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: kmer

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

Fast K-Mer Counting and Clustering for Biological Sequence Analysis
6 versions
Latest release: over 5 years ago
4 dependent packages
518 downloads last month

Papers Mentioning kmer 240

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
10.7717/peerj.11376
ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses
Cited by: 4
Author(s): Natasha Pavlovikj, João Carlos Gomes-Neto, Jitender S. Deogun, Andrew K. Benson
Software Mentions: 12
Published: over 3 years ago
10.1002/ece3.6594
A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses
Cited by: 36
Author(s): Devon O’Rourke, Nicholas A. Bokulich, Michelle A. Jusino, Matthew D. MacManes, Jeffrey T. Foster
Software Mentions: 10
Published: over 4 years ago
10.1371/journal.pcbi.1008918
Genome-wide analysis of lncRNA stability in human
Cited by: 17
Author(s): Kaiwen Shi, Tao Liu, Hanjiang Fu, Wuju Li, Xiaofei Zheng
Software Mentions: 9
Published: over 3 years ago
10.7554/eLife.36495
Firefly genomes illuminate parallel origins of bioluminescence in beetles
Cited by: 95
Author(s): Timothy R. Fallon, Sarah E. Lower, Ching-Ho Chang, Manabu Bessho-Uehara, Gavin J. Martin, Adam J. Bewick, Megan G Behringer, Humberto Julio Debat, Isaac Wong, John C. Day, Anton Suvorov, Christian J. Silva, Kathrin F. Stanger‐Hall, David W. Hall, Robert J. Schmitz, David R. Nelson, Sara M. Lewis, Shuji Shigenobu, Seth Bybee, Amanda M. Larracuente, Yuichi Oba, Jing‐Ke Weng
Software Mentions: 8
Published: about 6 years ago
10.1111/1755-0998.13187
A de novo chromosome‐level genome assembly of<i>Coregonus</i>sp. “<i>Balchen</i>”: One representative of the Swiss Alpine whitefish radiation
Cited by: 25
Author(s): Rishi De‐Kayne, Stefan Zoller, Philine G. D. Feulner
Software Mentions: 8
Published: over 4 years ago
10.1371/journal.pbio.2004830
Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species
Cited by: 73
Author(s): Reuben W. Nowell, Pedro Almeida, Christopher G. Wilson, Thomas P. Smith, Diego Fontaneto, Alastair Crisp, Gos Micklem, Alan Tunnacliffe, Chiara Boschetti, Timothy G. Barraclough
Software Mentions: 8
Published: over 6 years ago
10.1186/s12864-020-6764-0
Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum
Cited by: 15
Author(s): Alice B. Dennis, Gabriel I. Ballesteros, Stéphanie Robin, Lukas Schrader, Jens Bast, Jan Berghöfer, Leo W. Beukeboom, Maya Belghazi, Anthony Bretaudeau, Jan Buellesbach, Elizabeth Cash, Dominique Colinet, Zoé Dumas, Mohammed Errbii, Patrizia Falabella, Jean‐Luc Gatti, Elzemiek Geuverink, Joshua D. Gibson, Corinne Hertaeg, Stefanie Hartmann, Emmanuelle Jacquin‐Joly, Mark Lammers, Blas I. Lavandero, Ina Lindenbaum, Lauriane Massardier-Galatà, Camille Meslin, Nicolas Montagné, Nina Pak, Marylène Poirié, Rosanna Salvia, Chris R. Smith, Denis Tagu, Sophie Tarès, Heiko Vogel, Tanja Schwander, Jean Simon, Christian C. Figueroa, Christoph Vorburger, Fabrice Legeai, Jürgen Gadau
Software Mentions: 8
Published: over 4 years ago
10.1002/evl3.110
Comparative genomics of 10 new<i>Caenorhabditis</i>species
Cited by: 105
Author(s): Lewis Stevens, Marie‐Anne Félix, Toni Beltran, Christian Braendle, Carlos Caurcel, Sarah Fausett, David Fitch, Lise Frézal, Charlie Gosse, Taniya Kaur, Karin Kiontke, Matthew D. Newton, Luke M. Noble, Aurélien Richaud, Matthew V. Rockman, Walter Sudhaus, Mark Blaxter
Software Mentions: 8
Published: over 5 years ago
10.1098/rstb.2019.0086
Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes
Cited by: 22
Author(s): David M. Needham, Camille Poirier, Elisabeth Hehenberger, Valeria Jiménez, Jarred Swalwell, Alyson E. Santoro, Alexandra Z. Worden
Software Mentions: 7
Published: about 5 years ago
10.1038/s41598-018-26592-1
Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan
Cited by: 13
Author(s): Radek Šindelka, Pavel Abaffy, Yanyan Qu, Silvie Tománková, Monika Šídová, Ravindra Naraine, Michal Kolář, Elizabeth H. Peuchen, Liangliang Sun, Norman J. Dovic̀hi, Mikael Kubista
Software Mentions: 7
Published: over 6 years ago
10.1186/s12864-021-07489-2
Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture
Cited by: 5
Author(s): Alex Rajewski, Derreck Carter-House, Jason E. Stajich, Amy Litt
Software Mentions: 7
Published: over 3 years ago
10.1111/mec.15287
Landscape drivers of genomic diversity and divergence in woodland Eucalyptus
Cited by: 29
Author(s): Kevin Murray, Jasmine K. Janes, Ashley Jones, Helen M. Bothwell, Rose L. Andrew, Justin O. Borevitz
Software Mentions: 7
Published: about 5 years ago
10.3390/microorganisms9051060
Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America
Cited by: 42
Author(s): Keisha Harrison, Chris Curtin
Software Mentions: 6
Published: over 3 years ago
10.3390/microorganisms7120595
Dynamic Succession of Microbiota during Ensiling of Whole Plant Corn Following Inoculation with Lactobacillus buchneri and Lactobacillus hilgardii Alone or in Combination
Cited by: 40
Author(s): Pascal Drouin, Julien Tremblay, Frédérique Chaucheyras‐Durand
Software Mentions: 6
Published: about 5 years ago
10.1099/mgen.0.000064
In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages
Cited by: 95
Author(s): Danielle J. Ingle, Mary Valcanis, Alex Kuzevski, Marija Tauschek, Michael Inouye, Timothy P. Stinear, Myron M. Levine, Roy M. Robins-Browne, Kathryn E. Holt
Software Mentions: 6
Published: over 8 years ago
10.1186/s13321-016-0146-2
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions
Cited by: 36
Author(s): Jie Dong, Zhi‐Jiang Yao, Ming Wen, Min Zhu, Ningning Wang, Hongyu Miao, Aiping Lu, Wenbin Zeng, Dong‐Sheng Cao
Software Mentions: 6
Published: over 8 years ago
10.1186/s12864-021-07526-0
Transcriptional profiling of identified neurons in leech
Cited by: 6
Author(s): Elizabeth A. C. Heath‐Heckman, Shinja Yoo, Christopher J. Winchell, Maurizio Pellegrino, James D. Angstadt, Veronica B. Lammardo, Diana M. Bautista, Francisco F. De‐Miguel, David A. Weisblat
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pntd.0008018
Using affinity propagation clustering for identifying bacterial clades and subclades with whole-genome sequences of Francisella tularensis
Cited by: 5
Author(s): Anne Busch, Timo Homeier‐Bachmann, Mostafa Y. Abdel-Glil, Anja Hackbart, Helmut Hotzel, Herbert Tomaso
Software Mentions: 6
Published: about 4 years ago
10.1186/s12915-019-0713-x
Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi
Cited by: 31
Author(s): Yuanning Li, Michael G. Tassia, Damien S. Waits, Viktoria E. Bogantes, Kyle T. David, Kenneth M. Halanych
Software Mentions: 6
Published: about 5 years ago
10.1128/AEM.01285-16
Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis
Cited by: 46
Author(s): Sagar M. Utturkar, W. Nathan Cude, Michael S. Robeson, Zamin K. Yang, Dawn M. Klingeman, Miriam Land, S. L. Allman, Tse-Yuan S. Lu, Steven D. Brown, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz, Dale A. Pelletier
Software Mentions: 6
Published: about 8 years ago
10.1371/journal.pbio.3000241
Islands of retroelements are major components of Drosophila centromeres
Cited by: 117
Author(s): Ching-Ho Chang, Ankita Chavan, Jason Palladino, Xiaolu Wei, Nuno M. C. Martins, Bryce Santinello, Chin-Chi Chen, Jelena Erceg, Brian J. Beliveau, Chao-ting Wu, Amanda M. Larracuente, Barbara G. Mellone
Software Mentions: 6
Published: over 5 years ago
10.1186/s12915-021-01010-7
Engineered sex ratio distortion by X-shredding in the global agricultural pest Ceratitis capitata
Cited by: 22
Author(s): Angela Meccariello, Flávia Krsticevic, Rita Colonna, Giuseppe Del Corsano, Barbara Fasulo, Philippos Aris Papathanos, Nikolai Windbichler
Software Mentions: 6
Published: over 3 years ago
10.1080/19490976.2021.1900995
Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment
Cited by: 21
Author(s): Kang Kang, Lejla Imamovic, Maria-Anna Misiakou, Maria Bornakke Sørensen, Yoshitaro Heshiki, Yueqiong Ni, Tingting Zheng, Jun Li, Mostafa Mostafa Hashim Ellabaan, Marta Colomer-Lluch, Anne A Rode, Peter Bytzer, Gianni Panagiotou, Morten Otto Alexander Sommer
Software Mentions: 6
Published: almost 4 years ago
10.1128/mBio.01442-21
Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship
Cited by: 9
