Richard A Gibbs

Summary

Affiliation: Baylor College of Medicine
Country: USA

Publications

  1. pmc Finding the missing honey bee genes: lessons learned from a genome upgrade
    Christine G Elsik
    Division of Animal Sciences, Division of Plant Sciences, and MU Informatics Institute, University of Missouri, Columbia, MO 65211, USA
    BMC Genomics 15:86. 2014
  2. pmc The functional spectrum of low-frequency coding variation
    Gabor T Marth
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    Genome Biol 12:R84. 2011
  3. pmc Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
    Marilyn B Renfree
    The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
    Genome Biol 12:R81. 2011
  4. pmc Identification of genetic risk variants for deep vein thrombosis by multiplexed next-generation sequencing of 186 hemostatic/pro-inflammatory genes
    Luca A Lotta
    Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, U O S Dipartimentale per la Diagnosi e la Terapia delle Coagulopatie, Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico, Universita degli Studi di Milano, Milan, Italy
    BMC Med Genomics 5:7. 2012
  5. pmc Genetic diversity in India and the inference of Eurasian population expansion
    Jinchuan Xing
    Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112, USA
    Genome Biol 11:R113. 2010
  6. pmc Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby
    Emily S W Wong
    Faculty of Veterinary Sciences, University of Sydney, Sydney, NSW 2006, Australia
    BMC Genomics 12:420. 2011
  7. pmc Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta)
    Gloria L Fawcett
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    BMC Genomics 12:311. 2011
  8. pmc Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility
    Jean M Feugang
    Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS 39762, USA
    BMC Genomics 10:176. 2009
  9. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
  10. ncbi request reprint The DNA sequence, annotation and analysis of human chromosome 3
    Donna M Muzny
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 440:1194-8. 2006

Collaborators

Detail Information

Publications139 found, 100 shown here

  1. pmc Finding the missing honey bee genes: lessons learned from a genome upgrade
    Christine G Elsik
    Division of Animal Sciences, Division of Plant Sciences, and MU Informatics Institute, University of Missouri, Columbia, MO 65211, USA
    BMC Genomics 15:86. 2014
    ..0) compared to what would be expected based on other sequenced insect genomes...
  2. pmc The functional spectrum of low-frequency coding variation
    Gabor T Marth
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    Genome Biol 12:R84. 2011
    ....
  3. pmc Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
    Marilyn B Renfree
    The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
    Genome Biol 12:R81. 2011
    ..Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development...
  4. pmc Identification of genetic risk variants for deep vein thrombosis by multiplexed next-generation sequencing of 186 hemostatic/pro-inflammatory genes
    Luca A Lotta
    Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, U O S Dipartimentale per la Diagnosi e la Terapia delle Coagulopatie, Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico, Universita degli Studi di Milano, Milan, Italy
    BMC Med Genomics 5:7. 2012
    ....
  5. pmc Genetic diversity in India and the inference of Eurasian population expansion
    Jinchuan Xing
    Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112, USA
    Genome Biol 11:R113. 2010
    ..Despite recent large-scale efforts in discovering human genetic variation, India's vast reservoir of genetic diversity remains largely unexplored...
  6. pmc Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby
    Emily S W Wong
    Faculty of Veterinary Sciences, University of Sydney, Sydney, NSW 2006, Australia
    BMC Genomics 12:420. 2011
    ..Here, we used pyrosequencing to compare the transcriptomes of a cervical and thoracic thymus from a single 178 day old tammar wallaby...
  7. pmc Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta)
    Gloria L Fawcett
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    BMC Genomics 12:311. 2011
    ....
  8. pmc Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility
    Jean M Feugang
    Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS 39762, USA
    BMC Genomics 10:176. 2009
    ..We performed a comprehensive genome wide analysis of single nucleotide polymorphisms (SNP) for bull fertility followed by a second-stage replication in additional bulls for a restricted set of markers...
  9. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  10. ncbi request reprint The DNA sequence, annotation and analysis of human chromosome 3
    Donna M Muzny
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 440:1194-8. 2006
    ....
