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

10.12688/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
10.1186/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
10.3389/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
10.3389/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
10.1186/1944-3277-10-15
Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S
Cited by: 19
Author(s): Tobias Goris, Bastian Hornung, Thomas Kruse, Anika Reinhold, Martin Westermann, Peter J. Schaap, Hauke Smidt, Gabriele Diekert
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0053516
Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach
Cited by: 108
Author(s): Alexander Eiler, Stina Drakare, Stefan Bertilsson, Jakob Pernthaler, Sari Peura, Carina Rofner, Karel Šimek, Yang Yang, Petr Znachor, Eva S. Lindström
Software Mentions: 2
Published: almost 12 years ago
10.7717/peerj.5798
Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities
Cited by: 19
Author(s): Ella T. Sieradzki, Jed A. Fuhrman, Sara Rivero‐Calle, Laura Gómez‐Consarnau
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0151214
Comparative Genomic Analysis of Sulfurospirillum cavolei MES Reconstructed from the Metagenome of an Electrosynthetic Microbiome
Cited by: 20
Author(s): Daniel E. Ross, C. W. Marshall, Harold D. May, R. Sean Norman
Software Mentions: 2
Published: over 8 years ago
10.1038/s41598-019-50076-5
Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence
Cited by: 14
Author(s): Pamela Gan, Ayako Tsushima, Ryoko Hiroyama, Mari Narusaka, Yoshitaka Takano, Yoshihiro Narusaka, Mitsuo Kawaradani, Ulrike Damm, Ken Shirasu
Software Mentions: 2
Published: about 5 years ago
10.1038/srep08988
The vaginal microbiome during pregnancy and the postpartum period in a European population
Cited by: 381
Author(s): David A. MacIntyre, Manju Chandiramani, Yun Sok Lee, Lindsay Kindinger, Ann Smith, Nicos Angelopoulos, Benjamin Lehne, S. Arulkumaran, Richard Brown, Tiong Ghee Teoh, Elaine Holmes, Jeremy K. Nicoholson, Julian R. Marchesi, Phillip R. Bennett
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0134435
Formal Comment to Pettengill: The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence
Cited by: 2
Author(s): Mark Achtman, Zhemin Zhou, Xavier Didelot
Software Mentions: 2
Published: over 9 years ago
10.3389/fgene.2020.00760
EnACP: An Ensemble Learning Model for Identification of Anticancer Peptides
Cited by: 20
Author(s): Ruiquan Ge, Guanwen Feng, Xiaoyang Jing, Renfeng Zhang, Pu Wang, Qing Wu
Software Mentions: 2
Published: over 4 years ago
10.1186/s43008-021-00072-0
Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation
Cited by: 20
Author(s): Ole Christian Hagestad, L.W. Hou, Jeanette H. Andersen, Espen Hansen, Bjørn Altermark, Li Chun, Eric Kuhnert, Russell J. Cox, Pedro W. Crous, Joseph W. Spatafora, Kathleen Lail, Mojgan Amirebrahimi, Anna Lipzen, Jasmyn Pangilinan, William Andreopoulos, Richard H. Hayes, Vivian Ng, Igor V. Grigoriev, Stephen A. Jackson, Thomas D.S. Sutton, Alan D. W. Dobson, Teppo Rämä
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2013.00288
Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics
Cited by: 134
Author(s): Richard M. Leggett, Ricardo H. Ramírez-González, Bernardo Clavijo, Darren Waite, Robert P. Davey
Software Mentions: 2
Published: almost 12 years ago
10.1186/s12864-019-6172-5
Are personalities genetically determined? Inferences from subsocial spiders
Cited by: 11
Author(s): Jessica Purcell, Jonathan N. Pruitt
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12859-016-1031-8
ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data
Cited by: 16
Author(s): Navin Rustagi, Oliver A. Hampton, Jie Li, Xi Liu, Richard A. Gibbs, Sharon E. Plon, Marek Kimmel, David A. Wheeler
Software Mentions: 2
Published: over 8 years ago
10.1186/1756-0500-7-488
Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers
Cited by: 27
