cran: phangorn | Projects | Ecosyste.ms: Papers

10.1186/s12864-020-07263-w

Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains
Cited by: 22
Author(s): Eva Wagner, Andreas Zaiser, Rebekka Leitner, Narciso M. Quijada, Nadja Pracser, Ariane Pietzka, Werner Ruppitsch, Stephan Schmitz‐Esser, Martin Wagner, Kathrin Rychli
Software Mentions: 4
Published: almost 4 years ago

10.1002/ece3.5032

Dissimilarity of individual microsatellite profiles under different mutation models: Empirical approach
Cited by: 12
Author(s): Evsey Kosman, Jukka Jokela
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.10572

Genomic diversity of Escherichia coli from healthy children in rural Gambia
Cited by: 7
Author(s): Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Usman N. Ikumapayi, Golam Sarwar, Catherine Okoi, Peggy-Estelle Tientcheu, Marianne Defernez, Justin O’Grady, Martín Antonio, Mark J. Pallen
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.6098

Symmetry breaking of the cellular lobes closely relates to phylogenetic structure within green microalgae of theMicrasteriaslineage (Zygnematophyceae)
Cited by: 5
Author(s): Jiří Neustupa, J. Šťastný
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2020.01981

Rumen Microbiome Composition Is Altered in Sheep Divergent in Feed Efficiency
Cited by: 62
Author(s): Steven McLoughlin, Charles Spillane, Noel A. Claffey, Pamela M. Smith, Tommy O’Rourke, M.G. Diskin, Sinéad M. Waters
Software Mentions: 4
Published: about 4 years ago

10.1038/s42003-021-02637-6

DEVOLUTION—A method for phylogenetic reconstruction of aneuploid cancers based on multiregional genotyping data
Cited by: 6
Author(s): Natalie Andersson, Subhayan Chattopadhyay, Anders Valind, Jenny Karlsson, David Gisselsson
Software Mentions: 4
Published: almost 3 years ago

10.1038/s41598-020-58398-5

Phylogenomic Perspective on a Unique Mycobacterium bovis Clade Dominating Bovine Tuberculosis Infections among Cattle and Buffalos in Northern Brazil
Cited by: 8
Author(s): Marília Lima da Conceição, Emilyn Costa Conceição, Ismari Perini Furlaneto, Sandro Patroca da Silva, Arthur Emil dos Santos Guimarães, Pedro Gomes, María Laura Boschiroli, Lorraine Michelet, Thomas A. Kohl, Katharina Kranzer, Loreno da Costa Francez, Luana Nepomuceno Gondim Costa Lima, Isabel Portugal, João Perdigão, Karla Valéria Batista Lima
Software Mentions: 4
Published: over 4 years ago

10.1111/1755-0998.12567

apex : phylogenetics with multiple genes
Cited by: 22
Author(s): Thibaut Jombart, Frederick I. Archer, Klaus Schliep, Zhian N. Kamvar, Rebecca B. Harris, Emmanuel Paradis, Jérôme Goudet, Hilmar Lapp
Software Mentions: 4
Published: about 8 years ago

10.1128/mSystems.00236-18

Using Core Genome Alignments To Assign Bacterial Species
Cited by: 51
Author(s): Matthew Chung, James B. Munro, Hervé Tettelin, Julie C. Dunning Hotopp
Software Mentions: 4
Published: almost 6 years ago

10.3390/nu13051559

Maternal Vegetable and Fruit Consumption during Pregnancy and Its Effects on Infant Gut Microbiome
Cited by: 13
Author(s): Hsien Yu Fan, Yu Tang Tung, Yu Yang, Justin Bo-Kai Hsu, Cheng Yang Lee, Tzu Hao Chang, Emily Chia Yu Su, Rong Hong Hsieh, Yang Ching Chen
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1004410

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus
Cited by: 227
Author(s): Yaniv Brandvain, Amanda M. Kenney, Lex E. Flagel, Graham Coop, Andrea L. Sweigart
Software Mentions: 4
Published: about 10 years ago