  11. pmc The hypofunctional effect of P335L single nucleotide polymorphism on SSTR5 function
    Guisheng Zhou
    Michael E DeBakey Department of Surgery, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    World J Surg 35:1715-24. 2011
    ..In the present study we sought to determine the distribution of the SSTR5 P335L SNP in a cohort of pancreatic cancer patients and whether the P335L SNP affected cellular function of SSTR5 in human pancreatic cancer...
  12. pmc Building a comprehensive genomic program for hepatocellular carcinoma
    Theresa R Harring
    Michael E DeBakey Department of Surgery, Baylor College of Medicine, One Baylor Plaza, Jewish Bldg 404D, Houston, TX 77030, USA
    World J Surg 35:1746-50. 2011
    ..Various centers at Baylor are elucidating the genomics of HCC to improve treatment options, with a focus on three etiologies: hepatitis C virus, hepatitis B virus, and non-viral...
  13. pmc Developing a tissue resource to characterize the genome of pancreatic cancer
    Georgios Voidonikolas
    Michael E DeBakey Department of Surgery, Baylor College of Medicine, 1709 Dryden, Suite 1500, Houston, TX 77030, USA
    World J Surg 33:723-31. 2009
    ..This article summarizes the basic principles that guide the creation of such a repository, including sample processing and preservation techniques, sample size and composition, and collection of clinical data elements...
  14. pmc A SNP discovery method to assess variant allele probability from next-generation resequencing data
    Yufeng Shen
    The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 20:273-80. 2010
    ..Validation results show that Atlas-SNP2 achieves a false-positive rate of lower than 10%, with an approximately 5% or lower false-negative rate...
  15. pmc Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities
    Matthew N Bainbridge
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Genome Biol 12:R68. 2011
    ..The number of variants per base pair (variant density) and our ability to interrogate regions outside of the CCDS regions is consequently less well understood...
  16. pmc Exome capture sequencing identifies a novel mutation in BBS4
    Hui Wang
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
    Mol Vis 17:3529-40. 2011
    ..The purpose of this study was to identify a novel LCA disease allele or gene and to develop an approach combining genetic mapping with whole exome sequencing...
  17. doi request reprint The complete genome of an individual by massively parallel DNA sequencing
    David A Wheeler
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 452:872-6. 2008
    ..This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'...
  18. ncbi request reprint The finished DNA sequence of human chromosome 12
    Steven E Scherer
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 440:346-51. 2006
    ..The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents...
  19. pmc Bos taurus genome assembly
    Yue Liu
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    BMC Genomics 10:180. 2009
    ..The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque...
  20. pmc MLH1-silenced and non-silenced subgroups of hypermutated colorectal carcinomas have distinct mutational landscapes
    Lawrence A Donehower
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    J Pathol 229:99-110. 2013
    ..Examination of MLH1 expression status and frequencies of APC, KRAS, and BRAF mutation in CRC may provide a useful diagnostic tool that could supplement the standard microsatellite instability assays and influence therapeutic decisions...
  21. pmc Whole-exome sequencing identifies compound heterozygous mutations in WDR62 in siblings with recurrent polymicrogyria
    David R Murdock
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
    Am J Med Genet A 155:2071-7. 2011
    ..Further studies to identify mutation frequency in the population are needed...
  22. pmc Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate
    Wu Lin Charng
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
    BMC Med Genomics 9:42. 2016
    ..We applied whole exome sequencing (WES) for molecular diagnosis and in silico analysis to identify novel disease gene candidates in a cohort from Saudi Arabia with primarily Mendelian neurologic diseases...
  23. pmc Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease
    Ender Karaca
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Neuron 88:499-513. 2015
    ..Neuroimaging and in silico analysis of functional and expression proximity between candidate and known disease genes allowed for further understanding of genetic networks underlying specific types of brain malformations...
  24. pmc Structural variation and missense mutation in SBDS associated with Shwachman-Diamond syndrome
    Claudia M B Carvalho
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
    BMC Med Genet 15:64. 2014
    ..Structural variation (SV) involving the SBDS locus has been rarely reported in association with the disease. We aimed to determine whether an SV contributed to the pathogenesis of a case lacking biallelic SBDS point mutations...
  25. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  26. ncbi request reprint Large-scale RT-PCR recovery of full-length cDNA clones
    Jia Qian Wu
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Biotechniques 36:690-6, 698-700. 2004
    ..This systematic gene recovery pipeline allows both rescue of predicted human and rat genes and provides insight into the complexity of the transcriptome through comparisons with existing data sets...