Author(s): Shorash Amin, Peter J. Prentis, Edward K. Gilding, Ana Pavasovic
Software Mentions: 2
Published: over 10 years ago
10.1093/gigascience/giy029
Improving draft genome contiguity with reference-derived in silico mate-pair libraries
Cited by: 18
Author(s): José Horacio Grau, Thomas Hackl, Klaus‐Peter Koepfli, Michael Hofreiter
Software Mentions: 2
Published: over 6 years ago
10.1093/bioinformatics/btv120
IVA: accurate <i>de novo</i> assembly of RNA virus genomes
Cited by: 169
Author(s): Martin Hunt, Astrid Gall, Swee Hoe Ong, Jacqui Brener, Bridget Ferns, Philip Goulder, Eleni Nastouli, Jacqueline A. Keane, Paul Kellam, Thomas D. Otto
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0095599
The Genome Sequence of a Widespread Apex Predator, the Golden Eagle (Aquila chrysaetos)
Cited by: 46
Author(s): Jacqueline Doyle, Todd E. Katzner, Peter H. Bloom, Yanzhu Ji, Bhagya K. Wijayawardena, J. Andrew DeWoody
Software Mentions: 2
Published: over 10 years ago
10.3389/fgene.2019.00643
Depletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear (Ursus maritimus)
Cited by: 20
Author(s): Ashley Byrne, Megan A. Supple, Roger Volden, Kristin L. Laidre, Beth Shapiro, Christopher Vollmers
Software Mentions: 2
Published: over 5 years ago
10.1186/s12859-018-2243-x
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers
Cited by: 73
Author(s): Lauren Coombe, Jessica Zhang, Benjamin P. Vandervalk, Justin Chu, Shaun D. Jackman, İnanç Birol, René L. Warren
Software Mentions: 2
Published: over 6 years ago
10.3389/fmicb.2021.726847
The Hidden Genomic Diversity, Specialized Metabolite Capacity, and Revised Taxonomy of Burkholderia Sensu Lato
Cited by: 11
Author(s): Alex J. Mullins, Eshwar Mahenthiralingam
Software Mentions: 2
Published: about 3 years ago
10.1186/s13073-019-0654-6
Evolving neoantigen profiles in colorectal cancers with DNA repair defects
Cited by: 36
Author(s): Giuseppe Rospo, Annalisa Lorenzato, Nabil Amirouchene-Angelozzi, Alessandro Magrì, Carlotta Cancelliere, Giorgio Corti, Carola Negrino, Vito Amodio, Monica Montone, Alice Bartolini, Ludovic Barault, Luca Novara, Claudio Isella, Enzo Medico, Andrea Bertotti, Livio Trusolino, Giovanni Germano, Federica Di Nicolantonio, Alberto Bardelli
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0112420
Transcriptomic Analysis of the Mussel Elliptio complanata Identifies Candidate Stress-Response Genes and an Abundance of Novel or Noncoding Transcripts
Cited by: 14
Author(s): Robert S. Cornman, Laura S. Robertson, Heather S. Galbraith, Carrie J. Blakeslee
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pone.0210538
Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles
Cited by: 24
Author(s): Antoine Pagé, Julien Tremblay, Luke Masson, Charles W. Greer
Software Mentions: 2
Published: almost 6 years ago
10.3389/fmicb.2017.00013
Virome Assembly and Annotation: A Surprise in the Namib Desert
Cited by: 18
Author(s): Uljana Hesse, Peter van Heusden, Bronwyn M. Kirby, Israel Olonade, Leonardo Joaquim van Zyl, Marla Trindade
Software Mentions: 2
Published: almost 8 years ago
10.1155/2016/8527435
Recombination Hotspot/Coldspot Identification Combining Three Different Pseudocomponents via an Ensemble Learning Approach
Cited by: 1
Author(s): Bingquan Liu, Yumeng Liu, Dong Huang
Software Mentions: 2
Published: almost 9 years ago
10.3389/fmicb.2015.00771
Primer and platform effects on 16S rRNA tag sequencing
Cited by: 370
Author(s): Julien Tremblay, Kanwar Pal Singh, Alison Fern, Edward Kirton, Shaomei He, Tanja Woyke, Janey Lee, Feng Chen, Jeffery L. Dangl, Susannah G. Tringe
Software Mentions: 2
Published: over 9 years ago
10.1186/s13059-019-1872-3
Afann: bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression
Cited by: 17
Author(s): Kujin Tang, Jie Ren, Fengzhu Sun
Software Mentions: 2
Published: almost 5 years ago
10.3389/fmicb.2016.01333
