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ORCIDF1000Research, 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 A. 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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