  27. pmc Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology
    Adam C English
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
    PLoS ONE 7:e47768. 2012
    ..The accuracy of gap closure was validated by comparison to Sanger sequencing on gaps from the original D. pseudoobscura draft assembly and shown to be dependent on initial reference quality...
  28. pmc The KAT6B-related disorders genitopatellar syndrome and Ohdo/SBBYS syndrome have distinct clinical features reflecting distinct molecular mechanisms
    Philippe M Campeau
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Hum Mutat 33:1520-5. 2012
    ..LOVD.nl/KAT6B) might help tease out answers to these questions and understand the developmental programs dysregulated by the different truncations...
  29. pmc A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
    Oliver A Hampton
    Bioinformatics Research Laboratory, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 19:167-77. 2009
    ..We show that knock-down of SULF2 in cell lines causes tumorigenic phenotypes, including increased proliferation, enhanced survival, and increased anchorage-independent growth...
  30. pmc Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses
    Ian M Campbell
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030
    Hum Mutat 37:231-4. 2016
    ..We also briefly discuss some commonly utilized resources that fully support multiallelic sites. ..
  31. pmc Exome sequencing identifies a homozygous C5orf42 variant in a Turkish kindred with oral-facial-digital syndrome type VI
    Yavuz Bayram
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
    Am J Med Genet A 167:2132-7. 2015
    ..Whole exome sequencing (WES) identified a homozygous predicted damaging missense mutation (c.4034A > G; p.Gln1345Arg) in the C5orf42 gene. Our data contribute to the evidence that C5orf42 is one of the causative genes for OFDVI...
  32. pmc Effects of TP53 mutational status on gene expression patterns across 10 human cancer types
    Neha Parikh
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
    J Pathol 232:522-33. 2014
    ..The data indicate that tumours with wild-type TP53 retain some aspects of p53-mediated growth inhibitory signalling through activation of p53 target genes and suppression of cell cycle regulatory genes...
  33. pmc PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations
    Min Wang
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
    BMC Genomics 16:214. 2015
    ....
  34. doi request reprint The genome of the model beetle and pest Tribolium castaneum
    Stephen Richards
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 452:949-55. 2008
    ..Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control...
  35. pmc Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy
    James R Lupski
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
    N Engl J Med 362:1181-91. 2010
    ..We therefore aimed to assess the usefulness of human whole-genome sequencing for genetic diagnosis in a patient with Charcot-Marie-Tooth disease...
  36. pmc A primer on a hepatocellular carcinoma bioresource bank using the cancer genome atlas guidelines: practical issues and pitfalls
    N Thao T Nguyen
    Michael E DeBakey Department of Surgery, Baylor College of Medicine, 1709 Dryden Road, Suite 1500, BCM390, Houston, TX 77030, USA
    World J Surg 35:1732-7. 2011
    ..Since the advent of the human genome, the era of personalized genomic medicine is indisputably in progress...
  37. pmc Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution
    Stephen Richards
    Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas 77030, USA
    Genome Res 15:1-18. 2005
    ..Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila...
  38. pmc A collagen-binding adhesin, Acb, and ten other putative MSCRAMM and pilus family proteins of Streptococcus gallolyticus subsp. gallolyticus (Streptococcus bovis Group, biotype I)
    Jouko Sillanpaa
    Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School at Houston, Houston, Texas 77030, USA
    J Bacteriol 191:6643-53. 2009
    ..gallolyticus subsp. gallolyticus isolates may play an important role in the predominance of this subspecies in S. bovis endocarditis...
  39. pmc Loss-of-function variants influence the human serum metabolome
    Bing Yu
    Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
    Sci Adv 2:e1600800. 2016
    ..These results reveal new avenues into gene function and the understanding of disease etiology by integrating -omic technologies into a deeply phenotyped population study. ..
  40. pmc Molecular diagnostic experience of whole-exome sequencing in adult patients
    Jennifer E Posey
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
    Genet Med 18:678-85. 2016
    ..We describe the diagnostic yield and characteristics of WES in adults...
