May 2016

In many applications, Bayesian methods are increasingly recognized to yield high-quality results, while providing an accurate measure of uncertainty in the form of posterior distributions. However, they have also obtained a reputation of requiring enormous computational effort and being difficult to use, due to the expertise required in choosing prior distributions. In this article, we focus on Bayesian inference in Hidden Markov Models, which are central to segmentation tasks such as identification of Copy Number Variants (CNV). We achieve dramatic improvements in both speed and accuracy through the use of dynamic wavelet compression and automatically selected priors. Wiedenhoeft et al.

Image Credit: Wiedenhoeft et al.

Message from ISCB

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee)

Lonnie Welch, Cath Brooksbank, Russell Schwartz, Sarah L. Morgan, Bruno Gaeta, Alastair M. Kilpatrick, Daniel Mietchen, Benjamin L. Moore, Nicola Mulder, Mark Pauley, William Pearson, Predrag Radivojac, Naomi Rosenberg, Anne Rosenwald, Gabriella Rustici, Tandy Warnow

PLOS Computational Biology: published May 13, 2016 | https://doi.org/10.1371/journal.pcbi.1004943

Perspectives

Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants

David L. Masica, Rachel Karchin

PLOS Computational Biology: published May 12, 2016 | https://doi.org/10.1371/journal.pcbi.1004725

Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?

Erik van Nimwegen

PLOS Computational Biology: published May 12, 2016 | https://doi.org/10.1371/journal.pcbi.1004726

The Maximum Entropy Fallacy Redux?

Erik Aurell

PLOS Computational Biology: published May 12, 2016 | https://doi.org/10.1371/journal.pcbi.1004777

Research Articles

Control of Ca²⁺ Influx and Calmodulin Activation by SK-Channels in Dendritic Spines

Thom Griffith, Krasimira Tsaneva-Atanasova, Jack R. Mellor

PLOS Computational Biology: published May 27, 2016 | https://doi.org/10.1371/journal.pcbi.1004949

The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach

Pascal Giehr, Charalampos Kyriakopoulos, Gabriella Ficz, Verena Wolf, Jörn Walter

PLOS Computational Biology: published May 25, 2016 | https://doi.org/10.1371/journal.pcbi.1004905

Tuning Curves for Arm Posture Control in Motor Cortex Are Consistent with Random Connectivity

Hagai Lalazar, L. F. Abbott, Eilon Vaadia

PLOS Computational Biology: published May 25, 2016 | https://doi.org/10.1371/journal.pcbi.1004910

PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies

Wenchao Zhang, Xinbin Dai, Qishan Wang, Shizhong Xu, Patrick X. Zhao

PLOS Computational Biology: published May 25, 2016 | https://doi.org/10.1371/journal.pcbi.1004925

PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions

Jaroslav Bendl, Miloš Musil, Jan Štourač, Jaroslav Zendulka, Jiří Damborský, Jan Brezovský

PLOS Computational Biology: published May 25, 2016 | https://doi.org/10.1371/journal.pcbi.1004962

From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors

Ana Zafra Ruano, Elisa Cilia, José R. Couceiro, Javier Ruiz Sanz, Joost Schymkowitz, Frederic Rousseau, Irene Luque, Tom Lenaerts

PLOS Computational Biology: published May 23, 2016 | https://doi.org/10.1371/journal.pcbi.1004938

Modelling Virus and Antibody Dynamics during Dengue Virus Infection Suggests a Role for Antibody in Virus Clearance

Hannah E Clapham, Than Ha Quyen, Duong Thi Hue Kien, Ilaria Dorigatti, Cameron P Simmons, Neil M Ferguson

PLOS Computational Biology: published May 23, 2016 | https://doi.org/10.1371/journal.pcbi.1004951

Spike-Based Bayesian-Hebbian Learning of Temporal Sequences

Philip J. Tully, Henrik Lindén, Matthias H. Hennig, Anders Lansner

PLOS Computational Biology: published May 23, 2016 | https://doi.org/10.1371/journal.pcbi.1004954

Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation

Raphaël Mourad, Olivier Cuvier

PLOS Computational Biology: published May 20, 2016 | https://doi.org/10.1371/journal.pcbi.1004908

Biophysical Network Modelling of the dLGN Circuit: Different Effects of Triadic and Axonal Inhibition on Visual Responses of Relay Cells

Thomas Heiberg, Espen Hagen, Geir Halnes, Gaute T. Einevoll

PLOS Computational Biology: published May 20, 2016 | https://doi.org/10.1371/journal.pcbi.1004929

A Detailed Data-Driven Network Model of Prefrontal Cortex Reproduces Key Features of In Vivo Activity

