cran: ape | Projects | Ecosyste.ms: Papers

10.3390/ijms22063251

Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes
Cited 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 isolates
Cited by: 61
Author(s): Arun Gonzales Decano, Tim Downing
Software Mentions: 30
Published: about 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 Adenocarcinoma
Cited by: 9
Author(s): Jun-Ze Liang, Xiaoling Liang, Liye Zhong, Chutian Wu, Jing Zhang, Yang Wang
Software Mentions: 30
Published: almost 4 years ago

10.3389/fmicb.2018.01474

Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current
Cited 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 colonization
Cited by: 29
Author(s): Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard
Software Mentions: 27
Published: over 6 years ago

10.1371/journal.pone.0243927

A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences
Cited 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 colordistance
Cited by: 49
Author(s): Hannah Weller, Mark W. Westneat
Software Mentions: 23
Published: almost 6 years ago

10.1038/s41396-020-00814-9

Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere
Cited 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 Québec
Cited 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 Nodes
Cited by: 6
Author(s): Tina Begum, Marc Robinson‐Rechavi
Software Mentions: 22
Published: about 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 infections
Cited 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 Pipeline
Cited 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 Banks
Cited 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 plesiosaurians
Cited 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 Signatures
Cited 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 selection
Cited 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 Africa
Cited by: 7
Author(s): Zhongning Zhao, Neil Heideman, Phillip Armand Bester, Adriaan Jordaan, Margaretha D. Hofmeyr
Software Mentions: 18
Published: about 4 years ago

10.1371/journal.pone.0194899

Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in Mali
Cited 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 bryophytes
Cited 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 Toxoplasma
Cited 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 Species
Cited 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 Italy
Cited 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 bats
Cited 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 complex
Cited 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 Visualization
Cited by: 2
Author(s): Zhaoyuan Wei, Jiahe Sun, Qinhui Li, Ting Yao, Haiyue Zeng, Yi Wang
Software Mentions: 16
Published: over 3 years ago

10.1038/s41598-017-11514-4

Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles
Cited 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 thuringiensis
Cited 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 bryophytes
Cited by: 28
Author(s): Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
Software Mentions: 16
Published: over 6 years ago

10.1038/s41597-019-0344-7

A global database for metacommunity ecology, integrating species, traits, environment and space
Cited 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 mammals
Cited 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 Cameroonians
Cited 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 Microbiome
Cited 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 Savanna
Cited 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 Phenotypes
Cited 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 approach
Cited 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 Transfaunation
Cited 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 schrenkianum
Cited 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 sugarcane
Cited by: 23
Author(s): Nam V. Hoang, Agnelo Furtado, Angela O'Keeffe, Frederik C. Botha, Robert J. Henry
Software Mentions: 15
Published: over 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 Genus
Cited 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 oncology
Cited 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 Paternity
Cited 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 Study
Cited 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 microbiota
Cited 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 winery
Cited 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 types
Cited 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: about 4 years ago

10.1186/1471-2105-13-133

Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling
Cited 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 System
Cited 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 phylogeny
Cited 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 relatives
Cited 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 evolution
Cited 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 genomics
Cited 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: almost 8 years ago

10.3390/tropicalmed5020064

Disease Ecology of Rickettsial Species: A Data Science Approach
Cited 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 Colitis
Cited 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: over 4 years ago

10.7554/eLife.67784

Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe
Cited 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 barnacles
Cited 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 genes
Cited 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)species
Cited 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: almost 5 years ago

10.1093/molbev/msaa128

Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression
Cited 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 patterns
Cited 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 joint
Cited by: 6
Author(s): Matthew Wysocki, Z. Jack Tseng
Software Mentions: 12
Published: over 6 years ago

10.1371/journal.pone.0184652

The evolution of Lachancea thermotolerans is driven by geographical determination, anthropisation and flux between different ecosystems
Cited 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 Cohorts
Cited 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 oeni
Cited by: 9
Author(s): Ingrid Collombel, Chrats Melkonian, Douwe Molenaar, Francisco M. Campos, Tim Hogg
Software Mentions: 12
Published: about 5 years ago

10.1186/s12862-016-0661-9

Breeding system, shell size and age at sexual maturity affect sperm length in stylommatophoran gastropods
Cited 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 considerations
Cited 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 Challenges
Cited 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: almost 6 years ago

10.1371/journal.pcbi.1005404

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
Cited by: 437
Author(s): Zachary Foster, Thomas J. Sharpton, Niklaus J. Grünwald
Software Mentions: 12
Published: almost 8 years ago

10.1128/mBio.02782-18

Fitness Cost of Aflatoxin Production in Aspergillus flavus When Competing with Soil Microbes Could Maintain Balancing Selection
Cited 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 Drosophila
Cited 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 Europe
Cited 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 GenBank
Cited 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 vectors
Cited 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 rainforests
Cited 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 Wheat
Cited 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 Beetles
Cited 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 orders
Cited 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 history
Cited 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 content
Cited 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 event
Cited 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 Interactome
Cited 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 Proteins
Cited 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 genomes
Cited 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 sediments
Cited 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 models
Cited 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 scales
Cited 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 Features
Cited 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 bats
Cited 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: about 5 years ago

10.1371/journal.pone.0144779

Identifying Centres of Plant Biodiversity in South Australia
Cited 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 Bacteria
Cited 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 Tomato
Cited 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 data
Cited 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: almost 8 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 Hosts
Cited 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 Indonesia
Cited 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 avifauna
Cited by: 11
Author(s): Ian J. Ausprey
Software Mentions: 10
Published: over 3 years ago

Projects: cran: ape

Papers Mentioning ape 918