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
10.1038/s41598-021-83355-1
Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, CanadaCited by: 10
Author(s): Calvin Sjaarda, Nazneen Rustom, Gerald A. Evans, David Huang, Santiago Pérez-Patrigeón, Melissa Hudson, Henry Wong, Zhengxin Sun, T Hugh Guan, Muhammad Ayub, Cláudio N. Soares, Robert I. Colautti, Prameet M. Sheth
Software Mentions: 5
Published: almost 4 years ago
10.1007/s00442-019-04426-9
Low levels of intraspecific trait variation in a keystone invertebrate groupCited by: 25
Author(s): Clara A. Gaudard, Mark P. Robertson, Tom R. Bishop
Software Mentions: 5
Published: over 5 years ago
10.1038/s41598-021-88964-4
A morphometric approach to track opium poppy domesticationCited by: 18
Author(s): A.C. Assis Jesus, Vincent Bonhomme, Allowen Evin, Sarah Ivorra, Raül Soteras, Aurélie Salavert, Ferrán Antolín, Laurent Bouby
Software Mentions: 5
Published: over 3 years ago
10.1186/s12862-018-1297-8
Diversity of opisthokont septin proteins reveals structural constraints and conserved motifsCited by: 15
Author(s): Ben Auxier, Jaclyn Dee, Mary L. Berbee, Michelle Momany
Software Mentions: 5
Published: almost 6 years ago
10.3389/fmicb.2020.590944
Analyzing Ash Leaf-Colonizing Fungal Communities for Their Biological Control of Hymenoscyphus fraxineusCited by: 21
Author(s): Regina Becker, Kristina Ulrich, Undine Behrendt, Michael Kube, Andreas Ulrich
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pone.0164532
The Evolutionary Basis of Naturally Diverse Rice Leaves AnatomyCited by: 23
Author(s): Jolly Chatterjee, Jacqueline Dionora, Abigail Elmido-Mabilangan, Samart Wanchana, Vivek Thakur, Anindya Bandyopadhyay, D. S. Brar, W. Paul Quick
Software Mentions: 5
Published: about 8 years ago
10.1186/1471-2105-12-104
PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environmentCited by: 50
Author(s): Botond Sipos, Tim Massingham, Gregory E. Jordan, Nick Goldman
Software Mentions: 5
Published: over 13 years ago
10.1093/gbe/evz246
Reprogramming of retrotransposon activity during speciation of the genus CitrusCited by: 2
Author(s): Carles Borredà, Estela Pérez-Román, Victoria Ibáñez, Javier Terol, Manuel Talón
Software Mentions: 5
Published: about 5 years ago
10.1093/molbev/msaa309
A New Catalog of Structural Variants in 1,301 <i>A. thaliana</i> Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response GenesCited by: 22
Author(s): Mehmet Göktay, Andrea Fulgione, Angela M. Hancock
Software Mentions: 5
Published: almost 4 years ago
10.3389/fnana.2016.00099
Big Cat Coalitions: A Comparative Analysis of Regional Brain Volumes in FelidaeCited by: 19
Author(s): Sharleen T. Sakai, Bradley M. Arsznov, Ani E. Hristova, Elise Yoon, Barbara L. Lundrigan
Software Mentions: 5
Published: about 8 years ago
10.1093/molbev/msw285
Rapid expansion of immune-related gene families in the house fly, <i>Musca domestica</i>Cited by: 23
Author(s): Timothy B. Sackton, Brian P. Lazzaro, Andrew G. Clark
Software Mentions: 5
Published: almost 8 years ago
10.1002/ece3.7555
Scaling the extinction vortex: Body size as a predictor of population dynamics close to extinction eventsCited by: 7
Author(s): Nathan F. Williams, Louise McRae, Robin Freeman, Pol Capdevila, Christopher F. Clements
Software Mentions: 5
Published: over 3 years ago
10.1186/s13100-019-0190-3
Stowaway miniature inverted repeat transposable elements are important agents driving recent genomic diversity in wild and cultivated carrotCited by: 6
Author(s): Alicja Macko-Podgórni, Katarzyna Stelmach, Kornelia Kwolek, Dariusz Grzebelus
Software Mentions: 5
Published: almost 5 years ago
10.1371/journal.pone.0088805
Molecular Phylogenetics and Temporal Diversification in the Genus Aeromonas Based on the Sequences of Five Housekeeping GenesCited by: 13
