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  • Fungal microbiota profile in newly-diagnosed treatment-naïve children with Crohn's 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 ...
  • Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome 

    Xi, Hualin; Shulha, Hennaed P.; Lin, Jane M.; Vales, Teresa R.; Fu, Yutao; Bodine, David M.; McKay, Ronald D. G.; Chenoweth, Josh G.; Tesar, Paul J.; Furey, Terrence S.; Ren, Bing; Weng, Zhiping; Crawford, Gregory E. (Public Library of Science, 2007-8-17)
    The identification of regulatory elements from different cell types is necessary for understanding the mechanisms controlling cell type–specific and housekeeping gene expression. Mapping DNaseI hypersensitive (HS) sites ...
  • Small but Versatile: The Extraordinary Functional and Structural Diversity of the β-grasp Fold 

    Burroughs, A. Maxwell; Balaji, S.; Iyer, Lakshminarayan M.; Aravind, L. (BioMed Central, 2007-7-2)
    BACKGROUND. The β-grasp fold (β-GF), prototyped by ubiquitin (UB), has been recruited for a strikingly diverse range of biochemical functions. These functions include providing a scaffold for different enzymatic active ...
  • 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 ...
  • 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 ...
  • Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate 

    Xia, Yu; Franzosa, Eric A.; Gerstein, Mark B. (Public Library of Science, 2009-6-12)
    Rates of evolution differ widely among proteins, but the causes and consequences of such differences remain under debate. With the advent of high-throughput functional genomics, it is now possible to rigorously assess the ...
  • Comparison of Proteomic and Transcriptomic Profiles in the Bronchial Airway Epithelium of Current and Never Smokers 

    Steiling, Katrina; Kadar, Aran Y.; Bergerat, Agnes; Flanigon, James; Sridhar, Sriram; Shah, Vishal; Ahmad, Q. Rushdy; Brody, Jerome S.; Lenburg, Marc E.; Steffen, Martin; Spira, Avrum (Public Libary of Science, 2009-4-9)
    BACKGROUND. Although prior studies have demonstrated a smoking-induced field of molecular injury throughout the lung and airway, the impact of smoking on the airway epithelial proteome and its relationship to smoking-related ...
  • Multiplierz: An Extensible API Based Desktop Environment for Proteomics Data Analysis 

    Parikh, Jignesh R.; Askenazi, Manor; Ficarro, Scott B.; Cashorali, Tanya; Webber, James T.; Blank, Nathaniel C.; Zhang, Yi; Marto, Jarrod A. (BioMed Central, 2009-10-29)
    BACKGROUND. Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide ...
  • Design of a Combinatorial DNA Microarray for Protein-DNA Interaction Studies 

    Mintseris, Julian; Eisen, Michael B. (BioMed Central, 2006-10-3)
    BACKGROUND. Discovery of precise specificity of transcription factors is an important step on the way to understanding the complex mechanisms of gene regulation in eukaryotes. Recently, double-stranded protein-binding ...
  • Recurrent, Robust and Scalable Patterns Underlie Human Approach and Avoidance 

    Kim, Byoung Woo; Kennedy, David N.; Lehár, Joseph; Lee, Myung Joo; Blood, Anne J.; Lee, Sang; Perlis, Roy H.; Smoller, Jordan W.; Morris, Robert; Fava, Maurizio; Breiter, Hans C. (Public Library of Science, 2010-5-26)
    BACKGROUND. Approach and avoidance behavior provide a means for assessing the rewarding or aversive value of stimuli, and can be quantified by a keypress procedure whereby subjects work to increase (approach), decrease ...

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