  41. ncbi request reprint Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort
    Tomasz Gambin
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Nucleic Acids Res . 2016
    ..In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses...
  42. pmc Monoallelic and Biallelic Variants in EMC1 Identified in Individuals with Global Developmental Delay, Hypotonia, Scoliosis, and Cerebellar Atrophy
    Tamar Harel
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Electronic address
    Am J Hum Genet 98:562-70. 2016
    ..We propose EMC1 as a gene in which either biallelic or monoallelic variants might lead to a syndrome including intellectual disability and preferential degeneration of the cerebellum...
  43. pmc Molecular findings among patients referred for clinical whole-exome sequencing
    Yaping Yang
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
    JAMA 312:1870-9. 2014
    ..Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders...
  44. pmc Genetic and molecular alterations in pancreatic cancer: implications for personalized medicine
    Yantian Fang
    Molecular Surgeon Research Center, Division of Surgical Research, Michael E DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, U S A and Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, P R China
    Med Sci Monit 19:916-26. 2013
    ..This review aims to summarize recent advances of important genes, proteins, and microRNAs that play a critical role in the pathogenesis of pancreatic cancer, and to provide implications for personalized medicine in pancreatic cancer. ..
  45. pmc Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function
    Ender Karaca
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Cell 157:636-50. 2014
    ..Reduction of a founder mutation to homozygosity illustrates the importance of rare variations in disease and supports the clan genomics hypothesis...
  46. pmc An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data
    Yi Wang
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 23:833-42. 2013
    ..We apply SNPTools to the International 1000 Genomes Project (1000G) Phase 1 low-coverage data set and obtain genotyping accuracy comparable to that of SNP microarray...
  47. pmc Pooled genomic indexing of rhesus macaque
    Aleksandar Milosavljevic
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 15:292-301. 2005
    ..A further innovation, short-tag pooled genomic indexing (ST-PGI), was also introduced to further improve the economy of mapping by sequencing multiple, short, mapable tags within a single sequencing reaction...
  48. pmc Genomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genome
    Zhengdong Zhang
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 14:580-90. 2004
    ..Their higher nucleotide substitution rates may be related to the central role played by these two NRs in the metabolism of the foreign compounds and may have resulted from limited positive selection...
  49. pmc Identification of TP53 as an acute lymphocytic leukemia susceptibility gene through exome sequencing
    Bradford C Powell
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
    Pediatr Blood Cancer 60:E1-3. 2013
    ..This unexpected finding enabled identification of an appropriate sibling bone marrow donor and illustrates that exome sequencing will reveal atypical clinical presentations of even well-studied genes...
  50. pmc An integrative variant analysis suite for whole exome next-generation sequencing data
    Danny Challis
    The Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA
    BMC Bioinformatics 13:8. 2012
    ..Although the exome capture sequencing methods have become routine and well established, there is currently a lack of tools specialized for variant calling in this type of data...
  51. pmc Resequencing of IRS2 reveals rare variants for obesity but not fasting glucose homeostasis in Hispanic children
    Nancy F Butte
    Department of Pediatrics, Baylor College of Medicine, US Department of Agriculture Agricultural Research Service Children s Nutrition Research Center, Houston, TX, USA
    Physiol Genomics 43:1029-37. 2011
    ..Rare but not common IRS2 variants may play a role in the regulation of body weight but not an essential role in fasting glucose homeostasis in Hispanic children...
  52. pmc Identification of genetic susceptibility to childhood cancer through analysis of genes in parallel
    Sharon E Plon
    Texas Children s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
    Cancer Genet 204:19-25. 2011
    ..The failure to detect mutations in 87% of families highlights that a number of childhood cancer susceptibility genes remain to be discovered...
  53. pmc MIPEP recessive variants cause a syndrome of left ventricular non-compaction, hypotonia, and infantile death
    Mohammad K Eldomery
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
    Genome Med 8:106. 2016
    ..The mitochondrial intermediate presequence protease MIP/Oct1, which carries out precursor processing, has not yet been established to have a role in human disease...
  54. doi request reprint The role of combined SNV and CNV burden in patients with distal symmetric polyneuropathy
    Davut Pehlivan
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
    Genet Med 18:443-51. 2016
    ..We hypothesized that CNVs and/or single-nucleotide variants (SNVs) might exist in patients with CMT with an unknown molecular genetic etiology...
