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: cran: ape

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/ape

Analyses of Phylogenetics and Evolution
102 versions
Latest release: over 1 year ago
374 dependent packages
72,114 downloads last month

Papers Mentioning ape 918

10.1186/s12983-016-0141-5
How to build your dragon: scaling of muscle architecture from the world’s smallest to the world’s largest monitor lizard
Cited by: 31
Author(s): Taylor J. M. Dick, Christofer J. Clemente
Software Mentions: 4
Published: almost 9 years ago
10.1093/gbe/evy188
Genome Wide Identification of Mutational Hotspots in the Apicomplexan Parasite Neospora caninum and the Implications for Virulence
Cited by: 17
Author(s): Larissa Calarco, Joel Barratt, John Ellis
Software Mentions: 4
Published: about 6 years ago
10.1093/gbe/evz178
Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter
Cited by: 50
Author(s): Valeria Mateo-Estrada, Lucía Graña-Miraglia, Gamaliel López-Leal, Santiago Castillo-Ramírez
Software Mentions: 4
Published: over 5 years ago
10.1093/gbe/evab202
Horizontal Transfer of Microbial Toxin Genes to Gall Midge Genomes
Cited by: 7
Author(s): Kirsten I. Verster, Rebecca L. Tarnopol, Saron M. Akalu, Noah K. Whiteman
Software Mentions: 4
Published: about 3 years ago
10.1016/j.gpb.2016.06.003
Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins
Cited by: 37
Author(s): Obed Ramírez-Sánchez, Paulino Pérez‐Rodríguez, Luis Delaye, Axel Tiessen
Software Mentions: 4
Published: almost 8 years ago
10.1186/s42238-020-00036-y
A single nucleotide polymorphism assay sheds light on the extent and distribution of genetic diversity, population structure and functional basis of key traits in cultivated north American cannabis
Cited by: 12
Author(s): Philippe Henry, Surender Khatodia, Karan Kapoor, Britni Gonzales, Alexis Middleton, Kevin C. Hong, Aaron Hilyard, Steve L. Johnson, Davis Allen, Zachary Chester, Dan Jin, José Carlos Rodriguez Jule, Iain F. Wilson, Manu P. Gangola, Jason Broome, Deron Caplan, Dinesh Adhikary, Michael K. Deyholos, Michael Morgan, Oliver W. Hall, Brent J. Guppy, Cindy S. Orser
Software Mentions: 4
Published: about 4 years ago
10.1007/s10886-015-0631-5
Evolution of Cuticular Hydrocarbons in the Hymenoptera: a Meta-Analysis
Cited by: 87
Author(s): Ricarda Kather, Stephen J. Martin
Software Mentions: 4
Published: about 9 years ago
10.1128/JCM.00190-19
hicap: <i>In Silico</i> Serotyping of the Haemophilus influenzae Capsule Locus
Cited by: 30
Author(s): Stephen C. Watts, Kathryn E. Holt
Software Mentions: 4
Published: over 5 years ago
10.1111/jeb.12601
Functional constraints on the evolution of long butterfly proboscides: lessons from<scp>N</scp>eotropical skippers (<scp>L</scp>epidoptera:<scp>H</scp>esperiidae)
Cited by: 18
Author(s): Julia Bauder, Linde Morawetz, Andrew Warren, Harald W. Krenn
Software Mentions: 4
Published: over 9 years ago
10.1371/journal.ppat.1008998
Gallbladder carriage generates genetic variation and genome degradation in Salmonella Typhi
Cited by: 15
Author(s): Duy Pham Thanh, Nga Tran Vu Thieu, To Nguyen Thi Nguyen, Ho Ngoc Dan Thanh, Sabina Dongol, Abhilasha Karkey, Megan E Carey, Buddha Basnyat, Gordon Dougan, Maia A. Rabaa, Stephen Baker
Software Mentions: 4
Published: about 4 years ago
10.1098/rspb.2014.0321
Two waves of colonization straddling the K–Pg boundary formed the modern reef fish fauna
Cited by: 28
Author(s): Samantha A. Price, Lars Schmitz, Christopher E. Oufiero, Ron I. Eytan, Alex Dornburg, William L. Smith, Matt Friedman, Thomas J. Near, Peter C. Wainwright
Software Mentions: 4
Published: over 10 years ago
10.1098/rspb.2018.1473
Testing hypotheses for the function of the carnivoran baculum using finite-element analysis
Cited by: 11
Author(s): Charlotte A. Brassey, James Gardiner, Andrew C. Kitchener
Software Mentions: 4
Published: about 6 years ago
10.1098/rspb.2020.3150
Evolutionary versatility of the avian neck
Cited by: 9
Author(s): Ryan D. Marek, Peter L. Falkingham, Roger Benson, James Gardiner, Thomas W. Maddox, Karl T. Bates
Software Mentions: 4
Published: over 3 years ago
10.1098/rsos.150377
Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms
Cited by: 20
Author(s): Ronald M. Clouse, Gregorio V. Linchangco, Alexander M. Kerr, Robert W. Reid, Daniel Janies
Software Mentions: 4
