URI: http://hdl.handle.net/2144/2433

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  • Fungal microbiota profile in newly-diagnosed treatment-naïve children with Crohn disease 

    Korolev, Kirill; El Mouzan, Mohammad; Wang, Feng; Al Mofarreh, Mohammad; Menon, Rajita; Al Barrag, Ahmad; Al Sarkhy, Ahmad; Al Asmi, Mona; Hamed, Yassin; Saeed, Anjum; Dowd, Scot; Assiri, Asaad; Winter, Harland (Oxford University Press, 2016-11-03)
    BACKGROUND & AIMS: although increasing evidence suggests a role for fungi in inflammatory bowel disease (IBD), data are scarce and mostly from adults. Our aim was to define the characteristics of fungal microbiota in ...
  • Predicting Eukaryotic Transcriptional Cooperativity by Bayesian Network Integration of Genome-Wide Data 

    Wang, Yong; Zhang, Xiang-Sun; Xia, Yu (2009-10)
    Transcriptional cooperativity among several transcription factors (TFs) is believed to be the main mechanism of complexity and precision in transcriptional regulatory programs. Here, we present a Bayesian network framework ...
  • Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains 

    Ku, Manching; Koche, Richard P.; Rheinbay, Esther; Mendenhall, Eric M.; Endoh, Mitsuhiro; Mikkelsen, Tarjei S.; Presser, Aviva; Nusbaum, Chad; Xie, Xiaohui; Chi, Andrew S.; Adli, Mazhar; Kasif, Simon; Ptaszek, Leon M.; Cowan, Chad A.; Lander, Eric S.; Koseki, Haruhiko; Bernstein, Bradley E. (Public Library of Science, 2008-10-31)
    In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 ...
  • The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome 

    Fu, Yutao; Sinha, Manisha; Peterson, Craig L.; Weng, Zhiping (Public Library of Science, 2008-7-25)
    Chromatin structure plays an important role in modulating the accessibility of genomic DNA to regulatory proteins in eukaryotic cells. We performed an integrative analysis on dozens of recent datasets generated by ...
  • Towards a Holistic, Yet Gene-Centered Analysis of Gene Expression Profiles: A Case Study of Human Lung Cancers 

    Guo, Yuchun; Eichler, Gabriel S.; Feng, Ying; Ingber, Donald E.; Huang, Sui (Hindawi Publishing Corporation, 2006-11-2)
    Genome-wide gene expression profile studies encompass increasingly large number of samples, posing a challenge to their presentation and interpretation without losing the notion that each transcriptome constitutes a complex ...
  • Biological Process Linkage Networks 

    Dotan-Cohen, Dikla; Letovsky, Stan; Melkman, Avraham A.; Kasif, Simon (Public Library of Science, 2009-4-23)
    BACKGROUND. The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic pathways. By comparison, little is known ...
  • COMBREX: A Project to Accelerate the Functional Annotation of Prokaryotic Genomes 

    Roberts, Richard J.; Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John N.; Anton, Brian P.; Pokrzywa, Revonda M.; Choi, Han-Pil; Faller, Lina L.; Guleria, Jyotsna; Housman, Genevieve; Klitgord, Niels; Mazumdar, Varun; McGettrick, Mark G.; Osmani, Lais; Swaminathan, Rajeswari; Tao, Kevin R.; Letovsky, Stan; Vitkup, Dennis; Segrè, Daniel; Salzberg, Steven L.; DeLisi, Charles; Steffen, Martin; Kasif, Simon (2010-11-20)
    COMBREX (http://combrex.bu.edu) is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes. It consists of a database of functional predictions produced by computational biologists ...
  • PRECISE: A Database of Predicted and Consensus Interaction Sites in Enzymes 

    Sheu, Shu-Hsien; Lancia, David R.; Clodfelter, Karl H.; Landon, Melissa R.; Vajda, Sandor (Oxford University Press, 2004-12-17)
    PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between the amino acid residues of an enzyme and its ligands (substrate and transition state analogs, cofactors, inhibitors and ...
  • Systematic Variation in mRNA 3′-Processing Signals during Mouse Spermatogenesis 

    Liu, Donglin; Brockman, J. Michael; Dass, Brinda; Hutchins, Lucie N.; Singh, Priyam; McCarrey, John R.; MacDonald, Clinton C.; Graber, Joel H. (Oxford University Press, 2006-12-08)
    Gene expression and processing during mouse male germ cell maturation (spermatogenesis) is highly specialized. Previous reports have suggested that there is a high incidence of alternative 3′-processing in male germ cell ...
  • Comparative Assessment of Performance and Genome Dependence among Phylogenetic Profiling Methods 