  55. pmc DVL3 Alleles Resulting in a -1 Frameshift of the Last Exon Mediate Autosomal-Dominant Robinow Syndrome
    Janson J White
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Am J Hum Genet 98:553-61. 2016
    ..Here, we review the current knowledge of these peculiar variant alleles in DVL1- and DVL3-mediated Robinow syndrome and further elucidate the phenotypic features present in subjects with DVL1 and DVL3 frameshift mutations...
  56. pmc Recurrent De Novo and Biallelic Variation of ATAD3A, Encoding a Mitochondrial Membrane Protein, Results in Distinct Neurological Syndromes
    Tamar Harel
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Electronic address
    Am J Hum Genet 99:831-845. 2016
    ..ATAD3A variation represents an additional link between mitochondrial dynamics and recognizable neurological syndromes, as seen with MFN2, OPA1, DNM1L, and STAT2 mutations...
  57. pmc Rare variants in the notch signaling pathway describe a novel type of autosomal recessive Klippel-Feil syndrome
    Ender Karaca
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
    Am J Med Genet A 167:2795-9. 2015
    ..2015 Wiley Periodicals, Inc. ..
  58. pmc Whole-exome sequencing identifies homozygous GPR161 mutation in a family with pituitary stalk interruption syndrome
    Ender Karaca
    Department of Molecular and Human Genetics E K, D P, W L C, Y B, T G, M W, M M A, R A G, J R L, Baylor College of Medicine, Houston, Texas 77030 Department of Radiology R B, Duzce University Medical School, 81620 Duzce, Turkey Department of Medical Biology K O Y, Kahramanmaras Sutcu Imam University, Medical School, 46100 Kahramanmaras, Turkey Department of Pediatric Endocrinology I A, S B, Duzce University Medical School, 81620 Duzce, Turkey Center for Human Genetic Research S E, Massachussetts General Hospital, Boston, Massachussetts 02114 Department of Radiology A B, Duzce Ataturk Community Hospital, 81620 Duzce, Turkey Department of Medical Biology and Genetics E Y, Duzce University Institute of Health Science, 81620 Duzce, Turkey Human Genome Sequencing Center S N J, D M M, R A G, Baylor College of Medicine, Taiwan
    J Clin Endocrinol Metab 100:E140-7. 2015
    ..Mutations in HESX1, LHX4, OTX2, SOX3, and PROKR2 have been associated with PSIS in less than 5% of cases; thus, the underlying genetic etiology for the vast majority of cases remains to be determined...
  59. pmc Whole exome sequencing identifies three novel mutations in ANTXR1 in families with GAPO syndrome
    Yavuz Bayram
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
    Am J Med Genet A 164:2328-34. 2014
    ..1150G>A; p.Gly384Ser) mutation in the ANTXR1 gene. Our studies expand the allelic spectrum in this rare condition and potentially provide insight into the role of ANTXR1 in the regulation of the extracellular matrix...
  60. pmc Whole-exome sequencing links TMCO1 defect syndrome with cerebro-facio-thoracic dysplasia
    Davut Pehlivan
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
    Eur J Hum Genet 22:1145-8. 2014
    ..We propose that mutations of TMCO1 are not only responsible for craniofacial dysmorphism, skeletal anomalies and mental retardation syndrome but also for CFTD. ..
  61. pmc Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF
    Agathe Bourgogne
    Division of Infectious Diseases, Department of Medicine, University of Texas Medical School, Houston, Texas 77030, USA
    Genome Biol 9:R110. 2008
    ..Enterococcus faecalis has emerged as a major hospital pathogen. To explore its diversity, we sequenced E. faecalis strain OG1RF, which is commonly used for molecular manipulation and virulence studies...
  62. pmc Clan genomics and the complex architecture of human disease
    James R Lupski
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Cell 147:32-43. 2011
    ..One implication of this realization is that recent mutation may have a greater influence on disease susceptibility or protection than is conferred by variations that arose in distant ancestors...
  63. pmc Association between somatostatin receptor 5 gene polymorphisms and pancreatic cancer risk and survival
    Donghui Li
    Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
    Cancer 117:2863-72. 2011
    ..Genetic variation in SSTR had been associated with risk of human cancers but had never been investigated in pancreatic cancer...
