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- Towards computational prediction of microRNA function and activity
- An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes
- Genome-wide functional element detection using pairwise statistical alignment outperforms multi-genome footprinting techniques
- Mining metabolic pathways through gene expression
- Integration of pathway knowledge into a weighted recursive feature elimination approach for cancer patients risk stratification
- Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm
- A Poisson model for random multigraphs
- A Bayesian approach using covariance of SNP data to detect differences in linkage disequilibrium patterns between groups
- Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
- Over-optimism in bioinformatics: an illustration
Nucleic Acids Research
- Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm
- A flexible and efficient template format for circular consensus sequencing and SNP detection
- Towards computational prediction of microRNA function and activity
- Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology
- The synthetic integron: an in vivo genetic shuffling device
Bioinformatics
- Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins
- Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images
- Mass spectrometry data processing using zero-crossing lines in multi-scale of Gaussian derivative wavelet
- Author Index
- Utopia documents: linking scholarly literature with research data
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Chemistry
Functional Studies of Plasmodium falciparum Dipeptidyl Aminopeptidase I Using Small Molecule Inhibitors and Active Site Probes
Edgar Deu, Melissa J. Leyva, Victoria E. Albrow, Mark J. Rice, Jonathan A. Ellman, Matthew Bogyo. The widespread resistance of malaria parasites to all affordable drugs has made the identification of new targets urgent. Dipeptidyl aminopeptidases (DPAPs) represent potentially valuable new targ....
Application of Fragment-Based Drug Discovery to Membrane Proteins: Identification of Ligands of the Integral Membrane Enzyme DsbB
Virginie Früh, Yunpeng Zhou, Dan Chen, Caroline Loch, Eiso AB, Yelena N. Grinkova, Herman Verheij, Stephen G. Sligar, John H. Bushweller, Gregg Siegal. Membrane proteins are important pharmaceutical targets, but they pose significant challenges for fragment-based drug discovery approaches. Here, we present the first successful use of biophysical ....
Nitric Oxide-Mediated Histone Hyperacetylation in Oral Cancer: Target for a Water-Soluble HAT Inhibitor, CTK7A
Mohammed Arif, Bhusainahalli M. Vedamurthy, Ramesh Choudhari, Yogesh B. Ostwal, Kempegowda Mantelingu, Gopinath S. Kodaganur, Tapas K. Kundu. Altered histone acetylation is associated with several diseases, including cancer. We report here that, unlike in most cancers, histones are found to be highly hyperacetylated in oral squamous cel....
A Metabolomic View of Staphylococcus aureus and Its Ser/Thr Kinase and Phosphatase Deletion Mutants: Involvement in Cell Wall Biosynthesis
Manuel Liebeke, Hanna Meyer, Stefanie Donat, Knut Ohlsen, Michael Lalk. Little is known about intracellular metabolite pools in pathogens such as Staphylococcus aureus. We have studied a particular metabolome by means of the presented LC-MS method. By investiga....
The Awesome Power of Synergy from Chemical-Chemical Profiling
Jeff S. Piotrowski, Chuek Hei Ho, Charles Boone. Chemical-chemical profiling, as described in Farha and Brown (2010), delivers all the power of chemical-genomic profiling while untethering researchers from model systems and thereby enabling us t....
Expanding the Biological Periodic Table
Javier Seravalli, Stephen W. Ragsdale. Metal ions play an indispensable role in biology, enabling enzymes to perform their functions and lending support to the structures of numerous macromolecules. Despite their prevalence and importa....
Chemical Probes of Escherichia coli Uncovered through Chemical-Chemical Interaction Profiling with Compounds of Known Biological Activity
Maya A. Farha, Eric D. Brown. While cell-based screens have considerable power in identifying new chemical probes of biological systems and leads for new drugs, a major challenge to the utility of such compounds is in connecti....
The Glycerophospho Metabolome and Its Influence on Amino Acid Homeostasis Revealed by Brain Metabolomics of GDE1(−/−) Mice
Florian Kopp, Toru Komatsu, Daniel K. Nomura, Sunia A. Trauger, Jason R. Thomas, Gary Siuzdak, Gabriel M. Simon, Benjamin F. Cravatt. GDE1 is a mammalian glycerophosphodiesterase (GDE) implicated by in vitro studies in the regulation of glycerophophoinositol (GroPIns) and possibly other glycerophospho (GroP) metabolites. Here, w....
