Browsing by Author "Hide, Winston"

Now showing items 1-20 of 20

    • Comparison of Illumina and 454 Deep Sequencing in Participants Failing Raltegravir-Based Antiretroviral Therapy 

      Li, Jonathan Z.; Chapman, Brad; Charlebois, Patrick; Hofmann, Oliver; Weiner, Brian; Porter, Alyssa J.; Samuel, Reshmi; Vardhanabhuti, Saran; Zheng, Lu; Eron, Joseph; Taiwo, Babafemi; Zody, Michael C.; Henn, Matthew R.; Kuritzkes, Daniel R.; Hide, Winston; Wilson, Cara C.; Berzins, Baiba I.; Acosta, Edward P.; Bastow, Barbara; Kim, Peter S.; Read, Sarah W.; Janik, Jennifer; Meres, Debra S.; Lederman, Michael M.; Mong-Kryspin, Lori; Shaw, Karl E.; Zimmerman, Louis G.; Leavitt, Randi; De La Rosa, Guy; Jennings, Amy (Public Library of Science, 2014)
      Background: The impact of raltegravir-resistant HIV-1 minority variants (MVs) on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral ...

    • A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells 

      Sompallae, Ramakrishna; Hofmann, Oliver; Maher, Christopher A.; Gedye, Craig; Behren, Andreas; Vitezic, Morana; Daub, Carsten O.; Devalle, Sylvie; Caballero, Otavia L.; Carninci, Piero; Hayashizaki, Yoshihide; Lawlor, Elizabeth R.; Cebon, Jonathan; Hide, Winston (Frontiers Media S.A., 2013)
      PROM1 is the gene encoding prominin-1 or CD133, an important cell surface marker for the isolation of both normal and cancer stem cells. PROM1 transcripts initiate at a range of transcription start sites (TSS) associated ...

    • Divergent LIN28-mRNA associations result in translational suppression upon the initiation of differentiation 

      Tan, Shen Mynn; Altschuler, Gabriel; Zhao, Tian Yun; Ang, Haw Siang; Yang, Henry; Lim, Bing; Vardy, Leah; Hide, Winston; Thomson, Andrew M.; Lareu, Ricky R. (Oxford University Press, 2014)
      LIN28 function is fundamental to the activity and behavior of human embryonic stem cells (hESCs) and induced pluripotent stem cells. Its main roles in these cell types are the regulation of translational efficiency and ...

    • edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test 

      Dimont, Emmanuel; Shi, Jiantao; Kirchner, Rory; Hide, Winston (Oxford University Press, 2015)
      Summary: Next-generation sequencing platforms for measuring digital expression such as RNA-Seq are displacing traditional microarray-based methods in biological experiments. The detection of differentially expressed genes ...

    • Gateways to the FANTOM5 promoter level mammalian expression atlas 

      Lizio, Marina; Harshbarger, Jayson; Shimoji, Hisashi; Severin, Jessica; Kasukawa, Takeya; Sahin, Serkan; Abugessaisa, Imad; Fukuda, Shiro; Hori, Fumi; Ishikawa-Kato, Sachi; Mungall, Christopher J; Arner, Erik; Baillie, J Kenneth; Bertin, Nicolas; Bono, Hidemasa; de Hoon, Michiel; Diehl, Alexander D; Dimont, Emmanuel; Freeman, Tom C; Fujieda, Kaori; Hide, Winston; Kaliyaperumal, Rajaram; Katayama, Toshiaki; Lassmann, Timo; Meehan, Terrence F; Nishikata, Koro; Ono, Hiromasa; Rehli, Michael; Sandelin, Albin; Schultes, Erik A; ‘t Hoen, Peter AC; Tatum, Zuotian; Thompson, Mark; Toyoda, Tetsuro; Wright, Derek W; Daub, Carsten O; Itoh, Masayoshi; Carninci, Piero; Hayashizaki, Yoshihide; Forrest, Alistair RR; Kawaji, Hideya (BioMed Central, 2015)
      The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of ...

    • Genome-wide analysis of cancer/testis gene expression 

      Hofmann, Oliver Marc; Caballero, O. L.; Stevenson, B. J.; Chen, Yao-Tseng; Cohen, T.; Chua, R.; Maher, C. A.; Panji, S.; Schaefer, U.; Kruger, A.; Lehvaslaiho, M.; Carninci, P.; Hayashizaki, Y.; Jongeneel, C. V.; Simpson, A. J. G.; Old, L. J.; Hide, Winston (Proceedings of the National Academy of Sciences, 2008)
      Cancer/Testis (CT) genes, normally expressed in germ line cells but also activated in a wide range of cancer types, often encode antigens that are immunogenic in cancer patients, and present potential for use as biomarkers ...

    • Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium 

      Salomonis, Nathan; Dexheimer, Phillip J.; Omberg, Larsson; Schroll, Robin; Bush, Stacy; Huo, Jeffrey; Schriml, Lynn; Ho Sui, Shannan; Keddache, Mehdi; Mayhew, Christopher; Shanmukhappa, Shiva Kumar; Wells, James; Daily, Kenneth; Hubler, Shane; Wang, Yuliang; Zambidis, Elias; Margolin, Adam; Hide, Winston; Hatzopoulos, Antonis K.; Malik, Punam; Cancelas, Jose A.; Aronow, Bruce J.; Lutzko, Carolyn (Elsevier, 2016)
      Summary The rigorous characterization of distinct induced pluripotent stem cells (iPSC) derived from multiple reprogramming technologies, somatic sources, and donors is required to understand potential sources of variability ...

    • Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls 

      Zook, Justin M; Chapman, Brad Alan; Wang, Jason; Mittelman, David; Hofmann, Oliver Marc; Hide, Winston; Salit, Marc (Nature Publishing Group, 2014)
      Clinical adoption of human genome sequencing requires methods that output genotypes with known accuracy at millions or billions of positions across a genome. Because of substantial discordance among calls made by existing ...

    • Integrating Murine Gene Expression Studies to Understand Obstructive Lung Disease due to Chronic Inhaled Endotoxin 

      Lai, Peggy Sue; Hofmann, Oliver Marc; Baron, Rebecca Marlene; Cernadas, Manuela; Meng, Quanxin Ryan; Bresler, Herbert S.; Brass, David M.; Yang, Ivana V.; Schwartz, David A.; Christiani, David C.; Hide, Winston (Public Library of Science, 2013)
      Rationale: Endotoxin is a near ubiquitous environmental exposure that that has been associated with both asthma and chronic obstructive pulmonary disease (COPD). These obstructive lung diseases have a complex pathophysiology, ...

    • ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level 

      Rocca-Serra, Philippe; Brandizi, Marco; Maguire, Eamonn; Sklyar, Nataliya; Taylor, Chris; Begley, Kimberly; Field, Dawn; Harris, Stephen; Hide, Winston; Hofmann, Oliver Marc; Neumann, Steffen; Sterk, Peter; Tong, Weida; Sansone, Susanna-Assunta (Oxford University Press, 2010)
      Summary: The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination ...

    • ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus 

      Karp, Peter D.; Berger, Bonnie; Kovats, Diane; Lengauer, Thomas; Linial, Michal; Sabeti, Pardis; Hide, Winston; Rost, Burkhard (Public Library of Science, 2015)
      Speed is of the essence in combating Ebola; thus, computational approaches should form a significant component of Ebola research. As for the development of any modern drug, computational biology is uniquely positioned to ...

    • A Network of Epigenetic Regulators Guide Developmental Hematopoiesis In Vivo 

      Huang, Hsuan-Ting; Kathrein, Katie L.; Barton, Abby; Gitlin, Zachary; Huang, Yue-Hua; Ward, Thomas P.; Hofmann, Oliver; Dibiase, Anthony; Song, Anhua; Tyekucheva, Svitlana; Hide, Winston; Zhou, Yi; Zon, Leonard I. (2013)
      The initiation of cellular programs is orchestrated by key transcription factors and chromatin regulators that activate or inhibit target gene expression. To generate a compendium of chromatin factors that establish the ...

    • Novel Developmental Analyses Identify Longitudinal Patterns of Early Gut Microbiota that Affect Infant Growth 

      White, Richard A.; Bjørnholt, Jørgen V.; Baird, Donna D.; Midtvedt, Tore; Harris, Jennifer R.; Pagano, Marcello; Hide, Winston; Rudi, Knut; Moen, Birgitte; Iszatt, Nina; Peddada, Shyamal D.; Eggesbø, Merete (Public Library of Science, 2013)
      It is acknowledged that some obesity trajectories are set early in life, and that rapid weight gain in infancy is a risk factor for later development of obesity. Identifying modifiable factors associated with early rapid ...