New Genomic Insights into “Entotheonella” Symbionts in Theonella swinhoei: Mixotrophy, Anaerobic Adaptation, Resilience, and Interaction
Cited by: 13
Author(s): Fang Liu, Jinlong Li, Feng Gao, Zhiyong Li
Software Mentions: 2
Published: about 8 years ago
10.1186/gb-2014-15-1-r2
Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs
Cited by: 111
Author(s): Matthew B Friedersdorf, Jack D. Keene
Software Mentions: 2
Published: almost 11 years ago
10.3389/fmicb.2018.00711
Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer
Cited by: 8
Author(s): Kujin Tang, Yang Lu, Fengzhu Sun
Software Mentions: 2
Published: over 6 years ago
10.3390/cells8121570
Tristetraprolin/ZFP36 Regulates the Turnover of Autoimmune-Associated HLA-DQ mRNAs
Cited by: 4
Author(s): Laura Pisapia, Russell S. Hamilton, Federica Farina, Vito D’Agostino, Pasquale Barba, Maria Strazzullo, Alessandro Provenzani, Carmen Gianfrani, Giovanna Del Pozzo
Software Mentions: 2
Published: almost 5 years ago
10.3389/fmicb.2017.01585
Succession and Fermentation Products of Grass Carp (Ctenopharyngodon idellus) Hindgut Microbiota in Response to an Extreme Dietary Shift
Cited by: 68
Author(s): Yao Tong Hao, Shan Wu, Fan Xiong, Ngoc Tuan Tran, Ivan Jakovlić, Hong Zou, Wen Xiang Li, Gui Tang Wang
Software Mentions: 2
Published: over 7 years ago
10.1186/gb-2009-10-10-r112
Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels
Cited by: 37
Author(s): Ian Sudbery, Jim Stalker, Jared T. Simpson, Thomas Keane, Alistair G. Rust, Matthew E. Hurles, Klaudia Walter, Dee Lynch, Lydia Teboul, Steve Brown, Heng Li, Zemin Ning, Joseph H. Nadeau, Colleen M. Croniger, Richard Durbin, David J. Adams
Software Mentions: 2
Published: almost 16 years ago
10.1002/ece3.7611
The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat
Cited by: 5
Author(s): Changyi Xiao, Jingjin Li, Tingting Xie, Jianhai Chen, Sijia Zhang, Salma Hassan Elaksher, Jun Fan, Yaoxin Jiang, Lu Zhang, Wei Zhang, Yue Xiang, Zhenyang Wu, Shuhong Zhao, Xiaoyong Du
Software Mentions: 2
Published: over 3 years ago
10.1534/g3.118.200101
A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library
Cited by: 13
Author(s): Sandra L. Hoffberg, Nicholas J. Troendle, Travis C. Glenn, Ousman Mahmud, Swarnali Louha, Domitille Chalopin, Jeffrey L. Bennetzen, Rodney Mauricio
Software Mentions: 2
Published: over 6 years ago
10.1534/g3.117.043083
Annotated Draft Genome Assemblies for the Northern Bobwhite (<i>Colinus virginianus</i>) and the Scaled Quail (<i>Callipepla squamata</i>) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size
Cited by: 20
Author(s): David L. Oldeschulte, Yvette A. Halley, Miranda Wilson, Eric K. Bhattarai, Wesley Brashear, Joshua A. Hill, Richard P. Metz, Charles D. Johnson, Dale Rollins, Markus J. Peterson, Derek M. Bickhart, Jared E. Decker, John F. Sewell, Christopher M. Seabury
Software Mentions: 2
Published: about 7 years ago
10.1111/j.1462-2920.2010.02193.x
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Cited by: 1,150
Author(s): Susan M. Huse, David B. Mark Welch, Hilary G. Morrison, Mitchell L. Sogin
Software Mentions: 2
Published: over 14 years ago
10.2807/1560-7917.ES.2016.21.50.30423
Rise of multidrug-resistant non-vaccine serotype 15A Streptococcus pneumoniae in the United Kingdom, 2001 to 2014
Cited by: 39
Author(s): Carmen Sheppard, Norman K. Fry, Shazad Mushtaq, Neil Woodford, Rosy Reynolds, Regina Janes, Rachel Pike, Robert R.L. Hill, Maimuna Kimuli, Peter Staves, Michel Doumith, Timothy G. Harrison, David M. Livermore
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pcbi.1000844
The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies
Cited by: 313
Author(s): Patrick D. Schloss
Software Mentions: 2
Published: over 14 years ago
10.1016/j.plantsci.2014.12.004
New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing
Cited by: 18