Author(s): J. Gaspar Lorén, Maribel Farfán, M. Carmen Fusté
Software Mentions: 5
Published: almost 11 years ago
10.3390/microorganisms8081152
Population Structure of Non-ST6 Listeria monocytogenes Isolated in the Red Meat and Poultry Value Chain in South AfricaCited by: 11
Author(s): Itumeleng Matle, Thendo Mafuna, Evelyn Madoroba, Khanyisile R. Mbatha, Kudakwashe Magwedere, Rian Pierneef
Software Mentions: 5
Published: over 4 years ago
10.1128/mSphere.00738-20
Genomic Epidemiology and Evolution of <i>Escherichia coli</i> in Wild Animals in MexicoCited by: 14
Author(s): Robert S. Murphy, Martin Palm, Ville Mustonen, Jonas Warringer, Anne Farewell, Leopold Parts, Danesh Moradigaravand
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0154871
Fruiting Season Length Restricts Global Distribution of Female-Only Parental Care in Frugivorous Passerine BirdsCited by: 8
Author(s): Sahas Barve, Frank A. La Sorte
Software Mentions: 5
Published: over 8 years ago
10.1186/s12862-016-0758-1
Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae)Cited by: 15
Author(s): Laurent Vuataz, Sereina Rutschmann, Michael T. Monaghan, Michel Sartori
Software Mentions: 5
Published: about 8 years ago
10.3390/microorganisms8060905
First Detection of Paralytic Shellfish Toxins from Alexandrium pacificum above the Regulatory Limit in Blue Mussels (Mytilus galloprovincialis) in New South Wales, AustraliaCited by: 8
Author(s): Abanti Barua, Penelope Ajani, Rendy Ruvindy, H. Farrell, A. Zammit, Steve Brett, David R. Hill, Chowdhury Sarowar, Mona Hoppenrath, Shauna A. Murray
Software Mentions: 5
Published: over 4 years ago
10.3390/microorganisms9020229
Arbuscular Mycorrhizal Fungal Communities in the Soils of Desert HabitatsCited by: 15
Author(s): Martti Vasar, John Davison, Siim‐Kaarel Sepp, Maarja Öpik, Mari Moora, Kadri Koorem, Yiming Meng, Jane Oja, Asem A. Akhmetzhanova, Saleh Al‐Quraishy, В. Г. Онипченко, Juan José Cantero, Sydney I. Glassman, Wael N. Hozzein, Martin Zobel
Software Mentions: 5
Published: almost 4 years ago
10.1371/journal.pone.0239541
Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.)Cited by: 14
Author(s): Nikolaj Vendelbo, Pernille Sarup, Jihad Orabi, Peter Skov Kristensen, A. Jahoor
Software Mentions: 5
Published: about 4 years ago
10.3390/ijms22115876
Oral Microbiome in Relation to Periodontitis Severity and Systemic InflammationCited by: 31
Author(s): Adelina S. Plachokova, Sergio Andreu‐Sánchez, Marlies P. Noz, Jingyuan Fu, Niels P. Riksen
Software Mentions: 5
Published: over 3 years ago
10.1186/s40168-021-01119-5
Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineageCited by: 16
Author(s): Dominique Le Bœuf, John M. Eppley, Daniel Mende, Rex R. Malmstrom, Tanja Woyke, Edward F. DeLong
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0182270
Differential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C. elegansCited by: 4
Author(s): Kapil Dev Singh, Xue Zheng, Stuart Milstein, Martin Keller, Bernd Roschitzki, Jonas Grossmann, Michael O. Hengartner
Software Mentions: 5
Published: over 7 years ago
10.1186/s13059-020-01971-y
High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of lifeCited by: 22
Author(s): Michael Peeri, Tamir Tuller
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.pone.0140761
Relation between Water Balance and Climatic Variables Associated with the Geographical Distribution of AnuransCited by: 25
Author(s): Braz Titon, Fernando Ribeiro Gomes
Software Mentions: 5
Published: about 9 years ago
10.1371/journal.pone.0244803
Trypanosoma (Herpetosoma) diversity in rodents and lagomorphs of New Mexico with a focus on epizootological aspects of infection in Southern Plains woodrats (Neotoma micropus)Cited by: 0
Author(s): Irina Goodrich, Clifton McKee, Michael Kosoy
Software Mentions: 5
Published: almost 4 years ago
