Elliott H. Margulies, Ph.D. - Publications

2001 University of Michigan, Ann Arbor, Ann Arbor, MI 

49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Eberle MA, Fritzilas E, Krusche P, Källberg M, Moore BL, Bekritsky MA, Iqbal Z, Chuang HY, Humphray SJ, Halpern AL, Kruglyak S, Margulies EH, McVean G, Bentley DR. A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. Genome Research. PMID 27903644 DOI: 10.1101/gr.210500.116  1
2014 Prickett TD, Zerlanko B, Gartner JJ, Parker SC, Dutton-Regester K, Lin JC, Teer JK, Wei X, Jiang J, Chen G, Davies MA, Gershenwald JE, Robinson W, Robinson S, ... ... Margulies EH, et al. Somatic mutations in MAP3K5 attenuate its proapoptotic function in melanoma through increased binding to thioredoxin. The Journal of Investigative Dermatology. 134: 452-60. PMID 24008424 DOI: 10.1038/jid.2013.365  1
2013 Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK, ... ... Margulies EH, et al. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proceedings of the National Academy of Sciences of the United States of America. 110: 13481-6. PMID 23901115 DOI: 10.1073/pnas.1304227110  1
2013 Belgard TG, Montiel JF, Wang WZ, García-Moreno F, Margulies EH, Ponting CP, Molnár Z. Adult pallium transcriptomes surprise in not reflecting predicted homologies across diverse chicken and mouse pallial sectors. Proceedings of the National Academy of Sciences of the United States of America. 110: 13150-5. PMID 23878249 DOI: 10.1073/pnas.1307444110  1
2013 Goldstein DB, Allen A, Keebler J, Margulies EH, Petrou S, Petrovski S, Sunyaev S. Sequencing studies in human genetics: design and interpretation. Nature Reviews. Genetics. 14: 460-70. PMID 23752795 DOI: 10.1038/nrg3455  1
2013 Raczy C, Petrovski R, Saunders CT, Chorny I, Kruglyak S, Margulies EH, Chuang HY, Källberg M, Kumar SA, Liao A, Little KM, Strömberg MP, Tanner SW. Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. Bioinformatics (Oxford, England). 29: 2041-3. PMID 23736529 DOI: 10.1093/bioinformatics/btt314  1
2012 Saunders CJ, Miller NA, Soden SE, Dinwiddie DL, Noll A, Alnadi NA, Andraws N, Patterson ML, Krivohlavek LA, Fellis J, Humphray S, Saffrey P, Kingsbury Z, Weir JC, Betley J, ... ... Margulies EH, et al. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Science Translational Medicine. 4: 154ra135. PMID 23035047 DOI: 10.1126/scitranslmed.3004041  1
2012 Parker SC, Gartner J, Cardenas-Navia I, Wei X, Ozel Abaan H, Ajay SS, Hansen NF, Song L, Bhanot UK, Killian JK, Gindin Y, Walker RL, Meltzer PS, Mullikin JC, Furey TS, ... ... Margulies EH, et al. Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. Plos Genetics. 8: e1002871. PMID 22912592 DOI: 10.1371/journal.pgen.1002871  1
2012 Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. Plos Genetics. 8: e1002789. PMID 22761590 DOI: 10.1371/journal.pgen.1002789  1
2012 Hogart A, Lichtenberg J, Ajay SS, Anderson S, Margulies EH, Bodine DM. Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites. Genome Research. 22: 1407-18. PMID 22684279 DOI: 10.1101/gr.132878.111  1
2011 Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, ... ... Margulies EH, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/nature10530  1
2011 Prickett TD, Wei X, Cardenas-Navia I, Teer JK, Lin JC, Walia V, Gartner J, Jiang J, Cherukuri PF, Molinolo A, Davies MA, Gershenwald JE, Stemke-Hale K, Rosenberg SA, Margulies EH, et al. Exon capture analysis of G protein-coupled receptors identifies activating mutations in GRM3 in melanoma. Nature Genetics. 43: 1119-26. PMID 21946352 DOI: 10.1038/ng.950  1
2011 Pilon AM, Ajay SS, Kumar SA, Steiner LA, Cherukuri PF, Wincovitch S, Anderson SM, Mullikin JC, Gallagher PG, Hardison RC, Margulies EH, Bodine DM. Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation. Blood. 118: e139-48. PMID 21900194 DOI: 10.1182/blood-2011-05-355107  1
2011 Belgard TG, Marques AC, Oliver PL, Abaan HO, Sirey TM, Hoerder-Suabedissen A, García-Moreno F, Molnár Z, Margulies EH, Ponting CP. A transcriptomic atlas of mouse neocortical layers. Neuron. 71: 605-16. PMID 21867878 DOI: 10.1016/j.neuron.2011.06.039  1
