cran: kmer | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0008230

A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies
Cited by: 276
Author(s): Patrick D. Schloss
Software Mentions: 1
Published: almost 15 years ago

Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome
Cited by: 195
Author(s): Margaret L. Zupancic, Brandi L. Cantarel, Zhenqiu Liu, Elliott F. Drábek, Kathleen A. Ryan, Shana Cirimotich, Cheron Jones, Rob Knight, William A. Walters, Daniel Knights, Emmanuel F. Mongodin, Richard B. Horenstein, Braxton D. Mitchell, Nanette I. Steinle, Søren Snitker, Alan R. Shuldiner, Claire M. Fraser
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0220117

Metagenome of Acropora palmata coral rubble: Potential metabolic pathways and diversity in the reef ecosystem
Cited by: 11
Author(s): Andrés Sánchez-Quinto, Luisa I. Falcón
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0198526

Resistome of carbapenem- and colistin-resistant Klebsiella pneumoniae clinical isolates
Cited by: 48
Author(s): Sara Lomonaco, Matthew A. Crawford, Christine Lascols, Ruth Timme, Kevin Anderson, David R. Hodge, Debra J. Fisher, Segaran P. Pillai, Stephen Morse, Erum Khan, Molly A. Hughes, Marc W. Allard, Shashi Sharma
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0048995

Reference-Free Comparative Genomics of 174 Chloroplasts
Cited by: 4
Author(s): Chai-Shian Kua, Jue Ruan, John Harting, Cheng-Xi Ye, Matthew R. Helmus, Jun Yu, Charles H. Cannon
Software Mentions: 1
Published: about 12 years ago

10.1155/2017/4630621

Retrospective Identification of Herpes Simplex 2 Virus-Associated Acute Liver Failure in an Immunocompetent Patient Detected Using Whole Transcriptome Shotgun Sequencing
Cited by: 1
Author(s): Atsushi Ono, C. Nelson Hayes, Sakura Akamatsu, Michio Imamura, Kazuaki Chayama
Software Mentions: 1
Published: almost 8 years ago

10.1038/s42003-019-0678-x

Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei
Cited by: 18
Author(s): Claire Chewapreecha, Alison E. Mather, Simon R. Harris, Martin Hunt, Matthew T. G. Holden, Chutima Chaichana, Vanaporn Wuthiekanun, Gordon Dougan, Nicholas P. J. Day, Direk Limmathurotsakul, Julian Parkhill, Sharon J. Peacock
Software Mentions: 1
Published: almost 5 years ago

10.3390/foods10081794

Utilizing Big Data to Identify Tiny Toxic Components: Digitalis
Cited by: 2
Author(s): Elizabeth Sage Hunter, Robert Literman, Sara M. Handy
Software Mentions: 1
Published: over 3 years ago

10.3389/fimmu.2021.625311

Protein-Based Immunome Wide Association Studies (PIWAS) for the Discovery of Significant Disease-Associated Antigens
Cited by: 11
Author(s): Winston Haynes, Kathy Kamath, Rebecca Waitz, Patrick S. Daugherty, John Shon
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2020.00450

Rumen Virus Populations: Technological Advances Enhancing Current Understanding
Cited by: 16
Author(s): Rosalind A. Gilbert, Eleanor Townsend, Kathleen S. Crew, Thomas C. A. Hitch, Jessica C. A. Friedersdorff, Christopher J. Creevey, Phillip B. Pope, D. Ouwerkerk, Eleanor Jameson
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2015.00872

Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica
Cited by: 58
Author(s): Stephanie Carr, Beth N. Orcutt, Kevin W. Mandernack, John R. Spear
Software Mentions: 1
Published: about 9 years ago

10.3389/fmicb.2013.00323

The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling
Cited by: 74
Author(s): Stephen R. Lindemann, James J. Moran, James C. Stegen, Ryan Renslow, Janine R. Hutchison, Jesse Cole, Alice Dohnálková, Julien Tremblay, Kanwar Pal Singh, Stephanie Malfatti, Feng Chen, Susannah G. Tringe, Haluk Beyenal, James K. Fredrickson
Software Mentions: 1
Published: almost 12 years ago