10.1371/journal.pone.0148459
Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1Cited by: 28
Author(s): Luc Villandré, David A. Stephens, Aurélie Labbe, Huldrych F. Günthard, Roger D. Kouyos, Tanja Stadler
Software Mentions: 5
Published: almost 9 years ago
10.1186/s40168-020-00907-9
Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trialCited by: 33
Author(s): Suryang Kwak, Joo-Hee Choi, Tiffany Hink, Kimberly A. Reske, Kenneth Blount, Courtney Jones, Margaret H. Bost, Xiaoqing Sun, Carey-Ann D. Burnham, Erik R. Dubberke, Gautam Dantas
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pone.0127692
Revealing Beta-Diversity Patterns of Breeding Bird and Lizard Communities on Inundated Land-Bridge Islands by Separating the Turnover and Nestedness ComponentsCited by: 71
Author(s): Xingfeng Si, Andrés Baselga, Ping Ding
Software Mentions: 5
Published: over 9 years ago
10.1371/journal.pone.0188430
Diversification rates, host plant shifts and an updated molecular phylogeny of Andean Eois moths (Lepidoptera: Geometridae)Cited by: 14
Author(s): Patrick Strutzenberger, Gunnar Brehm, Brigitte Gottsberger, Florian Bodner, Carlo L. Seifert, Konrad Fiedler
Software Mentions: 5
Published: almost 7 years ago
10.3389/fonc.2020.00117
From the Clinic to the Bench and Back Again in One Dog Year: How a Cross-Species Pipeline to Identify New Treatments for Sarcoma Illuminates the Path Forward in Precision MedicineCited by: 17
Author(s): Satish Rao, Jason A. Somarelli, Erdem Altunel, Laura E. Selmic, Mark Byrum, Maya U. Sheth, Serene Cheng, Kathryn E. Ware, So Young Kim, Joseph A. Prinz, Nicolas Devos, David L. Corcoran, Arthur Moseley, Erik J. Soderblom, Shiaowen David Hsu, William C. Eward
Software Mentions: 5
Published: almost 5 years ago
10.3389/fphys.2020.00706
Integrating Mortality Risk and the Adaptiveness of HibernationCited by: 10
Author(s): Théo Constant, Sylvain Giroud, Vincent A. Viblanc, Mathilde L. Tissier, Patrick Bergeron, F. Stephen Dobson, Caroline Habold
Software Mentions: 5
Published: over 4 years ago
10.1128/mSphere.00104-18
The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset SepsisCited by: 95
Author(s): Stephen Wandro, Stephanie Osborne, Claudia Enriquez, Christine Bixby, Antonio Arrieta, Katrine Whiteson
Software Mentions: 5
Published: over 6 years ago
10.1002/ece3.7793
Common Buzzards wintering strategies as an effect of weather conditions and geographic barriersCited by: 1
Author(s): Emanuel Ștefan Baltag, István Kovács, Lucian Sfîcă
Software Mentions: 5
Published: over 3 years ago
10.3390/ani9100733
Virulence Genes, Shiga Toxin Subtypes, Serogroups, and Clonal Relationship of Shiga Toxin-Producing Escherichia Coli Strains Isolated from Livestock and Companion AnimalsCited by: 15
Author(s): Nicolás Galarce, Beatriz Escobar, Francisco Javier Sierro Sánchez, Esteban Paredes-Osses, Raúl Alegría-Morán, César Borie
Software Mentions: 5
Published: about 5 years ago
10.1371/journal.pone.0113429
Body Size, Extinction Risk and Knowledge Bias in New World SnakesCited by: 14
Author(s): Bruno Vilela, Fabricio Villalobos, Miguel Á. Rodrı́guez, Levi Carina Terribile
Software Mentions: 5
Published: about 10 years ago
10.1186/s12864-019-6114-2
Genus level analysis of PKS-NRPS and NRPS-PKS hybrids reveals their origin in AspergilliCited by: 14
Author(s): Sebastian Theobald, Tammi Camilla Vesth, Mikael Rørdam Andersen
Software Mentions: 5
Published: about 5 years ago
10.1128/mSphere.01070-20
Monitoring COVID-19 Transmission Risks by Quantitative Real-Time PCR Tracing of Droplets in Hospital and Living EnvironmentsCited by: 20
Author(s): Andrea Piana, Maria Eugenia Colucci, Federica Valeriani, Adriano Marcolongo, Giovanni Sotgiu, Cesira Pasquarella, Lory Marika Margarucci, Andrea Petrucca, Gianluca Gianfranceschi, Sergio Babudieri, Pietro Vitali, Giuseppe D’Ermo, Assunta Bizzarro, Flavio De Maio, Matteo Vitali, Antonio Azara, Ferdinando Romano, Maurizio Simmaco, Vincenzo Romano Spica
