Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: run
https://packages.ecosyste.ms/registries/pypi.org/packages/run
Python Process Run Control
2 versions
Latest release: over 14 years ago
2,133 downloads last month
Papers Mentioning run 35
10.1093/molbev/msaa288
Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication NodesCited by: 6
Author(s): Tina Begum, Marc Robinson‐Rechavi
Software Mentions: 22
Published: almost 4 years ago
10.1371/journal.pone.0232822
SimSurvey: An R package for comparing the design and analysis of surveys by simulating spatially-correlated populationsCited by: 5
Author(s): Paul M. Regular, Gregory J. Robertson, Keith P. Lewis, Jonathan Babyn, Brian Healey, Fran Mowbray
Software Mentions: 17
Published: over 4 years ago
10.1093/molbev/msu269
Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed LociCited by: 488
Author(s): Simon H. Martin, John W. Davey, Chris D. Jiggins
Software Mentions: 10
Published: about 10 years ago
10.3389/fmicb.2019.02476
Characterization of the Mycobiome of the Seagrass, Zostera marina, Reveals Putative Associations With Marine ChytridsCited by: 29
Author(s): Cassandra L. Ettinger, Jonathan A. Eisen
Software Mentions: 10
Published: about 5 years ago
10.1534/g3.119.400185
ARMOR: An <u>A</u>utomated <u>R</u>eproducible <u>MO</u>dular Workflow for Preprocessing and Differential Analysis of <u>R</u>NA-seq DataCited by: 35
Author(s): Stephany Orjuela, Ronald Huang, Katharina Hembach, Mark D. Robinson, Charlotte Soneson
Software Mentions: 8
Published: over 5 years ago
10.1038/s42003-020-01377-3
Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal wormCited by: 71
Author(s): Stephen R. Doyle, Alan S. Tracey, Roz Laing, Nancy Holroyd, David J. Bartley, Wojtek Bazant, Helen Beasley, Robin N. Beech, Collette Britton, Karen Brooks, Umer Chaudhry, Kirsty Maitland, Axel Martinelli, Jennifer D. Noonan, Michael Paulini, Michael A. Quail, Elizabeth Redman, Faye H. Rodgers, Guillaume Sallé, Muhammad Zubair Shabbir, Geetha Sankaranarayanan, Janneke Wit, Kevin Howe, Neil Sargison, Eileen Devaney, Matthew Berriman, John S. Gilleard, James A. Cotton
Software Mentions: 8
Published: almost 4 years ago
10.1371/journal.pgen.1004900
An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifoliaCited by: 41
Author(s): Aashish Ranjan, Brad T. Townsley, Yasunori Ichihashi, Neelima Sinha, Daniel H. Chitwood
Software Mentions: 7
Published: almost 10 years ago
10.1186/1471-2105-13-76
EpiFire: An open source C++ library and application for contact network epidemiologyCited by: 34
Author(s): Thomas J. Hladish, Eugene Melamud, Luis Barrera, Alison P. Galvani, Lauren Ancel Meyers
Software Mentions: 6
Published: over 12 years ago
10.1186/s12864-020-06987-z
Global transcriptomic responses orchestrate difenoconazole resistance in Penicillium spp. causing blue mold of stored apple fruitCited by: 6
Author(s): Franz J. Lichtner, Verneta L. Gaskins, Kerik D. Cox, Wayne M. Jurick
Software Mentions: 6
Published: about 4 years ago
10.1186/1471-2105-10-121
SNP HiTLink: a high-throughput linkage analysis system employing dense SNP dataCited by: 29
Author(s): Yoko Fukuda, Yukiko Nakahara, Hidetoshi Date, Yūji Takahashi, Jun Goto, Akinori Miyashita, Ryozo Kuwano, Hiroki Adachi, Eiji Nakamura, Shoji Tsuji
Software Mentions: 6
Published: over 15 years ago
10.1371/journal.pone.0092725
ss3sim: An R Package for Fisheries Stock Assessment Simulation with Stock SynthesisCited by: 19
Author(s): Sean C. Anderson, Cole C. Monnahan, Kelli F. Johnson, Kotaro Ono, Juan L. Valero
Software Mentions: 5
Published: over 10 years ago
10.1186/s13104-017-2616-7
fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence dataCited by: 6
Author(s): Damien M. O’Halloran
Software Mentions: 5
Published: over 7 years ago
10.1371/journal.pone.0034560
Skip the Alignment: Degenerate, Multiplex Primer and Probe Design Using K-mer Matching Instead of AlignmentsCited by: 37
Author(s): David Hysom, Pejman Naraghi-Arani, Maher Elsheikh, A.C. Carrillo, Peter Williams, Shea N. Gardner
Software Mentions: 5
Published: over 12 years ago
10.1371/journal.pone.0215054
Numerical simulations for the Toda lattices Hamiltonian system: Higher order symplectic illustrative perspectiveCited by: 1
Author(s): Asif Mushtaq, Amna Noreen, Muhammad Farooq
Software Mentions: 5
Published: over 5 years ago
10.1038/s42003-021-01656-7
Molecular characterization of a marine turtle tumor epizootic, profiling external, internal and postsurgical regrowth tumorsCited by: 19
Author(s): Kelsey Yetsko, Jessica Farrell, Nicholas B. Blackburn, Liam Whitmore, Maximilian R Stammnitz, Jenny Whilde, Catherine B. Eastman, Devon Rollinson Ramia, Rachel Thomas, Aleksandar Krstić, Paul J. Linser, Simon Creer, Gary R. Carvalho, Mariana A. Devlin, Nina Nahvi, Ana C Leandro, Thomas W. deMaar, Brooke Burkhalter, Elizabeth P. Murchison, Christine E. Schnitzler, David J. Duffy
Software Mentions: 5
Published: almost 4 years ago
10.3389/fmicb.2018.00771
GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus StenotrophomonasCited by: 101
Author(s): Pablo Vinuesa, Luz Edith Ochoa-Sánchez, Bruno Contreras‐Moreira
Software Mentions: 5
Published: over 6 years ago
10.1186/1471-2164-11-74
Automated design of genomic Southern blot probesCited by: 6
Author(s): Mike D. R. Croning, David Fricker, Noboru H. Komiyama, Seth G. N. Grant
Software Mentions: 4
Published: almost 15 years ago
10.1371/journal.pcbi.1006196
Simulations to benchmark time-varying connectivity methods for fMRICited by: 24
Author(s): William Hedley Thompson, Craig G. Richter, Pontus Plavén-Sigray, Peter Fransson
Software Mentions: 4
Published: over 6 years ago
10.3389/fmicb.2016.01768
Life without dUTPaseCited by: 20
Author(s): Csaba Kerepesi, J. Szabó, Veronika Papp‐Kádár, Orsolya Dobay, Dóra Szabó, Vince Grolmusz, Beáta G. Vértessy
Software Mentions: 4
Published: almost 8 years ago
10.18632/oncotarget.13346
Differentiated regulation of immune-response related genes between LUAD and LUSC subtypes of lung cancersCited by: 51
Author(s): Mengzhu Chen, Xiu Ying Liu, Jie Du, Xiu‐Jie Wang, Xia Lei
Software Mentions: 3
Published: almost 8 years ago
10.1038/s41598-017-07297-3
Desiccation tolerance in bryophytes: The dehydration and rehydration transcriptomes in the desiccation-tolerant bryophyte Bryum argenteumCited by: 37
Author(s): Bei Gao, Xiaoshuang Li, Daoyuan Zhang, Yuqing Liang, Yang Hong-yuan, Moxian Chen, Yuanming Zhang, Jianhua Zhang, Andrew J. Wood
Software Mentions: 3
Published: over 7 years ago
10.1186/s12864-020-07149-x
Systemic paralogy and function of retinal determination network homologs in arachnidsCited by: 16
Author(s): Guilherme Gainett, Jesús A. Ballesteros, Charlotte R. Kanzler, Jakob T. Zehms, John M. Zern, Shlomi Aharon, Efrat Gavish‐Regev, Prashant P. Sharma
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0058652
Genes Related to Ion-Transport and Energy Production Are Upregulated in Response to CO2-Driven pH Decrease in Corals: New Insights from Transcriptome AnalysisCited by: 133
Author(s): Jérémie Vidal-Dupiol, Didier Zoccola, Éric Tambutté, Christoph Grunau, Céline Cosseau, Kristina M. Smith, Michael Freitag, Nolwenn M. Dheilly, Denis Allemand, Sylvie Tambutté
Software Mentions: 2
Published: over 11 years ago
10.3390/microorganisms9081581
