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F1000Research, 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 R. 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 R. 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 - 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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