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-021-97556-1
De novo transcriptome assembly, polymorphic SSR markers development and population genetics analyses for southern corn rust (Puccinia polysora)Cited by: 3
Author(s): Qiuyu Sun, Jie Liu, Keyu Zhang, Chong Huang, Leifu Li, Jiayu Dong, Yong Luo, Zhanhong Ma
Software Mentions: 5
Published: about 3 years ago
10.1038/s41598-021-97519-6
Landscape genetics and the genetic legacy of Upper Paleolithic and Mesolithic hunter-gatherers in the modern CaucasusCited by: 1
Author(s): Alexander Gavashelishvili, Alexey Yanchukov, David Tarkhnishvili, Marine Murtskhvaladze, Irakli Akhvlediani, Ceren Kazancı
Software Mentions: 5
Published: about 3 years ago
10.1242/bio.014902
Feliform carnivores have a distinguished constitutive innate immune responseCited by: 23
Author(s): Sonja K. Heinrich, Bettina Wachter, Ortwin Aschenborn, Susanne Thalwitzer, Jörg Melzheimer, Heribert Hofer, Gábor Á. Czirják
Software Mentions: 5
Published: over 8 years ago
10.3389/fpls.2019.01434
Mapping and Dynamics of Regulatory DNA in Maturing Arabidopsis thaliana SiliquesCited by: 12
Author(s): Alessandra M. Sullivan, Andrej A Arsovski, Agnieszka Thompson, Richard Sandstrom, Robert E. Thurman, Shane Neph, Audra Johnson, Shawn Sullivan, Peter J. Sabo, Fidencio Neri, Molly Weaver, Morgan Diegel, Jennifer L. Nemhauser, J Stamatoyannopoulos, Kerry L Bubb, Christine Queitsch
Software Mentions: 5
Published: about 5 years ago
10.1128/mSphere.00071-20
Different Types of Atrial Fibrillation Share Patterns of Gut Microbiota DysbiosisCited by: 36
Author(s): Kun Zuo, Xiandong Yin, Kuibao Li, Jing Zhang, Pan Wang, Jie Jiao, Zheng Liu, Xiaoqing Liu, Jiapeng Liu, Jing Li, Xinchun Yang
Software Mentions: 5
Published: over 4 years ago
10.1186/s12898-019-0220-5
Ecological and life history traits are associated with Ross River virus infection among sylvatic mammals in AustraliaCited by: 11
Author(s): Michael Walsh
Software Mentions: 5
Published: almost 6 years ago
10.3389/fpls.2020.00022
Plastome Evolution and Phylogeny of Orchidaceae, With 24 New SequencesCited by: 50
Author(s): Sang Hyun Kim, Sangjin Jo, Se Hwan Cheon, Min Jung Joo, Ja Ram Hong, Myounghai Kwak, Ki Joong Kim
Software Mentions: 5
Published: over 4 years ago
10.1186/s12898-018-0171-2
Do avian blood parasites influence hypoxia physiology in a high elevation environment?Cited by: 20
Author(s): Farah Ishtiaq, Sahas Barve
Software Mentions: 5
Published: over 6 years ago
10.3389/fpls.2020.01140
Development of a Novel Phenotypic Roadmap to Improve Blueberry Quality and StorabilityCited by: 10
Author(s): Brian Farneti, F. Emanuelli, Iuliia Khomenko, M. Ajelli, Franco Biasioli, L. Giongo
Software Mentions: 5
Published: over 4 years ago
10.7554/eLife.46883
Proteome-wide signatures of function in highly diverged intrinsically disordered regionsCited by: 115
Author(s): Taraneh Zarin, Bob Strome, Alex N Nguyen Ba, Simon Alberti, Julie D. Forman‐Kay, Alan M. Moses
Software Mentions: 5
Published: over 5 years ago
10.1186/s12866-020-01884-7
Diversity and distribution of marine heterotrophic bacteria from a large culture collectionCited by: 24
Author(s): Isabel Sanz-Sáez, Guillem Salazar, Pablo Sánchez, Elena Lara, Marta Royo-Llonch, Elisabet L. Sà, Teresa Lucena, María J. Pujalte, Dolors Vaqué, Carlos M. Duarte, Josep M. Gasol, Carlos Pedrós‐Alió, Olga Sánchez, Silvia G. Acinas
Software Mentions: 5
Published: over 4 years ago
10.1186/s12866-021-02195-1
Characteristics and variation of fecal bacterial communities and functions in isolated systolic and diastolic hypertensive patientsCited by: 8
Author(s): Pan Wang, Ying Dong, Kun Zuo, Chide Han, Jie Jiao, Xinchun Yang, Jing Li