  64. pmc Whole-genome sequencing for optimized patient management
    Matthew N Bainbridge
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Sci Transl Med 3:87re3. 2011
    ..Supplementation of l-dopa therapy with 5-hydroxytryptophan, a serotonin precursor, resulted in clinical improvements in both twins...
  65. pmc Common and rare variants of DAOA in bipolar disorder
    Manjula Maheshwari
    Human Genome Sequencing Center, Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
    Am J Med Genet B Neuropsychiatr Genet 150:960-6. 2009
    ..Our results suggest that DAOA does not have a major effect on BP susceptibility. However, DAOA may contribute to bipolar susceptibility in some specific families as evidenced by the STEPC analysis...
  66. ncbi request reprint Meeting the growing demands of genetic research
    Amy L McGuire
    Center for Medical Ethics and Health Policy, Baylor College of Medicine, USA
    J Law Med Ethics 34:809-12. 2006
  67. pmc Pharmacogenetic characterization of naturally occurring germline NT5C1A variants to chemotherapeutic nucleoside analogs
    Jason Saliba
    Departments of aMolecular and Human Genetics bBiochemistry and Molecular Biology cMolecular and Cellular Biology dHuman Genome Sequencing Center, Baylor College of Medicine eDepartment of Pediatrics, Texas Children s Cancer Center, Baylor College of Medicine fDepartment of Statistics, Rice University, Houston, Texas, USA
    Pharmacogenet Genomics 26:271-9. 2016
    ..L254P NT5C1A missense variant in the substrate recognition motif. Given the paucity of cellular drug response data from the NT5C1A germline variation, we characterized p.L254P and eight rare variants of NT5C1A from genomic databases...
  68. pmc Assessing structural variation in a personal genome-towards a human reference diploid genome
    Adam C English
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
    BMC Genomics 16:286. 2015
    ..Here, we characterize the SV content of a personal genome with Parliament, a publicly available consensus SV-calling infrastructure that merges multiple data types and SV detection methods...
  69. pmc Adult presentation of X-linked Conradi-Hünermann-Happle syndrome
    Jennifer E Posey
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
    Am J Med Genet A 167:1309-14. 2015
    ..As in many genetic syndromes, the hallmark features of CDPX2 in pediatric patients are not readily identifiable in adults. This demonstrates the utility of WES as a diagnostic tool in the evaluation of adults with genetic disorders...
  70. pmc Exome sequencing reveals homozygous TRIM2 mutation in a patient with early onset CMT and bilateral vocal cord paralysis
    Davut Pehlivan
    Section of Neurology, Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX, 77030, USA
    Hum Genet 134:671-3. 2015
    ..We report a TRIM2 homozygous missense mutation (c.2000A>C; p.D667A) in a patient with peripheral neuropathy and bilateral vocal cord paralysis, allowing for further delineation of the associated phenotypic spectrum. ..
  71. pmc Targeted sequencing in chromosome 17q linkage region identifies familial glioma candidates in the Gliogene Consortium
    Ali Jalali
    Department of Neurosurgery, Baylor College of Medicine, Houston, Texas
    Sci Rep 5:8278. 2015
    ..1% frequency), non-synonymous variants. Our findings implicate the MYO19 and KIF18B genes and rare variants in SPAG9 and RUNDC1 as candidates worthy of further investigation. Burden testing and functional studies are planned. ..
  72. pmc Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline
    Jeffrey G Reid
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    BMC Bioinformatics 15:30. 2014
    ..This expanding scale creates analytical challenges: accommodating peak compute demand, coordinating secure access for multiple analysts, and sharing validated tools and results...
  73. pmc Mutations in COL27A1 cause Steel syndrome and suggest a founder mutation effect in the Puerto Rican population
    Claudia Gonzaga-Jauregui
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
    Eur J Hum Genet 23:342-6. 2015
    ..We identified a homozygous missense variant p.(Gly697Arg) in COL27A1, in a family with Steel syndrome and no consanguinity. Interestingly, the identified variant seems to have arisen as a founder mutation in the Puerto Rican population. ..