Author(s): Marcelo Helguera, Máximo Rivarola, Bernardo Clavijo, Mihaela M. Martis, Leonardo Sebastián Vanzetti, Sergio González, Ingrid Garbus, P. P. Leroy, Hana Šimková, Miroslav Valárik, Mario Cáccamo, J. Doležel, Klaus Mayer, Catherine Feuillet, Gabriela Tranquilli, Norma Paniego, Viviana Echenique
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2164-14-273
Six novel Y chromosome genes in Anophelesmosquitoes discovered by independently sequencing males and females
Cited by: 105
Author(s): Andrew Brantley Hall, Yumin Qi, Vladimir A. Timoshevskiy, Maria V. Sharakhova, Igor V. Sharakhov, Zhijian Tu
Software Mentions: 2
Published: over 11 years ago
10.1186/s12859-019-2918-y
Viral coinfection analysis using a MinHash toolkit
Cited by: 3
Author(s): Eric T. Dawson, Sarah Wagner, David A. Roberson, Meredith Yeager, Joseph F. Boland, Erik Garrison, Stephen J. Chanock, Mark Schiffman, Tina Raine‐Bennett, Thomas Lorey, Phillip E. Castle, Lisa Mirabello, Richard Durbin
Software Mentions: 2
Published: over 5 years ago
10.3389/fmicb.2015.01436
Transplanting Soil Microbiomes Leads to Lasting Effects on Willow Growth, but not on the Rhizosphere Microbiome
Cited by: 84
Author(s): Étienne Yergeau, Terrence H. Bell, Julie Champagne, Christine Maynard, Stacie Tardif, Julien Tremblay, Charles W. Greer
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.pcbi.1008727
Balrog: A universal protein model for prokaryotic gene prediction
Cited by: 15
Author(s): Markus J. Sommer
Software Mentions: 2
Published: over 3 years ago
10.1128/JVI.01583-20
A Founder Effect Led Early SARS-CoV-2 Transmission in Spain
Cited by: 49
Author(s): Francisco Díez-Fuertes, María Iglesias-Caballero, Javier García-Pérez, Sara Monzón, Pilar Jiménez, Sarai Varona, Isabel Cuesta, Ángel Zaballos, Mercedes Jiménez, Laura Checa, Francisco Pozo, Mayte Pérez‐Olmeda, Michael M. Thomson, José Alcamı́, Inmaculada Casas
Software Mentions: 2
Published: almost 4 years ago
10.3389/fcimb.2020.596917
Lactobacillus-Depleted Vaginal Microbiota in Pregnant Women Living With HIV-1 Infection Are Associated With Increased Local Inflammation and Preterm Birth
Cited by: 13
Author(s): Charlotte-Eve Short, Richard Brown, Rachael Quinlan, Yun Sok Lee, Ann Smith, Julian R. Marchesi, Robin J. Shattock, Phillip R. Bennett, Graham P. Taylor, David A. MacIntyre
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pgen.1008209
Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album
Cited by: 55
Author(s): Ching Man Wai, Sean E. Weise, Philip Ozersky, Todd C. Mockler, Todd P. Michael, Robert VanBuren
Software Mentions: 2
Published: over 5 years ago
10.1007/s11418-016-1041-x
De novo transcriptome assembly and characterization of nine tissues of Lonicera japonica to identify potential candidate genes involved in chlorogenic acid, luteolosides, and secoiridoid biosynthesis pathways
Cited by: 46
Author(s): Amit Rai, Hidetaka Kamochi, Hideyuki Suzuki, Michimi Nakamura, Hiroki Takahashi, Tomoki Hatada, Kazuki Saito, Mami Yamazaki
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pgen.1005895
Genomic Landscape Survey Identifies SRSF1 as a Key Oncodriver in Small Cell Lung Cancer
Cited by: 138
Author(s): Liyan Jiang, Jiaqi Huang, Brandon W. Higgs, Zhibin Hu, Xiaowei Zhan, Xin Yao, R. Scott Conley, Haihong Zhong, Zheng Liu, Philip Z. Brohawn, Dong Shen, Song Wu, Xiaoxiao Ge, Yue Jiang, Yupei Zhao, Yu‐Qing Lou, Chris Morehouse, Wei Zhu, Yinong Sebastian, Meggan Czapiga, Vaheh Oganesyan, Haihua Fu, Yiming Niu, Wei Zhang, Katie Streicher, David A. Tice, Heng Zhao, Meng Zhu, Lin Xu, Ronald Herbst, Xinying Su, Yi Gu, Shyoung Li, Lihua Huang, Jianren Gu, Baohui Han, Bahija Jallal, Hongbing Shen, Yihong Yao
Software Mentions: 2
Published: over 8 years ago
10.3389/fmicb.2015.00624
Distribution of iron- and sulfate-reducing bacteria across a coastal acid sulfate soil (CASS) environment: implications for passive bioremediation by tidal inundation
Cited by: 23
Author(s): Yu Ling, Richard T Bush, Kliti Grice, Svenja Tulipani, Lyndon Berwick, John W. Moreau
Software Mentions: 2
Published: over 9 years ago