    • Pathprinting: An integrative approach to understand the functional basis of disease 

      Altschuler, Gabriel M; Hofmann, Oliver Marc; Kalatskaya, Irina; Payne, Rebecca; Ho Sui, Shannan; Saxena, Uma; Krivtsov, Andrei V; Armstrong, Scott A; Cai, Tianxi; Stein, Lincoln; Hide, Winston (Springer Science + Business Media, 2013)
      New strategies to combat complex human disease require systems approaches to biology that integrate experiments from cell lines, primary tissues and model organisms. We have developed Pathprint, a functional approach that ...

    • Population Differences in Transcript-Regulator Expression Quantitative Trait Loci 

      Bushel, Pierre R.; McGovern, Ray; Liu, Liwen; Hofmann, Oliver Marc; Huda, Ahsan; Lu, Jun; Hide, Winston; Lin, Xihong (Public Library of Science, 2012)
      Gene expression quantitative trait loci (eQTL) are useful for identifying single nucleotide polymorphisms (SNPs) associated with diseases. At times, a genetic variant may be associated with a master regulator involved in ...

    • Prenatal Lead Levels, Plasma Amyloid β Levels, and Gene Expression in Young Adulthood 

      Mazumdar, Maitreyi; Xia, Weiming; Hofmann, Oliver Marc; Gregas, Matthew; Sui, Shannan Ho; Hide, Winston; Yang, Ting; Needleman, Herbert L.; Bellinger, David C. (National Institute of Environmental Health Sciences, 2012)
      Background: Animal studies suggest that early-life lead exposure influences gene expression and production of proteins associated with Alzheimer’s disease (AD). Objectives: We attempted to assess the relationship between ...

    • Sequencing of Captive Target Transcripts Identifies the Network of Regulated Genes and Functions of Primate-Specific miR-522 

      Tan, Shen Mynn; Kirchner, Rory D; Jin, Jingmin; Hofmann, Oliver Marc; McReynolds, Larry; Hide, Winston; Lieberman, Judy (Elsevier BV, 2014)
      Identifying microRNA (miRNA)-regulated genes is key to understanding miRNA function. However, many miRNA recognition elements (MREs) do not follow canonical “seed” base-pairing rules, making identification of bona fide ...

    • The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework 

      Sui, Shannan Ho; Merrill, Emily; Gehlenborg, Nils; Haseley, Psalm; Sytchev, Ilya; Park, Richard; Rocca-Serra, Philippe; Corlosquet, Stephane; Gonzalez-Beltran, Alejandra; Maguire, Eamonn; Hofmann, Oliver; Park, Peter; Das, Sudeshna; Sansone, Susanna-Assunta; Hide, Winston (American Medical Informatics Association, 2013)
      Comparisons of stem cell experiments at both molecular and semantic levels remain challenging due to inconsistencies in results, data formats, and descriptions among biomedical research discoveries. The Harvard Stem Cell ...

    • The Stem Cell Discovery Engine: An Integrated Repository and Analysis System for Cancer Stem Cell Comparisons 

      Begley, Kimberly; Reilly, Dorothy; McGovern, Ray; Rocca-Sera, Philippe; Maguire, Eamonn; Altschuler, Gabriel M.; Culhane, Aedín C.; Correll, Mick; Sansone, Susanna-Assunta; Ho Sui, Shannan; Chapman, Brad Alan; Hansen, Terah; Sompallae, Ramakrishna Rao; Krivtsov, Andrei V.; Shivdasani, Ramesh Arjun; Armstrong, Scott A.; Hofmann, Oliver Marc; Hide, Winston (Oxford University Press, 2011)
      Mounting evidence suggests that malignant tumors are initiated and maintained by a subpopulation of cancerous cells with biological properties similar to those of normal stem cells. However, descriptions of stem-like gene ...

    • Ten Simple Rules for Organizing a Virtual Conference—Anywhere 

      Gichora, Nelson N.; Fatumo, Segun A.; Ngara, Mtakai V.; Chelbat, Noura; Ramdayal, Kavisha; Opap, Kenneth B.; Siwo, Geoffrey H.; Adebiyi, Marion O.; El Gonnouni, Amina; Zofou, Denis; Maurady, Amal A. M.; Adebiyi, Ezekiel F.; de Villiers, Etienne P.; Masiga, Daniel K.; Bizzaro, Jeffrey W.; Suravajhala, Prashanth; Ommeh, Sheila C.; Bourne, Philip E.; Hide, Winston (Public Library of Science, 2010)