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: ape
https://packages.ecosyste.ms/registries/pypi.org/packages/ape
A Productive Environment - make/rake/ant/fab-like system with support for FOSD
3 versions
Latest release: over 10 years ago
62 downloads last month
Papers Mentioning ape 918
10.3390/ijms22063251
Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in BryophytesCited by: 11
Author(s): Kristian Peters, Gerd Ulrich Balcke, Niklas Kleinenkuhnen, Hendrik Treutler, Steffen Neumann
Software Mentions: 31
Published: over 3 years ago
10.1038/s41598-019-54004-5
An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolatesCited by: 61
Author(s): Arun Gonzales Decano, Tim Downing
Software Mentions: 30
Published: almost 5 years ago
10.3389/fonc.2020.617890
Comparative Proteome Identifies Complement Component 3-Mediated Immune Response as Key Difference of Colon Adenocarcinoma and Rectal AdenocarcinomaCited by: 9
Author(s): Jun-Ze Liang, Xiaoling Liang, Liye Zhong, Chutian Wu, Jing Zhang, Yang Wang
Software Mentions: 30
Published: over 3 years ago
10.3389/fmicb.2018.01474
Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar CurrentCited by: 24
Author(s): Flavia Flaviani, Declan C. Schroeder, Karen Lebret, Cecilia Balestreri, Andrea Highfield, Joanna L. Schroeder, Sally Thorpe, Karen Moore, Konrad Pasckiewicz, Maya C. Pfaff, Edward P. Rybicki
Software Mentions: 27
Published: over 6 years ago
10.1371/journal.pcbi.1006242
Phylogeny-corrected identification of microbial gene families relevant to human gut colonizationCited by: 29
Author(s): Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard
Software Mentions: 27
Published: about 6 years ago
10.1371/journal.pone.0243927
A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequencesCited by: 13
Author(s): Emine Toparslan, Kemal Karabağ, Uğur Bilge
Software Mentions: 24
Published: almost 4 years ago
10.7717/peerj.6398
Quantitative color profiling of digital images with earth mover’s distance using the R package colordistanceCited by: 49
Author(s): Hannah Weller, Mark W. Westneat
Software Mentions: 23
Published: over 5 years ago
10.1038/s41396-020-00814-9
Food or just a free ride? A meta-analysis reveals the global diversity of the PlastisphereCited by: 96
Author(s): Robyn J. Wright, Morgan G. I. Langille, Tony R. Walker
Software Mentions: 23
Published: about 4 years ago
10.3389/fvets.2020.547181
Impacts of Short-Term Antibiotic Withdrawal and Long-Term Judicious Antibiotic Use on Resistance Gene Abundance and Cecal Microbiota Composition on Commercial Broiler Chicken Farms in QuébecCited by: 9
Author(s): Catherine Turcotte, Alexandre Thibodeau, Sylvain Quessy, Edward Topp, Guy Beauchamp, Philippe Fravalo, Marie Archambault, Marie-Lou Gaucher
Software Mentions: 23
Published: almost 4 years ago
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
10.1080/19490976.2021.1940792
Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infectionsCited by: 13
Author(s): Robert Thänert, Anna Thänert, Jocelyn Ou, Adam Bajinting, Carey Ann D. Burnham, Holly J. Engelstad, Maria E. Tecos, I. Malick Ndao, Carla Hall-Moore, Colleen Rouggly-Nickless, Mike A. Carl, Deborah C. Rubin, Nicholas O. Davidson, Phillip I. Tarr, Barbara B. Warner, Gautam Dantas, Brad W. Warner
Software Mentions: 22
Published: almost 4 years ago
10.3389/fmicb.2020.550420
Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing PipelineCited by: 91
Author(s): Daniel Straub, Nia Blackwell, Adrian Langarica‐Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst
Software Mentions: 22
Published: about 4 years ago
10.3390/plants10020247
Machine Learning Applications and Optimization of Clustering Methods Improve the Selection of Descriptors in Blackberry Germplasm BanksCited by: 5
Author(s): Juan Camilo Henao-Rojas, María Gladis Rosero-Alpala, Carolina Ortiz-Muñoz, Carlos Enrique Velásquez-Arroyo, William A. León-Rueda, Joaquín Guillermo Ramírez‐Gil
Software Mentions: 19
Published: almost 4 years ago
10.1038/s41598-020-73413-5
