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: pypi: seqtk

https://packages.ecosyste.ms/registries/pypi.org/packages/seqtk

seqtk provides various tools for Sequence.
6 versions
Latest release: almost 3 years ago
1 dependent package
7,762 downloads last month

Papers Mentioning seqtk 213

10.1016/j.cell.2019.07.038
A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana
Cited by: 237
Author(s): Anna-Lena Van de Weyer, Freddy Monteiro, Oliver J. Furzer, Marc T. Nishimura, Volkan Çevik, Kamil Witek, Jonathan D. G. Jones, Jeffery L. Dangl, Detlef Weigel, Felix Bemm
Software Mentions: 23
Published: about 5 years ago
10.15252/msb.20209438
Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics
Cited by: 49
Author(s): Carmen Bravo González-Blas, Xiao‐Jiang Quan, Ramon Duran-Romaña, Ibrahim Ihsan Taskiran, Duygu Koldere, Kristofer Davie, Valerie Christiaens, Samira Makhzami, Gert Hulselmans, Maxime De Waegeneer, David Mauduit, Suresh Poovathingal, Sara Aibar, Stein Aerts
Software Mentions: 19
Published: over 4 years ago
10.1186/s13059-021-02335-w
Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits
Cited by: 15
Author(s): Lindsay F. Rizzardi, Peter Hickey, Adrian Idrizi, Rakel Tryggvadóttir, Colin M. Callahan, K Stephens, Sean D. Taverna, Hao Zhang, Sinan Ramazanoglu, Kasper D. Hansen, Andrew P. Feinberg
Software Mentions: 16
Published: over 3 years ago
10.1371/journal.pone.0183417
Association of gene expression with biomass content and composition in sugarcane
Cited by: 23
Author(s): Nam V. Hoang, Agnelo Furtado, Angela O'Keeffe, Frederik C. Botha, Robert J. Henry
Software Mentions: 15
Published: about 7 years ago
10.1186/s12859-020-03860-4
Finding a suitable library size to call variants in RNA-Seq
Cited by: 3
Author(s): Anna Quaglieri, Christoffer Flensburg, Terence P. Speed, Ian J. Majewski
Software Mentions: 15
Published: almost 4 years ago
10.1371/journal.pone.0240935
The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome
Cited by: 24
Author(s): Kris A. Christensen, Eric B. Rondeau, David R. Minkley, Dionne Sakhrani, Carlo A. Biagi, Anne-Marie Flores, Ruth E. Withler, Scott A. Pavey, Terry D. Beacham, Theresa Godin, Eric B. Taylor, Michael A. Russello, Robert H. Devlin, Ben F. Koop
Software Mentions: 15
Published: almost 4 years ago
10.1186/s13059-021-02349-4
PEPPRO: quality control and processing of nascent RNA profiling data
Cited by: 14
Author(s): Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin, Nathan C. Sheffield
Software Mentions: 14
Published: over 3 years ago
10.3389/fgene.2021.665888
A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells
Cited by: 2
Author(s): Simon Haile, Richard Corbett, Véronique G. LeBlanc, Lisa L. Wei, Stephen Pleasance, Steve Bilobram, Ka Ming Nip, Kirstin Brown, Eva Trinh, Jillian Smith, Diane L. Trinh, Miruna Bala, Eric Chuah, Robin Coope, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Martin Hirst, Samuel Aparicio, İnanç Birol, Steven J.M. Jones, Marco A. Marra
Software Mentions: 13
Published: over 3 years ago
10.1099/mgen.0.000552
Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen
Cited by: 6
Author(s): Josephine Grützke, Mayada Gwida, Carlus Deneke, Holger Brendebach, Michaela Projahn, Alexander Schattschneider, Dirk Hofreuter, Maged El-Ashker, Burkhard Malorny, Sascha Al Dahouk
Software Mentions: 10
Published: over 3 years ago
10.7554/eLife.69249
A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
Cited by: 38
Author(s): Ursula Oggenfuss, Thomas Badet, Thomas Wicker, Fanny E. Hartmann, Navreet Singh, Leen Nanchira Abraham, Petteri Karisto, Tiziana Vonlanthen, Christopher C. Mundt, Bruce A. McDonald, Daniel Croll
Software Mentions: 9