10.3389/fmicb.2021.684233

Maternal Antibiotic Treatment Disrupts the Intestinal Microbiota and Intestinal Development in Neonatal Mice
Cited by: 8
Author(s): Chung-Ming Chen, Hsiu Chu Chou, Yu Yang
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2021.716750

Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies and Genotypes
Cited by: 3
Author(s): Rahman Ebrahimzadegan, Fatemeh Orooji, Pengtao Ma, Ghader Mirzaghaderi
Software Mentions: 4
Published: about 3 years ago

10.1128/MRA.00832-19

Draft Genome Sequences of Enterococcus faecalis Strains Isolated from Healthy Japanese Individuals
Cited by: 2
Author(s): Kazuki Tanaka, Tsubasa Watabe, Koichi Kato, Tomoya Tsukimi, Mitsuhiko Sato, Toshitaka Odamaki, Masaru Tomita, Shinji Fukuda
Software Mentions: 4
Published: almost 5 years ago

10.1099/mgen.0.000543

The structure and diversity of strain-level variation in vaginal bacteria
Cited by: 8
Author(s): Brett A. Tortelli, Amanda L. Lewis, Justin C. Fay
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2019.02257

Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes
Cited by: 12
Author(s): Nico Salmaso
Software Mentions: 4
Published: almost 5 years ago

10.1002/ece3.8087

Large brain size is associated with low extra‐pair paternity across bird species
Cited by: 6
Author(s): Min Chen, Guopan Li, Jinlong Liu, Shaobin Li
Software Mentions: 4
Published: about 3 years ago

10.1099/mgen.0.000245

HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny
Cited by: 48
Author(s): Joseph Crispell, Daniel Balaz, Stephen V. Gordon
Software Mentions: 4
Published: over 5 years ago

10.1002/ece3.5984

Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era
Cited by: 5
Author(s): Shing Hei Zhan, Chun‐Chi Shih, Shao‐Lun Liu
Software Mentions: 3
Published: over 4 years ago

10.1186/s12862-015-0503-1

Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes
Cited by: 53
Author(s): Sara Ruane, Christopher J. Raxworthy, Alan R. Lemmon, Emily Moriarty Lemmon, Frank T. Burbrink
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13062-015-0073-6

Tradeoff between robustness and elaboration in carotenoid networks produces cycles of avian color diversification
Cited by: 21
Author(s): Alexander V. Badyaev, Erin S. Morrison, Virginia Belloni, Michael J. Sanderson
Software Mentions: 3
Published: about 9 years ago

10.1098/rsbl.2020.0368

Chytrid fungi shape bacterial communities on model particulate organic matter
Cited by: 11
Author(s): Cordelia Roberts, Ro Allen, Kimberley Bird, Michael Cunliffe
Software Mentions: 3
Published: about 4 years ago

10.3390/microorganisms7110576

Phylogeny of Anoxygenic Photosynthesis Based on Sequences of Photosynthetic Reaction Center Proteins and a Key Enzyme in Bacteriochlorophyll Biosynthesis, the Chlorophyllide Reductase
Cited by: 26
Author(s): Johannes F. Imhoff, Tanja Rahn, Sven Künzel, Sven C. Neulinger
Software Mentions: 3
Published: almost 5 years ago

10.3390/microorganisms9061117

Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification
Cited by: 1
Author(s): Parichate Tangkanchanapas, Annelies Haegeman, Monica Höfte, Kris De Jonghe
Software Mentions: 3
Published: over 3 years ago

10.1093/molbev/msx134

Patterns of Genome-Wide Diversity and Population Structure in the Drosophila athabasca Species Complex
Cited by: 16
Author(s): Karen Miller, Ryan Bracewell, Michael B. Eisen, Doris Bachtrog
Software Mentions: 3
Published: over 7 years ago

10.1093/molbev/msz263

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements
Cited by: 34
Author(s): Benjamin R. Karin, Tony Gamble, Todd R. Jackman
Software Mentions: 3
Published: almost 5 years ago