  74. pmc Osteogenesis imperfecta without features of type V caused by a mutation in the IFITM5 gene
    Monica Grover
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
    J Bone Miner Res 28:2333-7. 2013
    ..14C > T), now typical of OI type V. This highlights the variability of OI caused by IFITM5 mutations and suggests screening for mutations in this gene in most cases of OI where type 1 collagen mutations are absent...
  75. pmc Whole exome capture in solution with 3 Gbp of data
    Matthew N Bainbridge
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Genome Biol 11:R62. 2010
    ....
  76. pmc Whole-exome sequencing identifies mutations in the nucleoside transporter gene SLC29A3 in dysosteosclerosis, a form of osteopetrosis
    Philippe M Campeau
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Hum Mol Genet 21:4904-9. 2012
    ..Our report highlights the pleomorphic consequences of dysfunction of this nucleoside transporter, and importantly suggests a new mechanism for the control of osteoclast differentiation and function...
  77. pmc Yunis-Varón syndrome is caused by mutations in FIG4, encoding a phosphoinositide phosphatase
    Philippe M Campeau
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Am J Hum Genet 92:781-91. 2013
    ..Our results describe a role for PI(3,5)P(2) signaling in skeletal development and maintenance...
  78. pmc Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes
    Xiang Qin
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
    BMC Microbiol 12:135. 2012
    ..faecium strains in clinical environments. Systematic study of the molecular epidemiology and pathogenesis of E. faecium has been hindered by the lack of closed, complete E. faecium genomes that can be used as references...
  79. pmc Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms
    James T Lu
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Genome Biol 13:R15. 2012
    ..3 million indels shorter than 50 bp, of which over 890 were identified as potentially disruptive variants. Yet, despite their ubiquity, the local genomic characteristics of indels remain unexplored...
  80. doi request reprint Microarray analysis of somatostatin receptor 5-regulated gene expression profiles in murine pancreas
    Sanjeet G Patel
    The Michael E DeBakey Department of Surgery, Baylor College of Medicine, 1709 Dryden Street, Suite 1500, Houston, TX 77030, USA
    World J Surg 33:630-7. 2009
    ..We hypothesized that SSTR5 mediates the inhibitory effect of somatostatin (SST) on insulin secretion and islet proliferation by regulating a specific set of pancreatic genes...
  81. pmc Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project
    Rui Chen
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 14:679-84. 2004
    ..Combined with the assembled BAC fingerprint map, a set of BAC clones that covered >97% of the genome was identified and used in the RGSP...
  82. pmc Overview of the development of personalized genomic medicine and surgery
    F Charles Brunicardi
    Michael E DeBakey Department of Surgery, Baylor College of Medicine, 1709 Dryden Street, Suite 1500, Houston, TX 77030, USA
    World J Surg 35:1693-9. 2011
    ..Five years ago we developed a model for the development of PGMS in which genomic profile guides choice of therapy. In this article we discussed our progress, including an updating of the model, and a future vision of PGMS...
  83. pmc The Atlas genome assembly system
    Paul Havlak
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 14:721-32. 2004
    ..Atlas was used to assemble a draft DNA sequence of the rat genome; its major components including overlapper and split-scaffold are also being used in pure WGS projects...
  84. pmc Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication
    Eve Shinbrot
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 24:1740-50. 2014
    ..Taken together, the extremely high mutation frequency and strand specificity of mutations provide a unique identifier of eukaryotic origins of replication. ..
  85. pmc Comparative primate genomics: emerging patterns of genome content and dynamics
    Jeffrey Rogers
    Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nat Rev Genet 15:347-59. 2014
    ..This Review summarizes current knowledge regarding primate genome content and dynamics, and proposes a series of goals for the near future. ..
  86. pmc The genetic basis of DOORS syndrome: an exome-sequencing study
    Philippe M Campeau
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
    Lancet Neurol 13:44-58. 2014
    ..We aimed to identify the genetic basis of this syndrome by sequencing most coding exons in affected individuals...
  87. ncbi request reprint Human genetics. Primate shadow play
    Richard A Gibbs
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 299:1331-3. 2003
  88. pmc Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing
    Jia Qian Wu
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 14:665-71. 2004
    ..Spliced sequences were amplified in 46 cases (34%). We conclude that this procedure for elucidating gene structures with native cDNA sequences is cost-effective and will become even more so as it is further optimized...
