Ecosyste.ms: Papers

10.12688/f1000research.15949.2

The Mega2R package: R tools for accessing and processing genetic data in common formats
Cited by: 0
Author(s): R. Baron, Justin R. Stickel, Daniel E. Weeks
Software Mentions: 12
Published: over 5 years ago

10.1016/j.epidem.2020.100425

Responsible modelling: Unit testing for infectious disease epidemiology
Cited by: 6
Author(s): Tim Lucas, Timothy M. Pollington, Emma L Davis, T. Déirdre Hollingsworth
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pone.0254749

Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node
Cited by: 2
Author(s): Christopher Schölzel, Valeria Blesius, Gernot Ernst, Alexander Goesmann, Andreas Dominik
Software Mentions: 7
Published: over 3 years ago

10.1186/s13321-020-0408-x

Towards reproducible computational drug discovery
Cited by: 83
Author(s): Nalini Schaduangrat, Samuel Lampa, Saw Simeon, M. Paul Gleeson, Ola Spjuth, Chanin Nantasenamat
Software Mentions: 6
Published: almost 5 years ago

10.1186/s13029-015-0042-6

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols
Cited by: 3
Author(s): Alexandros Kanterakis, Joël Kuiper, George Potamias, Morris A. Swertz
Software Mentions: 6
Published: about 9 years ago

10.1186/s12859-019-3103-z

De novo Nanopore read quality improvement using deep learning
Cited by: 9
Author(s): Nathan LaPierre, Rob Egan, Wei Wang, Zhong Wang
Software Mentions: 5
Published: about 5 years ago

10.1186/s13321-019-0398-8

The chemfp project
Cited by: 21
Author(s): Andrew Dalke
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pcbi.1009041

Ten simple rules for making a vocabulary FAIR
Cited by: 19
Author(s): Simon J. Cox, Alejandra N. González-Beltrán, Barbara Magagna, Maria-Cristina Marinescu
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pcbi.1003376

Current Practice in Software Development for Computational Neuroscience and How to Improve It
Cited by: 27
Author(s): Marc‐Oliver Gewaltig, Robert C. Cannon
Software Mentions: 4
Published: almost 11 years ago

10.3390/e23030321

CEPS: An Open Access MATLAB Graphical User Interface (GUI) for the Analysis of Complexity and Entropy in Physiological Signals
Cited by: 11
Author(s): David Mayor, Deepak Panday, Hari Kala Kandel, Tony Steffert, Duncan Banks
Software Mentions: 3
Published: over 3 years ago

10.1007/s11306-019-1588-0

Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing
Cited by: 55
Author(s): Kevin Mendez, Leighton Pritchard, Stacey N. Reinke, David Broadhurst
Software Mentions: 3
Published: about 5 years ago

10.12688/f1000research.10137.1

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows
Cited by: 83
Author(s): Brian D. O’Connor, Denis Yuen, Vincent Chung, A. Duncan, Xiang Kun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti
Software Mentions: 3
Published: almost 8 years ago

10.1093/gigascience/gix136

Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data
Cited by: 24
Author(s): Quan Nguyen, Ross L. Tellam, Marina Naval-Sánchez, Laércio R. Porto-Neto, W. Barendse, Antônio Reverter, Ben J. Hayes, James W. Kijas, Brian P. Dalrymple
Software Mentions: 3
Published: almost 7 years ago

10.1093/gigascience/giaa107

The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition
Cited by: 10
Author(s): Daniel Arend, Patrick König, Astrid Junker, Uwe Scholz, Matthias Lange
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pbio.1002303

Computing Workflows for Biologists: A Roadmap
Cited by: 32
Author(s): Ashley Shade, Tracy K. Teal
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0257192

Free and Open Source Software organizations: A large-scale analysis of code, comments, and commits frequency
Cited by: 3
Author(s): Tadeusz Chełkowski, Dariusz Jemielniak, Kacper Macikowski
Software Mentions: 2
Published: about 3 years ago

10.3390/microorganisms9040767

Phylogenomic Investigation of Increasing Fluoroquinolone Resistance among Belgian Cases of Shigellosis between 2013 and 2018 Indicates Both Travel-Related Imports and Domestic Circulation
Cited by: 4
Author(s): Bert Bogaerts, Raf Winand, Julien Van Braekel, Wesley Mattheus, Sigrid C. J. De Keersmaecker, Nancy Roosens, Kathleen Marchal, Kevin Vanneste, Pieter‐Jan Ceyssens
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.06397

Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE
Cited by: 33
Author(s): Todd Riley, Allan Lazarovici, Richard S. Mann, Harmen J. Bussemaker
Software Mentions: 2
Published: almost 9 years ago

10.12688/gatesopenres.12772.1

The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics
Cited by: 14
Author(s): Heba Shaaban, David A. Westfall, Rawhi Mohammad, David Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Nicola Segata, Christopher E. Mason
Software Mentions: 2
Published: almost 7 years ago

10.1002/gepi.22362

On the application, reporting, and sharing of in silico simulations for genetic studies
Cited by: 3
Author(s): Kaleigh Riggs, Huann‐Sheng Chen, Melissa Rotunno, Bing Li, Naoko I. Simonds, Leah E. Mechanic, Bo Peng
Software Mentions: 2
Published: about 4 years ago

10.1093/bioinformatics/btu630

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature
Cited by: 32
Author(s): Reece K. Hart, Rudolph Rico, Emily E. Hare, John Garcia, Jody Westbrook, Vincent A. Fusaro
Software Mentions: 2
Published: about 10 years ago

10.1186/s12911-014-0123-5

A RESTful interface to pseudonymization services in modern web applications
Cited by: 54
Author(s): Martin Lablans, Andreas Borg, Frank Ückert
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pbio.1002614

Imagining the “open” university: Sharing scholarship to improve research and education
Cited by: 37
Author(s): Erin C. McKiernan
Software Mentions: 2
Published: about 7 years ago

10.1093/bioinformatics/btu051

PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
Cited by: 19
Author(s): Andrey Tovchigrechko, Pratap Venepally, Samuel H. Payne
Software Mentions: 1
Published: almost 11 years ago

10.3390/metabo8020031

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics
Cited by: 413
Author(s): Ivana Blaženović, Tobias Kind, Jian Ji, Oliver Fiehn
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2021.644153

Zika Virus Infection of Human Iris Pigment Epithelial Cells
Cited by: 6
Author(s): Feargal J. Ryan, Jillian M. Carr, João M. Furtado, Yuefang Ma, Liam M. Ashander, Milena Simões, Genevieve F. Oliver, Gustavo Bracho Granado, Abby C. Dawson, Michael Michael, Binoy Appukuttan, David J. Lynn, Justine R. Smith
Software Mentions: 1
Published: over 3 years ago

10.1186/1751-0473-8-7

Git can facilitate greater reproducibility and increased transparency in science
Cited by: 128
Author(s): Karthik Ram
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pcbi.1003542

Ten Simple Rules for the Care and Feeding of Scientific Data
Cited by: 146
Author(s): Alyssa A. Goodman, Alberto Pepe, Aljona Blöcker, Christine L. Borgman, K. Cranmer, Mercè Crosas, Rosanne Di Stefano, Yolanda Gil, Paul Groth, Margaret Hedstrom, David W. Hogg, Vinay Kashyap, A. Mahabal, Aneta Siemiginowska, Aleksandra Slavković
Software Mentions: 1
Published: over 10 years ago

10.7554/eLife.07571

Genetic and epigenetic variation in the lineage specification of regulatory T cells
Cited by: 44
Author(s): Aaron Arvey, Joris van der Veeken, George Plitas, Stephen S. Rich, Patrick Concannon, Alexander Y. Rudensky
Software Mentions: 1
Published: about 9 years ago

10.1093/gigascience/giy072

YAMP: a containerized workflow enabling reproducibility in metagenomics research
Cited by: 19
Author(s): Alessia Visconti, Tiphaine Martin, Mario Falchi
Software Mentions: 1
Published: over 6 years ago

10.1128/JVI.00908-17

Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution
Cited by: 74
Author(s): Daniel W. Renner, Moriah L. Szpara
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13326-017-0121-5

Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request
Cited by: 11
Author(s): William R. Hogan, Josh Hanna, Amanda Hicks, Samira Amirova, Baxter Bramblett, Matthew Diller, Rodel Enderez, Timothy Modzelewski, Mirela Vasconcelos, Chris Delcher
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1005419

Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network
Cited by: 10
Author(s): C. Victor Jongeneel, Ovokeraye H. Oduaran, Ezekiel Adebiyi, Marion O. Adebiyi, Oluwaseun J. Adeyemi, Matthew B. Akanle, Shaun Aron, Efejiro Ashano, Hocine Bendou, Gerrit Botha, Emile R. Chimusa, Ananyo Choudhury, Ravikiran Donthu, Jenny Drnevich, Oluwadamila Falola, Christopher J. Fields, Scott Hazelhurst, Liesl M. Hendry, Itunuoluwa Isewon, Radhika S. Khetani, Judit Kumuthini, Magambo Phillip Kimuda, Lerato E Magosi, Liudmila Sergeevna Mainzer, Suresh Maslamoney, Mamana Mbiyavanga, Ayton Meintjes, Danny Mugutso, Phelelani T. Mpangase, Richard Munthali, Victoria Nembaware, Andrew Ndhlovu, Trust Odia, Adaobi Okafor, Olaleye Oladipo, Sumir Panji, V Pillay, Gloria Rendon, Dhriti Sengupta, Nicola Mulder
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0210232

The PLOS ONE collection on machine learning in health and biomedicine: Towards open code and open data
Cited by: 21
Author(s): Leo Anthony Celi, Luca Citi, Marzyeh Ghassemi, Tom Pollard
Software Mentions: 1
Published: almost 6 years ago

10.1016/j.patter.2020.100099

Reproducibility Starts from You Today
Cited by: 5
Author(s): Yasemin Türkyilmaz-van der Velden, Nicolas Dintzner, Marta Teperek
Software Mentions: 1
Published: about 4 years ago

10.1186/s13321-015-0065-7

SpeckTackle: JavaScript charts for spectroscopy
Cited by: 10
Author(s): Stephan Beisken, Pablo Conesa, Kenneth Haug, Reza M. Salek, Christoph Steinbeck
Software Mentions: 1
Published: over 9 years ago

10.1093/database/bay088

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture
Cited by: 43
Author(s): Lisa C. Harper, Jacqueline Campbell, Ethalinda K. S. Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson M. Andorf, Elizabeth Arnaud, Tanya Z. Berardini, Clayton L. Birkett, Steven B. Cannon, James P. Carson, Bradford Condon, Laurel Cooper, Nathan Dunn, Christine G. Elsik, Andrew Farmer, Stephen P. Ficklin, David M. Grant, Emily Grau, Nic Herndon, Zhi-Liang Hu, Jodi L. Humann, Pankaj Jaiswal, Clément Jonquet, Marie‐Angélique Laporte, Pierre Larmande, Gerard R. Lazo, Fiona M. McCarthy, Naama Menda, Christopher J. Mungall, Monica Munoz‐Torres, Sushma Naithani, Rex T. Nelson, Daureen Nesdill, Carissa A. Park, James M. Reecy, Leonore Reiser, Lacey-Anne Sanderson, Taner Z. Sen, Margaret Staton, Sabarinath Subramaniam, Marcela K. Tello-Ruiz, Victor Unda, Deepak Unni, Liya Wang, Doreen Ware, Jill L. Wegrzyn, Jason Williams, Margaret R. Woodhouse, Jing Yu, Doreen Main
Software Mentions: 1
Published: almost 7 years ago

10.1002/minf.201400016

MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics
Cited by: 11
Author(s): Stephan Beisken, Mark Earll, David E. Portwood, Mark Seymour, Christoph Steinbeck
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1007704

Ten simple rules for innovative dissemination of research
Cited by: 42
Author(s): Tony Ross-Hellauer, Jonathan Tennant, Viltė Banelytė, Edit Görögh, Daniela Luzi, Peter Kraker, Lucio Pisacane, Roberta Ruggieri, Electra Sifacaki, Michela Vignoli
Software Mentions: 1
Published: over 4 years ago

10.12688/f1000research.23224.2

An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action
Cited by: 17
Author(s): Hartwig Anzt, Felix Bach, Stephan Druskat, Frank Löffler, Axel Loewe, Bernhard Y. Renard, Gunnar Seemann, Alexander Struck, Elke Achhammer, Piush Aggarwal, Franziska Appel, Michael Bäder, Lutz Brusch, Christian E. Busse, Gerasimos Chourdakis, Piotr Wojtek Dabrowski, Peter Ebert, Bernd Flemisch, Sven Friedl, Bernd Fritzsch, Maximilian D. Funk, Volker Gast, Florian Goth, Jean-Noël Grad, Jan Hegewald, Hermann Schmitz, Florian Hohmann, Stephan Janosch, Dominik Kutra, Jan Linxweiler, Thilo Muth, Wolfgang Peters-Kottig, Fabian Rack, Fabian H. C. Raters, Stephan Rave, Guido Reina, Malte Reißig, Timo Ropinski, Jörg Schaarschmidt, Heidi Seibold, Jan Philipp Thiele, Benjamin Uekérmann, Stefan Unger, Rudolf Weeber
Software Mentions: 1
Published: almost 4 years ago