Research Topics
Genomes and Genes
| Richard A GibbsSummaryAffiliation: Baylor College of Medicine Country: USA Publications
| Collaborators
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Detail Information
Publications
Genetics. No longer de-identifiedAmy L McGuire
Center for Medical Ethics and Health Policy, Baylor College of Medicine, Baylor College of Medicine, One Baylor Plaza, Suite 310D, Houston, TX 77030, USA
Science 312:370-1. 2006
The functional spectrum of low-frequency coding variationGabor T Marth
Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
Genome Biol 12:R84. 2011....- Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and developmentMarilyn 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... - Identification of genetic risk variants for deep vein thrombosis by multiplexed next-generation sequencing of 186 hemostatic/pro-inflammatory genesLuca 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.... - Genetic diversity in India and the inference of Eurasian population expansionJinchuan 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... - Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallabyEmily 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... - 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.... - Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertilityJean 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... - Evolutionary and biomedical insights from the rhesus macaque genomeRichard 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... 
Building a comprehensive genomic program for hepatocellular carcinomaTheresa 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...- The hypofunctional effect of P335L single nucleotide polymorphism on SSTR5 functionGuisheng 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... - Developing a tissue resource to characterize the genome of pancreatic cancerGeorgios 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... - The finished DNA sequence of human chromosome 12Steven 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... - A SNP discovery method to assess variant allele probability from next-generation resequencing dataYufeng 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... - The DNA sequence, annotation and analysis of human chromosome 3Donna M Muzny
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
Nature 440:1194-8. 2006.... - The complete genome of an individual by massively parallel DNA sequencingDavid 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'... - Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densitiesMatthew 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... - Exome capture sequencing identifies a novel mutation in BBS4Hui 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... - Whole-exome sequencing identifies compound heterozygous mutations in WDR62 in siblings with recurrent polymicrogyriaDavid 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... - Bos taurus genome assemblyYue 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... - A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genomeOliver 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... - Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathyJames 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... - A primer on a hepatocellular carcinoma bioresource bank using the cancer genome atlas guidelines: practical issues and pitfallsN 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... - 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... - Pooled genomic indexing of rhesus macaqueAleksandar 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... - Large-scale RT-PCR recovery of full-length cDNA clonesJia 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... - Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolutionStephen 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... - An integrative variant analysis suite for whole exome next-generation sequencing dataDanny 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... - Resequencing of IRS2 reveals rare variants for obesity but not fasting glucose homeostasis in Hispanic childrenNancy 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... - The genome of the model beetle and pest Tribolium castaneumStephen 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... - Identification of genetic susceptibility to childhood cancer through analysis of genes in parallelSharon 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... - Meeting the growing demands of genetic researchAmy L McGuire
Center for Medical Ethics and Health Policy, Baylor College of Medicine, USA
J Law Med Ethics 34:809-12. 2006 - Common and rare variants of DAOA in bipolar disorderManjula 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... - Clan genomics and the complex architecture of human diseaseJames 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... - Genomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genomeZhengdong 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... - Whole-genome sequencing for optimized patient managementMatthew 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... - Association between somatostatin receptor 5 gene polymorphisms and pancreatic cancer risk and survivalDonghui 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... - Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiaeMichael 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... - Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphismsJames 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... - Whole exome capture in solution with 3 Gbp of dataMatthew N Bainbridge
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
Genome Biol 11:R62. 2010.... - Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technologyAdam 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... - Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomesXiang 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... - The Atlas genome assembly systemPaul 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... - Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing ProjectRui 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... - Overview of the development of personalized genomic medicine and surgeryF 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... - Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RFAgathe 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... - Microarray analysis of somatostatin receptor 5-regulated gene expression profiles in murine pancreasSanjeet 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... - Human genetics. Primate shadow playRichard 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 - Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRichard 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 <http://www.hgsc.bcm.tmc.edu