10.3389/fmicb.2021.712106

Characterization of Campylobacter spp. Strains Isolated From Wild Birds in Turkey
Cited by: 7
Author(s): Cemil Kürekçi, Fatih Sakin, Lennard Epping, Marie-Theres Knüver, Torsten Semmler, Kerstin Stingl
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2019.02094

A Metataxonomic Tool to Investigate the Diversity of Treponema
Cited by: 3
Author(s): Luisa K. Hallmaier–Wacker, Simone Lüert, Sabine Gronow, Cathrin Spröer, Jörg Overmann, Nicky Buller, Rebecca Vaughan‐Higgins, Sascha Knauf
Software Mentions: 1
Published: about 5 years ago

10.3389/fpls.2021.634901

Evidence of Recombination Suppression Blocks on the Y Chromosome of Date Palm (Phoenix dactylifera)
Cited by: 4
Author(s): María Fernanda Torres, Yasmin Ali Mohamoud, Shameem Younuskunju, Karsten Suhre, Joel A. Malek
Software Mentions: 1
Published: over 3 years ago

10.3389/fpls.2016.00204

Transcriptome and Biochemical Analysis of a Flower Color Polymorphism in Silene littorea (Caryophyllaceae)
Cited by: 27
Author(s): Inés Casimiro-Soriguer, Eduardo Narbona, Ma Luisa Buide, José Carlos del Valle, Justen B. Whittall
Software Mentions: 1
Published: over 8 years ago

10.3389/fpls.2018.01961

Identifying Plant Pentatricopeptide Repeat Coding Gene/Protein Using Mixed Feature Extraction Methods
Cited by: 10
Author(s): Kaiyang Qu, Leyi Wei, Jinxin Yu, Chunyu Wang
Software Mentions: 1
Published: almost 6 years ago

10.3389/fpls.2018.01501

3D Molecular Cytology of Hop (Humulus lupulus) Meiotic Chromosomes Reveals Non-disomic Pairing and Segregation, Aneuploidy, and Genomic Structural Variation
Cited by: 11
Author(s): Katherine A. Easterling, Nicholi J. Pitra, Rod Jones, Lauren G. Lopes, Jenna R. Aquino, Dong Zhang, Paul D. Matthews, Hank W. Bass
Software Mentions: 1
Published: about 6 years ago

10.3389/fpubh.2019.00242

Using Genomics to Track Global Antimicrobial Resistance
Cited by: 230
Author(s): René S. Hendriksen, Valeria Bortolaia, Heather Tate, Gregory H. Tyson, Frank Møller Aarestrup, Patrick F. McDermott
Software Mentions: 1
Published: about 5 years ago

10.1534/g3.118.200204

The Draft Genome of the Invasive Walking Stick, <i>Medauroidea extradendata</i>, Reveals Extensive Lineage-Specific Gene Family Expansions of Cell Wall Degrading Enzymes in Phasmatodea
Cited by: 9
Author(s): Philipp Brand, Wei Lin, Brian R. Johnson
Software Mentions: 1
Published: over 6 years ago

10.3390/genes8120379

The Genome of the Northern Sea Otter (Enhydra lutris kenyoni)
Cited by: 22
Author(s): Samantha Jones, Martin Haulena, Gregory A. Taylor, Simon K. Chan, Steven Bilobram, René L. Warren, S. Austin Hammond, Andrew J. Mungall, Caleb Choo, Heather Kirk, Pawan Pandoh, Adrian Ally, Noreen Dhalla, Angela K Y Tam, Armelle Troussard, Daniel Paulino, Robin Coope, Richard A. Moore, Yongjun Zhao, İnanç Birol, Yussanne Ma, Marco A. Marra, Steven J.M. Jones
Software Mentions: 1
Published: almost 7 years ago

10.1093/gbe/evu121

Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi
Cited by: 45
Author(s): Jaqueline Hess, Inger Skrede, Benjamin E. Wolfe, Kurt LaButti, Robin A. Ohm, Igor V. Grigoriev, Anne Pringle
Software Mentions: 1
Published: over 10 years ago