10.1186/s12864-020-07347-7
Identify RNA-associated subcellular localizations based on multi-label learning using Chou’s 5-steps rule
Cited by: 15
Author(s): Hao Wang, Yongsheng Ding, Jijun Tang, Quan Zou, Fei Guo
Software Mentions: 2
Published: almost 4 years ago
10.7554/eLife.03737
Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition
Cited by: 167
Author(s): Xiaoyong Li, Melissa M. Harrison, Jacqueline E. Villalta, Tommy Kaplan, Michael B. Eisen
Software Mentions: 2
Published: about 10 years ago
10.1038/s41396-019-0580-z
Phage-specific metabolic reprogramming of virocells
Cited by: 118
Author(s): Cristina Howard-Varona, Morgan Lindback, G. Eric Bastien, Natalie Solonenko, Ahmed A. Zayed, Ho Bin Jang, Bill Andreopoulos, Heather M. Brewer, Tijana Glavina del Rio, Joshua N. Adkins, Subhadeep Paul, Matthew B. Sullivan, Melissa B. Duhaime
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pone.0138162
Transcriptome Analysis of Poplar during Leaf Spot Infection with Sphaerulina spp.
Cited by: 29
Author(s): Adam Foster, G. Pelletier, Philippe Tanguay, Armand Séguin
Software Mentions: 2
Published: about 9 years ago
10.1186/s12864-020-06916-0
Using full chloroplast genomes of ‘red’ and ‘yellow’ Bixa orellana (achiote) for kmer based identification and phylogenetic inference
Cited by: 2
Author(s): Jorge Villacrés-Vallejo, José Aranda-Ventura, Anna Wallis, Robin Cagle, Sara M. Handy, Jeffery Davis, Elizabeth Reed, Shu Zhang, Errol Strain, Monica Pava‐Ripoll, David L. Erickson, Padmini Ramachandran, Andrea Ottesen
Software Mentions: 2
Published: over 4 years ago
10.1186/s12864-015-1331-9
The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release
Cited by: 42
Author(s): Isabelle Lesur, Grégoire Le Provost, Pascal Bento, Corinne Da Silva, Jean‐Charles Leplé, Florent Murat, S. Ueno, Jérôme Bartholome, Céline Lalanne, François Ehrenmann, Céline Noirot, Christian Burban, Valérie Leger, Joëlle Amselem, Caroline Belser, Hadi Quesneville, Michael Stierschneider, Silvia Fluch, Lasse Feldhahn, Mika Tarkka, Sylvie Herrmann, François Buscot, Christophe Klopp, Antoine Kremer, Jérôme Salse, Jean‐Marc Aury, Christophe Plomion
Software Mentions: 2
Published: over 9 years ago
10.1186/s12967-019-2100-3
The tumor inflammation signature (TIS) is associated with anti-PD-1 treatment benefit in the CERTIM pan-cancer cohort
Cited by: 75
Author(s): Diane Damotte, Sarah Warren, Jennifer Arrondeau, Pascaline Boudou‐Rouquette, Audrey Lupo, Jérôme Biton, Hanane Ouakrim, Marco Alifano, Claire Gervais, Audrey Bellesœur, N. Kramkimel, Camille Tlemsani, Barbara Burroni, A Duché, Franck Letourneur, Han Si, Rebecca Halpin, Todd Creasy, Ronald Herbst, Xing Ren, Pascale Morel, Alessandra Cesano, François Goldwasser, Karen Leroy
Software Mentions: 1
Published: about 5 years ago
10.1186/s12859-019-2901-7
PaSS: a sequencing simulator for PacBio sequencing
Cited by: 14
Author(s): Wenmin Zhang, Ben Jia, Chaochun Wei
Software Mentions: 1
Published: over 5 years ago
10.1186/1471-2105-12-S1-S52
Repeat-aware modeling and correction of short read errors
Cited by: 26
Author(s): Xiao Yang, Srinivas Aluru, Karin S. Dorman
Software Mentions: 1
Published: almost 14 years ago
10.1186/1471-2105-12-293
FAAST: Flow-space Assisted Alignment Search Tool
Cited by: 11
Author(s): Fredrik Lysholm, Björn Andersson, Bengt Persson
Software Mentions: 1
Published: over 13 years ago
10.1186/s12859-015-0709-7
Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph
Cited by: 87
Author(s): Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drézen, Thibault Dayris, Raluca Uricaru, Guillaume Rizk
Software Mentions: 1
Published: about 9 years ago
10.1186/s12861-016-0106-0
Computational prediction and experimental validation of novel Hedgehog-responsive enhancers linked to genes of the Hedgehog pathway
Cited by: 8
Author(s): Katherine Gurdziel, Kyle R. Vogt, Gary K. Schneider, Neil Richards, Deborah L. Gumucio
