Ecosyste.ms: Papers

10.1093/gigascience/giz095

Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv
Cited by: 45
Author(s): Farah Zaib Khan, Stian Soiland‐Reyes, Richard O. Sinnott, Andrew Lonie, Carole Goble, Michael R. Crusoe
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pone.0173115

Altered regulation and expression of genes by BET family of proteins in COPD patients
Cited by: 11
Author(s): Rajneesh Malhotra, Nisha Kurian, Xin Zhou, Fang Jiang, Susan J. Monkley, Amy DeMicco, Ib Groth Clausen, Göran Dellgren, Goran Edenro, Miika J. Ahdesmäki, Maryam Clausen, Lisa Öberg, Elisabeth Israelsson, Graham Belfield, Outi Vaarala
Software Mentions: 7
Published: over 7 years ago

10.1093/gigascience/giab060

ISA API: An open platform for interoperable life science experimental metadata
Cited by: 13
Author(s): David Johnson, Dominique Batista, Keeva Cochrane, Robert P. Davey, Anthony Etuk, Alejandra González-Beltrán, Kenneth Haug, Massimiliano Izzo, Martin Larralde, Thomas N. Lawson, Alice Minotto, Pablo Moreno-Ger, Venkata Chandrasekhar Nainala, Claire O’Donovan, Luca Pireddu, Pierrick Roger, Felix Shaw, Christoph Steinbeck, Ralf Weber, Susanna-Assunta Sansone, Philippe Rocca-Serra
Software Mentions: 7
Published: about 3 years ago

10.1038/s41598-020-80111-9

FAK regulates IL-33 expression by controlling chromatin accessibility at c-Jun motifs
Cited by: 13
Author(s): Billie G. C. Griffith, Rosanna Upstill-Goddard, Holly Brunton, Graeme R. Grimes, Andrew V. Biankin, Bryan Serrels, Adam Byron, Margaret C. Frame
Software Mentions: 6
Published: almost 4 years ago

10.7717/peerj.10897

Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application
Cited by: 4
Author(s): Jakub Hynšt, Veronika Navrkalová, Karol Pál, Šárka Pospı́šilová
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms21249478

Toll-Like Receptor 7 Is Required for Lacrimal Gland Autoimmunity and Type 1 Diabetes Development in Male Nonobese Diabetic Mice
Cited by: 8
Author(s): Ivy L. Debreceni, Michael S. Chimenti, David Serreze, Aron M. Geurts, Yi-Guang Chen, Scott M. Lieberman
Software Mentions: 4
Published: almost 4 years ago

10.1093/gigascience/giz135

Arteria: An automation system for a sequencing core facility
Cited by: 2
Author(s): Johan Dahlberg, Johan Hermansson, Steinar Sturlaugsson, М. В. Лысенкова, Patrik Smeds, Claes Ladenvall, Roman Valls Guimerà, Florian Reisinger, Oliver Hofmann, Pontus Larsson
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12859-018-2440-7

Comparing the performance of selected variant callers using synthetic data and genome segmentation
Cited by: 35
Author(s): Xiaopeng Bian, Bin Zhu, Mingyi Wang, Ying Hu, Qingrong Chen, Cu Nguyen, Belynda Hicks, Daoud Meerzaman
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pcbi.1004572

Wham: Identifying Structural Variants of Biological Consequence
Cited by: 98
Author(s): Zev Kronenberg, Edward J. Osborne, Kelsey R. Cone, Brett Kennedy, Eric T. Domyan, Michael D. Shapiro, Nels C. Elde, Mark Yandell
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13063-021-05442-y

Does intervention with GLP-1 receptor agonist semaglutide modulate perception of sweet taste in women with obesity: study protocol of a randomized, single-blinded, placebo-controlled clinical trial
Cited by: 3
Author(s): Mojca Jensterle, Simona Ferjan, Tadej Battelino, Jernej Kovač, Saba Battelino, Dušan Šuput, Andrej Vovk, Andrej Janež
Software Mentions: 3
Published: over 3 years ago

10.1128/mSphere.00803-20

Human Keratinocyte Response to Superantigens
Cited by: 9
Author(s): Patrick M. Schlievert, Françoise A. Gourronc, Donald Y.M. Leung, Aloysius J. Klingelhutz
Software Mentions: 3
Published: about 4 years ago