Author(s): Candice L. Swift, Katherine Louie, Benjamin P. Bowen, Casey A. Hooker, Kevin Solomon, Vasanth Singan, Chris Daum, Christa Pennacchio, Kerrie Barry, V. Shutthanandan, James E. Evans, Igor V. Grigoriev, Trent Northen, Michelle O’Malley
Software Mentions: 5
Published: about 3 years ago
10.1186/s12864-020-6517-0
Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci
Cited by: 2
Author(s): Simon Renny‐Byfield, Andy Baumgarten
Software Mentions: 5
Published: almost 5 years ago
10.7717/peerj.12198
Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets
Cited by: 16
Author(s): Nicholas D. Youngblut, Ruth E. Ley
Software Mentions: 5
Published: about 3 years ago
10.3389/fmicb.2020.00308
Characterization of the Gut Microbiota of the Antarctic Heart Urchin (Spatangoida) Abatus agassizii
Cited by: 13
Author(s): Guillaume Schwob, Léa Cabrol, Élie Poulin, Julieta Orlando
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.pgen.1008566
The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants
Cited by: 54
Author(s): Takashi Akagi, Kenta Shirasawa, Hideki Nagasaki, Hideki Hirakawa, Ryutaro Tao, Luca Comai, Isabelle Henry
Software Mentions: 5
Published: almost 5 years ago
10.3389/fmicb.2019.01429
Microbial Diversity in Bulk and Rhizosphere Soil of Ranunculus glacialis Along a High-Alpine Altitudinal Gradient
Cited by: 72
Author(s): Nadine Praeg, Harald Pauli, Paul Illmer
Software Mentions: 5
Published: over 5 years ago
10.3390/plants10091870
The Arabinogalactan Protein Family of Centaurium erythraea Rafn
Cited by: 3
Author(s): Danijela M. Paunović, Katarina Ćuković, Milica Bogdanović, Slaðana Todorović, Milana Trifunović‐Momčilov, Angelina Subotić, Ana Simonović, Milan Dragićević
Software Mentions: 5
Published: about 3 years ago
10.1371/journal.pone.0034560
Skip the Alignment: Degenerate, Multiplex Primer and Probe Design Using K-mer Matching Instead of Alignments
Cited by: 37
Author(s): David Hysom, Pejman Naraghi-Arani, Maher Elsheikh, A.C. Carrillo, Peter Williams, Shea N. Gardner
Software Mentions: 5
Published: over 12 years ago
10.1186/s12859-021-04006-w
Comparative analysis and prediction of nucleosome positioning using integrative feature representation and machine learning algorithms
Cited by: 3
Author(s): Guoqing Han, Qi Li, Ying Li
Software Mentions: 5
Published: over 3 years ago
10.1186/s13742-016-0134-5
Genome sequence of the olive tree, Olea europaea
Cited by: 158
Author(s): Fernando Cruz, Irene Julca, Jèssica Gómez-Garrido, Damian Loska, Marina Marcet‐Houben, Emilio Cano, Beatriz Galán, Leonor Frías, Paolo Ribeca, Sophia Derdak, Marta Gut, Manuel Sánchez-Fernández, José Luis Garcı́a, Pablo Vargas, Tyler Alioto, Toni Gabaldón
Software Mentions: 5
Published: over 8 years ago
10.1038/sdata.2016.131
De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens
Cited by: 28
Author(s): Daniel Blande, Pauliina Halimaa, Arja Tervahauta, Mark G. M. Aarts, Sirpa Kärenlampi
Software Mentions: 5
Published: almost 8 years ago
10.3389/fgene.2019.00826
Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing
Cited by: 27
Author(s): Stephen R. Doyle, Geetha Sankaranarayanan, Fiona Allan, Duncan Berger, Pablo David Jimenez Castro, James B. Collins, Thomas Crellen, María A. Duque-Correa, Peter Ellis, Tegegn G. Jaleta, Roz Laing, Kirsty Maitland, Catherine McCarthy, Tchonfienet Moundai, Ben Softley, Elizabeth A. Thiele, Philippe Tchindebet Ouakou, John Vianney Tushabe, Joanne P. Webster, Adam Weiss, James B. Lok, Eileen Devaney, Ray M. Kaplan, James A. Cotton, Matthew Berriman, Nancy Holroyd
Software Mentions: 4
Published: about 5 years ago
10.3390/pathogens10050555
Microeukaryotic Communities on the Fruit of Gardenia thunbergia Thunb. with a Focus on Pathogenic Fungi
Cited by: 0
Author(s): Bastian Steudel, Himansu Baijnath, Thorben Schwedt, Armin O. Schmitt
Software Mentions: 4
Published: over 3 years ago
10.1038/s41396-020-0635-1
Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming
Cited by: 6
Author(s): Ruonan Wu, Benli Chai, James R. Cole, Santosh Gunturu, Xue Guo, Renmao Tian, Ji‐Dong Gu, Jizhong Zhou, James M. Tiedje
Software Mentions: 4
Published: over 4 years ago
10.1186/s40168-018-0603-4
A comparative study of the gut microbiota in immune-mediated inflammatory diseases—does a common dysbiosis exist?