Published: almost 9 years ago
10.1098/rsos.200517
Brain microRNAs among social and solitary bees
Cited by: 12
Author(s): Karen M. Kapheim, Beryl M. Jones, Eirik Søvik, Eckart Stolle, Robert M. Waterhouse, Guy Bloch, Yehuda Ben‐Shahar
Software Mentions: 4
Published: over 4 years ago
10.1126/sciadv.abe2778
The evolution of pelvic limb muscle moment arms in bird-line archosaurs
Cited by: 24
Author(s): Vivian Allen, Brandon M. Kilbourne, John R. Hutchinson
Software Mentions: 4
Published: over 3 years ago
10.1038/srep18061
Probiotic treatment reduces appetite and glucose level in the zebrafish model
Cited by: 80
Author(s): Silvia Falcinelli, Ana Rodiles, Suraj Unniappan, Simona Picchietti, Giorgia Gioacchini, Daniel L. Merrifield, Oliana Carnevali
Software Mentions: 4
Published: almost 9 years ago
10.1038/srep30115
Genomic content typifying a prevalent clade of bovine mastitis-associated Escherichia coli
Cited by: 39
Author(s): Robert Goldstone, Susan R. Harris, David George Emslie Smith
Software Mentions: 4
Published: over 8 years ago
10.1038/srep45824
Mushroom biomass and diversity are driven by different spatio-temporal scales along Mediterranean elevation gradients
Cited by: 42
Author(s): Josu G. Alday, Juán Martínez de Aragón, Sergio de-Miguel, J. A. Bonet
Software Mentions: 4
Published: over 7 years ago
10.1038/s41598-018-24120-9
Testing the impact of effective population size on speciation rates – a negative correlation or lack thereof in lichenized fungi
Cited by: 5
Author(s): Jen‐Pan Huang, Steven D. Leavitt, H. Thorsten Lumbsch
Software Mentions: 4
Published: over 6 years ago
10.1038/s41598-018-32252-1
Adjusting risk-taking to the annual cycle of long-distance migratory birds
Cited by: 21
Author(s): Peter Mikula, Mario Dı́az, Tomáš Albrecht, Jukka Jokimäki, Marja Liisa Kaisanlahti-Jokimäki, Gal Kroitero, Anders Pape Møller, Piotr Tryjanowski, Reuven Yosef, Martin Hromada
Software Mentions: 4
Published: about 6 years ago
10.1038/s41598-018-37505-7
Oral neonatal antibiotic treatment perturbs gut microbiota and aggravates central nervous system autoimmunity in Dark Agouti rats
Cited by: 27
Author(s): Suzana Stanisavljević, Aleksa Čepić, Svetlana Bojić, Katarina Veljović, Sanja Mihajlović, Neda Djedović, Bojan Jevtić, Miljana Momčilović, Milica Lazarević, Marija Mostarica Stojković, Djordje Miljković, Nataša Golić
Software Mentions: 4
Published: almost 6 years ago
10.1038/s41598-019-48296-w
Carbon assimilation profiles of mucoralean fungi show their metabolic versatility
Cited by: 17
Author(s): Julia Pawłowska, Alicja Okrasińska, Kamil Kisło, Tamara Aleksandrzak‐Piekarczyk, Katarzyna Szatraj, Somayeh Dolatabadi, Anna Muszewska
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-019-50442-3
Multiple introductions and secondary dispersion of Tubastraea spp. in the Southwestern Atlantic
Cited by: 26
Author(s): K. C. C. Capel, Joel Christopher Creed, Marcelo V. Kitahara, C. A. Chen, Carla Zilberberg
Software Mentions: 4
Published: about 5 years ago
10.1038/s41598-019-57249-2
Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae
Cited by: 12
Author(s): Sidonie Bellot, Thomas C. Mitchell, Hanno Schaefer
Software Mentions: 4
Published: almost 5 years ago
10.1038/s41598-020-68497-y
Species traits predict the aryl hydrocarbon receptor 1 (AHR1) subtypes responsible for dioxin sensitivity in birds
Cited by: 5
Author(s): Kristin Bianchini, Christy A. Morrissey
Software Mentions: 4
Published: over 4 years ago
10.1038/s41598-020-78090-y
Linear infrastructure habitats increase landscape-scale diversity of plants but not of flower-visiting insects
Cited by: 9
Author(s): Juliana Dániel‐Ferreira, Riccardo Bommarco, Jörgen Wissman, Erik Öckinger
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41598-020-80444-5
A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt
Cited by: 23
Author(s): Adrienn Tóth, István Csabai, Gergely Maróti, Ákos Jerzsele, Attila Dubecz, Árpád V. Patai, Maura Fiona Judge, Sára Ágnes Nagy, László Makrai, Krisztián Bànyai, G. Szita, Norbert Solymosi
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41598-021-81788-2
Relevance of ddRADseq method for species and population delimitation of closely related and widely distributed wolf spiders (Araneae, Lycosidae)
Cited by: 5
Author(s): Vladislav Ivanov, Yuri M. Marusik, Julien Pétillon, Marko Mutanen