10.14202/vetworld.2019.909-915

Prevalence and molecular characterization of infectious bronchitis virus isolated from chicken in Bangladesh
Cited by: 9
Author(s): Zafar Ahmed Bhuiyan, Zulfekar Ali, Mohammad Moktader Moula, M Giasuddin, Zahed Uddin Mahmood Khan
Software Mentions: 3
Published: over 5 years ago

10.12688/wellcomeopenres.15333.2

Neisseria meningitidis has acquired sequences within the capsule locus by horizontal genetic transfer
Cited by: 2
Author(s): Marianne E. A. Clemence, Odile B. Harrison, Martin C. J. Maiden
Software Mentions: 3
Published: about 5 years ago

10.7717/peerj.2832

Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes
Cited by: 32
Author(s): Daniela Beißer, Nadine Graupner, Christina Böck, Sabina Wodniok, Lars Großmann, Matthijs Vos, Bernd Sures, Sven Rahmann, Jens Boenigk
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1003323

Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci
Cited by: 343
Author(s): Christopher L. Schardl, Carolyn A. Young, Uljana Hesse, Stefan G. Amyotte, Kalina Andreeva, Patrick J. Calie, Damien J. Fleetwood, David Haws, Neil Moore, Birgitt Oeser, Daniel G. Panaccione, Kathryn Schweri, Christine R. Voisey, Mark L. Farman, Jerzy W. Jaromczyk, Bruce A. Roe, Donal M. O’Sullivan, Barry Scott, Paul Tudzynski, Zhiqiang An, Elissaveta G. Arnaoudova, Charles T. Bullock, Nikki D. Charlton, Li Chen, Murray P. Cox, Randy D. Dinkins, Simona Florea, Anthony E. Glenn, Anna Gordon, Ulrich Güldener, Daniel R. Harris, Walter Hollin, Jolanta Jaromczyk, Richard D. Johnson, Anar Khan, Eckhard Leistner, Adrian Leuchtmann, Chunjie Li, Jin Ge Liu, Jinze Liu, Miao Liu, Wade J. Mace, Caroline Machado, Padmaja Nagabhyru, Juan Pan, Jan Schmid, Kazuo Sugawara, Ulrike Steiner, Johanna E. Takach, Eiji Tanaka, James D. Webb, Ella V. Wilson, Jennifer L. Wiseman, Ruriko Yoshida, Zheng Zeng
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pgen.1006632

JMJD-5/KDM8 regulates H3K36me2 and is required for late steps of homologous recombination and genome integrity
Cited by: 29
Author(s): Pier Giorgio Amendola, Nico Zaghet, João J. Ramalho, Jens Vilstrup Johansen, Mike Boxem, Anna Elisabetta Salcini
Software Mentions: 3
Published: over 7 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: about 10 years ago

10.1371/journal.pone.0189838

Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru
Cited by: 19
Author(s): Louis Grandjean, Robert H. Gilman, Tomotada Iwamoto, Claudio U. Köser, Jorge Coronel, Mirko Zimic, M. Estée Török, Diepreye Ayabina, Michaela Kendall, Christophe Fraser, Simon R. Harris, Julian Parkhill, Sharon J. Peacock, David Moore, Caroline Colijn
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0162834

A Novel Colonial Ciliate Zoothamnium ignavum sp. nov. (Ciliophora, Oligohymenophorea) and Its Ectosymbiont Candidatus Navis piranensis gen. nov., sp. nov. from Shallow-Water Wood Falls
Cited by: 28
Author(s): Lukas Schuster, Monika Bright
Software Mentions: 3
Published: almost 8 years ago

10.1093/cid/ciz905

Diarrhea as a Potential Cause and Consequence of Reduced Gut Microbial Diversity Among Undernourished Children in Peru
Cited by: 32
Author(s): Saba Rouhani, Nicholas W. Griffin, Pablo Peñataro Yori, Jeanette L. Gehrig, Maribel Paredes Olórtegui, Mery Siguas Salas, Dixner Rengifo Trigoso, Lawrence H. Moulton, Eric R. Houpt, Michael J. Barratt, Margaret Kosek, Jeffrey I. Gordon
Software Mentions: 3
Published: almost 5 years ago

