo(a) level in LPA transgenic mice. Lipids Health Dis. May 11;3(1):8 (2004)


162-Tringe, S….Rubin, E.M.,  Comparative metagenomics of microbial communities, Science, April 22, 308 (5721):554-7 (2005)


163-Baroukh, N., Ahituv, N., Chang, J., Shoukry, M., Afzal, V., Rubin, E. M., and Pennacchio, L. A.  2005.  Comparative Genomic Analysis Reveals a Distant Liver Enhancer Upstream of the COUP-TFII gene. Mammalian Genome, 16(2):91-5 (2005)


164-Youngren kKK, Coveney D, Peng X, Bhattacharya C, Schmidt LS, Nickerson ML, Lamb BT, Deng J-M, Behringer RR, Capel B, Rubin EM, Nadeau JH, & Matin A. The Ter mutation in the dead end gene causes germ cell loss and testicular germ cell tumours.  Nature, May 19;435(7040):360-4 (2005).


165-Poulin, F., Nobrega, M., Plajzer-Frick, I., Holt, A., Afzal, V., Rubin, E. M., and Pennacchio, L. A.  In Vivo Characterization of a Vertebrate Ultra-conserved Enhancer.  Genomics, 85(6):774-781 (2005)


166-Loots GG, Kneissel M, Keller H, Baptist M, Chang J, Collette NM, Ovcharenko D, Plajzer-Frick I, Rubin EM.  Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease. Genome Res. Jul;15(7):928-35 (2005)


167-Noonan JP, Hofreiter M, Smith D, Priest JR, Rohland N, Rabeder G, Krause J, Detter JC, Paabo S, Rubin EM.. Genomic Sequencing of Pleistocene Cave Bears. Science, Jul 22;309(5734):597-9. (2005)


168-Nowak M, Helleboid-Chapman A, Jakel H, Martin G, Duran-Sandoval D, Staels B, Rubin EM, Pennacchio LA, Taskinen MR, Fruchart-Najib J, Fruchart JC.  Insulin-mediated down-regulation of apolipoprotein A5 gene expression through the phosphatidylinositol 3-kinase pathway: role of upstream stimulatory factor. Mol Cell Biol. Feb;25(4):1537-48. (2005)


169-Tabibiazar R, Wagner RA, Spin JM, Ashley EA, Narasimhan B, Rubin EM, Efron B, Tsao PS, Tibshirani R, Quertermous T.  Mouse strain-specific differences in vascular wall gene expression and their relationship to vascular disease. Arterioscler Thromb Vasc Biol. Feb;25(2):302-8 (2005)


170-Hughes JR, Cheng JF, Ventress N, Prabhakar S, Clark K, Anguita E, De Gobbi M, de Jong P, Rubin E, Higgs DR.  Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences. Proc Natl Acad Sci U S A. Jul 5; (2005)


171-Grosskopf I, Baroukh N, Lee SJ, Kamari Y, Harats D, Rubin EM, Pennacchio LA, Cooper AD.  Apolipoprotein A-V Deficiency Results in Marked Hypertriglyceridemia Attributable to Decreased Lipolysis of Triglyceride-Rich Lipoproteins and Removal of Their Remnants. Arterioscler Thromb Vasc Biol. Dec;25(12):2573-9 (2005)


172-Ahituv N, Prabhakar S, Poulin F, Rubin EM, Couronne O.  Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny.
Hum Mol Genet. Oct 15;14(20):3057-63 (2005)


173-Tringe SG, Rubin EM. Metagenomics: DNA sequencing of environmental samples.
Nat Rev Genet. Nov;6(11):805-14 (2005)


174-Parolini C, Chiesa G, Gong E, Caligari S, Cortese MM, Koga T, Forte TM, Rubin EM.   Apolipoprotein A-I and the molecular variant apoA-I(Milano): evaluation of the antiatherogenic effects in knock-in mouse model. Atherosclerosis. Dec;183(2):222-9 (2005).