Nature 428:493-521. 2004.... - Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencingJia 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... - Human genome sequencing in health and diseaseClaudia 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... - Shedding genomic light on Aristotle's lanternErica 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... - Basic principles and technologies for deciphering the genetic map of cancerGeorgios 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... - 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 duplexesJeffrey G Reid
Department of Chemistry, University of Houston, Houston, Texas 77204, USA
Genome Res 18:1571-81. 2008.... - Metagenomic pyrosequencing and microbial identificationJoseph 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... - MLH1-silenced and non-silenced subgroups of hypermutated colorectal carcinomas have distinct mutational landscapesLawrence 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... - Whole-exome sequencing identifies ALMS1, IQCB1, CNGA3, and MYO7A mutations in patients with Leber congenital amaurosisXia 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... - Role of somatic mutations in vascular disease formationSarah 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.... - Genome-wide linkage disequilibrium and haplotype mapsJohn W Belmont
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
Am J Pharmacogenomics 4:253-62. 2004..Significant challenges lie ahead in determining the best methods for the selection of markers in disease/phenotype studies, large-scale genotyping, and analysis of the resulting genetic data... - Single nucleotide polymorphisms in genes for 2'-5'-oligoadenylate synthetase and RNase L inpatients hospitalized with West Nile virus infectionImtiaz 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... - Genetics. The critical region in trisomy 21David L Nelson
Department of Molecular and Human Genetics and the Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
Science 306:619-21. 2004 - Positive selection of a pre-expansion CAG repeat of the human SCA2 geneFuli 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... - The KAT6B-related disorders genitopatellar syndrome and Ohdo/SBBYS syndrome have distinct clinical features reflecting distinct molecular mechanismsPhilippe 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... - Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomesDebra A Dederich
Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, ALKEK Building, N1409, Houston, TX 77030, USA
Nucleic Acids Res 30:e32. 2002..2% and 516 bases, respectively. The cost of this direct lysis/glass bead method in September 2001 was approximately 10 cents per clone, which is a significant cost saving in high throughput genomic sequencing efforts... - Oligogenic heterozygosity in individuals with high-functioning autism spectrum disordersChristian P Schaaf
Department of Molecular and Human Genetics, Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
Hum Mol Genet 20:3366-75. 2011..01) lower rate, suggesting oligogenic heterozygosity as a new potential mechanism in the pathogenesis of ASDs... - Spectrum of CHD7 mutations in 110 individuals with CHARGE syndrome and genotype-phenotype correlationSeema R Lalani
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Am J Hum Genet 78:303-14. 2006..We conclude that cardiovascular malformations, coloboma, and facial asymmetry are common findings in CHARGE syndrome caused by CHD7 mutation... - Molecular evidence of HIV-1 transmission in a criminal caseMichael L Metzker
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Proc Natl Acad Sci U S A 99:14292-7. 2002..Resampling of blood from the suspected transmission pair and independent sequencing by different laboratories provided precaution against laboratory error... - Pulmonary alveolar proteinosis caused by deletion of the GM-CSFRalpha gene in the X chromosome pseudoautosomal region 1Margarita Martinez-Moczygemba
Department of Medicine, Texas A and M College of Medicine, Texas A and M Health Science Center, Houston, TX 77030, USA
J Exp Med 205:2711-6. 2008..Using a combination of cellular, molecular, and genomic approaches, we provide the first evidence that PAP can result from a genetic deficiency of the GM-CSFR alpha chain, encoded in the X-chromosome pseudoautosomal region 1... - Sequencing the full-length of the phosphatase and tensin homolog (PTEN) gene in hepatocellular carcinoma (HCC) using the 454 GS20 and Illumina GA DNA sequencing platformsJoel A Rodriguez
Michael E DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA
World J Surg 33:647-52. 2009..To sequence the whole gene (including introns and exons), we have taken advantage of new technologies that allow for rapid, inexpensive sequencing to great depth... - Mutations in KAT6B, encoding a histone acetyltransferase, cause Genitopatellar syndromePhilippe M Campeau
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Am J Hum Genet 90:282-9. 2012..Together, the data support an epigenetic dysregulation of the limb, brain, and genital developmental programs... - Disruptive TP53 mutation is associated with aggressive disease characteristics in an orthotopic murine model of oral tongue cancerDaisuke Sano
Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
Clin Cancer Res 17:6658-70. 2011..To characterize tumor growth and metastatic potential in head and neck squamous cell carcinoma (HNSCC) cell lines in an orthotopic murine model of oral tongue cancer and to correlate TP53 mutation status with these findings... - Activation of multiple proto-oncogenic tyrosine kinases in breast cancer via loss of the PTPN12 phosphataseTingting Sun
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
Cell 144:703-18. 2011.... - Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cellsPeili Gu
Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
PLoS ONE 3:e2548. 2008..They can either continuously replenish themselves (self-renewal), or differentiate into cells that execute a limited number of specific actions (pluripotence)... - Concatenation cDNA sequencing for transcriptome analysisPreethi H Gunaratne
Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
C R Biol 326:971-7. 2003..Using this concatenation cDNA sequencing platform, we have contributed more than 13000 full-length cDNA sequences from human and mouse to the Mammalian Gene Collection (MGC)... - The genome of the sea urchin Strongylocentrotus purpuratusErica Sodergren