10.3390/genes10060461

Diversity of “Ca. Micrarchaeota” in Two Distinct Types of Acidic Environments and Their Associations with Thermoplasmatales
Cited by: 19
Author(s): Olga V. Golyshina, Rafael Bargiela, Stepan V. Toshchakov, N. A. Chernyh, Soshila Ramayah, Aleksei A. Korzhenkov, Ilya V. Kublanov, Peter N. Golyshin
Software Mentions: 3
Published: over 5 years ago

10.1128/JCM.01945-16

The EpiQuant Framework for Computing Epidemiological Concordance of Microbial Subtyping Data
Cited by: 2
Author(s): Benjamin M. Hetman, Steven K. Mutschall, James E. Thomas, Victor P. J. Gannon, Clifford G. Clark, Frank Pollari, Eduardo N. Taboada
Software Mentions: 3
Published: over 7 years ago

10.1128/JCM.00920-20

Rapid and Sensitive Direct Detection and Identification of Poliovirus from Stool and Environmental Surveillance Samples by Use of Nanopore Sequencing
Cited by: 28
Author(s): Alexander Shaw, Manasi Majumdar, Catherine Troman, Áine O’Toole, Blossom Benny, Dilip Abraham, Ira Praharaj, Gagandeep Kang, Salman Sharif, Muhammad Masroor Alam, Shahzad Shaukat, Mehar Angez, Adnan Khurshid, Nayab Mahmood, Yasir Arshad, Lubna Rehman, Ghulam Mujtaba, Ribqa Akthar, Muhammad Salman, Dimitra Klapsa, Yara Hajarha, Humayun Asghar, Ananda S Bandyopadhyay, Andrew Rambaut, Javier Martı́n, Nicholas C Grassly
Software Mentions: 3
Published: about 4 years ago

10.1111/jeb.13074

Diversity in warning coloration is easily recognized by avian predators
Cited by: 16
Author(s): Lina María Arenas, Martin Stevens
Software Mentions: 3
Published: over 7 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/s41598-019-51511-3

Thiotrophic bacterial symbiont induces polyphenism in giant ciliate host Zoothamnium niveum
Cited by: 7
Author(s): Monika Bright, Salvador Espada‐Hinojosa, Jean-Marie Volland, Judith Drexel, Julia Kesting, I. Kolar, Denny Morchner, Andrea D. Nussbaumer, Jörg Ott, Florian Scharhauser, Lukas Schuster, Helena Constance Zambalos, H. L. Nemeschkal
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-67487-4

Immune status, and not HIV infection or exposure, drives the development of the oral microbiota
Cited by: 14
Author(s): Modupe Coker, Emmanuel F. Mongodin, Samer S. El-Kamary, Paul Akhigbe, ON Obuekwe, AI Omoigberale, Patricia Langenberg, Cyril O. Enwonwu, Lauren E. Hittle, William A. Blattner, Manhattan Charurat
Software Mentions: 3
Published: about 4 years ago

10.1186/1944-3277-9-22

Genome sequence of Coxiella burnetii strain Namibia
Cited by: 12
Author(s): Mathias C. Walter, Caroline Öhrman, Kerstin Myrtennäs, Andreas Sjödin, Mona Byström, Pär Larsson, Anna Macellaro, Mats Forsman, Dimitrios Frangoulidis
Software Mentions: 3
Published: almost 10 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: almost 11 years ago

10.1186/s12859-016-1277-1

A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation
Cited by: 39
Author(s): Hussein A. Hejase, Kevin J. Liu
Software Mentions: 2
Published: almost 8 years ago

10.3390/molecules24010015

Genome-Wide Identification and Comparative Analysis for OPT Family Genes in Panax ginseng and Eleven Flowering Plants
Cited by: 9
Author(s): He Su, Yang Chu, Junqi Bai, Lu Gong, Juan Huang, Wen Xu, Jing Zhang, Xiaohui Qiu, Jiang Xu, Zhixing Huang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12862-021-01772-2

Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference
Cited by: 7
Author(s): Jennifer L Spillane, Troy M LaPolice, Matthew D. MacManes, David C. Plachetzki
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0184017

Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions
Cited by: 39
Author(s): Cecilia Conte-Grand, Ralf Britz, Neelesh Dahanukar, Rajeev Raghavan, Rohan Pethiyagoda, Heok Hui Tan, Renny Kurnia Hadiaty, Norsham Yaakob, Lukas Rüber
Software Mentions: 2
Published: almost 7 years ago

10.1093/aobpla/plw019

Conflicting genomic signals affect phylogenetic inference in four species of North American pines
Cited by: 2
Author(s): Tomasz E. Koralewski, Mariana Mateos, Konstantin V. Krutovsky
Software Mentions: 2
Published: about 9 years ago

10.1186/s13068-018-1274-x

Characterization and genome analysis of a butanol–isopropanol-producing Clostridium beijerinckii strain BGS1
Cited by: 32
Author(s): Chen Zhang, Tinggang Li, Jianzhong He
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0168288

Generalising Ward’s Method for Use with Manhattan Distances
Cited by: 121
Author(s): Trudie Strauss, Michael von Maltitz
Software Mentions: 2
Published: over 7 years ago

10.1186/s12870-017-1195-z

Comparative analysis of inverted repeats of polypod fern (Polypodiales) plastomes reveals two hypervariable regions
Cited by: 20
Author(s): Maria D. Logacheva, A.A. Krinitsina, Maxim S. Belenikin, K. Khafizov, Е. А. Коноров, С.В. Купцов, Anna S. Speranskaya
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12866-021-02327-7

Gut microbiota changes in preeclampsia, abnormal placental growth and healthy pregnant women
Cited by: 19
Author(s): Lihui Huang, Min Cai, Li Li, Xin Zhang, Yang Xu, Jianhua Xiao, Qian Huang, Guijuan Luo, Zhaoyang Zeng, Cuiyuan Jin, Yuanxiang Jin, Jun He, Weitao Yang
Software Mentions: 2
Published: almost 3 years ago

10.1186/s12862-018-1130-4

Phylogenomics of a rapid radiation: the Australian rainbow skinks
Cited by: 25
Author(s): Jason G. Bragg, Sally Potter, Ana C. Afonso Silva, Conrad J. Hoskin, Benjamin Y H Bai, Craig Moritz
Software Mentions: 2
Published: over 6 years ago

10.3390/genes12020223

Clonal Interference and Mutation Bias in Small Bacterial Populations in Droplets
Cited by: 4
Author(s): Philip Ruelens, Allerdien Visser
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-15-162

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data
Cited by: 366
Author(s): Tae Ho Lee, Hui Guo, Xiyin Wang, Changsoo Kim, Andrew H. Paterson
Software Mentions: 2
Published: over 10 years ago

10.3390/nu13041305

Dietary Curdlan Enhances Bifidobacteria and Reduces Intestinal Inflammation in Mice
Cited by: 9
Author(s): Shafaque Rahman, Mark Davids, Patricia H. P. van Hamersveld, Olaf Welting, H. Rahaoui, Frank Schuren, Sybren L. Meijer, René M. van den Wijngaard, Theodorus B. M. Hakvoort, Wouter J. de Jonge, Sigrid E. M. Heinsbroek
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2018.00138

Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum
Cited by: 42
Author(s): Éric Duchaud, Tatiana Rochat, Christophe Habib, Paul Barbier, Valentin Loux, Cyprien Guérin, Inger Dalsgaard, Lone Madsen, Hanne Nilsen, Krister Sundell, Tom Wıklund, Nicole Strepparava, Thomas Wahli, Greta Caburlotto, Amedeo Manfrin, Gregory D. Wiens, Erina Fujiwara-Nagata, Rubén Avendaño‐Herrera, Jean‐François Bernardet, Pierre Nicolas
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2018.02149