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0222527
Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicusCited by: 7
Author(s): Ragnhildur Guðmundsdóttir, Agnes-Katharina Kreiling, Bjarni K. Kristjánsson, V. Marteinsson, Snæbjörn Pálsson
Software Mentions: 5
Published: about 5 years ago
10.1371/journal.pone.0078392
Scale Effects between Body Size and Limb Design in Quadrupedal MammalsCited by: 55
Author(s): Brandon M. Kilbourne, Louwrens C. Hoffman
Software Mentions: 5
Published: about 11 years ago
10.1073/pnas.2008281117
A SARS-CoV-2 vaccine candidate would likely match all currently circulating variantsCited by: 192
Author(s): Bethany L. Dearlove, Éric Lewitus, Hongjun Bai, Yifan Li, Daniel B. Reeves, Michael Joyce, Paul T. Scott, Mihret F. Amare, Sandhya Vasan, Nelson L. Michael, Kayvon Modjarrad, Morgane Rolland
Software Mentions: 5
Published: about 4 years ago
10.1098/rsos.190939
Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micellesCited by: 8
Author(s): Jean Manguy, Denis C. Shields
Software Mentions: 5
Published: about 5 years ago
10.1098/rsos.181423
Geographical, temporal and individual factors influencing foraging behaviour and consistency in Australasian gannetsCited by: 4
Author(s): Marlenne A. Rodríguez‐Malagón, Elodie C. M. Camprasse, Lauren P. Angel, John P. Y. Arnould
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.pone.0217839
The allometry of proboscis length in Melittidae (Hymenoptera: Apoidae) and an estimate of their foraging distance using museum collectionsCited by: 5
Author(s): Annalie Melin, Harald W. Krenn, Raurie C.K. Bowie, Colin M. Beale, John C. Manning, Jonathan F. Colville
Software Mentions: 5
Published: over 5 years ago
10.1002/ece3.6126
Evolution of altitudinal migration in passerines is linked to dietCited by: 13
Author(s): Claudie Pageau, Mariana M. Vale, Márcio Argollo de Menezes, Luciana Barçante, Mateen Shaikh, Maria Alice S. Alves, Matthew W. Reudink
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.pone.0171870
Phylogenetic patterns and the adaptive evolution of osmoregulation in fiddler crabs (Brachyura, Uca)Cited by: 25
Author(s): Samuel Coelho Faria, Diogo B. Provete, Carl L. Thurman, John Campbell McNamara
Software Mentions: 5
Published: almost 8 years ago
10.1128/mSystems.00195-17
Developing a <i>Bacteroides</i> System for Function-Based Screening of DNA from the Human Gut MicrobiomeCited by: 8
Author(s): Kathy N. Lam, Eric C. Martens, Trevor C. Charles
Software Mentions: 5
Published: over 6 years ago
10.1371/journal.pone.0010429
Novel Weapons Testing: Are Invasive Plants More Chemically Defended than Native Plants?Cited by: 60
Author(s): Eric M. Lind, John D. Parker
Software Mentions: 5
Published: over 14 years ago
10.1371/journal.pone.0134817
Male Homosexual Preference: Where, When, Why?Cited by: 9
Author(s): Julien Barthes, Pierre‐André Crochet, M. Raymond
Software Mentions: 5
Published: over 9 years ago
10.1038/sdata.2014.15
Tree of Sex: A database of sexual systemsCited by: 199
Author(s): Tia‐Lynn Ashman, Doris Bachtrog, Heath Blackmon, Emma E. Goldberg, Matthew W. Hahn, Mark Kirkpatrick, Jun Kitano, Judith E. Mank, Itay Mayrose, Ray Ming, Sarah P. Otto, Catherine L. Peichel, Matthew W. Pennell, Nicolas Perrin, Laura Ross, Nicole Valenzuela, Jana C. Vamosi
Software Mentions: 5
Published: over 10 years ago
10.1002/ece3.4006
Low acclimation capacity of narrow‐ranging thermal specialists exposes susceptibility to global climate changeCited by: 40
Author(s): Tricia M. Markle, Kenneth H. Kozak
Software Mentions: 5
Published: over 6 years ago
10.1186/s12862-019-1545-6
Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by EricaCited by: 9
Author(s): Michael D. Pirie, Martha Kandziora, Nicolai M. Nürk, Nicholas C Le Maitre, A. Mugrabi de Kuppler, Berit Gehrke, E. G. H. Oliver, Dirk U. Bellstedt
