PLOS Computational Biology

AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments

Publishing date: 2020-08-18 Published on: PLOS Computational Biology summary: In this software paper, Page et al develop ‘AlbaTraDIS’; a software application for rapid large-scale comparative analysis of TraDIS experiments that predicts the impact of transposon insertions on nearby genes.

bigPint: A Bioconductor visualization package that makes big data pint-sized

Publishing date: 2020-08-18 Published on: PLOS Computational Biology summary: bigPint is a software package for interactive and static data visualisation in R. It scales comfortably to large datasets, sporting graphs that include scatterplots, violin plots, and litre plots.

OSS-DBS: Open-source simulation platform for deep brain stimulation with a comprehensive automated modeling

Publishing date: 2020-08-18 Published on: PLOS Computational Biology summary: In this study, Butenko et al propose a new open-source simulation platform that comprises computer-aided design and computer-aided engineering tools for highly automated evaluation of electric field distribution and neural activation during Deep Brain Stimulation (DBS).

The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies

Publishing date: 2020-08-18 Published on: PLOS Computational Biology summary: In this report, Zimin and Salzberg present the assembly polishing tool POLCA (POLishing by Calling Alternatives) and compare its performance with two other popular polishing programs, Pilon and Racon.

ProteinVR: Web-based molecular visualization in virtual reality

Publishing date: 2020-05-12 Published on: PLOS Computational Biology summary: Channel Editor Summary: Have you ever wondered what proteins look like? In fact, accurately conceptualizing 3D protein structures is vital to both scientific research and education.

Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis

Publishing date: 2020-04-27 Published on: PLOS Computational Biology summary: None authors: Yuanchao Zhang, Man S. Kim, Erin R. Reichenberger, Ben Stear, Deanne M. Taylor link to paper: 10.1371/journal.pcbi.1007794 Icons made by catkuro from www.

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Publishing date: 2020-04-06 Published on: PLOS Computational Biology summary: None authors: Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, J. Andrew McCammon, Ravi Ramamoorthi, Michael Holst, Padmini Rangamani

Ten simple rules for providing effective bioinformatics research support

Publishing date: 2020-03-26 Published on: PLOS Computational Biology summary: None authors: Judit Kumuthini, Michael Chimenti, Sven Nahnsen, Alexander Peltzer, Rebone Meraba, Ross McFadyen, Gordon Wells, Deanne Taylor, Mark Maienschein-Cline, Jian-Liang Li, Jyothi Thimmapuram, Radha Murthy-Karuturi, Lyndon Zass

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data

Publishing date: 2020-03-03 Published on: PLOS Computational Biology summary: Ribosome profiling, an application of nucleic acid sequencing for monitoring ribosome activity, has revolutionized our understanding of protein translation dynamics. This technique has been available for a decade, yet the current state and standardization of publicly available computational tools for these data is bleak.

RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method

Publishing date: 2020-02-14 Published on: PLOS Computational Biology summary: None authors: Kosuke Hamazaki, Hiroyoshi Iwata link to paper: 10.1371/journal.pcbi.1007663 Icons made by catkuro from www.flaticon.com