Now showing items 1-18 of 18

    • 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 ...
    • Comparison of multiplexed reduced representation bisulfite sequencing (mRRBS) with the 450K Illumina Human BeadChip: from concordance to practical applications for methylomic profiling in epigenetic epidemiologic studies 

      Carmona, Juan Jose; Izzi, Benedetta; Just, Allan Carpenter; Barupal, Jitendra; Binder, Alexandra Margaret Lynn; Hutchinson, John N; Hofmann, Oliver Marc; Schwartz, Joel David; Baccarelli, Andrea; Michels, Karin B. (BioMed Central, 2013)
    • 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 ...
    • Evidence-Based Annotation of the Malaria Parasite's Genome Using Comparative Expression Profiling 

      Zhou, Yingyao; Ramachandran, Vandana; Kumar, Kota Arun; Westenberger, Scott; Refour, Phillippe; Zhou, Bin; Li, Fengwu; Young, Jason A.; Chen, Kaisheng; Plouffe, David; Henson, Kerstin; Nussenzweig, Victor; Carlton, Jane; Vinetz, Joseph M.; Winzeler, Elizabeth A.; Duraisingh, Manoj T.; Hofmann, Oliver Marc (Public Library of Science, 2008)
      A fundamental problem in systems biology and whole genome sequence analysis is how to infer functions for the many uncharacterized proteins that are identified, whether they are conserved across organisms of different phyla ...
    • 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 ...
    • 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, ...
    • Integrative Genomic Data Mining for Discovery of Potential Blood-Borne Biomarkers for Early Diagnosis of Cancer 

      Yang, Yongliang; Iyer, Lakshmanan K.; Adelstein, S. James; Kassis, Amin Iskandar; Hofmann, Oliver Marc; Pospisil, Pavel (Public Library of Science, 2008)
      Background: With the arrival of the postgenomic era, there is increasing interest in the discovery of biomarkers for the accurate diagnosis, prognosis, and early detection of cancer. Blood-borne cancer markers are favored ...
    • 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 ...
    • Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009 

      Lister, Allyson L.; Datta, Ruchira S.; Krause, Roland; Kuhn, Michael; Roth, Bettina; Schneider, Reinhard; Troyanskaya, Olga; Hofmann, Oliver (Public Library of Science, 2010)
    • Live Coverage of Scientific Conferences Using Web Technologies 

      Lister, Allyson L.; Datta, Ruchira S.; Krause, Roland; Kuhn, Michael; Roth, Bettina; Schneider, Reinhard; Bourne, Philip E.; Hofmann, Oliver Marc (Public Library of Science, 2010)
    • 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 ...
    • Stem Cell-Like Gene Expression in Ovarian Cancer Predicts Type II Subtype and Prognosis 

      Schwede, Matthew; Spentzos, Dimitrios; Bentink, Stefan; Hofmann, Oliver Marc; Haibe-Kains, Benjamin; Harrington, David Paul; Quackenbush, John; Culhane, Aedín C. (Public Library of Science, 2013)
      Although ovarian cancer is often initially chemotherapy-sensitive, the vast majority of tumors eventually relapse and patients die of increasingly aggressive disease. Cancer stem cells are believed to have properties that ...