Software Mentions: 1
Published: over 8 years ago
10.1186/s12864-015-1747-2
Analysis of archived residual newborn screening blood spots after whole genome amplification
Cited by: 6
Author(s): Brandi L. Cantarel, Yunping Lei, Daniel Weaver, Huiping Zhu, Andrew Farrell, Graeme Benstead-Hume, Justin Reese, Richard H. Finnell
Software Mentions: 1
Published: over 9 years ago
10.1186/1471-2164-15-819
The Chironomus tentans genome sequence and the organization of the Balbiani ring genes
Cited by: 15
Author(s): Alexey S. Kutsenko, Thomas Svensson, Björn Nystedt, Joakim Lundeberg, Petra Björk, Erik L. L. Sonnhammer, Stefania Giacomello, Neus Visa, Lars Wieslander
Software Mentions: 1
Published: about 10 years ago
10.1186/1471-2164-13-439
De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus)
Cited by: 41
Author(s): Hilary C. Miller, Patrick J. Biggs, Claudia Voelckel, Nicola J. Nelson
Software Mentions: 1
Published: almost 13 years ago
10.1186/s12864-018-4889-1
Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks
Cited by: 182
Author(s): Xiaoyong Pan, Peter Rijnbeek, Junchi Yan, Hong‐Bin Shen
Software Mentions: 1
Published: over 6 years ago
10.1186/s12864-020-06798-2
Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae
Cited by: 36
Author(s): Dhafer A. Alzahrani, Samaila Yaradua, Enas Albokhari, Abidina Abba
Software Mentions: 1
Published: over 4 years ago
10.1186/s12866-016-0891-4
Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification
Cited by: 136
Author(s): Josef Wagner, Paul Coupland, Hilary P. Browne, Trevor D. Lawley, Suzanna C. Francis, Julian Parkhill
Software Mentions: 1
Published: about 8 years ago
10.1093/bioinformatics/btaa857
Automated download and clean-up of family-specific databases for kmer-based virus identification
Cited by: 3
Author(s): Rosa Lundbye Allesøe, Camilla K. Lemvigh, My V. T. Phan, Philip Thomas Lanken Conradsen Clausen, Alfred Ferrer Florensa, Marion Koopmans, Ole Lund, Matthew Cotten
Software Mentions: 1
Published: about 4 years ago
10.1093/bioinformatics/bty597
A fast adaptive algorithm for computing whole-genome homology maps
Cited by: 100
Author(s): Chirag Jain, Sergey Koren, Alexander Dilthey, Adam M. Phillippy, Srinivas Aluru
Software Mentions: 1
Published: about 6 years ago
10.3390/biology10080816
Gene Flow and Diversification in Himalopsyche martynovi Species Complex (Trichoptera: Rhyacophilidae) in the Hengduan Mountains
Cited by: 3
Author(s): Xi‐Ling Deng, Adrien Favre, Emily Moriarty Lemmon, Alan R. Lemmon, Steffen U. Pauls
Software Mentions: 1
Published: about 3 years ago
10.1155/2019/4370258
Complete Chloroplast Genome Sequence of<i> Justicia flava</i>: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae
Cited by: 20
Author(s): Samaila Yaradua, Dhafer A. Alzahrani, Enas J Albokhary, Abidina Abba, Abubakar Bello
Software Mentions: 1
Published: over 5 years ago
10.1099/mgen.0.000169
The lytic Myoviridae of Enterobacteriaceae form tight recombining assemblages separated by discontinuities in genome average nucleotide identity and lateral gene flow
Cited by: 3
Author(s): Tomaž Accetto, Nika Janež
Software Mentions: 1
Published: over 6 years ago
10.1002/mbo3.458
<i>Hugonella massiliensis</i> gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut
Cited by: 16
Author(s): Ziena Elsawi, Amadou Hamidou Togo, Mamadou Beye, Grégory Dubourg, Claudia Andrieu, Nicholas Armsrtong, Magali Richez, Fabrizio Di Pinto, Fadi Bittar, N. Labas, Pierre-Édouard Fournier, Didier Raoult, Saber Khelaifia
Software Mentions: 1
Published: over 7 years ago
10.1128/MRA.00825-19
Complete Genome Sequences and Transmission Electron Micrographs of Listeria Phages of the Genus Homburgvirus
Cited by: 2
Author(s): Lauren K. Hudson, Tracey L. Peters, Yaxiong Song, Thomas G. Denes
Software Mentions: 1
Published: about 5 years ago
10.1080/23802359.2021.1927222
Characterization of the complete chloroplast genome of<i>Dioscorea polystachya</i>Turcz.
