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F1000Research, Volume 5
Volume 5, 2016
- Ulrich Dirnagl
, Ingo Przesdzing
A pocket guide to electronic laboratory notebooks in the academic life sciences. 2 - Suzanne M. Paquette, Kalle Leinonen, William J. R. Longabaugh:
BioTapestry now provides a web application and improved drawing and layout tools. 39 - Xuejun Dong:
How to put plant root uptake into a soil water flow model. 43 - Bence Mátyás
A novel data storage logic in the cloud. 93 - Geoffrey Siwo, Andrew K. Rider, Asako Tan, Richard S. Pinapati
Prediction of fine-tuned promoter activity from DNA sequence. 158 - Simon Mitternacht
FreeSASA: An open source C library for solvent accessible surface area calculations. 189 - Darawan Rinchai
A compendium of monocyte transcriptome datasets to foster biomedical knowledge discovery. 291 - Jana Blazkova, Sabri Boughorbel
A curated transcriptome dataset collection to investigate the immunobiology of HIV infection. 327 - Tariq Daouda, Claude Perreault, Sébastien Lemieux:
pyGeno: A Python package for precision medicine and proteogenomics. 381 - José I. López, Jesús M. Cortés:
A divide-and-conquer strategy in tumor sampling enhances detection of intratumor heterogeneity in routine pathology: A modeling approach in clear cell renal cell carcinoma. 385 - Elise Ruark, Anthony Renwick, Matthew Clarke, Katie Snape, Emma Ramsay
The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis. 386 - Swarit Jasial
Activity-relevant similarity values for fingerprints and implications for similarity searching. 591 - Georgia B. McGaughey, W. Patrick Walters, Brian Goldman:
Understanding covariate shift in model performance. 597 - Maria Cecília D. Costa
CyLineUp: A Cytoscape app for visualizing data in network small multiples. 635 - Richard J. Naftalin
A computer model simulating human glucose absorption and metabolism in health and metabolic disease states. 647 - Ben Busby
Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping. 672 - Eric Moyer, Megan Hastings Hagenauer
MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis. 674 - Bianca Kramer
Innovations in scholarly communication - global survey on research tool usage. 692 - Richard Smith
Time for sharing data to become routine: the seven excuses for not doing so are all invalid. 781 - Glenn Hyman, Elizabeth Barona, Chandrashekhar M. Biradar
Priority regions for research on dryland cereals and legumes. 885 - Elizabeth Baskin, Peter De-Ford
A cloud-based learning environment for comparing RNA-seq aligners. 888 - Lennart C. Karssen
The GenABEL Project for statistical genomics. 914 - Aaron T. L. Lun, Malcolm Perry
Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments. 950 - Philip J. Chapman, Dominic I. James, Amanda J. Watson, Gemma V. Hopkins, Ian D. Waddell, Donald J. Ogilvie:
IncucyteDRC: An R package for the dose response analysis of live cell imaging data. 962 - Mohd Izzuddin Hairol, Qazi Mohamad Omair, Sharanjeet Kaur:
Effects of flanker type and position on foveal letter recognition. 1013 - Karina Salvatierra
Biomedical Mutation Analysis (BMA): A software tool for analyzing mutations associated with antiviral resistance. 1141 - Ye Hu, Jürgen Bajorath
Analyzing compound activity records and promiscuity degrees in light of publication statistics. 1227 - Andy G. Lynch
Decomposition of mutational context signatures using quadratic programming methods. 1253 - Jovana Maksimovic
A cross-package Bioconductor workflow for analysing methylation array data. 1281 - Rebecca C. Wilson, Oliver W. Butters
Digital methodology to implement the ECOUTER engagement process. 1307 - Alexandra Popa, Kevin Le Brigand, Agnes Paquet, Nicolas Nottet
RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing. 1309 - Achim Wolf:
Facebook and mental wellbeing: a crossover randomised controlled study. 1311 - Bernd Klaus:
An end to end workflow for differential gene expression using Affymetrix microarrays. 1384 - Dean A. Attali
ddpcr: an R package and web application for analysis of droplet digital PCR data. 1411 - Yunshun Chen, Aaron T. L. Lun
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. 1438 - Upendra Kumar Devisetty, Kathleen Kennedy, Paul Sarando, Nirav C. Merchant
Bringing your tools to CyVerse Discovery Environment using Docker. 1442 - M. Jonathan Vachon
VISIT-TS version 2: A multimedia tool for population studies on tic disorders. 1518 - Karoline Faust, Jeroen Raes
CoNet app: inference of biological association networks using Cytoscape. 1519 - Nicolas Alcaraz
Robust de novo pathway enrichment with KeyPathwayMiner 5. 1531 - Tiago Chedraoui Silva
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages. 1542 - Akila Subasinghe Arachchige, Jagath Samarabandu, YanXin Li, Ruth Wilkins
Centromere detection of human metaphase chromosome images using a candidate based method. 1565 - Jeffrey De Fauw, Pearse A. Keane
Automated analysis of retinal imaging using machine learning techniques for computer vision. 1573 - Zichen Wang
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study. 1574 - Willem Siers, Michiel Bakker, Bob Rubbens, Ruben Haasjes, Jacco Brandt, Stefano Schivo