Published: about 3 years ago
10.1371/journal.pone.0236084
Mating system is correlated with immunogenetic diversity in sympatric species of Peromyscine mice
Cited by: 0
Author(s): Jesyka Meléndez‐Rosa, Ke Bi, Eileen A. Lacey
Software Mentions: 9
Published: about 4 years ago
10.1038/s42003-018-0199-z
Improved reference genome for the domestic horse increases assembly contiguity and composition
Cited by: 137
Author(s): Theodore S. Kalbfleisch, Edward S. Rice, Michael S. DePriest, Brian P. Walenz, Matthew S. Hestand, Joris Vermeesch, Brendan O’Connell, Ian T. Fiddes, Alisa O. Vershinina, Nedda F. Saremi, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone, Molly E. McCue, Samantha A. Brooks, Ernest Bailey, Ludovic Orlando, Edward Green, Donald C. Miller, Douglas F. Antczak, James N. MacLeod
Software Mentions: 9
Published: almost 6 years ago
10.3389/fcimb.2020.582187
Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface
Cited by: 11
Author(s): Austin Yan, James Butcher, David Mack, Alain Stintzi
Software Mentions: 9
Published: almost 4 years ago
10.1111/mec.14054
The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB
Cited by: 60
Author(s): Rodrigo Pracana, Anurag Priyam, Levantis Ilya, Richard A. Nichols, Yannick Wurm
Software Mentions: 8
Published: over 7 years ago
10.1093/molbev/msaa135
Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome
Cited by: 25
Author(s): Jaelle C. Brealey, Henrique G. Leitão, Tom van der Valk, Wenbo Xu, Katia Bougiouri, Love Dalén, Katerina Guschanski
Software Mentions: 8
Published: over 4 years ago
10.1186/s40168-018-0434-3
Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing
Cited by: 20
Author(s): Ellen L. Young, Manus Carey, Andrew A. Meharg, Caroline Meharg
Software Mentions: 8
Published: over 6 years ago
10.3389/fmicb.2019.01805
Fishing in the Soup – Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing
Cited by: 44
Author(s): Josephine Grützke, Burkhard Malorny, Jens A. Hammerl, Anne Busch, Simon H. Tausch, Herbert Tomaso, Carlus Deneke
Software Mentions: 8
Published: about 5 years ago
10.1093/dnares/dsaa017
A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform
Cited by: 0
Author(s): Yuu Hirose, Takuhei Shiozaki, Itsuki Hamano, Shizue Yoshihara, Hayato Tokumoto, Toshihiko Eki, Naomi Harada
Software Mentions: 8
Published: about 4 years ago
10.1371/journal.pcbi.1005727
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
Cited by: 40
Author(s): Kevin Murray, Christfried Webers, Cheng Soon Ong, Justin O. Borevitz, Norman Warthmann
Software Mentions: 8
Published: about 7 years ago
10.1186/s12859-016-1274-4
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
Cited by: 95
Author(s): Qian Qin, Shenglin Mei, Qiu Liang Wu, Hanfei Sun, Lewyn Li, Len Taing, Sujun Chen, Fugen Li, Tao Liu, Chongzhi Zang, Xu Han, Yiwen Chen, Clifford A. Meyer, Yong Zhang, Myles Brown, Henry W. Long, X. Shirley Liu
Software Mentions: 7
Published: almost 8 years ago
10.1371/journal.pone.0187735
Transcriptome profile of lung dendritic cells after in vitro porcine reproductive and respiratory syndrome virus (PRRSV) infection
Cited by: 16
Author(s): Maren Pröll, Christiane Neuhoff, K. Schellander, Muhammad Jasim Uddin, Mehmet Ulaş Çınar, Sudeep Sahadevan, Xuecheng Qu, M. S. Islam, Mikhaël Poirier, Marcel A. Müller, Christian Drosten, Dawit Tesfaye, Ernst Tholen, Christine Große‐Brinkhaus
Software Mentions: 7
Published: almost 7 years ago
10.1371/journal.pone.0163962
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
Cited by: 1,226
Author(s): Wei Shen, Shuai Le, Yan Li, Fuquan Hu
Software Mentions: 7
Published: almost 8 years ago
10.1093/bib/bbz126
Systematic evaluation of differential splicing tools for RNA-seq studies