Recognition of Intermediate Functionality by Acyl Carrier Protein over a Complete Cycle of Fatty Acid Biosynthesis
Eliza Płoskoń, Christopher J. Arthur, Amelia L.P. Kanari, Pakorn Wattana-amorn, Christopher Williams, John Crosby, Thomas J. Simpson, Christine L. Willis, Matthew P. Crump. It remains unclear whether in a bacterial fatty acid synthase (FAS) acyl chain transfer is a programmed or diffusion controlled and random action. Acyl carrier protein (ACP), which delivers all in....
Bioactive Cell-Penetrating Peptides: Kill Two Birds with One Stone
Gilles Divita. Jones et al. (2010) propose an innovative strategy for the development of bioactive cell-penetrating peptides. They combine computer-based design with specific targeting to elaborate a potent cell....
A Eubacterial Riboswitch Class That Senses the Coenzyme Tetrahydrofolate
Tyler D. Ames, Dmitry A. Rodionov, Zasha Weinberg, Ronald R. Breaker. Comparative sequence analyses of bacterial genomes are revealing many structured RNA motifs that function as metabolite-binding riboswitches. We have identified an RNA motif frequently positioned ....
Red Fluorescent Protein with Reversibly Photoswitchable Absorbance for Photochromic FRET
Fedor V. Subach, Lijuan Zhang, Theodorus W.J. Gadella, Nadya G. Gurskaya, Konstantin A. Lukyanov, Vladislav V. Verkhusha. We have developed the first red fluorescent protein, named rsTagRFP, which possesses reversibly photoswitchable absorbance spectra. Illumination with blue and yellow light switches rsTagRFP into a....
Characterization of Bioactive Cell Penetrating Peptides from Human Cytochrome c: Protein Mimicry and the Development of a Novel Apoptogenic Agent
Sarah Jones, Tina Holm, Imre Mäger, Ülo Langel, John Howl. Cell penetrating peptides (CPPs) with intrinsic biological activities offer a novel strategy for the modulation of intracellular events. QSAR analysis identified CPPs within human cytochrome c<....
Microfluidic Compartmentalized Directed Evolution
Brian M. Paegel, Gerald F. Joyce. Directed evolution studies often make use of water-in-oil compartments, which conventionally are prepared by bulk emulsification, a crude process that generates nonuniform droplets and can damage ....
Accessing Protein Methyltransferase and Demethylase Enzymology Using Microfluidic Capillary Electrophoresis
Tim J. Wigle, Laurel M. Provencher, Jacqueline L. Norris, Jian Jin, Peter J. Brown, Stephen V. Frye, William P. Janzen. The discovery of small molecules targeting the >80 enzymes that add (methyltransferases) or remove (demethylases) methyl marks from lysine and arginine residues, most notably present in histone....
Dihydrosphingomyelin Impairs HIV-1 Infection by Rigidifying Liquid-Ordered Membrane Domains
Catarina R. Vieira, Jose M. Munoz-Olaya, Jesús Sot, Sonia Jiménez-Baranda, Nuria Izquierdo-Useros, Jose Luis Abad, Beatriz Apellániz, Rafael Delgado, Javier Martinez-Picado, Alicia Alonso, Josefina Casas, José L. Nieva, Gemma Fabriás, Santos Mañes, Félix M. Goñi. The lateral organization of lipids in cell membranes is thought to regulate numerous cell processes. Most studies focus on the coexistence of two fluid phases, the liquid crystalline (l
Insights into Protein-Protein and Enzyme-Substrate Interactions in Modular Polyketide Synthases
Lucky Tran, R. William Broadhurst, Manuela Tosin, Andrea Cavalli, Kira J. Weissman. Numerous natural products of clinical value are biosynthesized by polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs), which are multienzymes comprising modules of catalytic d....
Application of Chemoproteomics to Drug Discovery: Identification of a Clinical Candidate Targeting Hsp90
Patrick Fadden, Kenneth H. Huang, James M. Veal, Paul M. Steed, Amy F. Barabasz, Briana Foley, Mei Hu, Jeffrey M. Partridge, John Rice, Anisa Scott, Laura G. Dubois, Tiffany A. Freed, Melanie A. Rehder Silinski, Thomas E. Barta, Philip F. Hughes, Andy Ommen, Wei Ma, Emilie D. Smith, Angela Woodward Spangenberg, Jeron Eaves, Gunnar J. Hanson, Lindsay Hinkley, Matthew Jenks, Meredith Lewis, James Otto, Gijsbertus J. Pronk, Katleen Verleysen, Timothy A. Haystead, Steven E. Hall. A chemoproteomics-based drug discovery strategy is presented that utilizes a highly parallel screening platform, encompassing more than 1000 targets, with a focused chemical library prior t....