  89. pmc Bioactivity and bioavailability of ginsenosides are dependent on the glycosidase activities of the A/J mouse intestinal microbiome defined by pyrosequencing
    Tao Niu
    Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 1441 Moursund Street, Houston, Texas, 77030, USA
    Pharm Res 30:836-46. 2013
    ..To investigate the ability of bacteria in the intestinal microbiome to convert naturally occurring primary ginsenosides in red ginseng extract to active secondary ginsenosides...
  90. pmc Human genome sequencing in health and disease
    Claudia Gonzaga-Jauregui
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Annu Rev Med 63:35-61. 2012
    ..Personal genome sequencing may eventually become an instrument of common medical practice, providing information that assists in the formulation of a differential diagnosis. We outline herein some of the remaining challenges...
  91. pmc Metagenomic pyrosequencing and microbial identification
    Joseph F Petrosino
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
    Clin Chem 55:856-66. 2009
    ..The Human Microbiome Project has ushered in a new era for human metagenomics and high-throughput next-generation sequencing strategies...
  92. pmc Basic principles and technologies for deciphering the genetic map of cancer
    Georgios Voidonikolas
    Michael E DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA
    World J Surg 33:615-29. 2009
    ..We also describe the possible applications of the discovery of DNA changes to the approach of this disease and cite preliminary efforts where the knowledge has been translated into the clinical or preclinical setting...
  93. ncbi request reprint Shedding genomic light on Aristotle's lantern
    Erica Sodergren
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1519, Houston, TX 77030, USA
    Dev Biol 300:2-8. 2006
    ..Analysis of the basic deuterostome genetic complement supports the sea urchin's role as a model system for deuterostome and, by extension, chordate development...
  94. pmc Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes
    Jeffrey G Reid
    Department of Chemistry, University of Houston, Houston, Texas 77204, USA
    Genome Res 18:1571-81. 2008
    ....
  95. pmc Clinical whole-exome sequencing for the diagnosis of mendelian disorders
    Yaping Yang
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    N Engl J Med 369:1502-11. 2013
    ..Whole-exome sequencing is a diagnostic approach for the identification of molecular defects in patients with suspected genetic disorders...
  96. pmc Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae
    Michael P McLeod
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1519, Houston, TX 77030 7783, USA
    J Bacteriol 186:5842-55. 2004
    ..conorii) groups diverged. The three-way comparison allowed further in silico analysis of the SpoT split genes, leading us to propose that the stringent response system is still functional in these rickettsiae...
  97. pmc Deep sequencing of systematic combinatorial libraries reveals β-lactamase sequence constraints at high resolution
    Zhifeng Deng
    Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    J Mol Biol 424:150-67. 2012
    ..An analysis of the TEM-1 and other class A structures suggests that residues that vary in the alignment may nevertheless make unique, but important, interactions within individual enzymes...
  98. pmc Positive selection of a pre-expansion CAG repeat of the human SCA2 gene
    Fuli Yu
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
    PLoS Genet 1:e41. 2005
    ..These results suggest that a recent positive selection of the pre-expansion SCA2 CAG repeat has occurred in Utah residents with European ancestry...
  99. pmc Whole-exome sequencing identifies ALMS1, IQCB1, CNGA3, and MYO7A mutations in patients with Leber congenital amaurosis
    Xia Wang
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Hum Mutat 32:1450-9. 2011
    ..Thus, to obtain accurate diagnosis and gain a complete picture of the disease, it is essential to sequence a larger set of retinal disease genes and combine the clinical phenotype with molecular diagnosis...
  100. pmc Role of somatic mutations in vascular disease formation
    Sarah M Weakley
    Michael E DeBakey Department of Surgery, Molecular Surgeon Research Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop BCM391, Houston, TX 77030, USA
    Expert Rev Mol Diagn 10:173-85. 2010
    ....
  101. ncbi request reprint Single nucleotide polymorphisms in genes for 2'-5'-oligoadenylate synthetase and RNase L inpatients hospitalized with West Nile virus infection
    Imtiaz Yakub
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    J Infect Dis 192:1741-8. 2005
    ..Genetic susceptibility to severe WNV disease in humans has not been determined...