10.1186/s13073-021-00947-2

Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK
Cited by: 27
Author(s): Samuel Lipworth, Karina-Doris Vihta, Kevin Chau, Leanne Barker, Sophie George, James Kavanagh, Timothy Davies, Alison Vaughan, Monique Andersson, Katie Jeffery, Sarah Oakley, Marcus Morgan, Susan Hopkins, Timothy E. A. Peto, Derrick W. Crook, A Sarah Walker, Nicole Stoesser
Software Mentions: 1
Published: about 3 years ago

10.1093/gigascience/giy087

Chromosome-level reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression
Cited by: 22
Author(s): Guangyi Fan, Judy Yuet-Wa Chan, Kailong Ma, Bong Min Yang, He Zhang, Xianwei Yang, Chengcheng Shi, Henry C.-H. Law, Zhitao Ren, Qiwu Xu, Qun Li, Jiahao Wang, Wenbin Chen, Libin Shao, David Gonçalves, A.R. Ramos, Sara D. Cardoso, Min Guo, Jing Cai, Xun Xu, Jian Wang, Huanming Yang, Xin Liu, Ying Wang
Software Mentions: 1
Published: over 6 years ago

10.1093/gigascience/giab053

0s and 1s in marine molecular research: a regional HPC perspective
Cited by: 16
Author(s): Haris Zafeiropoulos, Αnastasia Gioti, Stelios Ninidakis, Antonis Potirakis, Savvas Paragkamian, Nelina Angelova, Aglaia Antoniou, Theodoros Danis, Eliza Kaitetzidou, Panagiotis Kasapidis, Jon Bent Kristoffersen, Vasileios Papadogiannis, Christina Pavloudi, Quoc Viet Ha, Jacques Lagnel, Nikos Pattakos, Giorgos Perantinos, Dimitris Sidirokastritis, Panagiotis Vavilis, Georgios Kotoulas, Tereza Manousaki, Elena Sarropoulou, Costas S. Tsigenopoulos, Christos Arvanitidis, Antoniοs Magoulas, Evangelos Pafilis
Software Mentions: 1
Published: over 3 years ago

10.3390/insects12070591

Annotating the Insect Regulatory Genome
Cited by: 3
Author(s): Hasiba Asma, Marc S. Halfon
Software Mentions: 1
Published: over 3 years ago

10.1128/JCM.00432-16

Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines
Cited by: 44
Author(s): Sophia David, M. Mentasti, Rediat Tewolde, Martin Aslett, Simon R. Harris, Baharak Afshar, Anthony Underwood, Norman K. Fry, Julian Parkhill, Timothy G. Harrison
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.ppat.1005001

Recombinant Murine Gamma Herpesvirus 68 Carrying KSHV G Protein-Coupled Receptor Induces Angiogenic Lesions in Mice
Cited by: 16
Author(s): Junjie Zhang, Lifei Zhu, Xiaolu Lu, Emily R. Feldman, Lisa R. Keyes, Yi Wang, Haijun Fan, Hao Feng, Zanxian Xia, Jiya Sun, Taijiao Jiang, Shou‐Jiang Gao, Scott A. Tibbetts, Pinghui Feng
Software Mentions: 1
Published: over 9 years ago

10.1038/s41597-020-0417-7

Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods
Cited by: 13
Author(s): Nanna Sophia Mucha Munck, Pimlapas Leekitcharoenphon, Eva Litrup, Rolf Sommer Kaas, Anika Meinen, Laurent Guillier, Yue Tang, Burkhard Malorny, Federica Di Palma, Maria Blettner, Michèle Gourmelon, Sandra Simon, Sangeeta Banerji, Liljana Petrovska, Timothy J. Dallman, Tine Hald
Software Mentions: 1
Published: over 4 years ago

10.1038/srep34983

Moku virus; a new Iflavirus found in wasps, honey bees and Varroa
Cited by: 54
Author(s): Gideon Mordecai, Laura E. Brettell, Purnima Pachori, Ethel M. Villalobos, Stephen J. Martin, Ian M. Jones, Declan C. Schroeder
Software Mentions: 1
Published: about 8 years ago

