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ORCIDPLoS Computational Biology, Volume 1
Volume 1, Number 1, June 2005
- Philip E. Bourne, Steven E. Brenner, Michael B. Eisen
:
PLoS Computational Biology: A New Community Journal.
- Michael Gribskov:
An Open Forum for Computational Biology.
- Sean R. Eddy:
"Antedisciplinary" Science.
- Olaf Sporns, Giulio Tononi, Rolf Kötter:
The Human Connectome: A Structural Description of the Human Brain.
- Tommy Kaplan, Nir Friedman, Hanah Margalit:
Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge. - Johan Elf, Måns Ehrenberg:
What Makes Ribosome-Mediated Transcriptional Attenuation Sensitive to Amino Acid Limitation? - Daniel Barker, Mark Pagel:
Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes. - Prashanth Ak, Craig J. Benham:
Susceptibility to Superhelically Driven DNA Duplex Destabilization: A Highly Conserved Property of Yeast Replication Origins. - Laxmi Parida, Ruhong Zhou:
Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a β-Hairpin. - Boris E. Shakhnovich:
Improving the Precision of the Structure-Function Relationship by Considering Phylogenetic Context. - Parantu K. Shah, Lars Juhl Jensen, Stéphanie Boué, Peer Bork:
Extraction of Transcript Diversity from Scientific Literature. - Bagrat R. Amirikian:
A Phenomenological Theory of Spatially Structured Local Synaptic Connectivity. - David H. Ardell, Leif A. Kirsebom:
The Genomic Pattern of tDNA Operon Expression in E. coli. - Dominic Grün, Yi-Lu Wang, David Langenberger, Kristin C. Gunsalus, Nikolaus Rajewsky:
microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets.
Volume 1, Number 2, July 2005
- Mercedes Pascual:
Computational Ecology: From the Complex to the Simple and Back.
- Kevin C. Chen, Lior Pachter:
Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities.
- Arnold Hayer, Upinder S. Bhalla:
Molecular Switches at the Synapse Emerge from Receptor and Kinase Traffic. - Marian Groenenboom, Athanasius F. M. Marée, Paulien Hogeweg:
The RNA Silencing Pathway: The Bits and Pieces That Matter. - Hadi Quesneville, Casey M. Bergman, Olivier Andrieu, Delphine Autard, Danielle Nouaud, Michael Ashburner, Dominique Anxolabéhère:
Combined Evidence Annotation of Transposable Elements in Genome Sequences. - Andrew M. Bisits, Roger Smith, Sam Mesiano, George Yeo, Kenneth Kwek, David MacIntyre, Eng C. Chan:
Inflammatory Aetiology of Human Myometrial Activation Tested Using Directed Graphs. - Adriana Migliaro, Angel A. Caputi, Ruben Budelli:
Theoretical Analysis of Pre-Receptor Image Conditioning in Weakly Electric Fish. - Uwe Ohler, Noam Shomron, Christopher B. Burge:
Recognition of Unknown Conserved Alternatively Spliced Exons.
Volume 1, Number 3, August 2005
- B. J. Morrison McKay:
ISMB 2005 Conference Report.
- Philip E. Bourne:
Will a Biological Database Be Different from a Biological Journal?
- Sagar D. Khare, Feng Ding, Kenneth N. Gwanmesia, Nikolay V. Dokholyan:
Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases. - Lauren Ancel Meyers, Fredric D. Ancel, Michael Lachmann:
Evolution of Genetic Potential. - Qinghu Ren, Ian T. Paulsen:
Comparative Analyses of Fundamental Differences in Membrane Transport Capabilities in Prokaryotes and Eukaryotes. - Lei Xie, Philip E. Bourne:
Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models. - Michiel J. L. de Hoon, Yuko Makita, Kenta Nakai, Satoru Miyano:
Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species. - Pedro Beltrão, Luis Serrano:
Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions. - Subbulakshmi Latha Cherukuvada, Aswin Sai Narain Seshasayee, Krishnan Raghunathan, Sharmila Anishetty, Pennathur Gautam:
Evidence of a Double-Lid Movement in Pseudomonas aeruginosa Lipase: Insights from Molecular Dynamics Simulations.
- Boris E. Shakhnovich:
Correction: Improving the Precision of the Structure-Function Relationship by Considering Phylogenetic Context.
Volume 1, Number 4, September 2005
- Dale J. Hedges, Richard Cordaux, Jinchuan Xing, David J. Witherspoon, Alan R. Rogers, Lynn B. Jorde, Mark A. Batzer:
Modeling the Amplification Dynamics of Human Alu Retrotransposons. - Igor N. Berezovsky, William W. Chen, Paul J. Choi, Eugene I. Shakhnovich:
Entropic Stabilization of Proteins and Its Proteomic Consequences. - Carsten Rautengarten, Dirk Steinhauser, Dirk Büssis, Annick Stintzi, Andreas Schaller, Joachim Kopka, Thomas Altmann:
Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family. - James P. Carson, Tao Ju, Hui-Chen Lu, Christina Thaller, Mei Xu, Sarah L. Pallas, Michael C. Crair, Joe D. Warren, Wah Chiu, Gregor Eichele:
A Digital Atlas to Characterize the Mouse Brain Transcriptome. - Ruiqiang Li, Jia Ye, Songgang Li, Jing Wang, Yujun Han, Chen Ye, Jian Wang, Huanming Yang, Jun Yu, Gane Ka-Shu Wong, Jun Wang:
ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun. - Andrew B. Goryachev, Da-Jun Toh, Keng Boon Wee, Travis Lee, Hai-Bao Zhang, Lian-Hui Zhang:
Transition to Quorum Sensing in an Agrobacterium Population: A Stochastic Model. - Yuanyuan Xiao, Yee Hwa Yang, Todd A. Burckin, Lily Shiue, Grant A. Hartzog, Mark R. Segal:
Analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4-5 in Splicing. - Daniel A. Beard:
A Biophysical Model of the Mitochondrial Respiratory System and Oxidative Phosphorylation.
