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F1000Research, Volume 4
Volume 4, 2015
- Ghose Bishwajit
:
Nutrition transition in South Asia: the emergence of non-communicable chronic diseases. 8 - Vitaly V. Babenko, Daria Alekseeva, Denis V. Yavna
:
Possible significance of spatial heterogeneities of local visual features for face perception. 10 - Ian Dunham
, Eugene Kulesha, Valentina Iotchkova
, Sandro Morganella, Ewan Birney
:
FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions. 18 - Christopher R. Madan
:
Every scientist is a memory researcher: Suggestions for making research more memorable. 19 - Priti Kumari, Raja Mazumder
, Vahan Simonyan, Konstantinos Krampis:
Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly. 20 - Michael Considine, Hilary S. Parker, Yingying Wei
, Xaio Xia, Leslie Cope, Michael F. Ochs, Elana J. Fertig
:
AGA: Interactive pipeline for reproducible genomics analyses. 28 - Benjamin Siranosian
, Sudheesha Perera
, Edward Williams, Chen Ye, Christopher de Graffenried
, Peter Shank:
Tetranucleotide usage highlights genomic heterogeneity among mycobacteriophages. 36 - Betty J. Kreakie, Kristopher Winiarski, Richard McKinney:
Developing a wintering waterfowl community baseline for environmental monitoring of Narragansett Bay, Rhode Island. 40 - Erinija Pranckeviciene
:
Procedure and datasets to compute links between genes and phenotypes defined by MeSH keywords. 47 - Sean Ekins
, Christopher Southan
, Megan Coffee
:
Finding small molecules for the 'next Ebola'. 58 - Jason E. McDermott, Paul J. Bruillard, Christopher C. Overall, Luke J. Gosink, Stephen R. Lindemann:
Prediction of multi-drug resistance transporters using a novel sequence analysis method. 60 - Disha Gupta-Ostermann, Yoichiro Hirose, Takenao Odagami, Hiroyuki Kouji, Jürgen Bajorath
:
Follow-up: Prospective compound design using the 'SAR Matrix' method and matrix-derived conditional probabilities of activity. 75 - Bjørn Fjukstad, Karina Standahl Olsen, Mie Jareid, Eiliv Lund, Lars Ailo Bongo
:
Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies. 81 - Lauren Soluk, Christopher Buddle
:
Tweets from the forest: using Twitter to increase student engagement in an undergraduate field biology course. 82 - Ernesto Borrayo, Masaru Takeya:
Signal-processing tools for core-collection selection from genetic-resource collections. 97 - Sonia Vaida, Davide Cattano
, Debra Hurwitz, Berend Mets:
Algorithm for the anesthetic management of cesarean delivery in patients with unsatisfactory labor epidural analgesia. 98 - Leonardo Collado-Torres
, Andrew E. Jaffe
, Jeffrey T. Leek
:
regionReport: Interactive reports for region-based analyses. 105 - Anita E. Bandrowski
, Matthew H. Brush, Jeffrey S. Grethe
, Melissa A. Haendel, David N. Kennedy
, Sean L. Hill
, Patrick R. Hof, Maryann E. Martone
, Maaike Pols, Serena S. Tan, Nicole L. Washington, Elena V. Zudilova-Seinstra, Nicole A. Vasilevsky
:
The Resource Identification Initiative: A cultural shift in publishing. 134 - Asier Erramuzpe
, J. M. Encinas, Amanda Sierra
, Mirjana Maletic-Savatic, A. L. Brewster, Anne E. Anderson, Sebastiano Stramaglia
, Jesús M. Cortés
:
Longitudinal variations of brain functional connectivity: A case report study based on a mouse model of epilepsy. 144 - Sandeep Chakraborty
, Monica Britton, Jill L. Wegrzyn, Timothy Butterfield, Basuthkar J. Rao, Charles A. Leslie, Mallikarjuna Aradhaya, David B. Neale, Keith Woeste, Abhay Dandekar
:
YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut. 155 - Yan Tan, Felix Wu, Pablo Tamayo, W. Nicholas Haining, Jill P. Mesirov:
Constellation Map: Downstream visualization and interpretation of gene set enrichment results. 167 - Ye Hu, Norbert Furtmann, Dagmar Stumpfe, Jürgen Bajorath
:
Comprehensive knowledge base of two- and three-dimensional activity cliffs for medicinal and computational chemistry. 168 - Michael Hanke, Richard Dinga, Christian Olaf Häusler, J. Swaroop Guntupalli, Michael Casey, Falko R. Kaule, Jörg Stadler:
High-resolution 7-Tesla fMRI data on the perception of musical genres - an extension to the studyforrest dataset. 174 - Nicky J. D. Slee, Marty H. Jacobs:
Trialling the Use of Google Apps Together with Online Marking to Enhance Collaborative Learning and Provide Effective Feedback. 177 - João Mendes Moreira
, Alcino Cunha
, Nuno Macedo
:
An ORCID based synchronization framework for a national CRIS ecosystem. 181 - Damir Madjarevic:
Connecting Altmetric: Integrating with Institutional Publications Systems. 192 - Muriel Swijghuisen Reigersberg
:
Problematizing Digital Research Evaluation using DOIs in Practice-Based Arts, Humanities and Social Science Research. 193 - Mohamed Baessa
, Thibaut Lery
, Daryl Grenz
, J. K. Vijayakumar
:
Connecting the pieces: Using ORCIDs to improve research impact and repositories. 195 - Andrea Bonaccorsi, Tindaro Cicero
, Antonio Ferrara
, Marco Malgarini
:
Journal ratings as predictors of articles quality in Arts, Humanities and Social Sciences: an analysis based on the Italian Research Evaluation Exercise. 196 - Fabrizio Celli, Johannes Keizer, Yves Jaques, Stasinos Konstantopoulos, Dusan Vudragovic:
Discovering, Indexing and Interlinking Information Resources. 432 - Faizaan Shaik
, Srikanth Bezawada, Neena Goveas:
CySpanningTree: Minimal Spanning Tree computation in Cytoscape. 476 - Emily Olorin
, Kevin T. O'Brien, Nicolas Palopoli
, Åsa Pérez-Bercoff, Denis C. Shields
, Richard J. Edwards
:
SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks. 477 - Keiichiro Ono, Tanja Muetze, Georgi Kolishovski, Paul Shannon, Barry Demchak
:
CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. 478 - Fabio Rinnone
, Giovanni Micale, Vincenzo Bonnici, Gary D. Bader
, Dennis E. Shasha, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
:
NetMatchStar: an enhanced Cytoscape network querying app. 479 - Lilit Nersisyan, Graham Johnson, Megan Riel-Mehan, Alexander R. Pico
, Arsen Arakelyan
:
PSFC: a Pathway Signal Flow Calculator App for Cytoscape. 480 - Victor Kofia
, Ruth Isserlin
, Alison Buchan, Gary D. Bader
:
Social Network: a Cytoscape app for visualizing co-publication networks. 481 - John H. Morris
, Vijay Dhameliya, Steven Federowicz, Alexander R. Pico
, Thomas E. Ferrin
:
CyAnimator: Simple Animations of Cytoscape Networks. 482 - Christopher Dardis
, Eric C. Woolf, Adrienne C. Scheck
:
Towards reproducible research: From data analysis (in R) to a typeset laboratory notebook (as .pdf) using the text editor Emacs with the 'mp' package. 483 - Giovanni Scardoni, Gabriele Tosadori, Sakshi Pratap, Fausto Spoto, Carlo Laudanna:
Finding the shortest path with PesCa: a tool for network reconstruction. 484 - Lili Wang, Daniel S. Himmelstein
, Adam Santaniello, Parvin Mousavi, Sergio E. Baranzini
:
iCTNet2: integrating heterogeneous biological interactions to understand complex traits. 485 - Raivo Kolde
, Jaak Vilo
:
GOsummaries: an R Package for Visual Functional Annotation of Experimental Data. 574 - Edward P. Randviir, Samuel M. Illingworth
, Matthew J. Baker, Matthew Cude, Craig E. Banks:
Twittering About Research: A Case Study of the World's First Twitter Poster Competition. 798 - Roslyn Gleadow
, Barbara Macfarlan
:
Design for learning - a case study of blended learning in a science unit. 898 - Michael R. Crusoe
, Hussien F. Alameldin, Sherine Awad, Elmar Boucher
, Adam Caldwell, Reed Cartwright
, Amanda Charbonneau, Bede Constantinides
, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan A. Fish, Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R. Herr, Adina Howe
, Alex Hyer, Andreas Härpfer, Luiz Irber
, Rhys Kidd, David Lin, Justin Lippi, Tamer Mansour
, Pamela McA'Nulty, Eric McDonald, Jessica Mizzi, Kevin D. Murray
, Joshua R. Nahum, Kaben Nanlohy, Alexander Johan Nederbragt
, Humberto Ortiz-Zuazaga
, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N. Russ, Erich M. Schwarz
, Camille Scott
, Josiah D. Seaman, Scott Sievert, Jared Simpson, Connor Skennerton, James Spencer, Ramakrishnan Srinivasan, Daniel S. Standage
