Ecosyste.ms: Papers

10.1093/molbev/msaa288

Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes
Cited by: 6
Author(s): Tina Begum, Marc Robinson‐Rechavi
Software Mentions: 22
Published: about 4 years ago

10.1371/journal.pone.0232822

SimSurvey: An R package for comparing the design and analysis of surveys by simulating spatially-correlated populations
Cited 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 Loci
Cited 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 Chytrids
Cited 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 Data
Cited 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 worm
Cited 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: about 4 years ago

10.1371/journal.pgen.1004900

An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifolia
Cited 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 epidemiology
Cited 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 fruit
Cited 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 data
Cited 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 Synthesis
Cited 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 data
Cited 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 Alignments
Cited 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 perspective
Cited 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 tumors
Cited 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 Stenotrophomonas
Cited 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 probes
Cited 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 fMRI
Cited 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 dUTPase
Cited by: 20
Author(s): Csaba Kerepesi, J. Szabó, Veronika Papp‐Kádár, Orsolya Dobay, Dóra Szabó, Vince Grolmusz, Beáta G. Vértessy
Software Mentions: 4
Published: about 8 years ago

10.18632/oncotarget.13346

Differentiated regulation of immune-response related genes between LUAD and LUSC subtypes of lung cancers
Cited by: 51
Author(s): Mengzhu Chen, Xiu Ying Liu, Jie Du, Xiu‐Jie Wang, Xia Lei
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-017-07297-3

Desiccation tolerance in bryophytes: The dehydration and rehydration transcriptomes in the desiccation-tolerant bryophyte Bryum argenteum
Cited 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 arachnids
Cited 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 Analysis
Cited 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 Biomass
Cited 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 Plant
Cited 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 Conditions
Cited 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 forms
Cited 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 light
Cited 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 thetaiotaomicron
Cited 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 size
Cited 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-Heterocycles
Cited 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 approach
Cited 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 multilayers
Cited 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 Ceratopsia
Cited by: 14
Author(s): Fenglu Han, Catherine A. Forster, James M. Clark, Xing Xu
Software Mentions: 1
Published: almost 9 years ago