The macroevolutionary landscape of short-necked plesiosauriansCited by: 13
Author(s): Valentin Fischer, Jamie A. MacLaren, Laura C. Soul, Rebecca Bennion, Patrick S. Druckenmiller, Roger Benson
Software Mentions: 19
Published: about 4 years ago
10.1128/mBio.01054-19
Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial SignaturesCited by: 28
Author(s): Miles Richardson, Neil Gottel, Jack A. Gilbert, Simon Lax
Software Mentions: 18
Published: about 5 years ago
10.1186/s40168-019-0702-x
Understanding microbial community dynamics to improve optimal microbiome selectionCited by: 193
Author(s): Robyn J. Wright, Matthew I. Gibson, Joseph Alexander Christie-Oleza
Software Mentions: 18
Published: over 5 years ago
10.1186/s12862-020-01717-1
Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern AfricaCited by: 7
Author(s): Zhongning Zhao, Neil Heideman, Phillip Armand Bester, Adriaan Jordaan, Margaretha D. Hofmeyr
Software Mentions: 18
Published: almost 4 years ago
10.1371/journal.pone.0194899
Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in MaliCited by: 34
Author(s): Benjamin J Krajacich, Diana L. Huestis, Adama Dao, Alpha Seydou Yaro, Moussa Diallo, Asha Krishna, Jianchu Xu, Tovi Lehmann
Software Mentions: 18
Published: over 6 years ago
10.1038/s41598-020-75345-6
High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae)Cited by: 9
Author(s): Sara L. Martin, Leshawn Benedict, Wei Wei, Connie A. Sauder, Hugh J. Beckie, Linda M. Hall
Software Mentions: 17
Published: about 4 years ago
10.1038/sdata.2018.179
Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytesCited by: 13
Author(s): Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
Software Mentions: 17
Published: about 6 years ago
10.1016/j.cell.2019.12.013
Identification of a Master Regulator of Differentiation in ToxoplasmaCited by: 154
Author(s): Benjamin S. Waldman, Dominic Schwarz, Marc H. Wadsworth, Jeroen P. J. Saeij, Alex K. Shalek, Sebastian Lourido
Software Mentions: 17
Published: almost 5 years ago
10.1016/j.cell.2015.01.006
Enhancer Evolution across 20 Mammalian SpeciesCited by: 626
Author(s): Diego Villar, Camille Berthelot, Sarah Aldridge, Tim Rayner, Margus Lukk, Miguel Pignatelli, Thomas J. Park, Robert Deaville, Jonathan Thor Erichsen, Anna J. Jasinska, James M. A. Turner, Mads F. Bertelsen, Elizabeth P. Murchison, Paul Flicek, Duncan T. Odom
Software Mentions: 17
Published: almost 10 years ago
10.1038/s42003-021-02025-0
SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in ItalyCited by: 23
Author(s): Marta Giovanetti, Eleonora Cella, Francesca Benedetti, Brittany Rife Magalis, Vagner Fonseca, Silvia Fabris, Giovanni Campisi, Alessandra Ciccozzi, Silvia Angeletti, Alessândra Borsetti, Vittoradolfo Tambone, Caterina Sagnelli, Stefano Pascarella, Alberto Riva, Giancarlo Ceccarelli, Alessandro Marcello, Taj Azarian, Eduan Wilkinson, Túlio de Oliveira, Luiz Carlos Júnior Alcântara, Roberto Cauda, Arnaldo Caruso, Natalie E. Dean, Cameron J. Browne, José Lourenço, Marco Salemi, Davide Zella, Massimo Ciccozzi
Software Mentions: 17
Published: over 3 years ago
10.1111/mec.15250
Demographic and environmental drivers of metagenomic viral diversity in vampire batsCited by: 57
Author(s): Laura M. Bergner, Richard Orton, Julio A. Benavides, Daniel J. Becker, Carlos Tello, Roman Biek, Daniel G. Streicker
Software Mentions: 16
Published: about 5 years ago
10.1371/journal.pone.0189789
An integrative framework to reevaluate the Neotropical catfish genus Guyanancistrus (Siluriformes: Loricariidae) with particular emphasis on the Guyanancistrus brevispinis complexCited by: 11
Author(s): Sonia Fisch-Muller, Jan H. Mol, Raphaël Covain
Software Mentions: 16
Published: almost 7 years ago
10.3389/fgene.2021.719204
RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and VisualizationCited by: 2
Author(s): Zhaoyuan Wei, Jiahe Sun, Qinhui Li, Ting Yao, Haiyue Zeng, Yi Wang
Software Mentions: 16
Published: about 3 years ago
10.1038/s41598-017-11514-4