, James A. Stapleton, Susan R. Steinman, Joe Stein, Benjamin Taylor, Will Trimble, Heather Wiencko, Michael Wright, Brian Wyss, Qingpeng Zhang, en zyme, C. Titus Brown
:
The khmer software package: enabling efficient nucleotide sequence analysis. 900 - Thomas Cokelaer
, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M. Bot
, Elias Chaibub Neto, Federica Eduati, Mehmet Gönen, Steven M. Hill, Bruce R. Hoff, Jonathan R. Karr, Robert Küffner, Michael P. Menden
, Pablo Meyer
, Raquel Norel
, Abhishek Pratap, Robert J. Prill, Matthew T. Weirauch, James C. Costello
, Gustavo Stolovitzky, Julio Saez-Rodriguez
:
DREAMTools: a Python package for scoring collaborative challenges. 1030 - Ye Hu, Bijun Zhang, Martin Vogt
, Jürgen Bajorath
:
AnalogExplorer2 - Stereochemistry sensitive graphical analysis of large analog series. 1031 - David G. Bonsall
, M. Azim Ansari
, Camilla Ip
, Amy Trebes, Anthony Brown
, Paul Klenerman
, David Buck, STOP-HCV Consortium, Paolo Piazza
, Eleanor Barnes
, Rory J. Bowden
:
ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens. 1062 - Camilla L. C. Ip, Matthew Loose
, John R. Tyson
, Mariateresa de Cesare
, Bonnie L. Brown, Miten Jain
, Richard M. Leggett
, David A. Eccles
, Vadim Zalunin
, John M. Urban
, Paolo Piazza
, Rory J. Bowden
, Benedict Paten, Solomon Mwaigwisya, Elizabeth M. Batty, Jared T. Simpson, Terrance P. Snutch, Ewan Birney
, David Buck, Sara Goodwin, Hans J. Jansen
, Justin O'Grady
, Hugh E. Olsen, MinION Analysis, Reference Consortium:
MinION Analysis and Reference Consortium: Phase 1 data release and analysis. 1075 - Sean Ekins
, Joel S. Freundlich, Alex M. Clark, Manu Anantpadma
, Robert A. Davey, Peter B. Madrid:
Machine learning models identify molecules active against the Ebola virus in vitro. 1091 - David P. Cavanaugh
, Krishnan K. Chittur:
A hydrophobic proclivity index for protein alignments. 1097 - Andrew R. Segerdahl
, Melvin Mezue, Thomas W. Okell
, John T. Farrar, Irene Tracey
:
The dorsal posterior insula is not an island in pain but subserves a fundamental role - Response to: "Evidence against pain specificity in the dorsal posterior insula" by Davis et al.. 1207 - Jean-Louis Vincent
:
A new Critical Care channel in F1000Research. 1295 - Steven W. Wingett
, Philip Ewels
, Mayra Furlan-Magaril
, Takashi Nagano, Stefan Schoenfelder, Peter Fraser
, Simon Andrews
:
HiCUP: pipeline for mapping and processing Hi-C data. 1310 - Eshini Perera, Neiraja Gnaneswaran, Marlon Perera
, Rodney Sinclair
:
Validating the use of Medicare Australia billing data to examine trends in skin cancer. 1341 - Michael Liu, Aaron E. Darling
:
Metagenomic Chromosome Conformation Capture (3C): techniques, applications, and challenges. 1377 - Andy G. Lynch
:
Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimates. 1407 - François Moreews
, Olivier Sallou, Hervé Ménager
, Yvan Le Bras
, Cyril Monjeaud, Christophe Blanchet, Olivier Collin
:
BioShaDock: a community driven bioinformatics shared Docker-based tools registry. 1443 - Zeeshan Ahmed, Thomas Dandekar:
MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format. 1453 - Bartholomew Jardine, Gary M. Raymond, James B. Bassingthwaighte
:
Semi-automated Modular Program Constructor for physiological modeling: Building cell and organ models. 1461 - Stefan A. Koestler
, Begum Alaybeyoglu
, Christian X. Weichenberger
, Arzu Celik
:
FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development. 1484 - Santiago L. Poggio
, Sarina Macfadyen, David A. Bohan
:
Reconciling Techno-simplicity and Eco-complexity for future food security. 1507 - Liang Wang, Kaiyong Zhao:
Detecting "protein words" through unsupervised word segmentation. 1517 - Daniel Stöckel, Florian Schmidt
, Patrick Trampert
, Hans-Peter Lenhof:
CausalTrail: Testing hypothesis using causal Bayesian networks. 1520 - Angela U. Makolo
, Temitayo A. Olagunju:
Computational identification of signaling pathways in protein interaction networks. 1522
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