Tracing Antibody Repertoire Evolution by Systems Phylogeny
Cited by: 25
Author(s): Alexander Yermanos, Andreas Dounas, Tanja Stadler, Annette Oxenius, Sai T. Reddy
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0148967

Circumpolar Genetic Structure and Recent Gene Flow of Polar Bears: A Reanalysis
Cited by: 51
Author(s): René M. Malenfant, Corey S. Davis, Catherine I. Cullingham, David W. Coltman
Software Mentions: 2
Published: over 8 years ago

10.3390/jof7080665

Virulence Traits and Population Genomics of the Black Yeast Aureobasidium melanogenum
Cited by: 6
Author(s): Anja Černoša, Xiaohuan Sun, Chao Fang, Nina Gunde‐Cimerman, Zewei Song
Software Mentions: 2
Published: about 3 years ago

10.1038/s41598-019-55689-4

SimpactCyan 1.0: An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces
Cited by: 6
Author(s): Jori Liesenborgs, Diana M. Hendrickx, Elise Kuylen, David Niyukuri, Niel Hens, Wim Delva
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0101755

Molecular Identification of Adult and Juvenile Linyphiid and Theridiid Spiders in Alpine Glacier Foreland Communities
Cited by: 10
Author(s): Lorna Raso, Daniela Sint, Alexander Rief, Rüdiger Kaufmann, Michael Traugott
Software Mentions: 2
Published: about 10 years ago

10.3390/v12111218

Metagenomic Approach with the NetoVIR Enrichment Protocol Reveals Virus Diversity within Ethiopian Honey Bees (Apis mellifera simensis)
Cited by: 15
Author(s): Haftom Gebremedhn, Ward Deboutte, Karel Schoonvaere, Peter Demaeght, Lina De Smet, Amssalu Bezabeh, Jelle Matthijnssens, Dirk C. de Graaf
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0162454

Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution
Cited by: 2
Author(s): Fabrícia F. Nascimento, Allen G. Rodrigo
Software Mentions: 2
Published: almost 8 years ago

10.1093/g3journal/jkaa062

Linking anthocyanin diversity, hue, and genetics in purple corn
Cited by: 18
Author(s): Laura A. Chatham, John A. Juvik
Software Mentions: 2
Published: over 3 years ago

10.1002/ece3.4092

The puzzling phylogeography of the haplochromine cichlid fish Astatotilapia burtoni
Cited by: 12
Author(s): Gaëlle Pauquet, Walter Salzburger, Bernhard Egger
Software Mentions: 1
Published: over 6 years ago

10.1016/j.dib.2016.08.015

Data on the multilocus molecular phylogenies of the Neotropical fish family Prochilodontidae (Teleostei: Characiformes)
Cited by: 3
Author(s): Benjamin W. Frable, Bruno Francelino de Melo, Brian L. Sidlauskas, Kendra Hoekzema, Richard P. Vari, Cláudio Oliveira
Software Mentions: 1
Published: almost 8 years ago

10.1155/2019/4259479

K-mer-Based Motif Analysis in Insect Species across Anopheles, Drosophila, and Glossina Genera and Its Application to Species Classification
Cited by: 5
Author(s): Mátyás Cserháti, Peng Xiao, Chittibabu Guda
Software Mentions: 1
Published: almost 5 years ago

10.1038/s42003-019-0539-7

Nested retrotransposition in the East Asian mouse genome causes the classical nonagouti mutation
Cited by: 7
Author(s): Akira Tanave, Yuji Imai, Tsuyoshi Koide
Software Mentions: 1
Published: about 5 years ago

10.1111/1462-2920.14760

Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease
Cited by: 59
Author(s): Evangelos Mourkas, Diego Florez‐Cuadrado, Ben Pascoe, Jessica K. Calland, Sion C. Bayliss, Leonardos Mageiros, Guillaume Méric, Matthew D. Hitchings, Alberto Quesada, Concepción Porrero, María Ugarte‐Ruiz, José Gutiérrez‐Fernández, Lucas Domı́nguez, Samuel K. Sheppard
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-017-4199-z