175-Lee JY, Timmins JM, Mulya A, Smith TL, Zhu Y, Rubin EM, Chisholm JW, Colvin PL, Parks JS.  HDLs in apoA-I transgenic Abca1 knockout mice are remodeled normally in plasma but are hypercatabolized by the kidney. J Lipid Res. Oct;46(10):2233-45 (2005).


176-De Gobbi  M, Viprakasit V, Hughes J,  Fisher C,  Buckle VJ,  Ayyub H,  Gibbons RJ,  Vernimmen D, Yoshinaga Y,  de Jong P, Cheng J-F,  Rubin EM,  Wood WG,  Bowden D,  Higgs DR.  A remote, gain of function regulatory SNP illustrating a novel mechanism for human genetic disease.  Science.  May 26; 312 (5777_:1215-7 (2006).


177-Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D.  A distal enhancer and an ultraconserved exon are derived from a novel retroposon.  Nature.  May 4; 441(7089); 87-90 (2006).


178-Weng L, Rubin EM, Bristow J.  Application of sequence-based methods in human microbial ecology.  Genome Res. Mar;16(3):316-22 (2006).


179-Prabhakar S, Poulin F, Shoukry M, Afzal V, Rubin EM, Couronne O, Pennacchio LA.  Close sequence comparisons are sufficient to identify human cis-regulatory elements.  Genome Res. Jul, 16(7):855-63 (2006).


180-Prabhakar S, Noonan JP, Pääbo S, Rubin EM.  Accelerated evolution of conserved noncoding sequences in humans.  Science. 2006 Nov 3;314(5800):786.


181-Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, Gloeckner FO, Boffelli D, Anderson IJ, Barry KW, Shapiro HJ, Szeto E, Kyrpides NC, Mussmann M, Amann R, Bergin C, Ruehland C, Rubin EM* and Dubilier N.  Symbiosis insights through metagenomic analysis of a microbial consortium.  Nature.  Oct 26; 443(7114):950-5 (2006) *(Corresponding author).


182-Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Paabo S, Pritchard JK, Rubin EM.  Sequencing and analysis of Neanderthal Genomic DNA.  Science, Nov 17:314 (5802):1045 (2006).


183-Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM.  In vivo enhancer analysis of human conserved non-coding sequences.

Nature Nov 23;444(7118):499-502 (2006).


184-Wang QF, Prabhakar S, Chanan S, Cheng JF, Boffelli D, Rubin EM. Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons. Genome Biol. Jan 3;8(1) (2007).


185-Ward RD, Davis SW, Cho M, Esposito C, Lyons RH, Cheng JF, Rubin EM, Rhodes SJ, Raetzman LT, Smith TP, Camper SA. Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene.  Mamm Genome, Jul;18(6-7):521-37 (2007).

186-Nottingham WT, Jarratt A, Burgess M, Speck CL, Cheng JF, Prabhakar S, Rubin EM, Li PS, Sloane-Stanley J, Kong-A-San J, de Bruijn MF. Runx1-mediated hematopoietic stem cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer. Blood. Dec 15;110(13):4188-97 (2007).


187-Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, Pennacchio LA, Rubin EM.  Deletion of ultraconserved elements yields viable mice.PLoS Biol. Sept 5(9):234. (2007)


188-Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin HG, Kunin V, Dalevi D, Madejska J, Kirton E, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang X, Hernández M, Murillo C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Hugenholtz P, Leadbetter JR.  Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature Nov 22;450(7169):560-5 (2007).


189-Rachidi M, Lopes C, Vayssettes C, Smith DJ, Rubin EM, Delabar JM.  New cerebellar phenotypes in YAC transgenic mouse in vivo library of human Down syndrome critical region-1. Biochem Biophys Res Commun. Dec 21;364(3):488-94 (2007).