Science 314:941-52. 2006..This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes... - The DNA sequence of the human X chromosomeMark T Ross
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 434:325-37. 2005..Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence... - What everybody should know about the rat genome and its online resourcesSimon N Twigger
Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
Nat Genet 40:523-7. 2008.... - Initial sequencing and comparative analysis of the mouse genomeRobert H Waterston
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 420:520-62. 2002.... - Recurrent duplication-driven transposition of DNA during hominoid evolutionMatthew E Johnson
Department of Genome Sciences and the Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 103:17626-31. 2006..Our data support a model of duplication where the probability that a segment of DNA becomes duplicated is determined by its proximity to core duplicons, such as LCR16a... - Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assayPaul Hardenbol
ParAllele BioScience, Inc, South San Francisco, California 94080, USA
Genome Res 15:269-75. 2005..The results of this study demonstrate the suitability of this technology for comprehensive association studies that use targeted SNPs in indirect linkage disequilibrium studies or that directly screen for causative mutations... - Variation in GRM3 affects cognition, prefrontal glutamate, and risk for schizophreniaMichael F Egan
Clinical Brain Disorders Branch, Intramural Research Program, National Institute of Mental Health NIH DHHS, Building 10, Center Drive, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 101:12604-9. 2004..These convergent data point to a specific molecular pathway by which GRM3 genotype alters glutamate neurotransmission, prefrontal and hippocampal physiology and cognition, and thereby increased risk for schizophrenia... - Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequencesRobert L Strausberg
National Cancer Institute, Bethessda, MD 20892 2580, USA
Proc Natl Acad Sci U S A 99:16899-903. 2002..All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:mgc.nci.nih.gov)... - Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequenceSusan E Celniker
Berkeley Drosophila Genome Project, Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Genome Biol 3:RESEARCH0079. 2002.... - Polymorphisms at the G72/G30 gene locus, on 13q33, are associated with bipolar disorder in two independent pedigree seriesEiji Hattori
Department of Psychiatry, The University of Chicago, IL 60637, USA
Am J Hum Genet 72:1131-40. 2003..Taken together with the earlier report, this is the first demonstration of a novel gene(s), discovered through a positional approach, independently associated with both bipolar illness and schizophrenia... - Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomesAdam Siepel
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
Genome Res 15:1034-50. 2005..Noncoding HCEs also show strong statistical evidence of an enrichment for RNA secondary structure... - 28-way vertebrate alignment and conservation track in the UCSC Genome BrowserWebb Miller
Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA
Genome Res 17:1797-808. 2007..Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions... - Characterizing the cancer genome in lung adenocarcinomaBarbara A Weir
Department of Medical Oncology and Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
Nature 450:893-8. 2007..More generally, our results indicate that many of the genes that are involved in lung adenocarcinoma remain to be discovered... - Genome-wide detection and characterization of positive selection in human populationsPardis C Sabeti
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
Nature 449:913-8. 2007.... - A second generation human haplotype map of over 3.1 million SNPsKelly A Frazer
The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
Nature 449:851-61. 2007..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations... - Direct selection of human genomic loci by microarray hybridizationThomas J Albert
NimbleGen Systems Inc, 1 Science Court, Madison, Wisconsin 53711, USA
Nat Methods 4:903-5. 2007..These direct selection methods supersede multiplex PCR for the large-scale analysis of genomic regions... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genomeElliott H Margulies
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Genome Res 17:760-74. 2007..Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization... - The genome of Apis mellifera: dialog between linkage mapping and sequence assemblyMichel Solignac
Genome Biol 8:403. 2007..Each construct was used to control the quality of the other. The co-linearity of markers in the sequence and the map is almost perfect and argues in favor of the high quality of both... - Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insectsJoel Savard
Abteilung für Evolutionsgenetik, Institut fur Genetik, Universitat zu Koln, Köln 50674, Germany
Genome Res 16:1334-8. 2006..We validate our results by meticulous examination of potential confounding factors. Phylogenomic approaches are thus able to resolve long-standing questions about the phylogeny of insects... - Community annotation: procedures, protocols, and supporting toolsChristine G Elsik
Department of Animal Science, Texas A and M University, College Station, Texas 77843, USA
Genome Res 16:1329-33. 2006..We present annotation procedures, standard protocols, and tools used for sequence analysis, data submission, and data management. We also report lessons learned from this dispersed community annotation effort for a metazoan genome... - Analysis of transcriptome data in the red flour beetle, Tribolium castaneumYoonseong Park
Department of Entomology, Kansas State University, Manhattan, KS 66506 4004, USA
Insect Biochem Mol Biol 38:380-6. 2008..We conservatively estimate that the current EST set represents more than 7,500 transcription units... - SNPdetector: a software tool for sensitive and accurate SNP detectionJinghui Zhang
Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
PLoS Comput Biol 1:e53. 2005..SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov)... - The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorseTim Durfee
DNASTAR, Inc, Madison, Wisconsin 53705, USA
J Bacteriol 190:2597-606. 2008..Finally, while the sequence confirms most of the reported alleles, the sequence of deoR is wild type, necessitating reexamination of the assumed basis for the high transformability of DH10B...