Microbial communities in placentas from term normal pregnancy exhibit spatially variable profilesCited by: 121
Author(s): Lindsay A. Parnell, Catherine Briggs, Bin Cao, Omar Delannoy-Bruno, Andrew E. Schrieffer, Indira U. Mysorekar
Software Mentions: 16
Published: about 7 years ago
10.3390/ijms22052244
The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensisCited by: 4
Author(s): Anton E. Shikov, Yury V. Malovichko, Arseniy Lobov, Maria Belousova, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 16
Published: over 3 years ago
10.1002/ece3.4361
Seasonal variation of secondary metabolites in nine different bryophytesCited by: 28
Author(s): Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
Software Mentions: 16
Published: about 6 years ago
10.1038/s41597-019-0344-7
A global database for metacommunity ecology, integrating species, traits, environment and spaceCited by: 21
Author(s): Aliénor Jeliazkov, Darko Mijatovic, Stéphane Chantepie, Nigel R. Andrew, Raphaël Arlettaz, Luc Barbaro, Nadia Barsoum, Alena Sucháčková Bartoňová, Elena Belskaya, Núria Bonada, Anik Brind’Amour, Rodrigo Assis de Carvalho, Helena Castro, Damian Chmura, Philippe Choler, Karen M. Chong‐Seng, Daniel F. R. Cleary, A. Cormont, William K. Cornwell, Ramiro de Campos, Nicole J. de Voogd, Sylvain Dolédec, Joshua Adam Drew, Frank Dziock, Anthony S. Eallonardo, Melanie J. Edgar, Fábio Z. Farneda, Domingo Flores Hernández, Cédric Frenette‐Dussault, Guillaume Fried, Belinda Gallardo, Heloise Gibb, Thiago Gonçalves‐Souza, Janet Higuti, Jean‐Yves Humbert, Boris R. Krasnov, Eric Le Saux, Zoë Lindo, Adrià López‐Baucells, E. Cronin Lowe, Bryndís Marteinsdóttir, Koenraad Martens, Peter J. Meffert, Andrés Mellado‐Díaz, Myles H. M. Menz, Christoph F. J. Meyer, Julia Ramos-Miranda, David Mouillot, Alessandro Ossola, Robin J. Pakeman, Sandrine Pavoine, Burak K. Pekin, Joan Pino, Arnaud Pocheville, Francesco Pomati, Peter Poschlod, Honor C. Prentice, Oliver Purschke, Valérie Raevel, Triin Reitalu, Willem Renema, Ignacio Ribera, Natalie Robinson, Bjorn J. M. Robroek, Ricardo Rocha, Sen-Her Shieh, Rebecca Spake, Monika Staniaszek‐Kik, Michał Stanko, Francisco Leonardo Tejerina‐Garro, Cajo J. F. ter Braak, Mark C. Urban, Roel van Klink, Sébastien Villéger, R.J.M. Wegman, Martin J. Westgate, Jonas Wolff, Jan Żarnowiec, М. П. Золотарев, Jonathan M. Chase
Software Mentions: 16
Published: almost 5 years ago
10.1038/s42003-021-01757-3
Jaw shape and mechanical advantage are indicative of diet in Mesozoic mammalsCited by: 20
Author(s): Nuria Melisa Morales-García, Pamela G. Gill, Christine M. Janis, Emily J. Rayfield
Software Mentions: 16
Published: over 3 years ago
10.1186/s13059-020-02020-4
Lifestyle and the presence of helminths is associated with gut microbiome composition in CamerooniansCited by: 43
Author(s): Meagan A Rubel, Arwa Abbas, Louis J. Taylor, Andrew Jesse Connell, Ceylan Tanes, Kyle Bittinger, Valantine Ngum Ndze, Julius Y. Fonsah, Eric Ngwang, André Essiane, Charles Fokunang, Alfred K. Njamnshi, Frederic D. Bushman, Sarah A. Tishkoff
Software Mentions: 16
Published: over 4 years ago
10.1093/gbe/evab127
Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild <i>Drosophila</i> Gut MicrobiomeCited by: 4
Author(s): Jeffery S. McMullen, Eduardo Bueno, Frances Blow, Angela E. Douglas
Software Mentions: 16
Published: over 3 years ago
10.3389/fpls.2021.618028
Floral UV Features of Plant Species From a Neotropical SavannaCited by: 6
Author(s): Priscila Tunes, Maria Gabriela Gutierrez Camargo, Elza Guimarães
Software Mentions: 15
Published: over 3 years ago
10.1128/mBio.00034-20
Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial PhenotypesCited by: 98
Author(s): Laura M. Carroll, Martin Wiedmann, Jasna Kovač
Software Mentions: 15
Published: over 4 years ago
10.1186/s40168-020-00961-3
Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approachCited by: 30
Author(s): Wang Ya, Yan Yan, Kelsey N. Thompson, Sena Bae, Emma K. Accorsi, Yancong Zhang, Jiaxian Shen, Hera Vlamakis, Erica M. Hartmann, Curtis Huttenhower