10.1186/s40425-019-0794-7

Longitudinal immune characterization of syngeneic tumor models to enable model selection for immune oncology drug discovery
Cited by: 54
Author(s): Molly A. Taylor, Adina Hughes, Josephine Walton, Anna M.L. Coenen-Stass, Łukasz Magiera, Lorraine Mooney, Sigourney Bell, Anna D. Staniszewska, Linda C. Sandin, Simon T. Barry, Amanda Watkins, Larissa S. Carnevalli, Elizabeth Hardaker
Software Mentions: 3
Published: almost 5 years ago

10.3390/cancers13174430

Prevalence of Germline Pathogenic Variants in Cancer Predisposing Genes in Czech and Belgian Pancreatic Cancer Patients
Cited by: 7
Author(s): Greet Wieme, J Král, Toon Rosseel, Petra Zemánková, Bram Parton, Michal Vočka, Mattias Van Heetvelde, Petra Kleiblová, Bettina Blaumeiser, Jana Soukupová, Jenneke van den Ende, Petr Nehasil, Sabine Tejpar, Marianna Borecká, Encarna B. Gómez García, Marinus J. Blok, Markéta Šafaříková, Marta Kalousová, Karen Geboes, Robin De Putter, Bruce Poppe, Kim De Leeneer, Zdeněk Kleibl, Markéta Janatová, Kathleen Claes
Software Mentions: 2
Published: about 3 years ago

10.1186/1471-2164-15-244

Comparison of somatic mutation calling methods in amplicon and whole exome sequence data
Cited by: 132
Author(s): Huilei Xu, John DiCarlo, Ravi Vijaya Satya, Peng Quan, Yexun Wang
Software Mentions: 2
Published: over 10 years ago

10.1002/sctm.19-0069

Discovery of retinoic acid receptor agonists as proliferators of cardiac progenitor cells through a phenotypic screening approach
Cited by: 20
Author(s): Lauren Drowley, Jane McPheat, Anneli Nordqvist, Samantha Peel, Ulla Karlsson, Svante Martinsson, Erik Müllers, Anita Dellsén, Sinéad Knight, Ian P. Barrett, Jose Gonzalo Sanchez, Björn Magnusson, Boris Greber, Qingdong Wang, Alleyn T. Plowright
Software Mentions: 2
Published: about 5 years ago

10.1186/s12931-021-01617-y

Potential interactions between the TBX4-FGF10 and SHH-FOXF1 signaling during human lung development revealed using ChIP-seq
Cited by: 11
Author(s): Justyna A. Karolak, Tomasz Gambin, Przemysław Szafrański, Paweł Stankiewicz
Software Mentions: 2
Published: almost 4 years ago

10.1186/s40425-018-0457-0

PI3Kα/δ inhibition promotes anti-tumor immunity through direct enhancement of effector CD8+ T-cell activity
Cited by: 57
Author(s): Larissa S. Carnevalli, Charles Sinclair, Molly A. Taylor, Pablo Morentin Gutierrez, Sophie Langdon, Anna M.L. Coenen-Stass, Lorraine Mooney, Adina Hughes, Laura Jarvis, Anna D. Staniszewska, Claire Crafter, Ben S. Sidders, Elizabeth Hardaker, Kevin Hudson, Simon T. Barry
Software Mentions: 2
Published: almost 6 years ago

10.12688/f1000research.10082.2

Disambiguate: An open-source application for disambiguating two species in next generation sequencing data from grafted samples
Cited by: 10
Author(s): Miika J. Ahdesmäki, Stuart R. Gray, Justin Johnson, Zhongwu Lai
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-018-2227-x

ToTem: a tool for variant calling pipeline optimization
Cited by: 1
Author(s): Nikola Tom, Ondřej Tom, Jitka Malčíková, Šárka Pavlová, Blanka Kubešová, Tobias Rausch, Miroslav Kolařík, Vladimı́r Beneš, Vojtěch Bystrý, Šárka Pospı́šilová
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-018-2532-4

VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database
Cited by: 24
Author(s): Francesco Musacchia, Andrea Ciolfi, Margherita Mutarelli, Alessandro Bruselles, Raffaele Castello, Michele Pinelli, Swaraj Basu, Sandro Banfi, Giorgio Casari, Marco Tartaglia, Vincenzo Nigro
Software Mentions: 1
Published: almost 6 years ago