Genomic divergence and cohesion in a species of pelagic freshwater bacteria
Cited by: 14
Author(s): Matthias Hoetzinger, Martin W. Hahn
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13059-021-02467-z

Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation
Cited by: 24
Author(s): Abraham Morales‐Cruz, Jonás A. Aguirre‐Liguori, Yongfeng Zhou, Andrea Minio, Summaira Riaz, A. M. Walker, Dario Cantu
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0194908

Unmasking the complexity of species identification in Australasian flying-foxes
Cited by: 5
Author(s): Linda E. Neaves, Melissa Danks, Matthew J. Lott, Siobhan Dennison, Greta J. Frankham, Andrew King, Mark D. B. Eldridge, Rebecca N. Johnson, Anja Divljan
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0130942

Segregating the Effects of Seed Traits and Common Ancestry of Hardwood Trees on Eastern Gray Squirrel Foraging Decisions
Cited by: 25
Author(s): Mekala Sundaram, Janna R. Willoughby, Nathanael I. Lichti, Michael Steele, Robert K. Swihart
Software Mentions: 1
Published: about 9 years ago

10.1186/s12862-018-1153-x

The effects of repeated whole genome duplication events on the evolution of cytokinin signaling pathway
Cited by: 21
Author(s): Elisabeth Kaltenegger, Svetlana Leng, Alexander Heyl
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0090786

Gene Sequence Variability of the Three Surface Proteins of Human Respiratory Syncytial Virus (HRSV) in Texas
Cited by: 54
Author(s): Lorena I. Tapia, Chad A. Shaw, Letisha Aideyan, Alan M. Jewell, Brian Dawson, T. Haq, Pedro A. Piedra
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0118019

Are Differences in Genomic Data Sets due to True Biological Variants or Errors in Genome Assembly: An Example from Two Chloroplast Genomes
Cited by: 40
Author(s): Zhiqiang Wu, Luke R. Tembrock, Song Ge
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1007018

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters
Cited by: 66
Author(s): Mario López‐Pérez, José M. Haro-Moreno, Rafael Gonzalez-Serrano, Marcos Parras-Moltó, Francisco Rodrı́guez-Valera
Software Mentions: 1
Published: almost 7 years ago

10.1111/tpj.13767

Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds
Cited by: 49
Author(s): Lenka Havlíčková, Zhesi He, Lihong Wang, Swen Langer, Andrea L. Harper, Harjeevan Kaur, Martin R. Broadley, Vasilis C. Gegas, Ian Bancroft
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.2767

A large and unusually colored new snake species of the genusTantilla(Squamata; Colubridae) from the Peruvian Andes
Cited by: 3
Author(s): Claudia Koch, Pablo J. Venegas
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep17104

Elevated Extinction Rates as a Trigger for Diversification Rate Shifts: Early Amniotes as a Case Study
Cited by: 28
Author(s): Neil Brocklehurst, Marcello Ruta, Johannes Müller, Jörg Fröbisch
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-018-25474-w

Acquisition and dissemination of cephalosporin-resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis
Cited by: 54
Author(s): Christina A. Ahlstrom, Jonas Bonnedahl, Hanna Woksepp, Jorge Hernández, Björn Olsén, Andrew M. Ramey
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-29738-3

The identification of novel single nucleotide polymorphisms to assist in mapping the spread of Bacillus anthracis across the Southern Caucasus
Cited by: 6
Author(s): Mitat Şahin, Fatih Büyük, Les Baillie, Roman Wölfel, Adam Kotorashvili, Alexandra Rehn, Markus Antwerpen, Gregor Grass
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-35421-4

A Fréchet tree distance measure to compare phylogeographic spread paths across trees
Cited by: 2
Author(s): Susanne Reimering, Sebastian Muñoz, Alice C. McHardy
Software Mentions: 1
Published: almost 6 years ago

