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ORCIDF1000Research, Volume 6
Volume 6, 2017
- Aleksandr Agafonov, Kimmo Mattila, Cuong Duong Tuan, Lars Tiede, Inge Alexander Raknes, Lars Ailo Bongo:
META-pipe cloud setup and execution. 2060- - Timothy Puckering
, Jake Thompson, Sushruth Sathyamurthy, Sinduja Sukumar, Tirosh Shapira, Paul Ebert:
Automated Wormscan. 192- - Darrell O. Ricke, Steven Schwartz:
Fast P(RMNE): Fast forensic DNA probability of random man not excluded calculation. 2154- - Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth:
Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. 2055- - Jonathan K. Black, Kevin J. Black:
Software for web-based tic suppression training. 2150- - Andrea Tacchella, Silvia Romano, Michela Ferraldeschi, Marco Salvetti, Andrea Zaccaria, Andrea Crisanti, Francesca Grassi:
Collaboration between a human group and artificial intelligence can improve prediction of multiple sclerosis course: a proof-of-principle study. 2172- - Michael J. Steinbaugh, Lorena Pantano, Rory D. Kirchner, Víctor Barrera, Brad A. Chapman, Mary E. Piper, Meeta Mistry, Radhika S. Khetani, Kayleigh Rutherford, Oliver Hofmann, John N. Hutchinson, Shannan J. Ho Sui:
bcbioRNASeq: R package for bcbio RNA-seq analysis. 1976- - Philippa C. Griffin, Jyoti Khadake, Kate S. LeMay, Suzanna E. Lewis, Sandra E. Orchard, Andrew Pask, Bernard J. Pope, Ute Roessner, Keith Russell, Torsten Seemann, Andrew E. Treloar, Sonika Tyagi, Jeffrey H. Christiansen, Saravanan Dayalan, Simon Gladman, Sandra B. Hangartner, Helen L. Hayden, William W. H. Ho, Gabriel Keeble-Gagnère, Pasi K. Korhonen, Peter Neish, Priscilla R. Prestes, Mark F. Richardson, Nathan S. Watson-Haigh, Kelly L. Wyres, Neil D. Young, Maria Victoria Schneider:
Best practice data life cycle approaches for the life sciences. 1618- - Adva Yeheskel, Adam Reiter, Metsada Pasmanik-Chor, Amir Rubinstein:
Simulation and visualization of multiple KEGG pathways using BioNSi. 2120- - Travis L. Jensen, Michael Frasketi, Kevin Conway, Leigh Villarroel, Heather Hill, Konstantinos Krampis, Johannes B. Goll:
RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting. 2162- - Francois Berenger, David Simoncini, Arnout R. D. Voet, Rojan Shrestha, Kam Y. J. Zhang:
Fragger: a protein fragment picker for structural queries. 1722- - Chiara Gabella, Christine Durinx, Ron Appel:
Funding knowledgebases: Towards a sustainable funding model for the UniProt use case. 2051- - Matthias Egger, Leigh F. Johnson, Christian Althaus, Anna Schöni, Georgia Salanti, Nicola Low, Susan L. Norris:
Developing WHO guidelines: Time to formally include evidence from mathematical modelling studies. 1584- - Xinyan Zhang, Manali Rupji, Jeanne Kowalski:
GAC: Gene Associations with Clinical, a web based application. 1039- - Mehdi Benchoufi, Raphaël Porcher, Philippe Ravaud:
Blockchain protocols in clinical trials: Transparency and traceability of consent. 66- - Daniel E. Carlin, Kassi Kosnicki, Sara Garamszegi, Trey Ideker, Helga Thorvaldsdóttir, Michael Reich, Jill P. Mesirov:
A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. 784- - Karolina Wartolowska, David Beard, Andrew Carr:
Blinding in trials of interventional procedures is possible and worthwhile. 1663- - Hashem Koohy:
The rise and fall of machine learning methods in biomedical research. 2012- - Jonathan K. Black, Jonathan M. Koller, Kevin J. Black:
TicTimer software for measuring tic suppression. 1560- - Nancy Baker, Thomas Knudsen, Antony J. Williams:
Abstract Sifter: a comprehensive front-end system to PubMed. 2164- - Giselle Zambrano-Gonzalez, Gustavo Ramírez-González, Martha Almanza-Pinzon:
The evolution of knowledge in sericultural research as observed through a science mapping approach. 2075- - Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Eric Rasche, Michael R. Crusoe, Hedi Peterson, Jon C. Ison, Hervé Ménager:
Using bio.tools to generate and annotate workbench tool descriptions. 2074- - Jonathan P. Tennant, Jonathan M. Dugan, Daniel Graziotin, Damien C. Jacques, François Waldner, Daniel Mietchen, Yehia Elkhatib, Lauren B. Collister, Christina K. Pikas, Tom Crick, Paola Masuzzo, Anthony Caravaggi, Devin R. Berg, Kyle E. Niemeyer, Tony Ross-Hellauer, Sara Mannheimer, Lillian Rigling, Daniel S. Katz, Bastian Greshake Tzovaras, Josmel Pacheco-Mendoza, Nazeefa Fatima, Marta Poblet, Marios Isaakidis, Dasapta Erwin Irawan, Sébastien Renaut, Christopher R. Madan, Lisa Matthias, Jesper Nørgaard Kjær, Daniel Paul O'Donnell, Cameron Neylon, Sarah Kearns, Manojkumar Selvaraju, Julien Colomb:
A multi-disciplinary perspective on emergent and future innovations in peer review. 1151- - Lauren Kemperman, Matthew N. McCall:
miRcomp-Shiny: Interactive assessment of qPCR-based microRNA quantification and quality control algorithms. 2046- - Shruti Kane, Himanshu Garg, Neeraja M. Krishnan, Aditya Singh, Binay Panda:
RNAtor: an Android-based application for biologists to plan RNA sequencing experiments. 997- - Annemarie H. Eckes, Tomasz Gubala, Piotr Nowakowski, Tomasz Szymczyszyn, Rachel Wells, Judith A. Irwin, Carlos Horro, John M. Hancock, Graham J. King, Sarah C. Dyer, Wiktor Jurkowski:
Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data. 465- - Robert Carroll, Sreeram V. Ramagopalan, Javier Cid-Ruzafa, Dimitra Lambrelli, Laura McDonald:
An analysis of characteristics of post-authorisation studies registered on the ENCePP EU PAS Register. 1447- - Virginia Barbour, Theodora Bloom, Jennifer Lin, Elizabeth Moylan:
Amending published articles: time to rethink retractions and corrections? 1960- - Thomas Kesteman, Milijaona Randrianarivelojosia, Christophe Rogier:
The protective effectiveness of control interventions for malaria prevention: a systematic review of the literature. 1932- - Jiandong Zhao, Jiazhou Wang, Mingxia Cheng:
Development of a deep neural network derived from contours defined by consensus-based guidelines for automatic target segmentation in hepatocellular carcinoma radiotherapy: A study protocol. 1929- - Merlijn N. van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez Del Angel, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-García, Rafael C. Jiménez, Fabien Jourdan, Namrata Kale, Maria I. Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Nicholas K. Moschonas, Steffen Neumann, Claire O'Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M. Salek, Susanna-Assunta Sansone, Venkata P. Satagopam, Daniel Schober, Ruth Shimmo, Rachel A. Spicer, Ola Spjuth, Etienne A. Thévenot, Mark R. Viant, Ralf J. M. Weber, Egon L. Willighagen, Gianluigi Zanetti, Christoph Steinbeck:
The future of metabolomics in ELIXIR. 1649- - Nomi L. Harris, Peter J. A. Cock, Brad Chapman, Christopher J. Fields, Karsten Hokamp, Hilmar Lapp, Monica C. Munoz-Torres, Bastian Greshake Tzovaras, Heather Wiencko:
