Affiliation: Baylor College of Medicine
- mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communitiesJun Ma
Departments of Obstetrics and Gynecology, Baylor College of Medicine and Texas Children s Hospital, Houston, TX, USA
BMC Genomics 15:257. 2014....
- Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and bloodMatthew N Davies
Institute of Psychiatry, King s College London, De Crespigny Park, London, UK
Genome Biol 13:R43. 2012..We characterized intra- and inter-individual methylomic variation across whole blood and multiple regions of the brain from multiple donors...
- Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrainPreethi H Gunaratne
Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
BMC Genomics 12:277. 2011..To test this, we used massively parallel Illumina sequencing to analyse small RNAs from auditory forebrain of adult zebra finches exposed to tape-recorded birdsong or silence...
- Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencingCristian Coarfa
Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza Houston, TX 77030, USA
BMC Bioinformatics 11:572. 2010..Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing...
- Atlas2 Cloud: a framework for personal genome analysis in the cloudUday S Evani
The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
BMC Genomics 13:S19. 2012..To this end, the cloud computing and Software-as-a-Service (SaaS) technologies can help address these issues...
- Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAsViren Amin
Epigenome Center, Bioinformatics Research Laboratory, Department of Molecular and Human, Genetics, Baylor College of Medicine, One Baylor Plaza, BCMD 400D, Houston, Texas 77030, USA
Nat Commun 6:6370. 2015..The exquisitely tissue-specific epigenetic regulation of lincRNAs and the assignment of a majority of them to specific tissue types will inform future studies of this newly discovered class of genes. ..
- Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencingGovindarajan Kunde-Ramamoorthy
Department of Pediatrics, Baylor College of Medicine, USDA ARS Children s Nutrition Research Center, Houston, TX 77030, USA, Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Nucleic Acids Res 42:e43. 2014..Of these algorithms, Bismark provides an attractive combination of processing speed, genomic coverage and quantitative accuracy, whereas Pash offers considerably higher genomic coverage. ..
- Upregulation of EGFR signaling is correlated with tumor stroma remodeling and tumor recurrence in FGFR1-driven breast cancerXue B Holdman
Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
Breast Cancer Res 17:141. 2015..However, the mechanisms underlying this process are not completely understood. In this study, we investigated the mechanisms of tumor dormancy and recurrence in a preclinical mouse model of breast cancer...
- The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequencesKevin Riehle
Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
BMC Bioinformatics 13:S11. 2012..Installation, integration, and maintenance of the tools poses significant burden on many researchers and creates a barrier to adoption of microbiome analysis, particularly in translational settings...
- 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...
- Mammary Stem Cells and Tumor-Initiating Cells Are More Resistant to Apoptosis and Exhibit Increased DNA Repair Activity in Response to DNA DamageChi Hsuan Chang
Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
Stem Cell Reports 5:378-91. 2015..These results have important implications for understanding DDR mechanisms involved in both tumorigenesis and therapy resistance. ..
- CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinomaKalpana Kannan
Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
PLoS Genet 10:e1004216. 2014..CDKN2D-WDFY2 fusion could be an important molecular signature for understanding and classifying sub-lineages among heterogeneous high-grade serous ovarian carcinomas. ..