Cited by: 238
Author(s): Jessica D. Forbes, Chih-Yu Chen, Natalie Knox, Ruth Ann Marrie, Hani El-Gabalawy, Teresa de Kievit, Michelle J. Alfa, Çharles N. Bernstein, Gary Van Domselaar
Software Mentions: 4
Published: almost 6 years ago
10.1186/s12864-017-4294-1
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes
Cited by: 44
Author(s): Bhavya Papudeshi, John M. Haggerty, Michael P. Doane, Megan M. Morris, Kevin Walsh, Douglas T. Beattie, Dnyanada Pande, Parisa Zaeri, Genivaldo G. Z. Silva, Fabiano L. Thompson, Robert A. Edwards, Elizabeth A. Dinsdale
Software Mentions: 4
Published: almost 7 years ago
10.1371/journal.pone.0094447
Analysis of the Salivary Gland Transcriptome of Frankliniella occidentalis
Cited by: 69
Author(s): Candice A. Stafford-Banks, Dorith Rotenberg, Brian R. Johnson, Anna E. Whitfield, Diane E. Ullman
Software Mentions: 4
Published: over 10 years ago
10.1099/mgen.0.000531
Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods
Cited by: 20
Author(s): Bert Bogaerts, Stéphanie Nouws, Bavo Verhaegen, Sarah Denayer, Julien Van Braekel, Raf Winand, Qiang Fu, Florence Crombé, Denis Piérard, Kathleen Marchal, Nancy Roosens, Sigrid C. J. De Keersmaecker, Kevin Vanneste
Software Mentions: 4
Published: over 3 years ago
10.1002/ece3.5965
Draft genome of the famous ornamental plant <i>Paeonia suffruticosa</i>
Cited by: 31
Author(s): Shuzuo Lv, Shu Cheng, Zhanying Wang, Shiming Li, Xin Jin, Lei Lan, Bing Yang, Kun Yu, Xiliang Ni, Ning Li, Xiaogai Hou, Gang Huang, Jie Wang, Yang Dong, Erqiang Wang, Jun Huang, Gengyun Zhang, Zhang Can-jun
Software Mentions: 4
Published: over 4 years ago
10.3389/fpls.2018.00902
Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence
Cited by: 74
Author(s): Gloria Torres-Cortés, Sophie Bonneau, Olivier Bouchez, Clémence Genthon, Martial Briand, Marie‐Agnès Jacques, Matthieu Barret
Software Mentions: 4
Published: over 6 years ago
10.1093/gbe/evz158
Geography Shapes the Population Genomics of Salmonella enterica Dublin
Cited by: 19
Author(s): Gavin Fenske, Anil J. Thachil, Patrick L. McDonough, Amy L. Glaser, Joy Scaria
Software Mentions: 4
Published: over 5 years ago
10.1186/s13059-016-1145-3
Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
Cited by: 539
Author(s): Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, Patrice Bâa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamás Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldón, Anna Jordan, Irene Julca, Graeme J. Kettles, Krissana Kowitwanich, Dominique Lavenier, Paolo Lenzi, Sara López-Gomollón, Damian Loska, Daniel Mapleson, Florian Maumus, Simon Moxon, Daniel D. Price, Akiko Sugio, Manuella van Munster, Marilyne Uzest, Darren Waite, Georg Jander, Denis Tagu, Alex C. C. Wilson, Cock van Oosterhout, David Swarbreck, Saskia A. Hogenhout
Software Mentions: 4
Published: almost 8 years ago
10.1186/s12859-017-1881-8
K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity
Cited by: 14
Author(s): Chang Sik Kim, Martyn Winn, Vipin Sachdeva, Kirk E. Jordan
Software Mentions: 4
Published: about 7 years ago
10.1186/s12864-021-07897-4
A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses
Cited by: 4
Author(s): Jun Fan, Yaoxin Jiang, Wenxuan Wang, Changyi Xiao, Ruiyi Lin, Tingting Xie, Wing‐Kin Sung, Shijun Li, Ivan Jakovlić, Jianhai Chen, Xiaoyong Du
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0174930
Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater
Cited by: 24
Author(s): William B. Ludington, Thaddeus D. Seher, Olin Applegate, Xunde Li, J.I. Kliegman, Charles Langelier, Edward R. Atwill, Thomas Harter, Joseph L. DeRisi
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.pone.0200423
Analytical “bake-off” of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis
Cited by: 6