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41598-021-93552-7
Electrophysiological characterization of a diverse group of sugar transporters from Trichoderma reesei
Cited by: 7
Author(s): Sami Havukainen, Jonai Pujol‐Giménez, Mari Valkonen, Ann Westerholm-Parvinen, Matthias A. Hediger, Christopher P. Landowski
Software Mentions: 4
Published: over 3 years ago
10.1038/s41598-021-95676-2
Small pigmented eukaryote assemblages of the western tropical North Atlantic around the Amazon River plume during spring discharge
Cited by: 1
Author(s): Sophie Charvet, Eun-Soo Kim, Ajit Subramaniam, Joseph P. Montoya, Solange Duhamel
Software Mentions: 4
Published: over 3 years ago
10.3390/toxins9030103
How the Cobra Got Its Flesh-Eating Venom: Cytotoxicity as a Defensive Innovation and Its Co-Evolution with Hooding, Aposematic Marking, and Spitting
Cited by: 72
Author(s): Nadya Panagides, Timothy N. W. Jackson, Maria P. Ikonomopoulou, Kevin Arbuckle, Rudolf Pretzler, Daryl C. Yang, Syed Abid Ali, Ivan Koludarov, James Dobson, Brittany Sanker, Angelique K. Asselin, Renan Castro Santana, Iwan Hendrikx, Harold van der Ploeg, Jeremie Tai-A-Pin, Romilly van den Bergh, Harald M. I. Kerkkamp, Freek J. Vonk, Arno Naude, Morné Strydom, Louis Jacobsz, Nathan Dunstan, Marc Jaeger, Wayne C. Hodgson, John J. Miles, Bryan G. Fry
Software Mentions: 4
Published: over 7 years ago
10.1128/mBio.00802-17
Evolution of the <i>Staphylococcus argenteus</i> ST2250 Clone in Northeastern Thailand Is Linked with the Acquisition of Livestock-Associated Staphylococcal Genes
Cited by: 37
Author(s): Danesh Moradigaravand, Dorota Jamrozy, Rafal Mostowy, Annaliesa S. Anderson, Emma K. Nickerson, Janjira Thaipadungpanit, Vanaporn Wuthiekanun, Direk Limmathurotsakul, Sarunporn Tandhavanant, Chanthiwa Wikraiphat, Gumphol Wongsuvan, Nittaya Teerawattanasook, Yaowaruk Jutrakul, Nuttiya Srisurat, Prajuab Chaimanee, T. Eoin West, Beth Blane, Julian Parkhill, Narisara Chantratita, Sharon J. Peacock
Software Mentions: 4
Published: about 7 years ago
10.1128/mBio.02318-20
Adaptation of Arginine Synthesis among Uropathogenic Branches of the Escherichia coli Phylogeny Reveals Adjustment to the Urinary Tract Habitat
Cited by: 11
Author(s): Michael E. Hibbing, Karen W. Dodson, Vasilios Kalas, Swaine L. Chen, Scott J. Hultgren
Software Mentions: 4
Published: about 4 years ago
10.1128/mBio.03281-20
Longitudinal Multi-omics and Microbiome Meta-analysis Identify an Asymptomatic Gingival State That Links Gingivitis, Periodontitis, and Aging
Cited by: 21
Author(s): Shi Huang, Tao He, Yue Feng, Xiang Xu, Lijiang Wang, Pengfei Zhu, Fei Teng, Zheng Sun, Xiaohui Liu, Gongchao Jing, Xiaoquan Su, Lijian Jin, Jiquan Liu, Jian Xu
Software Mentions: 4
Published: over 3 years ago
10.1128/mSphere.00550-17
Convergent Evolution Driven by Rifampin Exacerbates the Global Burden of Drug-Resistant Staphylococcus aureus
Cited by: 47
Author(s): Romain Guérillot, Anders Gonçalves da Silva, Ian R. Monk, Stefano Giulieri, Takehiro Tomita, Eloise Alison, Jessica L. Porter, Sacha J. Pidot, Wei Gao, Anton Y. Peleg, Torsten Seemann, Timothy P. Stinear, Benjamin P Howden
Software Mentions: 4
Published: over 6 years ago
10.1128/mSystems.00296-19
Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities
Cited by: 47
Author(s): Zhou Shi, Huaqun Yin, Joy D. Van Nostrand, James W. Voordeckers, Qichao Tu, Ye Deng, Mengting Yuan, Aifen Zhou, Ping Zhang, Naijia Xiao, Daliang Ning, Zhili He, Liyou Wu, Jizhong Zhou
Software Mentions: 4
Published: about 5 years ago
10.1128/mSystems.00633-21
Cross-Scale Analyses of Animal and Human Gut Microbiome Assemblies from Metacommunity to Global Landscape
Cited by: 13
Author(s): Zhanshan Sam
Software Mentions: 4
Published: about 3 years ago
10.1038/s41396-020-0694-3
Coexistence of genetically different Rhizophagus irregularis isolates induces genes involved in a putative fungal mating response
Cited by: 9
Author(s): Ivan D. Mateus, Edward C. Rojas, Romain Savary, Cindy Dupuis, Frédéric G. Masclaux, Consolée Aletti, Ian R. Sanders
Software Mentions: 4
Published: over 4 years ago
10.3390/ijerph15061146
Which Compounds Contribute Most to Elevated Soil Pollution and the Corresponding Health Risks in Floodplains in the Headwater Areas of the Central European Watershed?