webANIMO: Improving the accessibility of ANIMO. 1714 - Ganesh M. Babulal, Aaron Addison, Nupur Ghoshal, Sarah H. Stout
Development and interval testing of a naturalistic driving methodology to evaluate driving behavior in clinical research. 1716 - Mike Kucera, Ruth Isserlin
AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. 1717 - Matthias König
cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK. 1736 - Oliver W. Butters
The Biomedical Research Infrastructure Software as a Service Kit (BRISSKit): technical description. 1905 - Gopal P. Sarma
Unit testing, model validation, and biological simulation. 1946 - Haydee Artaza
Top 10 metrics for life science software good practices. 2000 - Rosa Guarch, Jesús M. Cortés, Charles H. Lawrie
Multi-site tumor sampling (MSTS) improves the performance of histological detection of intratumor heterogeneity in clear cell renal cell carcinoma (CCRCC). 2020 - Carlton Chu, Jeffrey De Fauw, Nenad Tomasev
Applying machine learning to automated segmentation of head and neck tumour volumes and organs at risk on radiotherapy planning CT and MRI scans. 2104 - Iman Rezaeian, Eliseos J. Mucaki, Katherina Baranova, Huy Quang Pham, Dimo Angelov, Alioune Ngom, Luis Rueda, Peter K. Rogan
Predicting Outcomes of Hormone and Chemotherapy in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) Study by Biochemically-inspired Machine Learning. 2124 - Nicolas Torquet, Fabrice de Chaumont, Philippe Faure, Thomas Bourgeron, Elodie Ey
mouseTube - a database to collaboratively unravel mouse ultrasonic communication. 2332 - Evert van den Broek, Stef van Lieshout, Christian Rausch, Bauke Ylstra
GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes. 2340 - Nirupama Benis
Building pathway graphs from BioPAX data in R. 2414 - Martin Scharm, Dagmar Waltemath
A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. 2421 - Nomi L. Harris
The 2016 Bioinformatics Open Source Conference (BOSC). 2464 - Jawoo Koo
CELL5M: A geospatial database of agricultural indicators for Africa South of the Sahara. 2490 - Dylan Collins
Simple and adaptable R implementation of WHO/ISH cardiovascular risk charts for all epidemiological subregions of the world. 2522 - Gabriele Tosadori, Ivan Bestvina, Fausto Spoto, Carlo Laudanna, Giovanni Scardoni:
Creating, generating and comparing random network models with Network Randomizer. 2524 - Timothy Nugent, David Upton, Mihai Cimpoesu:
Improving data transparency in clinical trials using blockchain smart contracts. 2541 - Braxton Fitts, Ziran Zhang
dot-app: a Graphviz-Cytoscape conversion plug-in. 2543 - Aprameya Mysore, Andreas Velten, Kevin W. Eliceiri
Sonification of hyperspectral fluorescence microscopy datasets. 2572 - Thomas P. Quinn
exprso: an R-package for the rapid implementation of machine learning algorithms. 2588 - Antonio de la Vega de León
Design of chemical space networks incorporating compound distance relationships. 2634 - Ivan Kondofersky, Michael Laimighofer, Christoph Kurz, Norbert Krautenbacher, Julia F. Söllner, Philip Dargatz, Hagen Scherb, Donna P. Ankerst
Three general concepts to improve risk prediction: good data, wisdom of the crowd, recalibration. 2671 - Detian Deng, Yu Du, Zhicheng Ji, Karthik Rao, Zhenke Wu, Yuxin Zhu
Predicting survival time for metastatic castration resistant prostate cancer: An iterative imputation approach. 2672 - Daniel Kristiyanto
Predicting discontinuation of docetaxel treatment for metastatic castration-resistant prostate cancer (mCRPC) with random forest. 2673 - Mehrad Mahmoudian, Fatemeh Seyednasrollah, Liisa Koivu, Outi Hirvonen, Sirkku Jyrkkiö, Laura L. Elo
A predictive model of overall survival in patients with metastatic castration-resistant prostate cancer. 2674 - Massimiliano Zanin
Using complex networks for refining survival prognosis in prostate cancer patient. 2675 - Richard Meier, Stefan Graw
An ensemble-based Cox proportional hazards regression framework for predicting survival in metastatic castration-resistant prostate cancer (mCRPC) patients. 2677 - Miika Ahdesmäki
Disambiguate: An open-source application for disambiguating two species in next generation sequencing data from grafted samples. 2741 - Andrea Komljenovic, Julien Roux, Marc Robinson-Rechavi, Frederic B. Bastian:
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests. 2748 - Nitesh Turaga, Mallory Ann Freeberg
A guide and best practices for R/Bioconductor tool integration in Galaxy. 2757 - Ignacio Enrique Sanchez
Optimal threshold estimation for binary classifiers using game theory. 2762 - Michael A. Carson
Approaches to R education in Canadian universities. 2802 - Antoine Zambelli
A data-driven approach to estimating the number of clusters in hierarchical clustering. 2809 - Daniel Chubb
CanVar: A resource for sharing germline variation in cancer patients. 2813 - Philip Ewels
Cluster Flow: A user-friendly bioinformatics workflow tool. 2824 - Youri Hoogstrate
Integration of EGA secure data access into Galaxy. 2841 - Martin Ryberg
Phylommand - a command line software package for phylogenetics. 2903 - Lisa M. Breckels
A Bioconductor workflow for processing and analysing spatial proteomics data. 2926
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