Author(s): Daria V. Zhernakova, Sergei Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Pavel Dobrynin, Andrey A. Yurchenko, Valentin Shimansky, Irina V. Shcherbakova, Andrey S. Glotov, David Valle, Minzhong Tang, Emilia Shin, Kathleen B. Schwarz, Stephen J. O’Brien
Software Mentions: 4
Published: over 6 years ago
10.1186/s12711-021-00668-5
A near complete genome for goat genetic and genomic research
Cited by: 11
Author(s): Ran Li, Peng Yang, Xuelei Dai, Hojjat Asadollahpour Nanaei, Wenwen Fang, Zhirui Yang, Yi Cai, Zhuqing Zheng, Xihong Wang, Yu Jiang
Software Mentions: 4
Published: about 3 years ago
10.1093/bib/bbz020
New approaches for metagenome assembly with short reads
Cited by: 113
Author(s): Martin Ayling, Matthew D. Clark, Richard M. Leggett
Software Mentions: 4
Published: over 5 years ago
10.1186/s12864-020-6672-3
De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly
Cited by: 19
Author(s): Anthony Bayega, Haïg Djambazian, Konstantina T. Tsoumani, Maria‐Eleni Gregoriou, Efthimia Sagri, Elena Drosopoulou, Penelope Mavragani-Tsipidou, Kristina Giorda, George Tsiamis, Kostas Bourtzis, Spyridon Oikonomopoulos, Ken Dewar, Deanna M. Church, Alexie Papanicolaou, Kostas D. Mathiopoulos, Jiannis Ragoussis
Software Mentions: 4
Published: over 4 years ago
10.3389/fmicb.2016.00603
Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity
Cited by: 22
Author(s): Beverly E. Flood, Palmer Fliss, Daniel S. Jones, Gregory J. Dick, Sunit Jain, Anne‐Kristin Kaster, Matthias Winkel, Marc Mußmann, Jake V. Bailey
Software Mentions: 4
Published: over 8 years ago
10.1186/1471-2164-14-87
The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus
Cited by: 8
Author(s): Emanuel Heitlinger, Stephen Bridgett, Anna Montazam, Horst Taraschewski, Mark Blaxter
Software Mentions: 4
Published: almost 12 years ago
10.3389/fmicb.2020.531404
Cross Inoculation of Rumen Fluid to Improve Dry Matter Disappearance and Its Effect on Bacterial Composition Using an in vitro Batch Culture Model
Cited by: 2
Author(s): Katie McDermott, Michael R. F. Lee, Kenneth J. McDowall, H.M.R. Greathead
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pgen.1007807
Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay
Cited by: 79
Author(s): Michael J. Roach, Daniel L. Johnson, Jöerg Bohlmann, H. J. J. Van Vuuren, Steven J.M. Jones, Isak S. Pretorius, Simon A. Schmidt, Anthony R. Borneman
Software Mentions: 4
Published: about 6 years ago
10.7717/peerj.6293
Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota
Cited by: 9
Author(s): Kim De Paepe, Joran Verspreet, Mohammad Naser Rezaei, Silvia Hidalgo Martinez, Filip J. R. Meysman, Davy Van de Walle, Koen Dewettinck, Jeroen Raes, Tom Van de Wiele
Software Mentions: 4
Published: almost 6 years ago
10.1371/journal.pone.0145031
Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing
Cited by: 27
Author(s): Margaret Staton, Teodora Best, Sudhir Khodwekar, Sandra A. Owusu, Tao Xu, Yi Xu, Tara Jennings, Richard Cronn, Aru K. Arumuganathan, Mark V. Coggeshall, Oliver Gailing, Haiying Liang, Jeanne Romero‐Severson, Scott E. Schlarbaum, John E. Carlson
Software Mentions: 4
Published: almost 9 years ago
10.7554/eLife.26580
Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
Cited by: 56
Author(s): Feiqiao Brian Yu, Paul C. Blainey, Frederik Schulz, Tanja Woyke, Mark Horowitz, Stephen R. Quake
Software Mentions: 4
Published: over 7 years ago
10.3389/fpls.2020.567249
Molecular Mechanism Underlying Derepressed Male Production in Hexaploid Persimmon
Cited by: 7
Author(s): Kanae Masuda, Naoko Fujita, Ho Wen Yang, Koichiro Ushijima, Yasutaka Kubo, Ryutaro Tao, Takashi Akagi
Software Mentions: 4
Published: almost 4 years ago
10.1093/molbev/msab096
Novelty and Convergence in Adaptation to Whole Genome Duplication
Cited by: 20
Author(s): Magdalena Bohutínská, Mark Alston, Patrick J. Monnahan, Terezie Mandáková, Sian Bray, Pirita Paajanen, Filip Kolář, Levi Yant
Software Mentions: 4
Published: over 3 years ago
