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ORCIDF1000Research, Volume 8
Volume 8, 2019
- Md Shahjaman
, Habiba Akter, Md. Mamunur Rashid, Md. Ibnul Asifuzzaman, Md Bipul Hossen, Md. Rezanur Rahman:
Robust and efficient identification of biomarkers from RNA-Seq data using median control chart. 7 - Thomas R. Wood, Christopher Kelly, Megan Roberts, Bryan Walsh:
An interpretable machine learning model of biological age. 17 - Shweta Gopaulakrishnan, Samuela Pollack, BJ Stubbs, Hervé Pagès, John Readey, Sean Davis, Levi Waldron, Martin Morgan, Vincent J. Carey:
restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor. 21 - Gerben ter Riet, Bram W. C. Storosum, Aeilko H. Zwinderman:
What is reproducibility? 36 - Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz:
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python. 42 - Marco Bilucaglia, Luciano Pederzoli, William Giroldini, Elena Prati, Patrizio Tressoldi:
EEG correlation at a distance: A re-analysis of two studies using a machine learning approach. 43 - Zaria C. Ali, Savana Shakir, Tariq Mehmood Aslam:
Perceptions and use of technology in older people with ophthalmic conditions. 86 - Matthieu Schapira, The Open Lab Notebook Consortium, Rachel J. Harding:
Open laboratory notebooks: good for science, good for society, good for scientists. 87 - Claire Garnett, Susan Michie, Robert West, Jamie Brown:
Updating the evidence on the effectiveness of the alcohol reduction app, Drink Less: using Bayes factors to analyse trial datasets supplemented with extended recruitment. 114 - Michael Prummer:
Enhancing gene set enrichment using networks. 129 - Zhian N. Kamvar, Jun Cai, Juliet R. C. Pulliam, Jakob Schumacher, Thibaut Jombart:
Epidemic curves made easy using the R package incidence. 139 - Alex Hawkins-Hooker, Henry Kenlay, John E. Reid:
Projection layers improve deep learning models of regulatory DNA function. 151 - Doaa Ahmed Fouad Hamed, Reham Mohamed Hamdy, Sahar Hosny El Dessouky:
Accuracy of linear measurements obtained from stitched cone beam computed tomography images versus direct skull measurements. 166 - Modhusudon Shaha, Sadia Farzana Sifat, Md. Al Mamun, Md. Baki Billah, Nadim Sharif, Nasir Uddin Nobel, Md. Anowar Khasru Parvez, Ali Azam Talukder, Akiko Nomura, Hiroshi Ushijima, Shuvra Kanti Dey:
Comparative evaluation of sensitivity and specificity of immunochromatography kit for the rapid detection of norovirus and rotavirus in Bangladesh. 173 - Nur Asiah, Junianto Junianto, Ayi Yustiati, Sukendi Sukendi, Melta Rini Fahmi, Zainal A. Muchlisin, Muhamad Kadapi:
Biometric and genetic differences in kelabau (Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1. 177 - Cender Udai Quispe-Juli, Victor Hugo Moquillaza-Alcántara, Katherine Arapa-Apaza:
Massive open online courses on biomedical informatics. 180 - Peter Kokol, Helena Blazun Vosner, Jernej Zavrsnik, Marko Turcin:
How 'smart' is smart dentistry? 183 - Kimon Froussios, Kira Mourão, Gordon G. Simpson, Geoffrey J. Barton, Nicholas J. Schurch:
Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seq. 213 - Mauricio Oberti, Iosif I. Vaisman:
shiny-pred: a server for the prediction of protein disordered regions. 230 - Lorena Pantano, Francisco Pantano, Eulalia Martí, Shannan J. Ho Sui:
Visualization of the small RNA transcriptome using seqclusterViz. 232 - Yi-An Chen, Erika Yogo, Naoko Kurihara, Tomoshige Ohno, Chihiro Higuchi, Masatomo Rokushima, Kenji Mizuguchi:
Assessing drug target suitability using TargetMine. 233 - Juneman Abraham:
National culture as a correlate of research impact and productivity. 237 - John D. Van Horn, Sumiko Abe, José Luis Ambite, Teresa K. Attwood, Niall Beard, Louisa Bellis, Avnish Bhattrai, Alex A. T. Bui, Gully Burns, Lily Fierro, Jonathan Gordon, Jeffrey S. Grethe, Jeana Kamdar, Xiaoyu Lei, Kristina Lerman, Annette McGrath, Nicola J. Mulder, Caroline O'Driscoll, Crystal Stewart, Sonika Tyagi:
Advancing the international data science workforce through shared training and education. 251 - Saif Aldeen AlRyalat, Mohammad Saleh, Mohammad Alaqraa, Alaa Alfukaha, Yara Alkayed, Maryann Abaza, Hadeel Abu Saa, Mohamed Alshamiry:
The impact of the open-access status on journal indices: a review of medical journals. 266 - Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker:
