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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

Research Articles

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

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

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

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

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

Hagai Lalazar, L. F. Abbott, Eilon Vaadia

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

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

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

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

Spike-Based Bayesian-Hebbian Learning of Temporal Sequences

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

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

Joachim Hass, Loreen Hertäg, Daniel Durstewitz

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

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

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

Cellular Architecture Regulates Collective Calcium Signaling and Cell Contractility

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

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

Andrew F. Neuwald, Stephen F. Altschul

Neuroprosthetic Decoder Training as Imitation Learning

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

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

John Wiedenhoeft, Eric Brugel, Alexander Schliep

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models

Hugo Jacquin, Amy Gilson, Eugene Shakhnovich, Simona Cocco, Rémi Monasson

Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics

Lisa M. Breckels, Sean B. Holden, David Wojnar, Claire M. Mulvey, Andy Christoforou, Arnoud Groen, Matthew W. B. Trotter, Oliver Kohlbacher, Kathryn S. Lilley, Laurent Gatto

Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions

Natalie S. Scholes, Robert O. J. Weinzierl

A Molecular Clock Infers Heterogeneous Tissue Age Among Patients with Barrett’s Esophagus

Kit Curtius, Chao-Jen Wong, William D. Hazelton, Andrew M. Kaz, Amitabh Chak, Joseph E. Willis, William M. Grady, E. Georg Luebeck

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