10.3389/fimmu.2020.583013
Accurate and Efficient KIR Gene and Haplotype Inference From Genome Sequencing Reads With Novel K-mer Signatures
Cited by: 10
Author(s): David Roe, Rui Kuang
Software Mentions: 4
Published: almost 4 years ago
10.3390/ijms19092483
IDP–CRF: Intrinsically Disordered Protein/Region Identification Based on Conditional Random Fields
Cited by: 18
Author(s): Yumeng Liu, Xiaolong Wang, Bin Liu
Software Mentions: 4
Published: over 6 years ago
10.1186/s12864-017-4075-x
Analysis of the genome sequence of Phomopsis longicolla: a fungal pathogen causing Phomopsis seed decay in soybean
Cited by: 21
Author(s): Shuxian Li, Omar Darwish, Nadim W. Alkharouf, Bryan Musungu, Benjamin F. Matthews
Software Mentions: 3
Published: about 7 years ago
10.12688/f1000research.10443.1
ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services
Cited by: 7
Author(s): Espen Mikal Robertsen, Hubert Denise, Alex L. Mitchell, Alex Bateman, Lars Ailo Bongo, Nils Peder Willassen
Software Mentions: 3
Published: almost 8 years ago
10.1038/s41598-020-61992-2
Tumor fitness, immune exhaustion and clinical outcomes: impact of immune checkpoint inhibitors
Cited by: 5
Author(s): Adrian Bubie, Edgar Gonzalez-Kozlova, Nicholas K. Akers, Augusto Villanueva, Bojan Losic
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-020-79143-y
Microbial community composition in the rhizosphere of Larix decidua under different light regimes with additional focus on methane cycling microorganisms
Cited by: 17
Author(s): Nadine Praeg, Paul Illmer
Software Mentions: 3
Published: almost 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
10.1186/s12859-017-1561-8
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach
Cited by: 153
Author(s): Xiaoyong Pan, Hong‐Bin Shen
Software Mentions: 3
Published: over 7 years ago
10.1186/s40168-021-01059-0
Identifying biases and their potential solutions in human microbiome studies
Cited by: 60
Author(s): Jacob T. Nearing, A. Comeau, Morgan G. I. Langille
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-018-23641-7
Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol
Cited by: 43
Author(s): Joseph A. Russell, Brittany Campos, Jennifer Stone, Erik M. Blosser, Nathan D. Burkett‐Cadena, Jonathan L. Jacobs
Software Mentions: 3
Published: over 6 years ago
10.1038/srep33782
The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae
Cited by: 22
Author(s): Jamal S. M. Sabir, Robert K. Jansen, Dhivya Arasappan, Virginie Calderon, Emmanuel Noutahi, Chunfang Zheng, Seongjun Park, Meshaal J. Sabir, Mohammed N. Baeshen, Nahid H. Hajrah, Mohammad A. Khiyami, Nabih A. Baeshen, Abdullah Y. Obaid, Abdulrahman L. Al-Malki, David Sankoff, Nadia El-Mabrouk, Tracey A. Ruhlman
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pgen.1008647
A fly model establishes distinct mechanisms for synthetic CRISPR/Cas9 sex distorters
Cited by: 35
Author(s): Barbara Fasulo, Angela Meccariello, Maya Morgan, Carl Borufka, Philippos Aris Papathanos, Nikolai Windbichler
Software Mentions: 3
Published: over 4 years ago
10.1186/s12859-019-2999-7
IRESpy: an XGBoost model for prediction of internal ribosome entry sites
Cited by: 40
Author(s): Junhui Wang, Michael Gribskov
Software Mentions: 3
Published: over 5 years ago
10.1038/s42003-021-02559-3
Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing
Cited by: 63
Author(s): Caroline Belser, Franc-Christophe Baurens, Benjamin Noël, Guillaume Martin, Corinne Cruaud, Benjamin Istace, Nabila Yahiaoui, Karine Labadie, Eva Hřibová, Jaroslav Doležel, Arnaud Lemainque, Patrick Wincker, Angélique D’Hont, Jean‐Marc Aury
Software Mentions: 3
Published: about 3 years ago
10.1038/s41598-018-19430-x
Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)
Cited by: 9
Author(s): Iria Fernandez‐Silva, James Henderson, Luiz A. Rocha, W. Brian Simison
Software Mentions: 3
Published: almost 7 years ago