Volume 1, Number 5, October 2005
- Philip E. Bourne:
Ten Simple Rules for Getting Published.
- Michael Gribskov:
The ISCB: Growing and Evolving in Step with Science.
- Jinghui Zhang, David A. Wheeler, Imtiaz Yakub, Sharon Wei, Raman Sood, William Rowe, Paul P. Liu, Richard A. Gibbs, Kenneth H. Buetow:
SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection. - Stefan Legewie, Nils Blüthgen, Reinhold Schäfer, Hanspeter Herzel:
Ultrasensitization: Switch-Like Regulation of Cellular Signaling by Transcriptional Induction. - Dmitry A. Rodionov, Inna Dubchak, Adam P. Arkin, Eric J. Alm, Mikhail S. Gelfand:
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks. - Eric D. Scheeff, Philip E. Bourne:
Structural Evolution of the Protein Kinase-Like Superfamily. - Karthik Raman, Preethi Rajagopalan, Nagasuma R. Chandra:
Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs. - Barbara E. Engelhardt, Michael I. Jordan, Kathryn E. Muratore, Steven E. Brenner:
Protein Molecular Function Prediction by Bayesian Phylogenomics.
Volume 1, Number 6, November 2005
- Shoba Ranganathan:
Bioinformatics Education - Perspectives and Challenges.
- Michael F. Huerta, Gregory K. Farber, Elizabeth L. Wilder, Dushanka V. Kleinman, Patricia A. Grady, David A. Schwartz, Lawrence A. Tabak:
NIH Roadmap Interdisciplinary Research Initiatives.
- James J. Bull, Lauren Ancel Meyers, Michael Lachmann:
Quasispecies Made Simple.
- Alon Kaufman, Alon Keinan, Isaac Meilijson, Martin Kupiec, Eytan Ruppin:
Quantitative Analysis of Genetic and Neuronal Multi-Perturbation Experiments. - Thomas LaFramboise, Barbara A. Weir, Xiaojun Zhao, Rameen Beroukhim, Cheng Li, David Harrington, William R. Sellers, Matthew Meyerson:
Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis. - Michelle S. Scott, Sara J. Calafell, David Y. Thomas, Michael T. Hallett:
Refining Protein Subcellular Localization. - Deqiang Zhang, James Andrew McCammon:
The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis. - Peter Sperisen, Christoph D. Schmid, Philipp Bucher, Olav Zilian:
Stealth Proteins: In Silico Identification of a Novel Protein Family Rendering Bacterial Pathogens Invisible to Host Immune Defense. - Rajeev K. Azad, Jeffrey G. Lawrence:
Use of Artificial Genomes in Assessing Methods for Atypical Gene Detection. - Daniel H. Haft, Jeremy D. Selengut, Emmanuel F. Mongodin, Karen E. Nelson:
A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes. - Dan Frumkin, Adam Wasserstrom, Shai Kaplan, Uriel Feige, Ehud Shapiro:
Genomic Variability within an Organism Exposes Its Cell Lineage Tree.
Volume 1, Number 7, December 2005
- Phillip W. Lord, Robert Stevens, James A. Butler, Robin McEntire:
The Eighth Annual Bio-Ontologies Meeting.
- Nicola Cannata, Emanuela Merelli, Russ B. Altman:
Time to Organize the Bioinformatics Resourceome.
- Quan Wen, Dmitri B. Chklovskii:
Segregation of the Brain into Gray and White Matter: A Design Minimizing Conduction Delays. - Hung D. Nguyen, Maki Yoshihama, Naoya Kenmochi:
New Maximum Likelihood Estimators for Eukaryotic Intron Evolution. - Ala Trusina, Kim Sneppen, Ian B. Dodd, Keith E. Shearwin, J. Barry Egan:
Functional Alignment of Regulatory Networks: A Study of Temperate Phages. - Eivind Almaas, Zoltán N. Oltvai, Albert-László Barabási:
The Activity Reaction Core and Plasticity of Metabolic Networks. - Jie Song, Qikai Xu, Rolf Olsen, William F. Loomis, Gad Shaulsky, Adam Kuspa, Richard Sucgang:
Comparing the Dictyostelium and Entamoeba Genomes Reveals an Ancient Split in the Conosa Lineage. - Eliot C. Bush, Bruce T. Lahn:
Selective Constraint on Noncoding Regions of Hominid Genomes. - Fredj Tekaia, Edouard Yeramian:
Genome Trees from Conservation Profiles. - Rahul Siddharthan, Eric D. Siggia, Erik van Nimwegen:
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny. - Chang S. Chan, Olivier Elemento, Saeed Tavazoie:
Revealing Posttranscriptional Regulatory Elements Through Network-Level Conservation. - Markus Ringnér, Morten Krogh:
Folding Free Energies of 5′-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast.
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