2011 Goldfeder RL, Parker SC, Ajay SS, Ozel Abaan H, Margulies EH. A bioinformatics approach for determining sample identity from different lanes of high-throughput sequencing data. Plos One. 6: e23683. PMID 21858207 DOI: 10.1371/journal.pone.0023683  1
2011 Ajay SS, Parker SC, Abaan HO, Fajardo KV, Margulies EH. Accurate and comprehensive sequencing of personal genomes. Genome Research. 21: 1498-505. PMID 21771779 DOI: 10.1101/gr.123638.111  1
2011 Catalona WJ, Bailey-Wilson JE, Camp NJ, Chanock SJ, Cooney KA, Easton DF, Eeles RA, FitzGerald LM, Freedman ML, Gudmundsson J, Kittles RA, Margulies EH, McGuire BB, Ostrander EA, Rebbeck TR, et al. National Cancer Institute Prostate Cancer Genetics Workshop. Cancer Research. 71: 3442-6. PMID 21558387 DOI: 10.1158/0008-5472.CAN-11-0314  1
2010 Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ, Margulies EH, Boehnke M, Furey TS, Crawford GE, et al. Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metabolism. 12: 443-55. PMID 21035756 DOI: 10.1016/j.cmet.2010.11.013  1
2010 Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, Swift AJ, Abaan HO, Albert TJ, Margulies EH, Green ED, Collins FS, Mullikin JC, Biesecker LG. Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Research. 20: 1420-31. PMID 20810667 DOI: 10.1101/gr.106716.110  1
2010 Sommer WH, Lidström J, Sun H, Passer D, Eskay R, Parker SC, Witt SH, Zimmermann US, Nieratschker V, Rietschel M, Margulies EH, Palkovits M, Laucht M, Heilig M. Human NPY promoter variation rs16147:T>C as a moderator of prefrontal NPY gene expression and negative affect. Human Mutation. 31: E1594-608. PMID 20648632 DOI: 10.1002/humu.21299  1
2010 Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH. A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Research. 20: 249-56. PMID 20123915 DOI: 10.1101/gr.097956.109  1
2009 Zerbino DR, McEwen GK, Margulies EH, Birney E. Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. Plos One. 4: e8407. PMID 20027311 DOI: 10.1371/journal.pone.0008407  1
2009 Parker HG, VonHoldt BM, Quignon P, Margulies EH, Shao S, Mosher DS, Spady TC, Elkahloun A, Cargill M, Jones PG, Maslen CL, Acland GM, Sutter NB, Kuroki K, Bustamante CD, et al. An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs. Science (New York, N.Y.). 325: 995-8. PMID 19608863 DOI: 10.1126/science.1173275  1
2009 Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH. Local DNA topography correlates with functional noncoding regions of the human genome. Science (New York, N.Y.). 324: 389-92. PMID 19286520 DOI: 10.1126/science.1169050  1
2008 Parker SC, Margulies EH, Tullius TD. The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome. Genome Informatics. International Conference On Genome Informatics. 20: 199-211. PMID 19425134  1
2008 Margulies EH, Birney E. Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes. Nature Reviews. Genetics. 9: 303-13. PMID 18347593 DOI: 10.1038/nrg2185  1
2008 Margulies EH. Confidence in comparative genomics. Genome Research. 18: 199-200. PMID 18245452 DOI: 10.1101/gr.7228008  0.01
2008 Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 132: 311-22. PMID 18243105 DOI: 10.1016/j.cell.2007.12.014  1
2007 Nikolaev SI, Montoya-Burgos JI, Popadin K, Parand L, Margulies EH, Antonarakis SE. Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements. Proceedings of the National Academy of Sciences of the United States of America. 104: 20443-8. PMID 18077382 DOI: 10.1073/pnas.0705658104  1
2007 Clark TG, Andrew T, Cooper GM, Margulies EH, Mullikin JC, Balding DJ. Functional constraint and small insertions and deletions in the ENCODE regions of the human genome Genome Biology. 8. PMID 17784950 DOI: 10.1186/gb-2007-8-9-r180  1
2007 McCauley JL, Kenealy SJ, Margulies EH, Schnetz-Boutaud N, Gregory SG, Hauser SL, Oksenberg JR, Pericak-Vance MA, Haines JL, Mortlock DP. SNPs in Multi-species Conserved Sequences (MCS) as useful markers in association studies: a practical approach. Bmc Genomics. 8: 266. PMID 17683615 DOI: 10.1186/1471-2164-8-266  1