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. 287 - Adam P. Cribbs, Sebastian Luna-Valero, Charlotte George, Ian M. Sudbery, Antonio J. Berlanga-Taylor, Stephen N. Sansom, Tom Smith, Nicholas E. Ilott, Jethro S. Johnson, Jakub Scaber, Katherine Brown, David Sims, Andreas Heger:
CGAT-core: a python framework for building scalable, reproducible computational biology workflows. 377 - (Withdrawn) Consumer perspectives on reproductive health after using the Jakpros smart mobile health application: A cross-sectional, qualitative study. 396
- Oliver M. Crook, Lisa M. Breckels, Kathryn S. Lilley, Paul D. W. Kirk, Laurent Gatto:
A Bioconductor workflow for the Bayesian analysis of spatial proteomics. 446 - Saket Choudhary:
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. 532 - Afolakemi S. Ogunbanwo, Julius Olatunji Okesola, Sheryl Buckley:
Knowledge management awareness assessment in Nigerian tertiary institutions. 608 - Dániel Leitold, Ágnes Vathy-Fogarassy, János Abonyi:
Network-based Observability and Controllability Analysis of Dynamical Systems: the NOCAD toolbox. 646 - Jernej Zavrsnik, Peter Kokol, Helena Blazun Vosner:
The impact of physical activity to the child's quality of life: a bibliometric study. 672 - Jin Hyun Cheong, Sawyer Brooks, Luke J. Chang:
FaceSync: Open source framework for recording facial expressions with head-mounted cameras. 702 - Diane E. Kovats, Ron Shamir, Christiana N. Fogg:
2019 ISCB Overton Prize: Christophe Dessimoz. 722 - Diane E. Kovats, Ron Shamir, Christiana N. Fogg:
2019 ISCB Innovator Award recognizes William Stafford Noble. 723 - Chris A. Boulton, Timothy M. Lenton:
A new method for detecting abrupt shifts in time series. 746 - Shian Su, Vincent J. Carey, Lori A. Shepherd, Matthew E. Ritchie, Martin T. Morgan, Sean Davis:
BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem. 752 - Sirinthip Roomkham, Michael Hittle, Joseph Cheung, David R. Lovell, Emmanuel Mignot, Dimitri Perrin:
Sleep monitoring with the Apple Watch: comparison to a clinically validated actigraph. 754 - Trevor K. McAllister-Day, Tara M. Madhyastha, Mary K. Askren, Peter Boord, Thomas J. Montine, Thomas J. Grabowski:
Attention Network Test fMRI data for participants with Parkinson's disease and healthy elderly. 780 - Paraic A. Kenny:
InferCNV, a python web app for copy number inference from discrete gene-level amplification signals noted in clinical tumor profiling reports. 807 - Kira Mourão, Nicholas J. Schurch, Radek Lucoszek, Kimon Froussios, Katarzyna Mackinnon, Céline Duc, Gordon G. Simpson, Geoffrey J. Barton:
Detection and mitigation of spurious antisense expression with RoSA. 819 - Peter Belmann, Björn Fischer, Jan Krüger, Michal Procházka, Helena Rasche, Manuel Prinz, Maximilian Hanussek, Martin Lang, Felix Bartusch, Benjamin Gläßle, Jens Krüger, Alfred Pühler, Alexander Sczyrba:
de.NBI Cloud federation through ELIXIR AAI. 842 - Andrea Chiarelli, Rob Johnson, Stephen Pinfield, Emma Richens:
Preprints and Scholarly Communication: Adoption, Practices, Drivers and Barriers. 971 - Jürgen Bajorath:
Repositioning the Chemical Information Science Gateway. 976 - Susan Guthrie, Gavin Cochrane, Advait Deshpande, Benoit Macaluso, Vincent Larivière:
Understanding the contribution of UK public health research to clinical guidelines: a bibliometric analysis. 1093 - Gloria C. Ferreira, Jenna Oberstaller, Renée Fonseca, Thomas E. Keller, Swamy Rakesh Adapa, Justin Gibbons, Chengqi Wang, Xiaoming Liu, Chang Li, Minh Pham, Guy W. Dayhoff II, Linh M. Duong, Luis Tañón Reyes, Luciano Enrique Laratelli, Douglas Franz, Segun A. Fatumo, ATM Golam Bari, Audrey Freischel, Lindsey Fiedler, Omkar Dokur, Krishna Sharma, Deborah Cragun, Ben Busby, Rays H. Y. Jiang:
Iron Hack - A symposium/hackathon focused on porphyrias, Friedreich's ataxia, and other rare iron-related diseases. 1135 - Nickil Agni, Caroline Fairhurst, Catriona McDaid, Mike Reed, David J. Torgerson:
Protocol for a factorial randomised controlled trial, embedded within WHiTE 8 COPAL, of an Enhanced Trainee Principal Investigator Package and Additional Digital Nudge to increase recruitment rates. 1153 - Carlos Biagolini-Jr., Regina H. Macedo:
bwimage: A package to describe image patterns in natural structures. 1168 - Mark Wong, Rhodri Ivor Leng:
On the design of linked datasets mapping networks of collaboration in the genomic sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa. 1200 - Ruben Esse:
ChIPdig: a comprehensive user-friendly tool for mining multi-sample ChIP-seq data. 1295 - Teresa Gomez-Diaz, Tomás Recio:
On the evaluation of research software: the CDUR procedure. 1353 - Vivek Navale, Michele Ji, Olga Vovk, Leonie Misquitta, Tsega Gebremichael, Alison Garcia, Yang Fann, Matthew J. McAuliffe:
Development of an informatics system for accelerating biomedical research. 1430 - Lukas M. Weber, Charlotte Soneson:
HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats. 1459 - Gian Marco Duma, Giovanni Mento, Luca Semenzato, Patrizio Tressoldi:
EEG anticipation of random high and low arousal faces and sounds. 1508 - Jason L. Oke, Benjamin G. Feakins, Iryna Schlackow, Borislava Mihaylova, Claire Simons, Chris A O'Callaghan, Daniel S. Lasserson, F. D. Richard Hobbs, Richard J. Stevens, Rafael Perera-Salazar:
Statistical models for the deterioration of kidney function in a primary care population: A retrospective database analysis. 1618 - Taha Abdelhalim Nakabi, Pekka J. Toivanen:
Optimal price-based control of heterogeneous thermostatically controlled loads under uncertainty using LSTM networks and genetic algorithms. 1619 - Aravind Venkatesan, Nikiforos Karamanis, Michele Ide-Smith, Jonathan Hickford, Johanna R. McEntyre:
Understanding life sciences data curation practices via user research. 1622 - Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Hidemasa Bono, Jesualdo Tomás Fernández-Breis, Robert M. Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla J. García, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick S. Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Pérez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala M. Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi:
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. 1677 - Catherine Morgan, Dietrich Samuel Schwarzkopf:
Comparison of human population receptive field estimates between scanners and the effect of temporal filtering. 1681 - Thomas M. Polasek, Sepehr Shakib, Amin Rostami-Hodjegan:
Precision medicine technology hype or reality? The example of computer-guided dosing. 1709 - Goran Medic, Melodi Kosaner Kließ, Louis Atallah, Jochen Weichert, Saswat Panda, Maarten J. Postma, Amer EL-Kerdi:
Evidence-based Clinical Decision Support Systems for the prediction and detection of three disease states in critical care: A systematic literature review. 1728 - John D. Blischak, Peter Carbonetto, Matthew Stephens:
Creating and sharing reproducible research code the workflowr way. 1749 - Michael C. Ryan, Mark Stucky, Chris Wakefield, James M. Melott, Rehan Akbani, John N. Weinstein, Bradley M. Broom:
Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps. 1750 - Justin Williams, Héctor Corrada Bravo, Jennifer Tom, Joseph N. Paulson:
microbiomeDASim: Simulating longitudinal differential abundance for microbiome data. 1769 - Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico:
RCy3: Network biology using Cytoscape from within R. 1774 - Sameera Senanayake, Adrian G. Barnett, Nicholas Graves, Helen Healy, Keshwar Baboolal, Sanjeewa Kularatna:
Using machine learning techniques to develop risk prediction models to predict graft failure following kidney transplantation: protocol for a retrospective cohort study. 1810 - Ana Claudia Sima, Christophe Dessimoz, Kurt Stockinger, Monique Zahn-Zabal, Tarcisio Mendes de Farias:
A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL. 1822 - Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn A. Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan, Andreas Tauch, Ulrike Trojahn, Björn Usadel, Oliver Kohlbacher:
The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. 1877 - Christopher Ryan King, Joanna Abraham, Thomas George Kannampallil, Bradley A. Fritz, Arbi Ben Abdallah, Yixin Chen, Bernadette Henrichs, Mary C. Politi, Brian A. Torres, Angela Mickle, Thaddeus P. Budelier, Sherry McKinnon, Stephen Gregory, Sachin Kheterpal, Troy Wildes, Michael S. Avidan, TECTONICS Research Group:
Protocol for the Effectiveness of an Anesthesiology Control Tower System in Improving Perioperative Quality Metrics and Clinical Outcomes: the TECTONICS randomized, pragmatic trial. 2032 - Garrett M. Dancik, Kevin Williams, Myron Zhang, Nataliia Romanenko:
Cancer Publication Portal: an online tool for summarizing and searching human cancer-genomic publications. 2073 - Muaed Alomar, Subish Palaian, Moawia M. Al-tabakha:
Pharmacovigilance in perspective: drug withdrawals, data mining and policy implications. 2109
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