Software Mentions: 15
Published: almost 4 years ago
10.3390/biomedicines9020144
Dietary Rice Bran-Modified Human Gut Microbial Consortia Confers Protection against Colon Carcinogenesis Following Fecal TransfaunationCited by: 19
Author(s): Kristopher D. Parker, Akhilendra Kumar Maurya, Hend Ibrahim, Sangeeta Rao, Petronella R. Hove, Dileep Kumar, Rama Kant, B. L. Raina, Rajesh Agarwal, Kristine A. Kuhn, Komal Raina, Elizabeth P. Ryan
Software Mentions: 15
Published: almost 4 years ago
10.3390/microorganisms9051050
Effect of Ionizing Radiation on the Bacterial and Fungal Endophytes of the Halophytic Plant Kalidium schrenkianumCited by: 5
Author(s): Jing Zhu, Xiang Sun, Zhidong Zhang, Qi-Yong Tang, Minghong Gu, Lijuan Zhang, Min Hou, Amir Sharon, Hongli Yuan
Software Mentions: 15
Published: over 3 years ago
10.1371/journal.pone.0183417
Association of gene expression with biomass content and composition in sugarcaneCited by: 23
Author(s): Nam V. Hoang, Agnelo Furtado, Angela O'Keeffe, Frederik C. Botha, Robert J. Henry
Software Mentions: 15
Published: about 7 years ago
10.1093/molbev/msab063
Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte GenusCited by: 42
Author(s): Olena Meleshko, Michael D. Martin, Thorfinn Sand Korneliussen, C. Schluechter, P. Lamkowski, Jeremy Schmutz, Adam Healey, Bryan Piatkowski, A. Jonathan Shaw, David J. Weston, Kjell Ivar Flatberg, Péter Szövényi, Kristian Hassel, Hans K. Stenøien
Software Mentions: 14
Published: over 3 years ago
10.1186/s12920-017-0261-6
CVE: an R package for interactive variant prioritisation in precision oncologyCited by: 6
Author(s): Andreas Möck, Suzanne Murphy, James A. Morris, Francesco Marass, Nitzan Rosenfeld, Charles E. Massie
Software Mentions: 14
Published: over 7 years ago
10.3390/cells10030620
Measuring Pre- and Post-Copulatory Sexual Selection and Their Interaction in Socially Monogamous Species with Extra-Pair PaternityCited by: 6
Author(s): Emily R. A. Cramer
Software Mentions: 14
Published: over 3 years ago
10.3390/microorganisms9061222
Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index—A Pilot StudyCited by: 5
Author(s): Hend Alqaderi, Meganathan P. Ramakodi, Rasheeba Nizam, Sindhu Jacob, Sriraman Devarajan, Muthukrishnan Eaaswarkhanth, Fahd Al-Mulla
Software Mentions: 14
Published: over 3 years ago
10.1186/s42523-020-00027-7
Domesticated equine species and their derived hybrids differ in their fecal microbiotaCited by: 18
Author(s): Joan E. Edwards, A. Schennink, Faith Burden, Stuart A. Long, D.A. van Doorn, W.F. Pellikaan, J. Dijkstra, Edoardo Saccenti, Hauke Smidt
Software Mentions: 14
Published: over 4 years ago
10.1371/journal.pone.0225615
An indigenous Saccharomyces uvarum population with high genetic diversity dominates uninoculated Chardonnay fermentations at a Canadian wineryCited by: 9
Author(s): Garrett C. McCarthy, Sydney Morgan, Jonathan T. Martiniuk, Brianne L. Newman, Stephanie McCann, Vivien Measday, Daniel M. Durall
Software Mentions: 14
Published: almost 4 years ago
10.1093/iob/obab004
Patterns of Body Shape Diversity and Evolution in Intertidal and Subtidal Lineages of Combtooth Blennies (Blenniidae)Cited by: 4
Author(s): Joshua Egan, Thaddaeus John Buser, Michael D. Burns, Andrew M. Simons, Peter J. Hundt
Software Mentions: 14
Published: almost 4 years ago
10.1371/journal.pone.0242060
The difference between cellulolytic ‘culturomes’ and microbiomes inhabiting two contrasting soil typesCited by: 3
Author(s): Elizaveta V. Evdokimova, Grigory Gladkov, Natalya I. Kuzina, Е. А. Иванова, Anastasiia K. Kimeklis, Aleksei Zverev, Arina Kichko, Tatyana S. Aksenova, А. Г. Пинаев, Evgeny Andronov
Software Mentions: 14
Published: almost 4 years ago
10.1186/1471-2105-13-133
Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scalingCited by: 30
Author(s): Julien Pelé, Jean Michel Bécu, Hervé Abdi, Marie Chabbert
Software Mentions: 14
Published: over 12 years ago
10.3389/fmicb.2021.709611
Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture SystemCited by: 2
Author(s): Yousri Abdelhafiz, Jorge M. O. Fernandes, Simone Larger, Davide Albanese, Claudio Donati, Omid Jafari, Artem Nedoluzhko, Viswanath Kiron
Software Mentions: 14
Published: about 3 years ago
10.1099/mgen.0.000225
Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogenyCited by: 20
Author(s): Cameron J. Reid, Matthew Z. DeMaere, Steven P. Djordjevic
Software Mentions: 14
Published: over 5 years ago
10.1038/s42003-021-01887-8
The impact of locomotion on the brain evolution of squirrels and close relativesCited by: 23
Author(s): Ornella Bertrand, Hans P. Püschel, Julia A. Schwab, Mary Silcox, Stephen L. Brusatte
Software Mentions: 13
Published: over 3 years ago
10.7717/peerj.1668
Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolutionCited by: 26
Author(s): Tsung Fei Khang, Oi Yoon Michelle Soo, Wooi Boon Tan, L. H. S. Lim
Software Mentions: 13
Published: almost 9 years ago
10.1038/srep42130
Dissecting the brown adipogenic regulatory network using integrative genomicsCited by: 20
Author(s): Rachana Pradhan, Johannes Bues, Vincent Gardeux, Petra Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K. Raghav, Bart Deplancke
Software Mentions: 13
Published: over 7 years ago
10.3390/tropicalmed5020064
Disease Ecology of Rickettsial Species: A Data Science ApproachCited by: 6
Author(s): Sergé Morand, Kittipong Chaisiri, Anamika Kritiyakan, Rawadee Kumlert
Software Mentions: 13
Published: over 4 years ago
10.3389/fmicb.2020.02028
Assessment of Inter-Laboratory Variation in the Characterization and Analysis of the Mucosal Microbiota in Crohn’s Disease and Ulcerative ColitisCited by: 8
Author(s): Jake C. Szamosi, Jessica D. Forbes, John W. Copeland, Natalie Knox, Shahrokh Shekarriz, Laura Rossi, Morag Graham, Christine Bonner, David S. Guttman, Gary Van Domselaar, Michael G. Surette, Çharles N. Bernstein
Software Mentions: 13
Published: about 4 years ago
10.7554/eLife.67784
Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across EuropeCited by: 26
Author(s): Ella Katz, Jiajie Li, Benjamin Jaegle, Haim Ashkenazy, R. Shawn Abrahams, Clement Bagaza, Samuel Holden, Chris J Pires, Ruthie Angelovici, Daniel J. Kliebenstein
Software Mentions: 13
Published: over 3 years ago
10.1002/ece3.5645
Testing adaptive hypotheses on the evolution of larval life history in acorn and stalked barnaclesCited by: 11
Author(s): Christine Ewers‐Saucedo, Paula Pappalardo
Software Mentions: 13
Published: about 5 years ago
10.1186/s40168-018-0569-2
Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genesCited by: 107
Author(s): Joshua P. Earl, Nithin D. Adappa, Jarosław Król, Archana Bhat, Sergey Balashov, Rachel Ehrlich, James N. Palmer, Alan D. Workman, Mariel Blasetti, Bhaswati Sen, Jocelyn Hammond, Noam A. Cohen, Garth D. Ehrlich, Joshua Chang Mell
Software Mentions: 13
Published: about 6 years ago
10.1186/s42523-020-0023-1
Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)speciesCited by: 31
Author(s): Joan E. Edwards, Sudarshan A. Shetty, Pim van den Berg, Faith Burden, D.A. van Doorn, W.F. Pellikaan, J. Dijkstra, Hauke Smidt
Software Mentions: 13
Published: over 4 years ago
10.1093/molbev/msaa128
Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic IntrogressionCited by: 25
Author(s): Xavier Grau‐Bové, Sean Tomlinson, Andrias O. O’Reilly, Nicholas J. Harding, Alistair Miles, Dominic Kwiatkowski, Martin Donnelly, David Weetman
Software Mentions: 12
Published: over 4 years ago
10.1371/journal.pone.0219698
Analysis of gene expression in rheumatoid arthritis and related conditions offers insights into sex-bias, gene biotypes and co-expression patternsCited by: 11
Author(s): Alexander Platzer, Thomas Nußbaumer, Thomas Karonitsch, Josef S. Smolen, Daniel Aletaha
Software Mentions: 12
Published: over 5 years ago
10.1371/journal.pone.0202824
Allometry predicts trabecular bone structural properties in the carnivoran jaw jointCited by: 6
Author(s): Matthew Wysocki, Z. Jack Tseng
Software Mentions: 12