10.1155/2015/292950
Challenges of the Unknown: Clinical Application of Microbial Metagenomics
Cited by: 14
Author(s): Graham Rose, David Wooldridge, Catherine Anscombe, Edward T. Mee, Raju Misra, Saheer E. Gharbia
Software Mentions: 3
Published: almost 10 years ago
10.1371/journal.pone.0222271
ViraMiner: Deep learning on raw DNA sequences for identifying viral genomes in human samples
Cited by: 79
Author(s): Ardi Tampuu, Zurab Bzhalava, Joakim Dillner, Rául Vicente
Software Mentions: 3
Published: about 5 years ago
10.1371/journal.pone.0027121
Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage
Cited by: 27
Author(s): Patrick J. Biggs, Paul Fearnhead, Grant S. Hotter, Vathsala Mohan, Julie Collins-Emerson, Errol Kwan, Thomas E. Besser, Adrian L. Cookson, Philip E. Carter, Nigel P. French
Software Mentions: 3
Published: about 13 years ago
10.1093/gigascience/giz007
Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden
Cited by: 36
Author(s): Huan Liu, Jinpu Wei, Ting Yang, Weixue Mu, Bo Song, Tuo Yang, Yuan Fang, Xuebing Wang, Guohai Hu, Wangsheng Li, Hong Zhou, Xiaoli Chen, Hongyun Chen, Lei Cheng, Xiao Shun He, Hechen Cai, Xianchu Cai, Mei Wang, Yang Li, Sunil Kumar Sahu, Jing Yang, Yu Wang, Ranchang Mu, Jie Liu, Jianming Zhao, Ziheng Huang, Xun Xu, Xin Liu
Software Mentions: 3
Published: almost 6 years ago
10.1186/1471-2164-9-551
Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays
Cited by: 10
Author(s): Katerina Kechris, Jean Yee Hwa Yang, Ru-Fang Yeh
Software Mentions: 3
Published: almost 17 years ago
10.1371/journal.pone.0200323
Consensus assessment of the contamination level of publicly available cyanobacterial genomes
Cited by: 38
Author(s): Luc Cornet, Loïc Meunier, Mick Van Vlierberghe, Raphaël R. Léonard, Benoit Durieu, Yannick Lara, Agnieszka Misztak, Damien Sirjacobs, Emmanuelle Javaux, Hervé Piégay, Annick Wilmotte, Denis Baurain
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pcbi.1003711
Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
Cited by: 421
Author(s): Mahmoud Ghandi, Dongwon Lee, M. Mohammad-Noori, M Beer
Software Mentions: 3
Published: over 10 years ago
10.1186/s13059-019-1643-1
bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes
Cited by: 60
Author(s): Matthew Z. DeMaere, Aaron E. Darling
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0116955
Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform
Cited by: 262
Author(s): Lucas Sinclair, Omneya Ahmed Osman, Stefan Bertilsson, Alexander Eiler
Software Mentions: 3
Published: almost 10 years ago
10.1186/s13059-014-0558-0
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data
Cited by: 40
Author(s): Lynnette Fernández-Cuesta, Ruping Sun, Roopika Menon, Julie George, Susanne Lorenz, Leonardo A. Meza‐Zepeda, Martin Peifer, Dennis Plenker, Johannes M. Heuckmann, Frauke Leenders, Thomas Zander, Ilona Dahmen, Mirjam Koker, Jakob Schöttle, Roland T. Ullrich, Janine Altmüller, Christian Becker, Peter Nürnberg, Henrik Seidel, Diana Böhm, Friederike Göke, Sascha Ansén, Prudence A. Russell, Gavin Wright, Zoe Wainer, Benjamin Solomon, Iver Petersen, Joachim H. Clement, Jörg Sänger, O.T. Brustugun, Åslaug Helland, Steinar Solberg, Marius Lund‐Iversen, Reinhard Buettner, Jürgen Wolf, Élisabeth Brambilla, Martin Vingron, Sven Perner, Stefan A. Haas, Roman K. Thomas
Software Mentions: 3
Published: almost 10 years ago
10.1186/s13059-020-02134-9
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Cited by: 637
Author(s): Arang Rhie, Brian P. Walenz, Sergey Koren, Adam M. Phillippy
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pone.0060058
Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs
Cited by: 26
Author(s): Richard M. Leggett, Ricardo H. Ramírez-González, Walter Verweij, Cintia Goulart Kawashima, Zamin Iqbal, Jonathan D. G. Jones, Mario Cáccamo, Dan MacLean
Software Mentions: 3