190-Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM.  Genome-wide experimental determination of barriers to horizontal gene transfer.  Science Nov 30;318(5855):1449-52 (2007).


191-Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barbote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS.  Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina).  Nat Biotechnol May;26(5):553-60 (2008).


192-Blow MJ, Zhang T, Woyke T, Spelle CF, Krivoshapkin A, Yang D, Derevianko A, Rubin EM.  Identification of the source of ancient remains through genomic sequencing.  Genome Res. Apr 21 (2008).


193-Tringe SG, Zhang T, Liu X, Yu Y, Lee WH, Yap J, Yao F, Suan ST, Ing SK, Haynes M, Rohwer F, Wei CL, Tan P, Bristow J, Rubin EM, Ruan Y.  The airborne metagenome in an indoor urban environment.  PLoS ONE. Apr 2;3(4):e1862 (2008).


194-Visel A, Prabhakar S, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM, Pennacchio LA.  Ultraconservation identifies a small subset of extremely constrained developmental enhancers.  Nat Genet Jan 6; 40(2):158-60 (2008)


195-Mackelprang R, Rubin EM. Paleontology. New tricks with old bones. Science. Jul 11;321(5886):211-2. (2008)


196-Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barbote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol. May;26(5):553-60(2008)


197-Prabhakar S, Visel A, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, DR FitzPatrick, Afzal V, Pennacchio LA, Rubin EM & Noonan JP.  Human-specific gain of function in a developmental enhancer.  Science.  Sep 5;321(5894):1346-50 (2008).


198-Rubin EM.  Genomics of cellulosic biofuels.  Nature, August 14:  (2008)


199- Visel A, Blow MJ, Zirong L, Zhang T ,Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA. CHIP-seq Accurately Predicts Tissue-Specific Activity of Enhancers.  Nature, Feb 12: 457(7231):854-8 (2009).


200-Visel A, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA.  Functional autonomy of distant-acting human enhancers. Genomics. Mar 5 (2009)


201-Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, Tiedje JM, Sorek R  Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A. Mar 10;106(10):3976-81 (2009)


202- Visel A, Rubin EM, Pennacchio LA.  Genomic views of distant-acting enhancers. Nature. Sep 10;461(7261):199-205. (2009)


203- Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. Dec 24;462(7276):1056-60 (2009)


204- Tarantino-Hutchison LM, Sorrentino C, Nadas A, Zhu Y, Rubin EM, Tinkle SS, Weston A, Gordon T. Genetic determinants of sensitivity to beryllium in mice. J Immunotoxicol. Jun:6(2):130-5(2009).


205- Visel A, Zhu Y, May D, Afzal V, Gong E, Attanasio C, Blow MJ, Cohen JC, Rubin EM, Pennacchio.  A Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice.. Nature. Mar 18;464(7287):409-12. (2010)


206- Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Bristow J, Ren B, Black BL, Rubin EM, Visel A, Pennacchio LA.  ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet. Sep;42(9):806-10. (2010)


207- Hemme CL, Deng Y, Gentry TJ, Fields MW, Wu L, Barua S, Barry K, Tringe SG, Watson DB, He Z, Hazen TC, Tiedje JM, Rubin EM, Zhou J. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J. May; 4(5):660-72. (2010)


208- Hemme CL, Mouttaki H, Lee YJ, Zhang G, Goodwin L, Lucas S, Copeland A, Lapidus A, Glavina del Rio T, Tice H, Saunders E, Brettin T, Detter JC, Han CS, Pitluck S, Land ML, Hauser LJ, Kyrpides N, Mikhailova N, He Z, Wu L, Van Nostrand JD, Henrissat B, He Q, Lawson PA, Tanner RS, Lynd LR, Wiegel J, Fields MW, Arkin AP, Schadt CW, Stevenson BS, McInerney MJ, Yang Y, Dong H, Xing D, Ren N, Wang A, Huhnke RL, Mielenz JR, Ding SY, Himmel ME, Taghavi S, van der Lelie D, Rubin EM, Zhou J. Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. J Bacteriol. Dec;192(24):6494-6. (2010)