Published: about 6 years ago
10.1371/journal.pone.0184652
The evolution of Lachancea thermotolerans is driven by geographical determination, anthropisation and flux between different ecosystemsCited by: 48
Author(s): Ana Hranilović, Marina Bely, Isabelle Masneuf‐Pomarède, Vladimir Jiranek, Warren Albertin
Software Mentions: 12
Published: about 7 years ago
10.3390/nu13082639
Infants’ First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental CohortsCited by: 18
Author(s): Chiara-Maria Homann, Connor A J Rossel, Sara Dizzell, Liene Bervoets, Julia Simioni, Jenifer Li, Elizabeth Gunn, Michael G. Surette, Russell J. de Souza, Monique Mommers, Eileen K. Hutton, Katherine M. Morrison, John Penders, Niels van Best, Jennifer C. Stearns
Software Mentions: 12
Published: over 3 years ago
10.1371/journal.pntd.0007061
Population genetic structure and geographical variation in Neotricula aperta (Gastropoda: Pomatiopsidae), the snail intermediate host of Schistosoma mekongi (Digenea: Schistosomatidae)Cited by: 2
Author(s): Stephen W. Attwood, Liang Liu, Guan-Nan Huo
Software Mentions: 12
Published: almost 6 years ago
10.3389/fmicb.2019.02597
New Insights Into Cinnamoyl Esterase Activity of Oenococcus oeniCited by: 9
Author(s): Ingrid Collombel, Chrats Melkonian, Douwe Molenaar, Francisco M. Campos, Tim Hogg
Software Mentions: 12
Published: almost 5 years ago
10.1186/s12862-016-0661-9
Breeding system, shell size and age at sexual maturity affect sperm length in stylommatophoran gastropodsCited by: 4
Author(s): Dénes Schmera, Julia Pizá, Ellen Reinartz, Sylvain Ursenbacher, Bruno Baur
Software Mentions: 12
Published: over 8 years ago
10.1002/ece3.6784
Ecomorphology of the pectoral girdle in anurans (Amphibia, Anura): Shape diversity and biomechanical considerationsCited by: 10
Author(s): Karolin Engelkes, Lena Kath, Thomas Kleinteich, Jörg U. Hammel, André Beerlink, Alexander Haas
Software Mentions: 12
Published: about 4 years ago
10.3389/fmicb.2019.00144
Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic ChallengesCited by: 70
Author(s): Laura M. Carroll, Manjarí Mukherjee, David Nicholas, Lisa A. Mingle, Nellie B. Dumas, Jocelyn A. Cole, Jasna Kovač
Software Mentions: 12
Published: over 5 years ago
10.1371/journal.pcbi.1005404
Metacoder: An R package for visualization and manipulation of community taxonomic diversity dataCited by: 437
Author(s): Zachary Foster, Thomas J. Sharpton, Niklaus J. Grünwald
Software Mentions: 12
Published: over 7 years ago
10.1128/mBio.02782-18
Fitness Cost of Aflatoxin Production in Aspergillus flavus When Competing with Soil Microbes Could Maintain Balancing SelectionCited by: 21
Author(s): Milton T. Drott, Tracy Debenport, Steven A. Higgins, Daniel H. Buckley, Michael G. Milgroom
Software Mentions: 12
Published: over 5 years ago
10.1099/mgen.0.000503
Rapid molecular evolution of Spiroplasma symbionts of DrosophilaCited by: 13
Author(s): Michael Gerth, Humberto Martínez-Montoya, Paulino Ramirez, Florent Masson, Joanne S. Griffin, Rodolfo Aramayo, Stefanos Siozios, Bruno Lemaître, Mariana Mateos, Gregory D. D. Hurst
Software Mentions: 11
Published: almost 4 years ago
10.3389/fpls.2020.588856
So Closely Related and Yet So Different: Strong Contrasts Between the Evolutionary Histories of Species of the Cardamine pratensis Polyploid Complex in Central EuropeCited by: 16
Author(s): Andrea Melichárková, Marek Šlenker, Judita Zozomová‐Lihová, Katarína Skokanová, Barbora Šingliarová, Tatiana Kačmárová, Michaela Caboňová, Matúš Kempa, Gabriela Šrámková, Terezie Mandáková, Martin Lysák, Marek Svitok, Lenka Mártonfiová, Karol Marhold
Software Mentions: 11
Published: almost 4 years ago
10.3897/BDJ.9.e71378
Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBankCited by: 2
Author(s): Reginald H.F. Young, Rekkab Gill, Daniel Gillis, Robert Hanner
Software Mentions: 11
Published: about 3 years ago
10.1038/s41598-021-94656-w
A global assessment of surveillance methods for dominant malaria vectorsCited by: 4