Software Mentions: 5
Published: almost 5 years ago
10.1098/rspb.2018.2387
The <i>achaete–scute</i> complex contains a single gene that controls bristle development in the semi-aquatic bugsCited by: 13
Author(s): Cédric Finet, Amélie Decaras, David Armisén, Abderrahman Khila
Software Mentions: 5
Published: almost 6 years ago
10.1371/journal.pntd.0003284
Improvements on Restricted Insecticide Application Protocol for Control of Human and Animal African Trypanosomiasis in Eastern UgandaCited by: 30
Author(s): Dennis Muhanguzi, Kim Picozzi, Jan Hatendorf, Michael Thrusfield, Susan C. Welburn, John David Kabasa, Charles Waiswa
Software Mentions: 5
Published: about 10 years ago
10.1038/sdata.2019.7
The effect of 16S rRNA region choice on bacterial community metabarcoding resultsCited by: 222
Author(s): Yu. S. Bukin, Yuri P. Galachyants, И. В. Морозов, S. V. Bukin, А. S. Zakharenko, Т. I. Zemskaya
Software Mentions: 5
Published: almost 6 years ago
10.1371/journal.pone.0144147
The Independent Evolution Method Is Not a Viable Phylogenetic Comparative MethodCited by: 3
Author(s): Rodger W. Griffin, Gabriel Yapuncich
Software Mentions: 5
Published: almost 9 years ago
10.1371/journal.pone.0198367
Comprehensive evolutionary analysis of the Anthroherpon radiation (Coleoptera, Leiodidae, Leptodirini)Cited by: 10
Author(s): Iva Njunjić, A. Perrard, Kasper P. Hendriks, Menno Schilthuizen, Michel Perreau, Vincent Merckx, Michel Baylac, Louis Deharveng
Software Mentions: 5
Published: over 6 years ago
10.1098/rspb.2016.1587
Evolutionary heritage influences Amazon tree ecologyCited by: 44
Author(s): Fernanda Coelho de Souza, Kyle G. Dexter, Oliver L. Phillips, Roel Brienen, Jérôme Chave, David Galbraith, Gabriela Lopez‐Gonzalez, Abel Monteagudo Mendoza, R. Toby Pennington, Lourens Poorter, Miguel Alexiades, Esteban Álvarez-Dávila, Ana Andrade, L. E. O. C. Aragão, Alejandro Araujo‐Murakami, E.J.M.M. Arets, Gerardo A. Aymard C, Christopher Baraloto, Jorcely Barroso, Damien Bonal, René Boot, José L. Camargo, J. A. Comiskey, Fernando Cornejo Valverde, Plínio Barbosa de Camargo, Anthony Di Fiore, Fernando Elias, Terry L. Erwin, Ted R. Feldpausch, Leandro Valle Ferreira, Nikolaos M. Fyllas, Emanuel Gloor, Bruno Hérault, R. Herrera, Níro Higuchi, Eurídice N. Honorio Coronado, Timothy J. Killeen, William F. Laurance, Susan G. Laurance, J. Lloyd, Thomas Ε. Lovejoy, Yadvinder Malhi, Leandro Maracahipes, Beatriz Schwantes Marimon, Casimiro Mendoza, Paulo S. Morandi, David Neill, Percy Núñez Vargas, Edmar Almeida de Oliveira, Eddie Lenza, Walter A. Palacios, M. C. Peñuela, John J. Pipoly, Nigel C. A. Pitman, Adriana Prieto, Carlos Alberto Quesada, Hirma Ramírez‐Angulo, Agustín Rudas, Kalle Ruokolainen, Rafael de Paiva Salomão, Marcos Silveira, Juliana Stropp, Hans ter Steege, Raquel Thomas-Caesar, P. van der Hout, Geertje M. F. van der Heijden, P.J. van der Meer, Rodolfo Vásquez, Simone A. Vieira, Emilio Vilanova Torre, Vincent Vos, Ophelia Wang, Kenneth R. Young, Roderick Zagt, Timothy R. Baker
Software Mentions: 5
Published: almost 8 years ago
10.1098/rspb.2015.2840
Environmental drivers of crocodyliform extinction across the Jurassic/Cretaceous transitionCited by: 40
Author(s): Jonathan Tennant, Philip D. Mannion, Paul Upchurch
Software Mentions: 5
Published: over 8 years ago
10.1038/srep41393
Tree cover in Central Africa: determinants and sensitivity under contrasted scenarios of global changeCited by: 11
Author(s): Julie C. Aleman, Olivier Blarquez, Sylvie Gourlet‐Fleury, Laurent Brémond, Charly Favier
Software Mentions: 5
Published: almost 8 years ago
10.1371/journal.pone.0168441
Landscape Use and Co-Occurrence Patterns of Neotropical Spotted CatsCited by: 52