Genome and Secretome Analysis of Staphylotrichum longicolleum DSM105789 Cultured on Agro-Residual and Chitinous BiomassCited by: 2
Author(s): Asghar Ali, Bernhard Ellinger, Sophie Brandt, Christian Betzel, Martin Rühl, Carsten Wrenger, Hartmut Schlüter, Wilhelm Schäfer, H. Brognaro, Martin Gand
Software Mentions: 2
Published: over 3 years ago
10.3389/fpls.2017.01142
Molecular Mechanisms behind the Physiological Resistance to Intense Transient Warming in an Iconic Marine PlantCited by: 47
Author(s): Lázaro Marín-Guirao, Laura Entrambasaguas, Emanuela Dattolo, Juan Manuel García Ruiz, Gabriele Procaccini
Software Mentions: 2
Published: over 7 years ago
10.1534/g3.115.019620
Comparative Transcriptome Analysis of the Cosmopolitan Marine Fungus <i>Corollospora maritima</i> Under Two Physiological ConditionsCited by: 16
Author(s): Patricia Vélez, Naholi D. Alejandri-Ramírez, Martha Letícia Gaeta González, Karel Estrada, Alejandro Sánchez-Flores, Tzvetanka D. Dinkova
Software Mentions: 2
Published: about 9 years ago
10.1186/s13326-017-0133-1
An ontology-driven tool for structured data acquisition using Web formsCited by: 13
Author(s): Rafael S. Gonçalves, Samson W. Tu, Csongor Nyulas, Michael J. Tierney, Mark A. Musen
Software Mentions: 2
Published: over 7 years ago
10.1093/jxb/erx213
Effects of periodic photoinhibitory light exposure on physiology and productivity of Arabidopsis plants grown under low lightCited by: 17
Author(s): Yonglan Tian, Joanna Sacharz, Maxwell A. Ware, Huayong Zhang, Alexander V. Ruban
Software Mentions: 2
Published: over 7 years ago
10.1128/mSystems.00252-20
Metabolic Feedback Inhibition Influences Metabolite Secretion by the Human Gut Symbiont Bacteroides thetaiotaomicronCited by: 9
Author(s): Jennie L. Catlett, Jonathan Catazaro, Mikaela Cashman, Sean Carr, Robert Powers, Myra B. Cohen, Nicole R. Buan
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0215165
Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L.Cited by: 10
Author(s): Helen Pourmazaheri, Aboozar Soorni, Bahram Baghban Kohnerouz, Nafiseh Khosravi Dehaghi, Enayatollah Kalantar, Mansoor Omidi, Mohammad Reza Naghavi
Software Mentions: 1
Published: over 5 years ago
10.1038/srep36304
Transcriptional changes during ovule development in two genotypes of litchi (Litchi chinensis Sonn.) with contrast in seed sizeCited by: 7
Author(s): Ashish Kumar Pathak, Sudhir P. Singh, Yogesh K. Gupta, Anoop Kishor Singh Gurjar, Shrikant Mantri, Rakesh Tuli
Software Mentions: 1
Published: about 8 years ago
10.3390/ijms20133353
Directed Evolution of P450 BM3 towards Functionalization of Aromatic O-HeterocyclesCited by: 13
Author(s): Gustavo de Almeida Santos, Gaurao V. Dhoke, Mehdi D. Davari, Anna Joëlle Ruff, Ulrich Schwaneberg
Software Mentions: 1
Published: over 5 years ago
10.1186/s12983-021-00390-4
Rosaceae, Brassicaceae and pollen beetles: exploring relationships and evolution in an anthophilous beetle lineage (Nitidulidae, Meligethes-complex of genera) using an integrative approachCited by: 5
Author(s): Meike Liu, Min Huang, Andrew R. Cline, Emiliano Mancini, Andrea Scaramuzzi, Simone Paradisi, Paolo Audisio, Davide Badano, Simone Sabatelli
Software Mentions: 1
Published: over 3 years ago
10.1107/S1600576716018379
<i>CADEM</i>: calculate X-ray diffraction of epitaxial multilayersCited by: 11
Author(s): Paulina Komar, G. Jakob
Software Mentions: 1
Published: almost 8 years ago
10.1371/journal.pone.0143369
A New Taxon of Basal Ceratopsian from China and the Early Evolution of CeratopsiaCited by: 14
Author(s): Fenglu Han, Catherine A. Forster, James M. Clark, Xing Xu
Software Mentions: 1
Published: almost 9 years ago