Author(s): Bram van de Straat, Tanya L. Russell, Kyran M. Staunton, Marianne Sinka, Thomas R. Burkot
Software Mentions: 11
Published: over 3 years ago
10.1038/s41598-019-47595-6
Coordinated community structure among trees, fungi and invertebrate groups in Amazonian rainforestsCited by: 14
Author(s): Jason Vleminckx, Heidy Schimann, Thibaud Decaëns, Mélanie Fichaux, Vincent Vedel, Gaëlle Jaouen, Mélanie Roy, Emmanuel Lapied, Julien Engel, Aurélie Dourdain, Pascal Pétronelli, Jérôme Orivel, Christopher Baraloto
Software Mentions: 11
Published: over 5 years ago
10.3389/fpls.2021.657796
Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in WheatCited by: 8
Author(s): Eva C Henningsen, Vahid Omidvar, Rafael Della Coletta, Jean Michel Michno, Erin Gilbert, Feng Li, Marisa E. Miller, Chad L. Myers, Sean P. Gordon, John P. Vogel, Brian J. Steffenson, Shahryar F. Kianian, Cory D. Hirsch, Melania Figueroa
Software Mentions: 11
Published: over 3 years ago
10.1371/journal.pone.0151959
Physiological Limits along an Elevational Gradient in a Radiation of Montane Ground BeetlesCited by: 28
Author(s): R. O. Slatyer, Sean D. Schoville
Software Mentions: 11
Published: over 8 years ago
10.3389/fmicb.2017.00682
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)Cited by: 314
Author(s): David W. Waite, Inka Vanwonterghem, Christian Rinke, Donovan H. Parks, Ying Zhang, Ken Takai, Stefan M. Sievert, Jörg Simon, Barbara J. Campbell, Thomas E. Hanson, Tanja Woyke, Martin G. Klotz, Philip Hugenholtz
Software Mentions: 11
Published: over 7 years ago
10.1186/s42523-020-00045-5
Influences of claywater and greenwater on the skin microbiome of cultured larval sablefish (Anoplopoma fimbria)Cited by: 4
Author(s): Emily Dodd, Melissa L. Pierce, Jonathan S. F. Lee, Rachel Poretsky
Software Mentions: 11
Published: over 4 years ago
10.1098/rspb.2021.0616
Juvenile ecology drives adult morphology in two insect ordersCited by: 4
Author(s): Peter T. Rühr, Thomas van de Kamp, Tomáš Faragó, Jörg U. Hammel, Fabian Wilde, Elena Borisova, Carina Edel, Melina Frenzel, Tilo Baumbach, Alexander Blanke
Software Mentions: 11
Published: over 3 years ago
10.1038/s41598-017-17728-w
Enclaves of genetic diversity resisted Inca impacts on population historyCited by: 28
Author(s): Chiara Barbieri, José R. Sandoval, Jairo Valqui, Aviva Shimelman, Stefan Ziemendorff, Roland Schröder, Martin Geppert, Lutz Roewer, Russell D. Gray, Mark Stoneking, Ricardo Fujita, Paul Heggarty
Software Mentions: 11
Published: almost 7 years ago
10.1111/tpj.14784
Segmental duplications are hot spots of copy number variants affecting barley gene contentCited by: 4
Author(s): Gianluca Bretani, Laura Rossini, Chiara Ferrandi, Joanne Russell, Robbie Waugh, Benjamin Kilian, Paolo Bagnaresi, Luigi Cattivelli, Agostino Fricano
Software Mentions: 11
Published: over 4 years ago
10.1111/mec.13636
Escape from the cryptic species trap: lichen evolution on both sides of a cyanobacterial acquisition eventCited by: 34
Author(s): Kevin Schneider, Philipp Resl, Toby Spribille
Software Mentions: 11
Published: over 8 years ago
10.1128/mBio.02699-19
The Toxoplasma gondii Cyst Wall InteractomeCited by: 24
Author(s): Vincent Tu, Tadakimi Tomita, Tatsuki Sugi, Joshua Mayoral, Bing Han, Rama R. Yakubu, Tere Williams, Aline Luciano Horta, Yanfen Ma, Louis M. Weiss
Software Mentions: 11
Published: over 4 years ago
10.1177/1176934320956575
Vesicle Transport in Plants: A Revised Phylogeny of SNARE ProteinsCited by: 10
Author(s): Xiaoyan Gu, Adrian C. Brennan, Wenbin Wei, Guang-Qin Guo, Keith Lindsey
Software Mentions: 11
Published: almost 5 years ago
10.1098/rstb.2018.0303
Origin and evolution of papillomavirus (onco)genes and genomesCited by: 35
Author(s): Anouk Willemsen, Ignacio G. Bravo
Software Mentions: 11
Published: over 5 years ago
10.1186/s40168-019-0714-6
A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sedimentsCited by: 78
Author(s): Jiarui Chen, Shelby E. McIlroy, Anand Asundi, David M. Baker, Gianni Panagiotou