Author(s): Mariana B. Nagy‐Reis, James D. Nichols, Adriano Garcia Chiarello, Milton Cézar Ribeiro, Eleonore Zulnara Freire Setz
Software Mentions: 5
Published: almost 8 years ago
10.1371/journal.pcbi.1009256
Computational identification and experimental characterization of preferred downstream positions in human core promotersCited by: 2
Author(s): René Dreos, Anna Sloutskin, Nati Malachi, Diana Ideses, Philipp Bücher, Tamar Juven‐Gershon
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0094162
Geographic Variation of Melanisation Patterns in a Hornet Species: Genetic Differences, Climatic Pressures or Aposematic Constraints?Cited by: 39
Author(s): A. Perrard, Marcella Arca, Quentin Rome, Franck Müller, Jiang-Li Tan, Sanjaya Bista, Hari Nugroho, Raymond Baudoin, Michel Baylac, Jean François Silvain, James M. Carpenter, Claire Villemant
Software Mentions: 5
Published: over 10 years ago
10.1371/journal.ppat.1009313
Diverging patterns of introgression from Schistosoma bovis across S. haematobium African lineagesCited by: 24
Author(s): Olivier Rey, Ève Toulza, Cristian Chaparro, Jean‐François Allienne, Julien Kincaid-Smith, Eglantine Mathieu‐Bégné, Fiona Allan, David Rollinson, Bonnie L. Webster, Jérôme Boissier
Software Mentions: 5
Published: almost 4 years ago
10.1371/journal.pcbi.1008640
Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in AfricaCited by: 7
Author(s): Verena Ras, Gerrit Botha, Shaun Aron, Katie Lennard, Imane Allali, Shantelle Claassen-Weitz, Kilaza Samson Mwaikono, Dane Kennedy, Jessica R. Holmes, Gloria Rendon, Sumir Panji, Christopher J. Fields, Nicola Mulder
Software Mentions: 5
Published: over 3 years ago
10.1186/s12862-019-1479-z
Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)Cited by: 16
Author(s): Kévin Debray, Jordan Marie‐Magdelaine, Tom Ruttink, Jérémy Clotault, Fabrice Foucher, Valéry Malécot
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pcbi.1003457
Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic DataCited by: 207
Author(s): Thibaut Jombart, Anne Cori, Xavier Didelot, Simon Cauchemez, Christophe Fraser, Neil M. Ferguson
Software Mentions: 5
Published: almost 11 years ago
10.3389/fmicb.2019.02902
Exploring Soil Factors Determining Composition and Structure of the Bacterial Communities in Saline-Alkali Soils of Songnen PlainCited by: 42
Author(s): Shuang Wang, Lei Sun, Ning Ling, Chen Zhu, Fengqin Chi, Weiqun Li, Xiaoyu Hao, Wu Zhang, Jingyang Bian, Lei Chen, Dan Wei
Software Mentions: 5
Published: almost 5 years ago
10.1038/s41598-018-23292-8
Fungal spore diversity reflects substrate-specific deposition challengesCited by: 45
Author(s): Sara Calhim, Panu Halme, Jens H. Petersen, Thomas Læssøe, Claus Bässler, Jacob Heilmann‐Clausen
Software Mentions: 5
Published: over 6 years ago
10.1002/ece3.2527
Experimentally comparing the attractiveness of domestic lights to insects: Do LEDs attract fewer insects than conventional light types?Cited by: 44
Author(s): Andrew Wakefield, Moth Broyles, Emma L. Stone, Gareth Jones, Stephen Harris
Software Mentions: 5
Published: about 8 years ago
10.7717/peerj-cs.243
HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curvesCited by: 15
Author(s): Jarrett D. Phillips, Steven H. French, Robert Hanner, Daniel Gillis
Software Mentions: 5
Published: almost 5 years ago
10.1038/s41598-018-26181-2
Paddy-upland rotation for sustainable agriculture with regards to diverse soil microbial communityCited by: 31
Author(s): Ping Hou, Chia Hung Chien, Yi Fan Chiang-Hsieh, Kuan Chieh Tseng, Chi Nga Chow, Hao Huang, Wen Chi Chang
Software Mentions: 5
Published: over 6 years ago
10.3389/fmicb.2021.738129
Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of ChinaCited by: 3
Author(s): Jun Zhang, Pengcheng Xing, Mengyu Niu, Gehong Wei, Peng Shi
Software Mentions: 5
Published: about 3 years ago
10.3934/microbiol.2019.1.62
