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

Collections in this community

Recently Added

  • 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 ...
  • A Predictive Phosphorylation Signature of Lung Cancer 

    Wu, Chang-Jiun; Cai, Tianxi; Rikova, Klarisa; Merberg, David; Kasif, Simon; Steffen, Martin (Public Library of Science, 2009-11-25)
    BACKGROUND. Aberrant activation of signaling pathways drives many of the fundamental biological processes that accompany tumor initiation and progression. Inappropriate phosphorylation of intermediates in these signaling ...
  • 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 ...
  • Trichomonas Transmembrane Cyclases Result from Massive Gene Duplication and Concomitant Development of Pseudogenes 

    Cui, Jike; Das, Suchismita; Smith, Temple F.; Samuelson, John (Public Library of Science, 2010-8-3)
    BACKGROUND. Trichomonas vaginalis has an unusually large genome (∼160 Mb) encoding ∼60,000 proteins. With the goal of beginning to understand why some Trichomonas genes are present in so many copies, we characterized here ...
  • Chemical Combination Effects Predict Connectivity in Biological Systems 

    Lehár, Joseph; Zimmermann, Grant R.; Krueger, Andrew S.; Molnar, Raymond A.; Ledell, Jedediah T.; Heilbut, Adrian M.; Short, Glenn F.; Giusti, Leanne C.; Nolan, Garry P.; Magid, Omar A.; Lee, Margaret S.; Borisy, Alexis A.; Stockwell, Brent R.; Keith, Curtis T. (2007-02-27)
    Efforts to construct therapeutically useful models of biological systems require large and diverse sets of data on functional connections between their components. Here we show that cellular responses to combinations of ...
  • 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 ...
  • 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 ...
  • 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 ...
  • Architecture of Y-Family DNA Polymerases Relevant to Translesion DNA Synthesis as Revealed in Structural and Molecular Modeling Studies 

    Chandani, Sushil; Jacobs, Christopher; Loechler, Edward L. (SAGE-Hindawi Access to Research, 2010-9-16)
    DNA adducts, which block replicative DNA polymerases (DNAPs), are often bypassed by lesion-bypass DNAPs, which are mostly in the Y-Family. Y-Family DNAPs can do non-mutagenic or mutagenic dNTP insertion, and understanding ...
  • 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 ...
  • Bioinformatics Analysis of Macrophages Exposed to Porphyromonas gingivalis: Implications in Acute vs. Chronic Infections 

    Yu, Wen-Han; Hu, Han; Zhou, Qingde; Xia, Yu; Amar, Salomon (Public Library of Science, 2010-12-23)
    BACKGROUND. Periodontitis is the most common human infection affecting tooth-supporting structures. It was shown to play a role in aggravating atherosclerosis. To deepen our understanding of the pathogenesis of this disease, ...
  • Signatures of Arithmetic Simplicity in Metabolic Network Architecture 

    Riehl, William J.; Krapivsky, Paul L.; Redner, Sidney; Segrè, Daniel (Public Library of Science, 2010-4-1)
    Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding ...
  • Improving the Precision of the Structure–Function Relationship by Considering Phylogenetic Context 

    Shakhnovich, Boris E (Public Library of Science, 2005-6-24)
    Understanding the relationship between protein structure and function is one of the foremost challenges in post-genomic biology. Higher conservation of structure could, in principle, allow researchers to extend current ...
  • Many Sequence-Specific Chromatin Modifying Protein-Binding Motifs Show Strong Positional Preferences for Potential Regulatory Regions in the Saccharomyces Cerevisiae Genome 

    Hansen, Loren; Mariño-Ramírez, Leonardo; Landsman, David (Oxford University Press, 2010-01-04)
    Initiation and regulation of gene expression is critically dependent on the binding of transcriptional regulators, which is often temporal and position specific. Many transcriptional regulators recognize and bind specific ...
  • UniPROBE, Update 2011: Expanded Content and Search Tools in the Online Database of Protein-Binding Microarray Data on Protein–DNA Interactions 

    Robasky, Kimberly; Bulyk, Martha L. (Oxford University Press, 2010-10-30)
    The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray ...
  • 3'-UTR SIRF: A Database for Identifying Clusters of Whort Interspersed Repeats in 3' Untranslated Regions 

    Andken, Benjamin B.; Lim, In; Benson, Gary; Vincent, John J.; Ferenc, Matthew T.; Heinrich, Bianca; Jarzylo, Larissa A.; Man, Heng-Ye; Deshler, James O. (BioMed Central, 2007-7-30)
    BACKGROUND. Short (~5 nucleotides) interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a ...
  • Environments that Induce Synthetic Microbial Ecosystems 

    Klitgord, Niels; Segrè, Daniel (Public Library of Science, 2010-11-18)
    Interactions between microbial species are sometimes mediated by the exchange of small molecules, secreted by one species and metabolized by another. Both one-way (commensal) and two-way (mutualistic) interactions may ...
  • 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 ...
  • Spectral affinity in protein networks 

    Voevodski, Konstantin; Teng, Shang-Hua; Xia, Yu (BioMed Central, 2009-11-29)
    BACKGROUND. Protein-protein interaction (PPI) networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network ...

View more