10.18632/oncotarget.18678

Mutation landscape and intra-tumor heterogeneity of two MANECs of the esophagus revealed by multi-region sequencing
Cited by: 12
Author(s): Wenqing Yuan, Zhen Liu, Wanjun Liu, Li Sun, Haijun Yang, Yu Wang, Shweta Ramdas, Xiao Dong, Ruiping Xu, Hong Cai, Jun Z. Li, Yang Ke
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.6899

Order, please! Uncertainty in the ordinal-level classification of Chlorophyceae
Cited by: 22
Author(s): Karolina Fučíková, Paul O. Lewis, Suman Neupane, Kenneth G. Karol, Louise A. Lewis
Software Mentions: 1
Published: over 5 years ago

10.1186/s40168-019-0623-8

Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity
Cited by: 47
Author(s): Aleksei A. Korzhenkov, Stepan V. Toshchakov, Rafael Bargiela, Huw Gibbard, Manuel Ferrer, A. V. Teplyuk, Davey L. Jones, Ilya V. Kublanov, Peter N. Golyshin, Olga V. Golyshina
Software Mentions: 1
Published: over 5 years ago

10.1099/mgen.0.000528

Globetrotting strangles: the unbridled national and international transmission of Streptococcus equi between horses
Cited by: 11
Author(s): Catriona Mitchell, Karen F. Steward, Amelia R. L. Charbonneau, Saoirse Walsh, Hayley Wilson, John F. Timoney, U. Wernery, Marina Joseph, David Craig, Kees van Maanen, Annelies Hoogkamer-van Gennep, Albertine Léon, Lucjan Witkowski, Magdalena Rzewuska, Ilona Stefańska, Monika Żychska, Gunther van Loon, Raymond T. Cursons, Olivia Anne Patty, Els Acke, James R. Gilkerson, Charles El-Hage, Joanne L. Allen, Hiroshi Bannai, Yuta Kinoshita, Hidekazu Niwa, Teótimo Becú, John Pringle, Bengt Guss, Reinhard Böse, Y. Abbott, Lisa Katz, Bernadette Leggett, Tom Buckley, Shlomo E. Blum, Fátima Cruz López, Ana Fernández Ros, Maria Cristina Marotti Campi, Silvia Preziuso, Carl Robinson, J. R. Newton, Ellen Schofield, Ben T Brooke, Mike Boursnell, Nicolas de Brauwere, Roxane Kirton, Charlie Barton, Khalil Abudahab, Ben Taylor, Corin Yeats, Richard Goater, David M. Aanensen, Simon R. Harris, Julian Parkhill, Matthew T. G. Holden, Andrew S. Waller
Software Mentions: 1
Published: over 3 years ago

10.1186/s12918-017-0476-3

Reconstructing evolutionary trees in parallel for massive sequences
Cited by: 13
Author(s): Quan Zou, Shixiang Wan, Xiangxiang Zeng, Zhanshan Sam
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12866-018-1250-4

Genotyping and phylogenetic placement of Bacillus anthracis isolates from Finland, a country with rare anthrax cases
Cited by: 13
Author(s): Taru Lienemann, Wolfgang Beyer, Kirsti Pelkola, Heidi Rossow, Alexandra Rehn, Markus Antwerpen, Gregor Grass
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-017-3917-x

Genome analysis of E. coli isolated from Crohn’s disease patients
Cited by: 23
Author(s): Daria V. Rakitina, Alexander I. Manolov, Alexandra Kanygina, Sofya K. Garushyants, Julia Baikova, Dmitry Alexeev, V. G. Ladygina, Elena S. Kostryukova, Andrei K. Larin, Tatiana A. Semashko, Irina Y. Karpova, Vladislav V. Babenko, Р. К. Исмагилова, Sergey Malanin, Mikhail S. Gelfand, Elena N. Ilina, Roman Gorodnichev, Eugenia S. Lisitsyna, Г И Алешкин, Petr Scherbakov, И. Л. Халиф, М. В. Шапина, И. В. Маев, D. N. Andreev, Vadim M. Govorun
Software Mentions: 1
Published: about 7 years ago

Projects: cran: phangorn

Papers Mentioning phangorn 192