209- Zhang T,Datta S, Eichler J,Ivanova N, Axen SD, Kerfeld CA, Chen F, Kyrpides N,  Hugenholtz P,Cheng J-F, Sale KL,Simmons B and Rubin EM. Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance.  Green Chem., 13, 2083-2090 (2011)


210- Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.Science. Jan 28;331(6016):463-7. (2011)


211- May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Afzal V, Simpson PC, Rubin EM, Black BL, Bristow J, Pennacchio LA, Visel.  A Large-scale discovery of enhancers from human heart tissue. Nat Genet. Dec 4;44(1):89-93 (2011)


212- Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ, Rubin EM, Jansson JK. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature. Nov 6;480(7377):368-71 (2011)


213- Kim TW, Chokhawala HA, Hess M, Dana CM, Baer Z, Sczyrba A, Rubin EM, Blanch HW, Clark DS Angew.  High-throughput in vitro glycoside hydrolase (HIGH) screening for enzyme discovery. Chem Int Ed Engl. Nov 18;50(47):11215-8 (2011)


214- Mason OU, Hazen TC, Borglin S, Chain PS, Dubinsky EA, Fortney JL, Han J, Holman HY, Hultman J, Lamendella R, Mackelprang R, Malfatti S, Tom LM, Tringe SG, Woyke T, Zhou J, Rubin EM, Jansson JK. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J. Sep;6(9):1715-27 (2012)


215- Kimelman A, Levy A, Sberro H, Kidron S, Leavitt A, Amitai G, Yoder-Himes DR, Wurtzel O, Zhu Y, Rubin EM, Sorek R. A vast collection of microbial genes that are toxic to bacteria. Genome Res. Apr;22(4):802-9 (2012)


216- Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, McKinsey GL, Pattabiraman K, Silberberg SN, Blow MJ, Hansen DV, Nord AS, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Kaplan T, Kriegstein AR, Rubin EM, Ovcharenko I, Pennacchio LA, Rubenstein JL.  A high-resolution enhancer atlas of the developing telencephalon. Cell. Feb 14;152(4):895-908. (2013)


217- Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M, Kerfeld CA.  Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci U S A.  Jan 15;110(3):1053-8.(2013)


218-Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. Insights into the phylogeny and coding potential of microbial dark matter. Nature Jul 25;499(7459):431-7.( 2013)


219- Nord AS, Blow MJ, Attanasio C, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Rubenstein JL, Rubin EM, Pennacchio LA, Visel A.  Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development.  Cell. Dec 19;155(7):1521-31.( 2013)


220- Pedersen JS, Valen E, Vargas Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, Jones PA, Hoover CA, Tikhonov A, Prokhortchouk E, Rubin EM, Sandelin A, Gilbert MT, Krogh A, Willerslev E, Orlando L.  Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res. Dec 3, (2013).


221- Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R, Phouanenavong S, Akiyama JA, Shoukry M, Afzal V, Rubin EM, FitzPatrick DR, Ren B, Hallgrímsson B, Pennacchio LA, Visel A. Fine tuning of craniofacial morphology by distant-acting enhancers. Science. Oct 25;342(6157):1241006. (2013).


222- Nord AS, Blow MJ, Attanasio C, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Rubenstein JL, Rubin EM, Pennacchio LA, Visel A.  Rapid and pervasive changes in genome-wide enhancer usage during mammalian development. Cell. 2013 Dec 19;155(7):1521-31


223- Ivanova NN, Schwentek p, Tripp HJ, Rhinke C, Pati A, Huntemann M, Woyke T, Kyrpides N, Rubin EM.  Stop codon reassignments in the wild. Science. 2014 May 23;344(7):909-13

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