Published: over 11 years ago
10.1371/journal.pcbi.1007894
Predicting host taxonomic information from viral genomes: A comparison of feature representations
Cited by: 29
Author(s): Francesca Young, Simon Rogers, David L. Robertson
Software Mentions: 3
Published: over 4 years ago
10.1016/j.cell.2011.11.065
Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer
Cited by: 292
Author(s): Elizabeth P. Murchison, Ole Schulz-Trieglaff, Zemin Ning, Ludmil B. Alexandrov, Markus Bauer, Beiyuan Fu, Matthew M. Hims, Zhihao Ding, Sergii Ivakhno, Caitlin M. Stewart, Bee Ling Ng, Wendy S. W. Wong, Bronwen Aken, Simon White, Amber E. Alsop, Jennifer Becq, Graham R. Bignell, R. Keira Cheetham, William Cheng, Thomas R. Connor, A.J. Cox, Zhiping Feng, Yong Gu, Russell Grocock, Simon R. Harris, Irina Khrebtukova, Zoya Kingsbury, Mark Kowarsky, Alexandre Kreiss, Shujun Luo, John Marshall, David J. McBride, Lisa Murray, Anne-Maree Pearse, Keiran Raine, Isabelle Rasolonjatovo, Richard J. Shaw, Philip Tedder, Carolyn Tregidgo, Albert J. Vilella, David C. Wedge, Gregory M. Woods, Niall Gormley, Sean Humphray, Gary P. Schroth, Geoffrey Smith, Kevin P. Hall, Stephen M. J. Searle, Nigel P. Carter, Anthony T. Papenfuss, P. Andrew Futreal, Peter J. Campbell, Fengtang Yang, David Bentley, Dirk Evers, Michael R. Stratton
Software Mentions: 3
Published: almost 13 years ago
10.1186/s13059-020-02200-2
Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
Cited by: 36
Author(s): Daniel R. Utter, Gary G. Borisy, A. Murat Eren, Colleen M. Cavanaugh, Jessica L. Mark Welch
Software Mentions: 3
Published: almost 4 years ago
10.3389/fmicb.2021.644487
Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences
Cited by: 8
Author(s): Michał Ziemski, Treepop Wisanwanichthan, Nicholas A. Bokulich, Benjamin Kaehler
Software Mentions: 3
Published: over 3 years ago
10.1186/s12866-020-01759-x
The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection
Cited by: 23
Author(s): Harris Onywera, Anna‐Lise Williamson, Luca Cozzuto, Sarah Bonnin, Zizipho Z. A. Mbulawa, David Coetzee, Julia Ponomarenko, Tracy L. Meiring
Software Mentions: 3
Published: over 4 years ago
10.7717/peerj.9973
Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams
Cited by: 15
Author(s): Susheel Bhanu Busi, Paraskevi Pramateftaki, Jade Brandani, Stilianos Fodelianakis, Hannes Peter, Rashi Halder, Paul Wilmes, Tom J. Battin
Software Mentions: 3
Published: about 4 years ago
10.7717/peerj.10813
6mA-Pred: identifying DNA N6-methyladenine sites based on deep learning
Cited by: 10
Author(s): Qianfei Huang, Wenyang Zhou, Fei Guo, Lei Xu, Lichao Zhang
Software Mentions: 3
Published: almost 4 years ago
10.7717/peerj.3571
Clinical streptococcal isolates, distinct from<i>Streptococcus pneumoniae,</i>but containing the β-glucosyltransferase<i>tts</i>gene and expressing serotype 37 capsular polysaccharide
Cited by: 11
Author(s): Carmen Sheppard, Georgia Kapatai, Karen Broughton, Ulf Schaefer, Matthew J. Hannah, David Litt, Norman K. Fry
Software Mentions: 3
Published: over 7 years ago
10.7717/peerj.4073
Detection of bacterial contaminants and hybrid sequences in the genome of the kelp <i>Saccharina japonica</i> using Taxoblast
Cited by: 19
Author(s): Simon M. Dittami, Matthieu Le Corre
Software Mentions: 3
Published: about 7 years ago
10.3389/fmicb.2015.00674
Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes
Cited by: 45
Author(s): Jatta Saarenheimo, Marja Tiirola, Antti J. Rissanen
Software Mentions: 3
Published: over 9 years ago
10.1111/1755-0998.12240
Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome <i>c</i> oxidase subunit 1 (<scp>COI</scp>) <scp>DNA</scp> barcode sequences using a naïve Bayesian classifier
Cited by: 48
Author(s): Teresita M. Porter, Joel F. Gibson, Shadi Shokralla, Donald J. Baird, G. Brian Golding, Mehrdad Hajibabaei
Software Mentions: 3
Published: over 10 years ago