10.1038/srep37811

A genome-wide association study identifies a horizontally transferred bacterial surface adhesin gene associated with antimicrobial resistant strains
Cited by: 18
Author(s): Masato Suzuki, Keigo Shibayama, Koji Yahara
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-017-06153-8

Maize (Zea mays L.) genome size indicated by 180-bp knob abundance is associated with flowering time
Cited by: 24
Author(s): Yinqiao Jian, Cheng Xu, Zifeng Guo, Shanhong Wang, Yunbi Xu, Cheng Zou
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-39743-9

Identification of S-nitrosylation sites based on multiple features combination
Cited by: 10
Author(s): Taoying Li, Runyu Song, Qian Yin, Mingyue Gao, Yan Chen
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-56728-w

New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships
Cited by: 51
Author(s): Kevin M. Kocot, Albert J. Poustka, Isabella Stöger, Kenneth M. Halanych, Michael Schrödl
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-020-72177-2

New insights into the biodiversity of coliphages in the intestine of poultry
Cited by: 11
Author(s): Patricia Espenhain Sørensen, Wim Van Den Broeck, Kristoffer Kiil, Džiuginta Jasinskytė, Arshnee Moodley, An Garmyn, Hanne Ingmer, Patrick Butaye
Software Mentions: 1
Published: about 4 years ago

10.1186/s40793-016-0134-1

Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015)
Cited by: 60
Author(s): Scott Federhen, Ramon Rosselló‐Móra, Hans Peter Klenk, Brian J. Tindall, Konstantinos T. Konstantinidis, William B. Whitman, Daniel R. Brown, David P. Labeda, David W. Ussery, George M Garrity, Rita R. Colwell, Nur A. Hasan, Joerg Graf, Aidan Parte, Pablo Yarza, Brittany Goldberg, Heike Sichtig, Ilene Karsch‐Mizrachi, Karen Clark, Richard McVeigh, Kim D. Pruitt, Tatiana Tatusova, Robert P. Falk, Seán Turner, Thomas Madden, Paul Kitts, Avi Kimchi, William Klimke, Richa Agarwala, Michael DiCuccio, James Ostell
Software Mentions: 1
Published: almost 9 years ago

10.1093/jhered/esaa031

Genomic Features of Parthenogenetic Animals
Cited by: 47
Author(s): Kamil S. Jaroň, Jens Bast, Reuben W. Nowell, T. Rhyker Ranallo-Benavidez, Marc Robinson‐Rechavi, Tanja Schwander
Software Mentions: 1
Published: about 4 years ago

10.1093/infdis/jiy098

Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya
Cited by: 108
Author(s): Patience K. Kiyuka, Charles N. Agoti, Patrick K. Munywoki, Regina Njeru, Anne Bett, James R. Otieno, Grieven P. Otieno, Everlyn Kamau, Taane G. Clark, L. Van Hoek, Paul Kellam, D. James Nokes, Matthew Cotten
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms20153828

Comparative Analysis of two Sugarcane Ancestors Saccharum officinarum and S. spontaneum based on Complete Chloroplast Genome Sequences and Photosynthetic Ability in Cold Stress
Cited by: 14
Author(s): Feifei Xu, Lili He, Shaopei Gao, Yachun Su, Fusheng Li, Liping Xu
Software Mentions: 1
Published: over 5 years ago

10.1186/s13756-020-0699-8

Whole-genome sequencing to explore nosocomial transmission and virulence in neonatal methicillin-susceptible Staphylococcus aureus bacteremia
Cited by: 11
Author(s): Bibi C. G. C. Slingerland, Margreet C. Vos, Willeke Bras, René F. Kornelisse, Dieter De Coninck, Alex van Belkum, Irwin K M Reiss, W. H. F. Goessens, Corné H. W. Klaassen, Nelianne J. Verkaik
Software Mentions: 1
Published: over 4 years ago

Projects: cran: kmer

Papers Mentioning kmer 240