Software Mentions: 11
Published: over 5 years ago
10.1038/s41598-020-79875-x
Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive modelsCited by: 23
Author(s): Marta Relvas, Alba Regueira-Iglesias, Carlos Balsa-Castro, Filomena Salazar, José Júlio Pacheco, Cristina Cabral, Corsina Velazco de Henriques, Inmaculada Tomás
Software Mentions: 10
Published: almost 4 years ago
10.1186/s42523-021-00094-4
Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scalesCited by: 23
Author(s): Connie A. Rojas, Santiago Ramírez‐Barahona, Kay E. Holekamp, Kevin R. Theis
Software Mentions: 10
Published: over 3 years ago
10.1016/j.celrep.2020.107885
CD4+ T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical FeaturesCited by: 9
Author(s): Alexander Greenshields‐Watson, Meriem Attaf, Bruce J. MacLachlan, Thomas Whalley, Cristina Rius, Aaron Wall, Alun G. Lloyd, Hywel Hughes, Kathryn E. Strange, Georgina H Mason, Andrea J. A. Schauenburg, Sarah Hulin-Curtis, James Geary, Yuan Chen, Sarah N. Lauder, Kathryn Smart, Dhanasekaran Vijaykrishna, Miguel L. Grau, Mikhail Shugay, Robert Andrews, Garry Dolton, P.J. Rizkallah, Awen Gallimore, Andrew K. Sewell, Andrew Godkin, David K. Cole
Software Mentions: 10
Published: over 4 years ago
10.1371/journal.pone.0226203
Mating strategy is determinant of adenovirus prevalence in European batsCited by: 4
Author(s): Federica Rossetto, María Iglesias-Caballero, H. Christoph Liedtke, Iván Gómez-Mestre, José Miguel Berciano, Gonzalo Pérez-Suárez, Óscar de Paz, Carlos Ibáñez, Juan E. Echevarrı́a, Inmaculada Casas
Software Mentions: 10
Published: almost 5 years ago
10.1371/journal.pone.0224947
Does caching strategy vary with microclimate in endangered Mt. Graham red squirrels?Cited by: 1
Author(s): Calebe P. Mendes, John L. Koprowski
Software Mentions: 10
Published: almost 5 years ago
10.1371/journal.pone.0144779
Identifying Centres of Plant Biodiversity in South AustraliaCited by: 33
Author(s): Greg R. Guerin, Ed Biffin, Zdravko Baruch, Andrew J. Lowe
Software Mentions: 10
Published: almost 9 years ago
10.3389/fmicb.2021.685263
Exploring the Potential of Micrococcus luteus Culture Supernatant With Resuscitation-Promoting Factor for Enhancing the Culturability of Soil BacteriaCited by: 9
Author(s): Marco Antonio Lopez Marin, Michal Strejcek, Petra Junková, Jáchym Šuman, Jiří Šantrůček, Ondřej Uhlík
Software Mentions: 10
Published: over 3 years ago
10.3389/fpls.2020.00136
The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and TomatoCited by: 17
Author(s): Araceli Lamelas, Damaris Desgarennes, Daniel López-Lima, Luc Villain, Alexandro Alonso-Sánchez, Alejandro Artacho, Amparo Latorre, Andrés Moya, Gloria Carrión
Software Mentions: 10
Published: over 4 years ago
10.1038/srep42808
Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing dataCited by: 21
Author(s): Fredrick M. Mobegi, Amelieke J. H. Cremers, Marien I. de Jonge, Stephen D. Bentley, Sacha A. F. T. van Hijum, Aldert Zomer
Software Mentions: 10
Published: over 7 years ago
10.1371/journal.pone.0138031
The Effect of Host-Plant Phylogenetic Isolation on Species Richness, Composition and Specialization of Insect Herbivores: A Comparison between Native and Exotic HostsCited by: 16
Author(s): Julio Miguel Grandez-Rios, Leonardo Lima Bergamini, Walter Santos de Araújo, Fabricio Villalobos, Mário Almeida‐Neto
Software Mentions: 10
Published: about 9 years ago
10.1371/journal.pntd.0008934
An investig-ation into the epidemiology of chikungunya virus across neglected regions of IndonesiaCited by: 6
Author(s): Sam Stubbs, Edison Johar, Frilasita A. Yudhaputri, Benediktus Yohan, Marsha S. Santoso, Rahma Hayati, Dionisius Denis, Barbara Blacklaws, Ann M. Powers, R. Tedjo Sasmono, Khin Saw Aye Myint, Simon D. W. Frost
Software Mentions: 10
Published: almost 4 years ago
10.1098/rspb.2021.0853
Adaptations to light contribute to the ecological niches and evolution of the terrestrial avifaunaCited by: 11
Author(s): Ian J. Ausprey
Software Mentions: 10
Published: over 3 years ago