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/nature05874  1
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/gr.6034307  1
2007 Nikolaev S, Montoya-Burgos JI, Margulies EH, Rougemont J, Nyffeler B, Antonarakis SE. Early history of mammals is elucidated with the ENCODE multiple species sequencing data. Plos Genetics. 3: e2. PMID 17206863 DOI: 10.1371/journal.pgen.0030002  1
2006 Margulies EH, Chen CW, Green ED. Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons. Trends in Genetics : Tig. 22: 187-93. PMID 16499991 DOI: 10.1016/j.tig.2006.02.005  1
2006 Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, Zhou D, Luo S, Vasicek TJ, Daly MJ, Wolfsberg TG, et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Research. 16: 123-31. PMID 16344561 DOI: 10.1101/gr.4074106  1
2005 Portnoy ME, McDermott KJ, Antonellis A, Margulies EH, Prasad AB, Kingsley DM, Green ED, Mortlock DP. Detection of potential GDF6 regulatory elements by multispecies sequence comparisons and identification of a skeletal joint enhancer. Genomics. 86: 295-305. PMID 15979840 DOI: 10.1016/j.ygeno.2005.05.003  1
2005 Margulies EH, Vinson JP, Miller W, Jaffe DB, Lindblad-Toh K, Chang JL, Green ED, Lander ES, Mullikin JC, Clamp M. An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. Proceedings of the National Academy of Sciences of the United States of America. 102: 4795-800. PMID 15778292 DOI: 10.1073/pnas.0409882102  1
2005 Margulies EH, Maduro VV, Thomas PJ, Tomkins JP, Amemiya CT, Luo M, Green ED. Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes. Proceedings of the National Academy of Sciences of the United States of America. 102: 3354-9. PMID 15718282 DOI: 10.1073/pnas.0408539102  1
2004 Angata T, Margulies EH, Green ED, Varki A. Large-scale sequencing of the CD33-related Siglec gene cluster in five mammalian species reveals rapid evolution by multiple mechanisms. Proceedings of the National Academy of Sciences of the United States of America. 101: 13251-6. PMID 15331780 DOI: 10.1073/pnas.0404833101  1
2003 Margulies EH, Blanchette M, Haussler D, Green ED. Identification and characterization of multi-species conserved sequences. Genome Research. 13: 2507-18. PMID 14656959 DOI: 10.1101/gr.1602203  1
2003 Gottsch JD, Seitzman GD, Margulies EH, Bowers AL, Michels AJ, Saha S, Jun AS, Stark WJ, Liu SH. Gene expression in donor corneal endothelium. Archives of Ophthalmology (Chicago, Ill. : 1960). 121: 252-8. PMID 12583793  1
2003 Gottsch JD, Bowers AL, Margulies EH, Seitzman GD, Kim SW, Saha S, Jun AS, Stark WJ, Liu SH. Serial analysis of gene expression in the corneal endothelium of Fuchs' dystrophy. Investigative Ophthalmology & Visual Science. 44: 594-9. PMID 12556388 DOI: 10.1167/iovs.02-0300  1
2002 Innis JW, Margulies EH, Kardia S. Integrative biology and the developing limb bud. Evolution & Development. 4: 378-89. PMID 12356268  1
2001 Margulies EH, Kardia SL, Innis JW. A comparative molecular analysis of developing mouse forelimbs and hindlimbs using serial analysis of gene expression (SAGE). Genome Research. 11: 1686-98. PMID 11591645 DOI: 10.1101/gr.192601  1
2001 Margulies EH, Kardia SL, Innis JW. Identification and prevention of a GC content bias in SAGE libraries. Nucleic Acids Research. 29: E60-0. PMID 11410683  1
2000 Margulies EH, Innis JW. eSAGE: managing and analysing data generated with serial analysis of gene expression (SAGE). Bioinformatics (Oxford, England). 16: 650-1. PMID 11038335  1
2000 Post LC, Margulies EH, Kuo A, Innis JW. Severe limb defects in Hypodactyly mice result from the expression of a novel, mutant HOXA13 protein. Developmental Biology. 217: 290-300. PMID 10625554 DOI: 10.1006/dbio.1999.9550  1
2000 Margulies EH, Innis JW. Building arms or legs with molecular models. Pediatric Research. 47: 2-3. PMID 10625073  1
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