Cited by: 0
Author(s): Na Hu, Junbo Gong, Biming Zhang
Software Mentions: 1
Published: over 3 years ago
10.1080/23802359.2021.1967799
Characterization and phylogenetic analysis of the complete chloroplast genome of Tulipa patens (Liliaceae)
Cited by: 1
Author(s): Xiuting Ju, Guomin Shi, Shengrong Chen, Wubin Dai, Tao He
Software Mentions: 1
Published: about 3 years ago
10.1080/23802359.2019.1681315
The complete chloroplast genome of Blepharis ciliaris (Acanthaceae)
Cited by: 0
Author(s): Samaila Yaradua, Dhafer A. Alzahrani, Abidina Abba, Enas J Albokhary, Abubakar Bello
Software Mentions: 1
Published: over 5 years ago
10.1080/23802359.2017.1318679
The complete mitochondrial genome of the lesser sac-winged bat Saccopteryx leptura (Chiroptera: Emballonuridae) from Costa Rica
Cited by: 0
Author(s): José Horacio Grau, Martina Nagy, Emrah Çoraman, Frieder Mayer
Software Mentions: 1
Published: almost 8 years ago
10.1080/23802359.2017.1325341
The complete mitochondrial genome of the pentastomid Armillifer grandis (Pentastomida) from the Democratic Republic of Congo
Cited by: 2
Author(s): José Horacio Grau, Jason A. Dunlop, Martin Meixner, Dennis Tappe
Software Mentions: 1
Published: almost 8 years ago
10.1186/s40851-018-0102-2
Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians
Cited by: 28
Author(s): Yang An, Akane Kawaguchi, Chen Zhao, Atsushi Toyoda, Ali Sharifi-Zarchi, Seyed Ahmad Mousavi, Reza Bagherzadeh, Takeshi Inoue, Hitoshi Ogino, Asao Fujiyama, Hamidreza Chitsaz, Hossein Baharvand, Kiyokazu Agata
Software Mentions: 1
Published: about 6 years ago
10.7717/peerj.7055
Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting
Cited by: 5
Author(s): Jason McDermott, John Cort, Ernesto Nakayasu, Jonathan N. Pruneda, Christopher C. Overall, Joshua N. Adkins
Software Mentions: 1
Published: over 5 years ago
10.3390/plants9040478
The Complete Chloroplast Genome of Two Important Annual Clover Species, Trifolium alexandrinum and T. resupinatum: Genome Structure, Comparative Analyses and Phylogenetic Relationships with Relatives in Leguminosae
Cited by: 22
Author(s): Yanli Xiong, Jun He, Qingqing Yu, Junlong Zhao, Lei Xiong, Zhixiao Dong, Jian Yang, Yan Peng, Xinquan Zhang, Xiao Ma
Software Mentions: 1
Published: over 4 years ago
10.3390/plants9060748
The Complete Chloroplast Genome Sequencing and Comparative Analysis of Reed Canary Grass (Phalaris arundinacea) and Hardinggrass (P. aquatica)
Cited by: 8
Author(s): Yi Xiong, Shangang Jia, Xiao Ma
Software Mentions: 1
Published: over 4 years ago
10.3390/plants10020270
Complete Chloroplast Genome of Abutilon fruticosum: Genome Structure, Comparative and Phylogenetic Analysis
Cited by: 9
Author(s): Dhafer A. Alzahrani
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pcbi.1007134
ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates
Cited by: 48
Author(s): Oliver Schwengers, Andreas Hoek, Moritz Fritzenwanker, Linda Falgenhauer, Torsten Hain, Trinad Chakraborty, Alexander Goesmann
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pgen.1005323
Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes
Cited by: 100
Author(s): Janna L. Fierst, John H. Willis, Cristel G. Thomas, Weiwei Wang, Rose M. Reynolds, Timothy E. Ahearne, Asher D. Cutter, Patrick C. Phillips