Stability of temperate coral <em>Astrangia poculata</em> microbiome is reflected across different sequencing methodologiesCited by: 5
Author(s): Dawn B. Goldsmith, Zoe A. Pratte, Christina A. Kellogg, Sara E. Snader, Koty Sharp
Software Mentions: 4
Published: almost 6 years ago
10.1002/aps3.11442
Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe MalinaeCited by: 13
Author(s): Roman Ufimov, Vojtěch Zeisek, Soňa Píšová, William J. Baker, Tomáš Fér, Marcela van Loo, Christoph Dobeš, Roswitha Schmickl
Software Mentions: 4
Published: over 3 years ago
10.31557/APJCP.2021.22.1.105
Spatial Association between Gastric Cancer Mortality and Goiter in SardiniaCited by: 5
Author(s): Giovanni Mario Pes, Giuseppe Fanciulli, Alessandro Delitala, Andrea Piana, Maria Pina Dore
Software Mentions: 4
Published: almost 4 years ago
10.1186/s12859-019-3020-1
LSX: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inferenceCited by: 3
Author(s): Carlos Rivera-Rivera, Juan I. Montoya‐Burgos
Software Mentions: 4
Published: over 5 years ago
10.1186/s12898-017-0116-1
Wild pollinators enhance oilseed rape yield in small-holder farming systems in ChinaCited by: 35
Author(s): Yi Zou, Hai Xiao, Felix J.J.A. Bianchi, Frank Jauker, Shudong Luo, Wopke Van der Werf
Software Mentions: 4
Published: over 7 years ago
10.1186/1472-6785-14-22
Causes and consequences of fine-scale population structure in a critically endangered freshwater sealCited by: 28
Author(s): Mia Valtonen, Jukka U. Palo, Jouni Aspi, Minna Ruokonen, Mervi Kunnasranta, Tommi Nyman
Software Mentions: 4
Published: almost 11 years ago
10.1186/s12898-020-00298-3
The trinity of ecological contrasts: a case study on rich insect assemblages by means of species, functional and phylogenetic diversity measuresCited by: 6
Author(s): Elia Guariento, Patrick Strutzenberger, Christine Truxa, Konrad Fiedler
Software Mentions: 4
Published: over 4 years ago
10.1186/s12862-018-1299-6
Macroevolution of sexual size dimorphism and reproduction-related phenotypic traits in lizards of the Chaco DomainCited by: 12
Author(s): Guadalupe López Juri, Margarita Chiaraviglio, Gabriela Cardozo
Software Mentions: 4
Published: almost 6 years ago
10.1186/1471-2148-12-102
Bayesian models for comparative analysis integrating phylogenetic uncertaintyCited by: 85
Author(s): Pierre de Villemereuil, Jessie A. Wells, R. E. Edwards, Simon P. Blomberg
Software Mentions: 4
Published: over 12 years ago
10.1186/1471-2148-13-272
Explosive diversification following a benthic to pelagic shift in freshwater fishesCited by: 31
Author(s): Phillip R. Hollingsworth, Andrew M. Simons, James A. Fordyce, C. Darrin Hulsey
Software Mentions: 4
Published: almost 11 years ago
10.1186/1471-2148-12-182
Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of amaryllidaceaeCited by: 101
Author(s): Nina Rønsted, Matthew R. E. Symonds, Trine Birkholm, Søren Brøgger Christensen, Alan W. Meerow, Marianne Molander, Per Mølgaard, Gitte Petersen, Nina Rasmussen, J. Van Staden, G.I. Stafford, Anna K. Jäger
Software Mentions: 4
Published: almost 13 years ago
10.1186/s12862-014-0194-z
Basal metabolic rate and maternal energetic investment durations in mammalsCited by: 9
Author(s): Gabrielle Jackson, Arne Ø. Mooers, Evgenia Dubman, Jenna Hutchen, Mark Collard
Software Mentions: 4
Published: about 10 years ago
10.1186/1471-2148-11-371
Driving south: a multi-gene phylogeny of the brown algal family Fucaceae reveals relationships and recent drivers of a marine radiationCited by: 51
Author(s): Fernando Cánovas, Catarina Mota, Ester A. Serrão, Gareth A. Pearson
Software Mentions: 4
Published: almost 14 years ago
10.1186/s12862-017-1071-3
A reconstruction of sexual modes throughout animal evolutionCited by: 20
Author(s): Daniel A. Sasson, Joseph F. Ryan
Software Mentions: 4
Published: almost 7 years ago