Cited by: 5
Author(s): Jan Skála, Radim Vácha, Pavel Čupr
Software Mentions: 4
Published: over 6 years ago
10.1016/j.jinsphys.2017.12.005
Does plasticity in thermal tolerance trade off with inherent tolerance? The influence of setal tracheal gills on thermal tolerance and its plasticity in a group of European diving beetles
Cited by: 24
Author(s): Wilco C. E. P. Verberk, Piero Calosi, John I. Spicer, Siegfried Kehl, David T. Bilton
Software Mentions: 4
Published: over 6 years ago
10.7554/eLife.56830
Bedrock radioactivity influences the rate and spectrum of mutation
Cited by: 5
Author(s): Nathanaëlle Saclier, Patrick Chardon, Florian Malard, Lara Konecny‐Dupré, David Eme, Arnaud Bellec, Vincent Breton, Laurent Duret, Tristan Lefébure, Christophe J. Douady
Software Mentions: 4
Published: almost 4 years ago
10.7554/eLife.08904
Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals
Cited by: 57
Author(s): Alex de Mendoza, Hiroshi Suga, Joan Permanyer, Manuel Irimia, Iñaki Ruiz‐Trillo
Software Mentions: 4
Published: about 9 years ago
10.7554/eLife.56367
Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants
Cited by: 6
Author(s): Alan C. Hicks, Stephen M Kissler, Tatum D Mortimer, C Kévin, George Taiaroa, M Ashcroft, Deborah A. Williamson, Marc Lipsitch, Yonatan H. Grad
Software Mentions: 4
Published: over 4 years ago
10.18632/oncotarget.24365
New therapeutic targets for pulmonary sarcomatoid carcinomas based on their genomic and phylogenetic profiles
Cited by: 40
Author(s): Takahiro Nakagomi, Taichiro Goto, Yosuke Hirotsu, Daichi Shikata, Yujiro Yokoyama, Rumi Higuchi, Kenji Amemiya, Kenichiro Okimoto, Toshio Oyama, Hitoshi Mochizuki, Masao Omata
Software Mentions: 4
Published: almost 7 years ago
10.1186/s12862-014-0199-7
Causes of endemic radiation in the Caribbean: evidence from the historical biogeography and diversification of the butterfly genus Calisto(Nymphalidae: Satyrinae: Satyrini)
Cited by: 53
Author(s): Pável Matos‐Maraví, Rayner Núñez Águila, Carlos Peña, Jacqueline Y. Miller, Andrei Sourakov, Niklas Wahlberg
Software Mentions: 3
Published: about 10 years ago
10.1128/mSphere.00786-20
A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan
Cited by: 39
Author(s): Tsuyoshi Sekizuka, Kentaro Itokawa, Masanori Hashino, Tetsuro Kawano-Sugaya, Rina Tanaka, Koji Yatsu, Asami Ohnishi, Keiko Goto, Hiroyuki Tsukagoshi, Hayato Ehara, Kenji Sadamasu, Masakatsu Taira, Shuzo Shibata, Ryohei Nomoto, Satoshi Hiroi, Miho Toho, Tomoe Shimada, Takeshi Matsui, Tomimasa Sunagawa, Hajime Kamiya, Yuichiro Yahata, Takashi Yamagishi, Motoi Suzuki, Takaji Wakita, Makoto Kuroda
Software Mentions: 3
Published: almost 4 years ago
10.1111/jeb.13713
Environmental and morphological constraints interact to drive the evolution of communication signals in frogs
Cited by: 6
Author(s): Matías I. Muñoz, Stéphane Goutte, Jacintha Ellers, Wouter Halfwerk
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pone.0149531
Divergence Times and Phylogenetic Patterns of Sebacinales, a Highly Diverse and Widespread Fungal Lineage
Cited by: 34
Author(s): Sigisfredo Garnica, Kai Riess, Max Emil Schön, Franz Oberwinkler, Sabrina Setaro
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.ppat.1004369
Symbionts Commonly Provide Broad Spectrum Resistance to Viruses in Insects: A Comparative Analysis of Wolbachia Strains
Cited by: 220
Author(s): Julien Martinez, Ben Longdon, Simone Bauer, Yuk-Sang Chan, Wolfgang J. Miller, Kostas Bourtzis, Luı́s Teixeira, Francis M. Jiggins
Software Mentions: 3
Published: about 10 years ago
10.1371/journal.pone.0182318
Evolutionary implications of heterochromatin and rDNA in chromosome number and genome size changes during dysploidy: A case study in Reichardia genus
Cited by: 22
Author(s): Sonja Siljak‐Yakovlev, Bernard Godelle, Vlatka Zoldoš, Joan Vallès, Teresa Garnatje, Oriane Hidalgo
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0014355
Sex, Ecology and the Brain: Evolutionary Correlates of Brain Structure Volumes in Tanganyikan Cichlids