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pgen.1002692
Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome
Cited by: 78
Author(s): Jian Jian Li, R. Alan Harris, Sau Wai Cheung, Cristian Coarfa, Mira Jeong, Margaret A. Goodell, Lisa D. White, Ankita Patel, Sung-Hae L. Kang, Chad A. Shaw, A. Craig Chinault, Tomasz Gambin, Anna Gambin, James R. Lupski, Aleksandar Milosavljevic
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0174701
Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants
Cited by: 22
Author(s): Maureen H. Diaz, Heta P. Desai, Shatavia S. Morrison, Alvaro J. Benitez, Bernard J. Wolff, Jason Caravas, Timothy D. Read, Deborah Dean, Jonas M. Winchell
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pone.0006323
Mapping Accuracy of Short Reads from Massively Parallel Sequencing and the Implications for Quantitative Expression Profiling
Cited by: 20
Author(s): Nicola Palmieri, Christian Schlötterer
Software Mentions: 1
Published: over 15 years ago
10.1371/journal.pone.0088999
Impact of Technical Sources of Variation on the Hand Microbiome Dynamics of Healthcare Workers
Cited by: 20
Author(s): Mariana Rosenthal, Allison E. Aiello, Carol E. Chenoweth, Deborah E. Goldberg, Elaine Larson, Gregory B. Gloor, Betsy Foxman
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pone.0114829
Life-Style and Genome Structure of Marine Pseudoalteromonas Siphovirus B8b Isolated from the Northwestern Mediterranean Sea
Cited by: 13
Author(s): Elena Lara, Karin Holmfeldt, Natalie Solonenko, Elisabet Laia Sà, J. Cesar Ignacio‐Espinoza, Francisco M. Cornejo‐Castillo, Nathan C. VerBerkmoes, Dolors Vaqué, Matthew B. Sullivan, Silvia G. Acinas
Software Mentions: 1
Published: almost 10 years ago
10.1371/journal.pone.0101338
Transcriptome Analysis of a Petal Anthocyanin Polymorphism in the Arctic Mustard, Parrya nudicaulis
Cited by: 14
Author(s): Timothy Butler, Cynthia Dick, Matthew L. Carlson, Justen B. Whittall
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pone.0119284
Microbial Iron Mats at the Mid-Atlantic Ridge and Evidence that Zetaproteobacteria May Be Restricted to Iron-Oxidizing Marine Systems
Cited by: 57
Author(s): Jarrod J. Scott, J. A. Breier, George W. Luther, David Emerson
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pone.0242591
Complete chloroplast genomes of three important species, Abelmoschus moschatus, A. manihot and A. sagittifolius: Genome structures, mutational hotspots, comparative and phylogenetic analysis in Malvaceae
Cited by: 7
Author(s): Jie Li, Guang-ying Ye, Hailin Liu, Zaihua Wang
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pone.0252849
Immunogenic amino acid motifs and linear epitopes of COVID-19 mRNA vaccines
Cited by: 9
Author(s): Adam V. Wisnewski, Carrie A. Redlich, Jian Liu, Kathy Kamath, Queenie-Ann Abad, Richard Smith, Louis E. Fazen, Romero Santiago, Julian Campillo Luna, Brian Martinez, Elizabeth Baum-Jones, Rebecca Waitz, Winston Haynes, John Shon
Software Mentions: 1
Published: about 3 years ago
10.1371/journal.pone.0115037
Lentinula edodes-Derived Polysaccharide Alters the Spatial Structure of Gut Microbiota in Mice
Cited by: 65
Author(s): Xiaofei Xu, Xuewu Zhang
Software Mentions: 1
Published: almost 10 years ago