Joachim Hass, Loreen Hertäg, Daniel Durstewitz

PLOS Computational Biology: published May 20, 2016 | https://doi.org/10.1371/journal.pcbi.1004930

Reactome from a WikiPathways Perspective

Anwesha Bohler, Guanming Wu, Martina Kutmon, Leontius Adhika Pradhana, Susan L. Coort, Kristina Hanspers, Robin Haw, Alexander R. Pico, Chris T. Evelo

PLOS Computational Biology: published May 20, 2016 | https://doi.org/10.1371/journal.pcbi.1004941

Evaluation of the Phase-Dependent Rhythm Control of Human Walking Using Phase Response Curves

Tetsuro Funato, Yuki Yamamoto, Shinya Aoi, Takashi Imai, Toshio Aoyagi, Nozomi Tomita, Kazuo Tsuchiya

PLOS Computational Biology: published May 20, 2016 | https://doi.org/10.1371/journal.pcbi.1004950

A Single Mechanism Can Account for Human Perception of Depth in Mixed Correlation Random Dot Stereograms

Sid Henriksen, Bruce G. Cumming, Jenny C. A. Read

PLOS Computational Biology: published May 19, 2016 | https://doi.org/10.1371/journal.pcbi.1004906

Cellular Architecture Regulates Collective Calcium Signaling and Cell Contractility

Jian Sun, James B. Hoying, Pierre A. Deymier, Donna D. Zhang, Pak Kin Wong

PLOS Computational Biology: published May 19, 2016 | https://doi.org/10.1371/journal.pcbi.1004955

Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties

Andrew F. Neuwald, Stephen F. Altschul

PLOS Computational Biology: published May 18, 2016 | https://doi.org/10.1371/journal.pcbi.1004936

Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection

Zizhang Sheng, Chaim A. Schramm, Mark Connors, Lynn Morris, John R. Mascola, Peter D. Kwong, Lawrence Shapiro

PLOS Computational Biology: published May 18, 2016 | https://doi.org/10.1371/journal.pcbi.1004940

Neuroprosthetic Decoder Training as Imitation Learning

Josh Merel, David Carlson, Liam Paninski, John P. Cunningham

PLOS Computational Biology: published May 18, 2016 | https://doi.org/10.1371/journal.pcbi.1004948

Bridging Mechanistic and Phenomenological Models of Complex Biological Systems

Mark K. Transtrum, Peng Qiu

PLOS Computational Biology: published May 17, 2016 | https://doi.org/10.1371/journal.pcbi.1004915

Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression

John Wiedenhoeft, Eric Brugel, Alexander Schliep

PLOS Computational Biology: published May 13, 2016 | https://doi.org/10.1371/journal.pcbi.1004871

Estimating Time of Infection Using Prior Serological and Individual Information Can Greatly Improve Incidence Estimation of Human and Wildlife Infections

Benny Borremans, Niel Hens, Philippe Beutels, Herwig Leirs, Jonas Reijniers

PLOS Computational Biology: published May 13, 2016 | https://doi.org/10.1371/journal.pcbi.1004882

Conflicting Selection Pressures Will Constrain Viral Escape from Interfering Particles: Principles for Designing Resistance-Proof Antivirals

Luke I. Rast, Igor M. Rouzine, Ganna Rozhnova, Lisa Bishop, Ariel D. Weinberger, Leor S. Weinberger

PLOS Computational Biology: published May 6, 2016 | https://doi.org/10.1371/journal.pcbi.1004799

A Model for Direction Sensing in Dictyostelium discoideum: Ras Activity and Symmetry Breaking Driven by a G_βγ-Mediated, G_α2-Ric8 -- Dependent Signal Transduction Network

Yougan Cheng, Hans Othmer

PLOS Computational Biology: published May 6, 2016 | https://doi.org/10.1371/journal.pcbi.1004900

Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression

Tuoqi Liu, Jiajun Zhang, Tianshou Zhou

PLOS Computational Biology: published May 6, 2016 | https://doi.org/10.1371/journal.pcbi.1004917

To Cooperate or Not to Cooperate: Why Behavioural Mechanisms Matter

Arthur Bernard, Jean-Baptiste André, Nicolas Bredeche

PLOS Computational Biology: published May 5, 2016 | https://doi.org/10.1371/journal.pcbi.1004886

A Model for an Angular Velocity-Tuned Motion Detector Accounting for Deviations in the Corridor-Centering Response of the Bee

Alex J. Cope, Chelsea Sabo, Kevin Gurney, Eleni Vasilaki, James A. R. Marshall

PLOS Computational Biology: published May 5, 2016 | https://doi.org/10.1371/journal.pcbi.1004887

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