Cited by: 77
Author(s): Alejandro González-Voyer, Niclas Kolm
Software Mentions: 3
Published: almost 14 years ago
10.1371/journal.ppat.1009859
Metabolomics provide new insights into mechanisms of Wolbachia-induced paternal defects in Drosophila melanogaster
Cited by: 7
Author(s): Hua‐Bao Zhang, Zheng Cao, Jun-Xue Qiao, Zi-Qian Zhong, Chenchen Pan, Chen Liu, Limin Zhang, Yufeng Wang
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0138785
Eggshell Types and Their Evolutionary Correlation with Life-History Strategies in Squamates
Cited by: 16
Author(s): Konstantin Hallmann, Eva Maria Griebeler
Software Mentions: 3
Published: about 9 years ago
10.1038/ismej.2013.186
Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements
Cited by: 31
Author(s): Ola Brønstad Brynildsrud, Edward J. Feil, Jon Bohlin, Santiago Castillo-Ramírez, Duncan J. Colquhoun, Úna McCarthy, Iveta Matějusová, Linda D. Rhodes, Gregory D. Wiens, David W. Verner–Jeffreys
Software Mentions: 3
Published: about 11 years ago
10.1098/rspb.2018.1805
Fundamental and realized feeding niche breadths of sexual and asexual stick insects
Cited by: 6
Author(s): Chloé Larose, Darren J. Parker, Tanja Schwander
Software Mentions: 3
Published: almost 6 years ago
10.1371/journal.pone.0063570
Congruence and Diversity of Butterfly-Host Plant Associations at Higher Taxonomic Levels
Cited by: 37
Author(s): Ferrer-Paris José R., Ada Sánchez‐Mercado, Ángel L. Viloria, John S. Donaldson
Software Mentions: 3
Published: over 11 years ago
10.1371/journal.pone.0123952
Are Protected Areas Required to Maintain Functional Diversity in Human-Modified Landscapes?
Cited by: 12
Author(s): H. Eden W. Cottee-Jones, Thomas J. Matthews, Tom P. Bregman, Maan Barua, Jatin Tamuly, Robert J. Whittaker
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pone.0146537
An Integrative Approach for Understanding Diversity in the Punctelia rudecta Species Complex (Parmeliaceae, Ascomycota)
Cited by: 35
Author(s): David Alors, H. Thorsten Lumbsch, Pradeep K. Divakar, Steven D. Leavitt, Ana Crespo
Software Mentions: 3
Published: almost 9 years ago
10.1371/journal.pone.0079585
Functional Implications of Ubiquitous Semicircular Canal Non-Orthogonality in Mammals
Cited by: 74
Author(s): Jeri C Berlin, E. Christopher Kirk, Timothy Rowe
Software Mentions: 3
Published: about 11 years ago
10.1186/s12862-014-0259-z
Mitochondrial genomes of the Baltic clam Macoma balthica(Bivalvia: Tellinidae): setting the stage for studying mito-nuclear incompatibilities
Cited by: 16
Author(s): Alice Saunier, Pascale Garcia, Vanessa Becquet, Nathalie Marsaud, Frédéric Escudié, Eric Pante
Software Mentions: 3
Published: almost 10 years ago
10.1371/journal.pone.0085006
Cytochrome b Divergence between Avian Sister Species Is Linked to Generation Length and Body Mass
Cited by: 7
Author(s): Caroline Thomson, James D. J. Gilbert, M. de L. Brooke
Software Mentions: 3
Published: almost 11 years ago
10.1371/journal.pone.0075029
High Genetic Diversity and Distinctiveness of Rear-Edge Climate Relicts Maintained by Ancient Tetraploidisation for Alnus glutinosa
Cited by: 44
Author(s): Olivier Lepais, Serge Müller, Samia Ben Saad-Limam, Mohamed Benslama, Laïla Rhazi, Djamila Belouahem-Abed, Amina Daoud-Bouattour, Amor Mokhtar Gammar, Zeineb Ghrabi-Gammar, Cecile F. E. Bacles
Software Mentions: 3
Published: about 11 years ago
10.1371/journal.pone.0070501
Phylogenetic Relationships and Species Delimitation in Pinus Section Trifoliae Inferrred from Plastid DNA
Cited by: 78
Author(s): Sergio Hernández-León, David S. Gernandt, Jorge A. Pérez de la Rosa, Lev Jardón Barbolla
Software Mentions: 3
Published: over 11 years ago
10.1098/rsos.201195
Dinosaur diversification rates were not in decline prior to the K-Pg boundary
Cited by: 10
Author(s): Joseph A. Bonsor, Paul M. Barrett, Thomas J. Raven, Natalie Cooper
Software Mentions: 3
Published: about 4 years ago
10.1186/s12977-019-0510-1
Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study
Cited by: 10
Author(s): Hanwei Sudderuddin, Natalie N. Kinloch, Steven Jin, Rachel L. Miller, Bradley R. Jones, Chanson J. Brumme, Jeffrey B. Joy, Mark A. Brockman, Zabrina L. Brumme
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12284-020-00417-0
Natural Diversity in Stomatal Features of Cultivated and Wild Oryza Species
Cited by: 13
Author(s): Jolly Chatterjee, Vivek Thakur, Robert A. Nepomuceno, Robert A. Coe, Jacqueline Dionora, Abigail Elmido-Mabilangan, Abraham Darius Llave, Anna Mae Delos Reyes, Apollo Neil Monroy, Irma Canicosa, Anindya Bandyopadhyay, Kshirod K. Jena, D. S. Brar, W. Paul Quick
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0203762
A genome size and phylogenetic survey of Mediterranean Tripleurospermum and Matricaria (Anthemideae, Asteraceae)
Cited by: 11
Author(s): Hüseyin İnceer, Teresa Garnatje, Sema Hayırlıoğlu-Ayaz, Joan Pere Pascual-Díaz, Joan Vallès, Sònia Garcia
Software Mentions: 3
Published: about 6 years ago
10.1371/journal.pone.0041307
Genome-Wide Characterization of Genetic Variation in the Unicellular, Green Alga Chlamydomonas reinhardtii
Cited by: 20
Author(s): Hyo Sik Jang, Ian M. Ehrenreich
Software Mentions: 3
Published: over 12 years ago
10.1371/journal.pntd.0005731
The sero-epidemiology of Rift Valley fever in people in the Lake Victoria Basin of western Kenya
Cited by: 26
Author(s): Elizabeth A. J. Cook, Elysse N. Grossi-Soyster, William A. de Glanville, Lian F. Thomas, Samuel Kariuki, Barend Mark de Clare Bronsvoort, C. N. Wamae, A. Desirée LaBeaud, Eric M. Fèvre
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pntd.0002738
Contrasting Patterns in Mammal–Bacteria Coevolution: Bartonella and Leptospira in Bats and Rodents
Cited by: 72
Author(s): Bonnie R. Lei, Kevin J. Olival
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pgen.1003763
Dynamics of DNA Methylation in Recent Human and Great Ape Evolution
Cited by: 128
Author(s): Irene Hernando-Herraez, Javier Prado-Martinez, Paras Garg, Marcos Fernández-Callejo, Holger Heyn, Christina Hvilsom, Arcadi Navarro, Manel Esteller, Andrew J. Sharp, Tomàs Marquès‐Bonet
Software Mentions: 3
Published: about 11 years ago
10.1371/journal.pgen.1008313
RPW8/HR repeats control NLR activation in Arabidopsis thaliana
Cited by: 51
Author(s): Cristina A. Barragan, Rui Wu, Sang‐Tae Kim, Wanyan Xi, Anette Habring, Jörg Hagmann, Anna-Lena Van de Weyer, Maricris Zaidem, William Wing Ho Ho, George Wang, Ilja Bezrukov, Detlef Weigel, Eunyoung Chae
Software Mentions: 3
Published: over 5 years ago
10.1038/srep11021
Signal honesty and predation risk among a closely related group of aposematic species
Cited by: 50
Author(s): Lina María Arenas, Dominic Walter, Martin Stevens
Software Mentions: 3
Published: over 9 years ago
10.1038/srep14337
A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation
Cited by: 10
Author(s): Wenguang Shao, Min Zhang, Henry H N Lam, S. S. Lau
Software Mentions: 3
Published: about 9 years ago
10.1038/srep22908
In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River
Cited by: 51
Author(s): Matthew Cannon, James Hester, Amanda Shalkhauser, E. Ricky Chan, Kyle Logue, Scott T. Small, David Serre
Software Mentions: 3
Published: over 8 years ago
10.1038/srep26337
Mucosal adherent bacterial dysbiosis in patients with colorectal adenomas
Cited by: 142
Author(s): Yingying Lǚ, Jing Chen, Jun-Yuan Zheng, Guoyong Hu, Jingjing Wang, Chen Huang, Lihong Lou, Xingpeng Wang, Yue Zeng
Software Mentions: 3
Published: over 8 years ago
10.1038/srep27392
Transcriptional reprogramming and phenotypic switching associated with the adaptation of Lactobacillus plantarum C2 to plant niches
Cited by: 31
Author(s): Pasquale Filannino, Raffaella Di Cagno, Carmine Crecchio, Caterina De Virgilio, Maria De Angelis, Marco Gobbetti
Software Mentions: 3
Published: over 8 years ago
10.1111/jfb.13195
Do method and species lifestyle affect measures of maximum metabolic rate in fishes?
