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ORCIDF1000Research, Volume 7
Volume 7, 2018
- Jonathan Ronen
, Altuna Akalin:
netSmooth: Network-smoothing based imputation for single cell RNA-seq. 8 - Benjamin M. Delory, Mao Li, Christopher N. Topp, Guillaume Lobet:
archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems. 22 - Inge Alexander Raknes, Lars Ailo Bongo:
META-pipe Authorization service. 32 - Agnes Norbury, Ben Seymour:
Response heterogeneity: Challenges for personalised medicine and big data approaches in psychiatry and chronic pain. 55 - Anisa Rowhani-Farid, Adrian G. Barnett:
Badges for sharing data and code at Biostatistics: an observational study. 90 - Anis Fuad, Chien-Yeh Hsu:
UTAUT for HSS: initial framework to study health IT adoption in the developing countries. 101 - Elizama de Gregorio, Dayanna Hartmann Cambruzzi Mendes, Luan Henrique Patrzyk, Luana Felski, Guilherme Barroso Langoni de Freita, Anne Karine Bosetto, Bárbara Luisa Fermino, Maria Vaitsa Loch Haskel, Flávia Ivanski, Juliana Sartori Bonini, Camila Diedrich, Weber Cláudio Francisco Nunes da Silva:
Nutritional status, survival and mortality in Alzheimer patients - a cross-sectional study. 137 - Christian Ohmann, Steve Canham, Rita Banzi, Wolfgang Kuchinke, Serena Battaglia:
Classification of processes involved in sharing individual participant data from clinical trials. 138 - John Q. Wong, Nel Jason Haw, Jhanna Uy, Diana Beatriz Bayani:
Reflections on the use of the World Health Organization's (WHO) OneHealth Tool: Implications for health planning in low and middle income countries (LMICs). 157 - Ewy A. Mathé, Ben Busby, Helen Piontkivska, Team of Developers:
Matchmaking in Bioinformatics. 171 - Patrice Godard, Jonathan van Eyll:
BED: a Biological Entity Dictionary based on a graph data model. 195 - Steven A. Frank:
A biochemical logarithmic sensor with broad dynamic range. 200 - Richard G. Jackson, Rashmi Patel, Sumithra Velupillai, George Gkotsis, David Hoyle, Robert Stewart:
Knowledge discovery for Deep Phenotyping serious mental illness from Electronic Mental Health records. 210 - Bhakti Dwivedi, Jeanne Kowalski:
shinySISPA: A web tool for defining sample groups using gene sets from multiple-omics data. 213 - John Ksander, Sarah M. Kark, Christopher R. Madan:
Breathe Easy EDA: A MATLAB toolbox for psychophysiology data management, cleaning, and analysis. 216 - Jonathan Z. L. Zhao, Eliseos J. Mucaki, Peter K. Rogan:
Predicting ionizing radiation exposure using biochemically-inspired genomic machine learning. 233 - Kenneth W. Witwer:
Alternative miRNAs? Human sequences misidentified as plant miRNAs in plant studies and in human plasma. 244 - Laura Downey, Neethi Rao, Lorna Guinness, Miqdad Asaria, Shankar Prinja, Anju Sinha, Rajni Kant, Arvind Pandey, Francoise Cluzeau, Kalipso Chalkidou:
Identification of publicly available data sources to inform the conduct of Health Technology Assessment in India. 245 - Alejandra Duque-Torres, Carlos Rodriguez-Pabon, Juan Ruiz-Rosero, Giselle Zambrano-Gonzalez, Martha Almanza-Pinzon, Oscar Maurício Caicedo Rendón, Gustavo Ramírez-González:
A new environmental monitoring system for silkworm incubators. 248 - Wolfram Höps, Matt Jeffryes, Alex Bateman:
Gene Unprediction with Spurio: A tool to identify spurious protein sequences. 261 - Zachary S. L. Foster, Scott Chamberlain, Niklaus J. Grünwald:
Taxa: An R package implementing data standards and methods for taxonomic data. 272 - Bo Gao, Qingyao Huang, Michael Baudis:
segment_liftover : a Python tool to convert segments between genome assemblies. 319 - Ihab B. Abdalrahman, Mohammed Elsanousi Huzaifa Mohammed, Abdelmohaymin A Abdalla, Sulaf Ibrahim Abdelaziz, Aboaagla Abdalbagi Ali, Dina Nader Mutwakel Osman, Ahmed Abdelmoniem Ahmed, Hagir Emad Elwasila, Romaisa Hashim Mokhtar Mohammed, Mohamed Dafaalla:
Improving paper-based discharge process; a continuous full-cycle quality improvement project in low resource setting. 324 - Raghvendra Mall, Ehsan Ullah, Khalid Kunji, Michele Ceccarelli, Halima Bensmail:
An unsupervised disease module identification technique in biological networks using novel quality metric based on connectivity, conductance and modularity. 378 - Trung Huynh, Sen Xu:
Gene Annotation Easy Viewer (GAEV): Integrating KEGG's Gene Function Annotations and Associated Molecular Pathways. 416 - Mike L. Smith, Andrzej K. Oles, Wolfgang Huber:
Authoring Bioconductor workflows with BiocWorkflowTools. 431 - Tiago Chedraoui Silva, Antonio Colaprico, Catharina Olsen, Tathiane M. Malta, Gianluca Bontempi, Michele Ceccarelli, Benjamin P. Berman, Houtan Noushmehr:
TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data. 439 - Robert R. Butler III, Pablo V. Gejman:
Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts. 462 - Andy R. Eugene, Jolanta Masiak, Beata Eugene:
Predicting lithium treatment response in bipolar patients using gender-specific gene expression biomarkers and machine learning. 474 - Eric T. Leung, Roshan Noronha, Ali Mirza, Reva Shenwai, Asterios Mpatziakas:
ShinyDiversity - Understanding Alpha and Beta Diversity through Interactive Visualizations. 479 - Hiroyuki Akama:
Individual typological differences in a neurally distributed semantic processing system: Revisiting the Science article by Mitchell et al. on computational neurolinguistics. 487 - Lenin Javier Ramirez-Cando, Cesar I. Alvarez-Mendoza, Patricia Gutierrez-Salazar:
Verhulst-Pearl growth model versus Malthusian growth model for in vitro evaluation of lead removal in wastewater by Photobacterium sp. 491 - Philipp Spohr, Kasper Dinkla, Gunnar W. Klau, Mohammed El-Kebir:
eXamine: Visualizing annotated networks in Cytoscape. 519 - Fred Loney, Guanming Wu:
Automation of ReactomeFIViz via CyREST API. 531 - Ehsan Abdekhodaie, Javad Hatami, Hadi Bahrami Ehsan, Reza Kormi-Nouri:
WordCommentsAnalyzer: A windows software tool for qualitative research. 536 - Guillaume Brysbaert, Théo Mauri, Marc F. Lensink:
Comparing protein structures with RINspector automation in Cytoscape. 563 - V. P. Nagraj, Nistara Randhawa, Finlay Campbell, Thomas Crellen, Bertrand Sudre, Thibaut Jombart:
epicontacts: Handling, visualisation and analysis of epidemiological contacts. 566 - John Muschelli, Elizabeth M. Sweeney, Ciprian M. Crainiceanu:
freesurfer: Connecting the Freesurfer software with R. 599 - Parashkev Nachev, Geraint Rees, Richard S. Frackowiak:
Lost in translation. 620 - Duc-Hau Le, Trang T. H. Tran:
autoHGPEC: Automated prediction of novel disease-gene and disease-disease associations and evidence collection based on a random walk on heterogeneous network. 658 - Zhe Hui Hoo, Muhaned S. A. El-Gheryani, Rachael Curley, Martin J. Wildman:
Using different methods to process forced expiratory volume in one second (FEV1) data can impact on the interpretation of FEV1 as an outcome measure to understand the performance of an adult cystic fibrosis centre: A retrospective chart review. 691 - Pedro Morell Miranda, Francesca Bertolini, Haja N. Kadarmideen:
Investigation of gut microbiome association with inflammatory bowel disease and depression: a machine learning approach. 702 - Nya Mehnwolo Boayue, Gábor Csifcsák, Oula Puonti, Axel Thielscher, Matthias Mittner:
Head models of healthy and depressed adults for simulating the effects of non-invasive brain stimulation. 704 - Adam Treister, Alexander R. Pico:
Identifier Mapping in Cytoscape: idmapper. 725 - Li Jun Huang, Jeffrey N. Law, T. M. Murali:
Automating the PathLinker app for Cytoscape. 727 - Kevin C. Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron T. L. Lun:
iSEE: Interactive SummarizedExperiment Explorer. 741 - Björn A. Grüning, Olivier Sallou, Pablo A. Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel J. Blankenberg, Rafael C. Jiménez, Daniel Blankenberg, Yasset Pérez-Riverol:
Recommendations for the packaging and containerizing of bioinformatics software. 742 - Martina Kutmon, Friederike Ehrhart, Egon L. Willighagen, Chris T. A. Evelo, Susan L. Coort:
CyTargetLinker app update: A flexible solution for network extension in Cytoscape. 743 - Ruby Gupta, Samir Cayenne, Madhu Dyavaiah, Pragnya Srinivas, David Otohinoyi, Debjyoti Talukdar, Moheem Halari, Chidambra Halari, Ashok Ramani, Joshua Yusuf, Khushdeep Chahal, Rupinder Kaur, Ankit Patel, Avaniben Patel, Ravindrasingh Rajput, Harish Siddaiah, Shilpadevi Patil, Ashish Patil, Nikhilesh Anand:
Oncoyeasti: a web-based application to translate data obtained from Saccharomyces cerevisiae high-throughput drug screens into cancer therapeutics. 757 - Barry Demchak, David Otasek, Alexander R. Pico, Gary D. Bader, Keiichiro Ono, Brett Settle, Eric Sage, John H. Morris, William J. R. Longabaugh, Christian Tannus Lopes, Michael Kucera, Adam Treister, Benno Schwikowski, Piet Molenaar, Trey Ideker:
The Cytoscape Automation app article collection. 800 - Brett Settle, David Otasek, John H. Morris, Barry Demchak:
Copycat Layout: Network layout alignment via Cytoscape Automation. 822 - Brett Settle, David Otasek, John H. Morris, Barry Demchak:
aMatReader: Importing adjacency matrices via Cytoscape Automation. 823 - Musatafa Khosa, Ahmed Waqas, Mahnoor Javaid, Jessica Singh, Sadiq Naveed, Salman Majeed, Faisal Khosa:
Bibliometrics of the 100 most-cited articles on refugee populations. 878 - Jamie Kirkham, David Moher:
Who and why do researchers opt to publish in post-publication peer review platforms? - findings from a review and survey of F1000 Research. 920 - Michael I. Love, Charlotte Soneson, Rob Patro:
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification. 952 - Kidane M. Tekle, Sveinung Gundersen, Kjetil Klepper, Lars Ailo Bongo, Inge Alexander Raknes, Xiaxi Li, Wei Zhang, Christian Andreetta, Teshome Dagne Mulugeta, Matús Kalas, Morten B. Rye, Erik Hjerde, Jeevan Karloss Antony Samy, Ghislain Fornous, Abdulrahman Azab, Dag Inge Våge, Eivind Hovig, Nils Peder Willassen, Finn Drabløs, Ståle Nygård, Kjell Petersen, Inge Jonassen:
Norwegian e-Infrastructure for Life Sciences (NeLS). 968 - J. Jesús Naveja, Mariel P. Rico-Hidalgo, José L. Medina-Franco:
Analysis of a large food chemical database: chemical space, diversity, and complexity. 993 - Gilles Didier, Alberto Valdeolivas, Anaïs Baudot:
Identifying communities from multiplex biological networks by randomized optimization of modularity. 1042 - Sophie Graham, Laura McDonald, Radek Wasiak, Michael Lees, Sreeram V. Ramagopalan:
Time to really share real-world data? 1054 - Sara Rodgers, Illary Sbizzera, Sarah Cockayne, Caroline Fairhurst, Sarah E. Lamb, Wesley Vernon, Judith Watson, Catherine Hewitt, David J. Torgerson:
A nested randomised controlled trial of a newsletter and Post-it® note did not increase postal questionnaire response rates in a falls prevention trial. 1083 - Jayaram Kancherla, Alexander Zhang, Brian Gottfried, Héctor Corrada Bravo:
Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets. 1096 - Paul Brennan:
drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics. 1105 - Angelo Duò, Mark D. Robinson, Charlotte Soneson:
A systematic performance evaluation of clustering methods for single-cell RNA-seq data. 1141 - Samir A. Farooq, Samuel J. Weisenthal, Melissa Trayhan, Robert J. White, Kristen Bush, Peter R. Mariuz, Martin S. Zand:
Revealing HIV viral load patterns using unsupervised machine learning and cluster summarization. 1144 - Pedro L. Varela, Camila V. Ramos, Pedro T. Monteiro, Claudine Chaouiya:
EpiLog: A software for the logical modelling of epithelial dynamics. 1145 - Suyan Tian, Chi Wang, Howard H. Chang:
To select relevant features for longitudinal gene expression data by extending a pathway analysis method. 1166 - Sunil Munakomi, Deepak Poudel:
A pilot study on assessing the role of intra-operative Flow 800 vascular map model in predicting onset of vasospasm following micro vascular clipping of ruptured intracranial aneurysms. 1188 - Mikael Linden, Michal Procházka, Ilkka Lappalainen, Dominik Bucik, Pavel Vyskocil, Martin Kuba, Sami Silén, Peter Belmann, Alexander Sczyrba, Steven J. Newhouse, Ludek Matyska, Tommi H. Nyrönen:
Common ELIXIR Service for Researcher Authentication and Authorisation. 1199 - Juan Rincon-Patino, Gustavo-Adolfo Ramírez-González, Juan Carlos Corrales:
Exploring machine learning: A bibliometric general approach using SciMAT. 1210 - Kamil Erguler:
sPop: Age-structured discrete-time population dynamics model in C, Python, and R. 1220 - Juan Rincon-Patino, Gustavo-Adolfo Ramírez-González, Juan Carlos Corrales:
Exploring machine learning: A bibliometric general approach using Citespace. 1240 - Gabriele Scheler:
Neuromodulation influences synchronization and intrinsic read-out. 1277 - Thomas P. Quinn:
Visualizing balances of compositional data: A new alternative to balance dendrograms. 1278 - Dimitri Perrin, Guido Zuccon:
Recursive module extraction using Louvain and PageRank. 1286 - Saskia Freytag, Luyi Tian, Ingrid Lönnstedt, Milica Ng, Melanie Bahlo:
Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data. 1297 - Clarence K. Mah, Thorin Tabor, Jill P. Mesirov:
An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data. 1306 - Nomi L. Harris, Heather Wiencko, Brad Chapman, Peter J. A. Cock, Karsten Hokamp, Hilmar Lapp, Christopher J. Fields, Bastian Greshake Tzovaras:
The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018). 1309 - Stefan Mitrasinovic, Alexander P. Y. Brown, Andreas T. Schaefer, Steven D. Chang, Geoff Appelboom:
Silicon Valley new focus on brain computer interface: hype or hope for new applications? 1327 - Steven W. Wingett, Simon Andrews:
FastQ Screen: A tool for multi-genome mapping and quality control. 1338 - Robert V. Baron, Justin R. Stickel, Daniel E. Weeks:
The Mega2R package: R tools for accessing and processing genetic data in common formats. 1352 - Vivek Navale, Matthew J. McAuliffe:
Long-term preservation of biomedical research data. 1353 - Tyler Weirick, Patrick J. Trainor, Eric C. Rouchka, Andrew P. DeFilippis, Shizuka Uchida:
DRETools: A tool-suite for differential RNA editing detection. 1366 - Paula Moraga, Ilaria Dorigatti, Zhian N. Kamvar, Pawel Piatkowski, Salla E. Toikkanen, V. P. Nagraj, Christl A. Donnelly, Thibaut Jombart:
epiflows: an R package for risk assessment of travel-related spread of disease. 1374 - Friederike Ehrhart, Jonathan Mélius, Elisa Cirillo, Martina Kutmon, Egon L. Willighagen, Susan L. Coort, Leopold M. G. Curfs, Chris T. A. Evelo:
Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services. 1390 - Evan Biederstedt, Jeffrey C. Oliver, Nancy F. Hansen, Aarti Jajoo, Nathan A. Dunn, Andrew Olson, Ben Busby, Alexander T. Dilthey:
NovoGraph: Genome graph construction from multiple long-read de novo assemblies. 1391 - Adam R. Rivers, Kyle C. Weber, Terrence G. Gardner, Shuang Liu, Shalamar D. Armstrong:
ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. 1418 - Nima S. Hejazi, Rachael V. Phillips, Alan E. Hubbard, Mark J. van der Laan:
methyvim: Targeted, robust, and model-free differential methylation analysis in R. 1424 - Erik Fasterius, Cristina Al-Khalili Szigyarto:
seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data. 1466 - Tyler Weirick, Raphael Rene Müller, Shizuka Uchida:
Increasing workflow development speed and reproducibility with Vectools. 1499 - Michail Tsagris, Ioannis Tsamardinos:
Feature selection with the R package MXM. 1505 - Brendan T. Innes, Gary D. Bader:
scClustViz - Single-cell RNAseq cluster assessment and visualization. 1522 - David Crane, Harveen Kaur Ubhi, Jamie Brown, Robert West:
Relative effectiveness of a full versus reduced version of the 'Smoke Free' mobile application for smoking cessation: a randomised controlled trial. 1524 - Jesper L. V. Maag:
gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2. 1576 - Linhua Wang, Jeffrey N. Law, Shiv D. Kale, T. M. Murali, Gaurav Pandey:
Large-scale protein function prediction using heterogeneous ensembles. 1577 - Shoaib Sufi, Caroline Jay:
Raising the status of software in research: A survey-based evaluation of the Software Sustainability Institute Fellowship Programme. 1599 - Fatemeh Behjati-Ardakani, Florian Schmidt, Marcel H. Schulz:
Predicting transcription factor binding using ensemble random forest models. 1603 - James E. Johnson, Praveen Kumar, Caleb Easterly, Mark Esler, Subina P. Mehta, Arthur C. Eschenlauer, Adrian D. Hegeman, Pratik D. Jagtap, Timothy J. Griffin:
Improve your Galaxy text life: The Query Tabular Tool. 1604 - Ajit Singh, Christopher J. Rawlings, Keywan Hassani-Pak:
KnetMaps: a BioJS component to visualize biological knowledge networks. 1651 - Sean Davis, Marcel Ramos, Lori A. Shepherd, Nitesh Turaga, Ludwig Geistlinger, Martin T. Morgan, Benjamin Haibe-Kains, Levi Waldron:
Orchestrating a community-developed computational workshop and accompanying training materials. 1656 - Matt Buranosky, Elmar Stellnberger, Emily R. Pfaff, David Díaz-Gutiérrez, Cavin Ward-Caviness:
FDTool: a Python application to mine for functional dependencies and candidate keys in tabular data. 1667 - Eric Feng, Xijin Ge:
DataViz: visualization of high-dimensional data in virtual reality. 1687 - Eugene Tseytlin, Faina Linkov, Melissa Castine, Elizabeth Legowski, Rebecca S. Jacobson:
DomainBuilder: the knowledge authoring system for SlideTutor Intelligent Tutoring system. 1721 - Gaurav S. Kandlikar, Zachary J. Gold, Madeline C. Cowen, Rachel S. Meyer, Amanda C. Freise, Nathan J. B. Kraft, Jordan Moberg-Parker, Joshua Sprague, David J. Kushner, Emily Curd:
ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations. 1734 - Tallulah S. Andrews, Martin Hemberg:
False signals induced by single-cell imputation. 1740 - Dominik Sidler, Marc Lehner, Simon Frasch, Michael Cristófol-Clough, Sereina Riniker:
Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations. 1745 - Andrew D. Oxman, Iain Chalmers, Astrid Austvoll-Dahlgren, Informed Health Choices group:
Key Concepts for assessing claims about treatment effects and making well-informed treatment choices. 1784 - Daria Komkova, Rachel Lyne, Julie M. Sullivan, Yo Yehudi, Gos Micklem:
The InterMine Android app: Cross-organism genomic data in your pocket. 1837 - Marlon Burbano-Fernandez, Gustavo Ramírez-González:
Wearable technology and health: A bibliometric analysis using SciMAT. 1893 - Fahrul Agus, Muhammad Ihsan, Dyna Marisa Khairina, Krishna Purnawan Candra:
ESforRPD2: Expert System for Rice Plant Disease Diagnosis. 1902 - Daniel S. Katz, Gabrielle Allen, Lorena A. Barba, Devin R. Berg, Holly Bik, Carl Boettiger, Christine L. Borgman, C. Titus Brown, Stuart Buck, Randy Burd, Anita de Waard, Martin Paul Eve, Brian E. Granger, Josh Greenberg, Adina Howe, Bill Howe, May Khanna, Timothy L. Killeen, Matthew S. Mayernik, Erin C. McKiernan, Chris Mentzel, Nirav C. Merchant, Kyle E. Niemeyer, Laura Norén, Sarah M. Nusser, Daniel A. Reed, Edward Seidel, MacKenzie Smith, Jeffrey R. Spies, Matthew J. Turk, John D. Van Horn, Jay Walsh:
The principles of tomorrow's university. 1926 - Ruipeng Lu, Peter K. Rogan:
Transcription factor binding site clusters identify target genes with similar tissue-wide expression and buffer against mutations. 1933 - Yuan Liu, Dana C. Nickleach, Chao Zhang, Jeffrey M. Switchenko, Jeanne Kowalski:
Carrying out streamlined routine data analyses with reports for observational studies: introduction to a series of generic SAS® macros. 1955 - João P. G. L. M. Rodrigues, João M. C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin:
pdb-tools: a swiss army knife for molecular structures. 1961 - Bruno M. Grande, Arjun Baghela, Anna Cavalla, Florian Privé, Peter Zhang, Yisong Zhen:
Hackathon-driven tutorial development. 1974 - Pamela H. Russell, Debashis Ghosh:
Radtools: R utilities for smooth navigation of medical image data. 1976
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