The 2017 Bioinformatics Open Source Conference (BOSC). 1858- - Kishore R. Anekalla, J. P. Courneya, Nicolas Fiorini, Jake Lever, Michael Muchow, Ben Busby:
PubRunner: A light-weight framework for updating text mining results. 612- - Glenn Hyman, Herlin Espinosa, Paola Camargo, David Abreu, Medha Devare, Elizabeth Arnaud, Cheryl H. Porter, Leroy Mwanzia, Kai Sonder, Sibiry Traoré:
Improving agricultural knowledge management: The AgTrials experience. 317- - Scott Gigante:
Picopore: A tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality. 227- - Jürgen Bajorath:
Expanding the chemical information science gateway. 1764- - Krzysztof J. Gorgolewski, Joke Durnez, Russell A. Poldrack:
Preprocessed Consortium for Neuropsychiatric Phenomics dataset. 1262- - Jeffrey W. Hollister, Jemma Stachelek:
lakemorpho: Calculating lake morphometry metrics in R. 1718- - Clare Fiala, Eleftherios P. Diamandis:
Make researchers revisit past publications to improve reproducibility. 1717- - Laura McDonald, Sreeram V. Ramagopalan, Andrew P. Cox, Mustafa Oguz:
Unintended consequences of machine learning in medicine? 1707- - Ira Mills, Catherine Sheard, Meredith Hays, Kevin Douglas, Christopher C. Winchester, William T. Gattrell:
Professional medical writing support and the reporting quality of randomized controlled trial abstracts among high-impact general medical journals. 1489- - Hugues Gentillon, Ludomir Stefanczyk, Michal Strzelecki, Maria Respondek-Liberska:
Texture analysis of the developing human brain using customization of a knowledge-based system. 40- - Hugues Gentillon, Ludomir Stefanczyk, Michal Strzelecki, Maria Respondek-Liberska:
Prenatal brain MRI samples for development of automatic segmentation, target- recognition and machine-learning algorithms to detect anatomical structures. 93- - Tomoyuki Miyao, Kimito Funatsu, Jürgen Bajorath:
Exploring differential evolution for inverse QSAR analysis. 1285- - Stéphanie Boué, Thomas E. Exner, Samik Ghosh, Vincenzo Belcastro, Joh Dokler, David Page, Akash R. Boda, Filipe Bonjour, Barry J. Hardy, Patrick Vanscheeuwijck, Julia Hoeng, Manuel C. Peitsch:
Supporting evidence-based analysis for modified risk tobacco products through a toxicology data-sharing infrastructure. 12- - Tony Ross-Hellauer:
What is open peer review? A systematic review. 588- - Tung Manh Ho, Ha Viet Nguyen, Thu-Trang Vuong, Quang-Minh Dam, Hiep-Hung Pham, Quan-Hoang Vuong:
Exploring Vietnamese co-authorship patterns in social sciences with basic network measures of 2008-2017 Scopus data. 1559- - Akram Hernández-Vásquez, Diego Rosselli:
A bibliometric analysis of the global research on sofosbuvir. 1536- - Jing Ming, Eric Verner, Anand D. Sarwate, Ross Kelly, Cory Reed, Torran Kahleck, Rogers F. Silva, Sandeep R. Panta, Jessica A. Turner, Sergey M. Plis, Vince D. Calhoun:
COINSTAC: Decentralizing the future of brain imaging analysis. 1512- - Helene Kretzmer, Christian Otto, Steve Hoffmann:
BAT: Bisulfite Analysis Toolkit. 1490- - Chao Zhang, Jochem Bijlard, Christine Staiger, Serena A. Scollen, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia D. Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe, Bas Stringer, Jaap Heringa, Andrew Stubbs, Luiz Olavo Bonino da Silva Santos, Jeroen Beliën, Ward Weistra, Rita Azevedo, Kees van Bochove, Gerrit Meijer, Jan-Willem Boiten, Jordi Rambla, Remond J. A. Fijneman, J. Dylan Spalding, Sanne Abeln:
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. 1488- - J. Jesús Naveja, José L. Medina-Franco:
ChemMaps: Towards an approach for visualizing the chemical space based on adaptive satellite compounds. 1134- - Antony J. Williams, Lou Peck, Sean Ekins:
The new alchemy: Online networking, data sharing and research activity distribution tools for scientists. 1315- - Ilya Y. Zhbannikov, Konstantin G. Arbeev, Anatoliy I. Yashin:
cophesim: A comprehensive phenotype simulator for testing novel association methods. 1294- - Sadiq Naveed, Ahmed Waqas, Salman Majeed, Muhammad Zeshan, Nusrat Jahan, Muhammad Haaris Sheikh:
Child psychiatry: A scientometric analysis 1980-2016. 1293- - Dominik R. Laetsch, Mark L. Blaxter:
BlobTools: Interrogation of genome assemblies. 1287- - Manali Rupji, Xinyan Zhang, Jeanne Kowalski:
CASAS: Cancer Survival Analysis Suite, a web based application. 919- - Leila Nemati-Anaraki, Hamed Aghajani Koupaei, Mohammadreza Alibeyk:
The relationship between altmetric score with received citations in Iranian pediatrics articles. 1221- - Lance E. Palmer, Mitchell J. Weiss, Vikram R. Paralkar:
YODEL: Peak calling software for HITS-CLIP data. 1138- - Luís Bastião Silva, Rafael C. Jiménez, Niklas Blomberg, José Luís Oliveira:
General guidelines for biomedical software development. 273- - Aleksandra Pawlik, Celia W. G. van Gelder, Aleksandra Nenadic, Patricia M. Palagi, Eija Korpelainen, Philip Lijnzaad, Diana Marek, Susanna-Assunta Sansone, John M. Hancock, Carole A. Goble:
Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action. 1040- - Jesper Eisfeldt, Francesco Vezzi, Páll Ísólfur Ólason, Daniel Nilsson, Anna Lindstrand:
TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. 664- - Kent A. Riemondy, Ryan M. Sheridan, Austin Gillen, Yinni Yu, Christopher G. Bennett, Jay R. Hesselberth:
valr: Reproducible genome interval analysis in R. 1025- - Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner. 1001- - Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
2017 Outstanding Contributions to ISCB Award: Fran Lewitter. 1000- - Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
2017 ISCB Overton Prize: Christoph Bock. 999- - Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
2017 ISCB Innovator Award: Aviv Regev. 998- - Anthony R. Colombo, Timothy J. Triche Jr., Giridharan Ramsingh:
Arkas: Rapid reproducible RNAseq analysis. 586- - Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutiérrez, Neil P. Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla J. García, Josep Lluis Gelpí, Simon L. Gladman, Carole A. Goble, Montserrat González Ferreiro, Alejandra N. González-Beltrán, Philippa C. Griffin, Björn A. Grüning, Jonas Hagberg, Petr Holub, Rob W. W. Hooft, Jon C. Ison, Daniel S. Katz, Brane Leskosek, Federico López-Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola J. Mulder, Yasset Pérez-Riverol, Robert Pergl, Horst Pichler, Bernard J. Pope, Ferran Sanz, Maria Victoria Schneider, Victoria Stodden, Radoslaw Suchecki, Radka Svobodová Vareková, Harry-Anton Talvik, Ilian T. Todorov, Andrew E. Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch:
Four simple recommendations to encourage best practices in research software. 876- - James Kite, Philayrath Phongsavan:
Insights for conducting real-time focus groups online using a web conferencing service. 122- - Arlin Stoltzfus, Michael S. Rosenberg, Hilmar Lapp, Aidan Budd, Karen Cranston, Enrico Pontelli, Shann Oliver, Rutger A. Vos:
Community and Code: Nine Lessons from Nine NESCent Hackathons. 786- - Ferdinando Villa, Stefano Balbi, Ioannis N. Athanasiadis, Caterina Caracciolo:
Semantics for interoperability of distributed data and models: Foundations for better-connected information. 686- - Benjamin J. Stubbs, Keith Frankston, Marcel Ramos, Nancy Laranjo, Frank M. Sacks, Vincent J. Carey:
ogttMetrics: Data structures and algorithms for oral glucose tolerance tests. 684- - Ilya Y. Zhbannikov, Konstantin G. Arbeev, Anatoliy I. Yashin:
haploR: an R-package for querying web-based annotation tools. 97- - Eric M. Weitz, Lorena Pantano, Jingzhi Zhu, Bennett Upton, Ben Busby:
Viewing RNA-seq data on the entire human genome. 596- - Bastian Greshake:
Looking into Pandora's Box: The Content of Sci-Hub and its Usage. 541- - Chakravarthi Kanduri, Irma Järvelä:
GenRank: a R/Bioconductor package for prioritization of candidate genes. 463- - Igor Dolgalev, Fritz J. Sedlazeck, Ben Busby:
DangerTrack: A scoring system to detect difficult-to-assess regions. 443- - Christopher J. Mungall, Ian H. Holmes:
WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis. 423- - Shennan A. Weiss, Ali A Asadi-Pooya, Sitaram Vangala, Stephanie Moy, Dale H. Wyeth, Iren Orosz, Michael Gibbs, Lara Schrader, Jason Lerner, Christopher K. Cheng, Edward Chang, Rajsekar Rajaraman, Inna Keselman, Perdro Churchman, Christine Bower-Baca, Adam L. Numis, Michael G. Ho, Lekha Rao, Annapoorna Bhat, Joanna Suski, Marjan Asadollahi, Timothy Ambrose, Andres Fernandez, Maromi Nei, Christopher Skidmore, Scott Mintzer, Dawn S. Eliashiv, Gary W. Mathern, Marc R. Nuwer, Michael R. Sperling, Jerome Engel Jr., John M. Stern:
AR2, a novel automatic artifact reduction software method for ictal EEG interpretation: Validation and comparison of performance with commercially available software. 30- - Erin K. Wagner, Satyajeet Raje, Liz Amos, Jessica Kurata, Abhijit Badve, Yingquan Li, Ben Busby:
Extending TCGA queries to automatically identify analogous genomic data from dbGaP. 319- - Carlos Culquichicón, Jaime A. Cardona-Ospina, Andrés M. Patiño-Barbosa, Alfonso J. Rodriguez-Morales:
Bibliometric analysis of Oropouche research: impact on the surveillance of emerging arboviruses in Latin America. 194- - S. K. Chua, Ahmad M. Qureshi, Vijay Krishnan, Dinker R. Pai, Laila B. Kamal, Sharmilla Gunasegaran, M. Z. Afzal, Lahiru Ambawatta, Jin Yun Gan, P. Y. Kew, Than Winn, Suneet Sood:
The impact factor of an open access journal does not contribute to an article's citations. 208- - Kyle Hoedebecke, Lindsey Beaman, Joy Mugambi, Sanam Shah, Marwa Mohasseb, Cheyanne Vetter, Kim Yu, Irini Gergianaki, Emily Couvillon:
Health care and social media: What patients really understand. 118- - Corneel Coens, Jan Bogaerts, Laurence Collette:
Comment on the "TrialsTracker: Automated ongoing monitoring of failure to share clinical trial results by all major companies and research institutions". 71- - Espen Mikal Robertsen, Hubert Denise, Alex L. Mitchell, Robert D. Finn, Lars Ailo Bongo, Nils Peder Willassen:
ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services. 70- - Brian D. O'Connor, Denis Yuen, Vincent Chung, Andrew G. Duncan, Xiangkun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti:
The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. 52- - Karina Salvatierra, Hector Florez:
Pathogen Sequence Signature Analysis (PSSA): A software tool for analyzing sequences to identify microorganism genotypes. 21-
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