    Snitkin, Evan S.; Gustafson, Adam M.; Mellor, Joseph; Wu, Jie; DeLisi, Charles (BioMed Central, 2006-9-27)
    BACKGROUND. The rapidly increasing speed with which genome sequence data can be generated will be accompanied by an exponential increase in the number of sequenced eukaryotes. With the increasing number of sequenced ...
  • ELISA: Structure-Function Inferences Based on Statistically Significant and Evolutionarily Inspired Observations 

    Shakhnovich, Boris E.; Harvey, John M.; Comeau, Steve; Lorenz, David; DeLisi, Charles; Shakhnovich, Eugene (BioMed Central, 2003-9-2)
    The problem of functional annotation based on homology modeling is primary to current bioinformatics research. Researchers have noted regularities in sequence, structure and even chromosome organization that allow valid ...
  • Protein Evolution in Yeast Transcription Factor Subnetworks 

    Wang, Yong; Franzosa, Eric A.; Zhang, Xiang-Sun; Xia, Yu (Oxford University Press, 2010-5-13)
    When averaged over the full yeast protein–protein interaction and transcriptional regulatory networks, protein hubs with many interaction partners or regulators tend to evolve significantly more slowly due to increased ...
  • Pre-Bilaterian Origins of the Hox Cluster and the Hox Code: Evidence from the Sea Anemone, Nematostella Vectensis 

    Ryan, Joseph F.; Mazza, Maureen E.; Pang, Kevin; Matus, David Q.; Baxevanis, Andreas D.; Martindale, Mark Q.; Finnerty, John R. (Public Library of Science, 2007-1-24)
    BACKGROUND. Hox genes were critical to many morphological innovations of bilaterian animals. However, early Hox evolution remains obscure. Phylogenetic, developmental, and genomic analyses on the cnidarian sea anemone ...
  • High-Precision High-Coverage Functional Inference from Integrated Data Sources 

    Linghu, Bolan; Snitkin, Evan S.; Holloway, Dustin T.; Gustafson, Adam M.; Xia, Yu; DeLisi, Charles (BioMed Central, 2008-2-25)
    BACKGROUND. Information obtained from diverse data sources can be combined in a principled manner using various machine learning methods to increase the reliability and range of knowledge about protein function. The result ...
  • Phylogenetic Detection of Conserved Gene Clusters in Microbial Genomes 

    Zheng, Yu; Anton, Brian P.; Roberts, Richard J.; Kasif, Simon (BioMed Central, 2005-10-3)
    BACKGROUND. Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functional ...
  • Machine Learning for Regulatory Analysis and Transcription Factor Target Prediction in Yeast 

    Holloway, Dustin T.; Kon, Mark; DeLisi, Charles (Kluwer Academic Publishers, 2006-10-31)
    High throughput technologies, including array-based chromatin immunoprecipitation, have rapidly increased our knowledge of transcriptional maps-the identity and location of regulatory binding sites within genomes. Still, ...
  • Segmentally Variable Genes: A New Perspective on Adaptation 

    Zheng, Yu; Roberts, Richard J; Kasif, Simon (Public Library of Science, 2004-4-13)
    Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes suggests that genes are evolving ...
  • Functional Characterization of the YmcB and YqeV tRNA Methylthiotransferases of Bacillus Subtilis 

    Anton, Brian P.; Russell, Susan P.; Vertrees, Jason; Kasif, Simon; Raleigh, Elisabeth A.; Limbach, Patrick A.; Roberts, Richard J. (2010-5-14)
    Methylthiotransferases (MTTases) are a closely related family of proteins that perform both radical-S-adenosylmethionine (SAM) mediated sulfur insertion and SAM-dependent methylation to modify nucleic acid or protein targets ...
  • Size Matters: Network Inference Tackles the Genome Scale 

    Hayete, Boris; Gardner, Timothy S.; Collins, James J. (2007-02-13)
  • In Silico Regulatory Analysis for Exploring Human Disease Progression 

    Holloway, Dustin T; Kon, Mark; DeLisi, Charles (BioMed Central, 2008-6-18)
    BACKGROUND. An important goal in bioinformatics is to unravel the network of transcription factors (TFs) and their targets. This is important in the human genome, where many TFs are involved in disease progression. Here, ...

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