Cited by: 59
Author(s): Shaun S. Killen, Tommy Norin, Lewis G. Halsey
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pgen.1004462
Clonal Architecture of Secondary Acute Myeloid Leukemia Defined by Single-Cell Sequencing
Cited by: 114
Author(s): Andrew Hughes, Vincent Magrini, Ryan Demeter, Christopher A. Miller, Robert S. Fulton, Lucinda L. Fulton, William Eades, Kevin Elliott, Sharon E. Heath, Peter Westervelt, Ding Li, Donald F. Conrad, Brian S. White, Jin Shao, Daniel C. Link, John F. DiPersio, Elaine R. Mardis, Richard K. Wilson, Timothy J. Ley, Matthew J. Walter, Timothy A. Graubert
Software Mentions: 3
Published: over 10 years ago
10.1038/srep43095
The scaling and allometry of organ size associated with miniaturization in insects: A case study for Coleoptera and Hymenoptera
Cited by: 47
Author(s): Alexey A. Polilov, Anastasia A. Makarova
Software Mentions: 3
Published: over 7 years ago
10.1186/s12862-018-1289-8
Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data
Cited by: 10
Author(s): Ondine Filippi‐Codaccioni, Marie-Pauline Beugin, Damien M. de Vienne, Elodie Portanier, David Fouchet, Cécile Kaerle, Lina Muselet, Guillaume Queney, Éric Petit, Corinne Régis, Jean-Baptiste Pons, Dominique Pontier
Software Mentions: 3
Published: about 6 years ago
10.1371/journal.pgen.1009170
Culture-free genome-wide locus sequence typing (GLST) provides new perspectives on Trypanosoma cruzi dispersal and infection complexity
Cited by: 5
Author(s): Philipp Schwabl, Jalil Maiguashca Sánchez, Jaime A. Costales, Sofía Ocaña-Mayorga, Maikell Segovia, Hernán J. Carrasco, Carolina Hernández, Juan David Ramírez, Michael D. Lewis, Mario J. Grijalva, Martin S. Llewellyn
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-017-05306-z
Tree functional types simplify forest carbon stock estimates induced by carbon concentration variations among species in a subtropical area
Cited by: 17
Author(s): Wenhua Xiang, Wenhua Xiang, Xi Fang, Pifeng Lei, Shuai Ouyang, Xiaomin Deng
Software Mentions: 3
Published: over 7 years ago
10.1038/s41598-017-05147-w
Dietary lipid content reorganizes gut microbiota and probiotic L. rhamnosus attenuates obesity and enhances catabolic hormonal milieu in zebrafish
Cited by: 70
Author(s): Silvia Falcinelli, Ana Rodiles, Azadeh Hatef, Simona Picchietti, Lina Cossignani, Daniel L. Merrifield, Suraj Unniappan, Oliana Carnevali
Software Mentions: 3
Published: over 7 years ago
10.1038/s41598-017-06938-x
Fungal root symbionts of high-altitude vascular plants in the Himalayas
Cited by: 47
Author(s): Milan Kotilínek, Inga Hiiesalu, Jiří Košnar, Marie Šmilauerová, Petr Šmilauer, Jan Altman, Miroslav Dvorský, Martin Kopecký, Jiří Doležal
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pbio.3001185
Signatures of optimal codon usage in metabolic genes inform budding yeast ecology
Cited by: 18
Author(s): Abigail L. LaBella, Dana A. Opulente, Jacob L. Steenwyk, Chris Todd Hittinger, Antonis Rokas
Software Mentions: 3
Published: over 3 years ago
10.3390/plants9121687
Genome Size Evolution and Dynamics in Iris, with Special Focus on the Section Oncocyclus
Cited by: 2
Author(s): Nour Abdel Samad, Oriane Hidalgo, Élie Saliba, Sonja Siljak‐Yakovlev, Kit Strange, Ilia J. Leitch, Magda Bou Dagher Kharrat
Software Mentions: 3
Published: almost 4 years ago
10.3897/phytokeys.171.55397
Taxonomic updates in Amphitecna (Bignoniaceae): A new Mexican species and the re-establishment of the giant-leaved A. megalophylla
Cited by: 2
Author(s): Héctor Gómez‐Domínguez, Andrés Ernesto Ortiz-Rodríguez, Delfilia Velasco-Espino, Rene Hernández-Burguete
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-017-16810-7
Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering
Cited by: 78
Author(s): Richard G. J. Hodel, Shichao Chen, Adam C. Payton, Stuart F. McDaniel, Pamela S. Soltis, Douglas E. Soltis
Software Mentions: 3
Published: almost 7 years ago
10.1038/s41598-018-19153-z
Bacterial and Fungal Community Composition and Functional Activity Associated with Lake Wetland Water Level Gradients
Cited by: 37
Author(s): Yi Ma, LI Jinqian, Juan Wu, Zhaochen Kong, Larry M. Feinstein, Xia Ding, Gang Ge, Lang Wu
Software Mentions: 3
Published: almost 7 years ago
10.1038/s41598-018-19269-2
Efficient isolation on Vero.DogSLAMtag cells and full genome characterization of Dolphin Morbillivirus (DMV) by next generation sequencing
Cited by: 10
Author(s): Simone Peletto, Claudio Caruso, Francesco Cerutti, Paola Modesto, Cristina Biolatti, Alessandra Pautasso, Carla Grattarola, Federica Giorda, Sandro Mazzariol, Walter Mignone, Loretta Masoero, Cristina Casalone, Pier Luigi Acutis
Software Mentions: 3
Published: almost 7 years ago
10.1038/s41598-018-21188-1
Phylogenetic and environmental components of inter-specific variability in the antioxidant defense system in freshwater anomurans Aegla (Crustacea, Decapoda)
Cited by: 7
Author(s): Samuel Coelho Faria, Roberta Daniele Klein, Patrícia Gomes Costa, Marcelo Schüler Crivellaro, Sandro Santos, Sérgio Luiz de Siqueira Bueno, Adalto Bianchini
Software Mentions: 3
Published: almost 7 years ago
10.1016/j.jhep.2018.06.009
Mutational landscape of a chemically-induced mouse model of liver cancer
Cited by: 92
Author(s): Frances Connor, Tim Rayner, Sarah J. Aitken, Christine Feig, Margus Lukk, Javier Santoyo-López, Duncan T. Odom
Software Mentions: 3
Published: about 6 years ago
10.1038/s41598-018-35925-z
Endogenous toxins and the coupling of gregariousness to conspicuousness in Argidae and Pergidae sawflies
Cited by: 5
Author(s): Jean‐Luc Boevé, Tommi Nyman, Akihiko Shinohara, Stefan Schmidt
Software Mentions: 3
Published: almost 6 years ago
10.7717/peerj.2384
Evolution of the climatic tolerance and postglacial range changes of the most primitive orchids (Apostasioideae) within Sundaland, Wallacea and Sahul
Cited by: 4
Author(s): Marta Kolanowska, Katarzyna Mystkowska, Marta Kras, Magdalena Dudek, Kamil Konowalik
Software Mentions: 3
Published: about 8 years ago
10.7717/peerj.3200
Rates of morphological evolution in Captorhinidae: an adaptive radiation of Permian herbivores
Cited by: 18
Author(s): Neil Brocklehurst
Software Mentions: 3
Published: over 7 years ago
10.7717/peerj.1769
Analyzing the proximity to cover in a landscape of fear: a new approach applied to fine-scale habitat use by rabbits facing feral cat predation on Kerguelen archipelago
Cited by: 6
Author(s): Pierrick Blanchard, Christine Lauzeral, Simon Chamaillé‐Jammes, Nigel G. Yoccoz, Dominique Pontier
Software Mentions: 3
Published: over 8 years ago
10.1038/s41598-019-42793-8
Insight into the microbial world of Bemisia tabaci cryptic species complex and its relationships with its host
Cited by: 19
Author(s): Hua-Ling Wang, Teng Lei, Wei Xia, Stephen L. Cameron, Yin-Quan Liu, Zhen Zhang, Maruthi Midatharahally Narase Gowda, Paul De Barro, Jesús Navas‐Castillo, Christopher Omongo, Hélène Delatte, Kyeong-Yeoll Lee, Mitulkumar V. Patel, Renate Krause‐Sakate, Jillian Ng, Sanling Wu, Elvira Fiallo‐Olivé, Shu‐Sheng Liu, John Colvin, Xiaowei Wang
Software Mentions: 3
Published: over 5 years ago
10.7717/peerj.5067
Horizontally transferred genes in the ctenophore<i>Mnemiopsis leidyi</i>
Cited by: 7
Author(s): Alexandra M. Hernandez, Joseph F. Ryan
Software Mentions: 3
Published: over 6 years ago