Cited by: 99
Author(s): Arfa Mehmood, Asta Laiho, Mikko S Venäläinen, Aidan McGlinchey, Ning Wang, Laura L. Elo
Software Mentions: 7
Published: almost 5 years ago
10.1186/s40168-021-01044-7
Characterization of the public transit air microbiome and resistome reveals geographical specificity
Cited by: 20
Author(s): Marcus H. Y. Leung, Xinzhao Tong, Kari Oline Bøifot, Daniela Bezdan, Daniel Butler, David Danko, Jostein Gohli, D. C. Green, Mark Hernandez, Frank J. Kelly, Shawn Levy, Gabriella Mason-Buck, Marina Nieto-Caballero, Denise Syndercombe‐Court, Klas I. Udekwu, Brian P. Young, Christopher E. Mason, Marius Dybwad, P. K. H. Lee
Software Mentions: 7
Published: over 3 years ago
10.7717/peerj.6902
Optimizing <i>de novo</i> genome assembly from PCR-amplified metagenomes
Cited by: 26
Author(s): Simon Roux, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A. Ahlgren, Yuanchao Zhan, David Marsan, Feng Chen, Jed A. Fuhrman, Trent Northen, Matthew B. Sullivan, V. I. Rich, Rex R. Malmstrom, Emiley A. Eloe‐Fadrosh
Software Mentions: 7
Published: over 5 years ago
10.1371/journal.pgen.1007784
Maternal and zygotic gene regulatory effects of endogenous RNAi pathways
Cited by: 17
Author(s): Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, René F. Ketting
Software Mentions: 7
Published: over 5 years ago
10.1093/gigascience/giy023
The Scientific Filesystem
Cited by: 1
Author(s): Vanessa Sochat
Software Mentions: 7
Published: over 6 years ago
10.1186/s12859-021-04128-1
Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis
Cited by: 4
Author(s): José Francisco Sánchez-Herrero, Raquel Pluvinet, Antonio Luna de Haro, Lauro Sumoy
Software Mentions: 6
Published: over 3 years ago
10.1186/s13059-018-1407-3
Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
Cited by: 90
Author(s): Yohei Sasagawa, Hiroki Danno, Hitomi Takada, Masashi Ebisawa, Kaori Tanaka, Tetsutaro Hayashi, Akira Kurisaki, Itoshi Nikaido
Software Mentions: 6
Published: over 6 years ago
10.1093/gigascience/gix049
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
Cited by: 114
Author(s): Sarah S.T. Mak, Shyam Gopalakrishnan, Christian Carøe, Chunyu Geng, Shanlin Liu, Mikkel‐Holger S. Sinding, Lukas F. K. Kuderna, Wenwei Zhang, Shujin Fu, Filipe Garrett Vieira, Mietje Germonpré, Hervé Bocherens, Sergey Fedorov, Bent Petersen, Thomas Sicheritz-Pontén, Tomás Marquès-Bonet, Guojie Zhang, Hui Jiang, M. Thomas P. Gilbert
Software Mentions: 6
Published: about 7 years ago
10.1186/s13742-015-0060-y
VirAmp: a galaxy-based viral genome assembly pipeline
Cited by: 31
Author(s): Yinan Wan, Daniel W. Renner, István Albert, Moriah L. Szpara
Software Mentions: 6
Published: over 9 years ago
10.1186/s12864-020-07358-4
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
Cited by: 33
Author(s): Tracy M. Yamawaki, Daniel Lu, Daniel C. Ellwanger, Dev Bhatt, Paolo Manzanillo, Vanessa Arias, Hong Zhou, Oh Kyu Yoon, Oliver Homann, Songli Wang, Chi-Ming Li
Software Mentions: 6
Published: over 3 years ago
10.1186/s12864-020-6455-x
Comparison of multiple algorithms to reliably detect structural variants in pears
Cited by: 14
Author(s): Yueyuan Liu, Mingyue Zhang, Jieying Sun, Wenjing Chang, Manyi Sun, Shaoling Zhang, Wu Jun
Software Mentions: 6
Published: over 4 years ago
10.1186/s12864-018-4670-5
Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects
Cited by: 28
Author(s): Shobana Sekar, Lori Cuyugan, Jonathan Adkins, Philipp Geiger, Winnie S. Liang
Software Mentions: 6
Published: over 6 years ago
10.3390/microorganisms8010134
Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota
Cited by: 34
Author(s): Rodrigo García-López, Fernanda Cornejo‐Granados, Alonso A. López-Zavala, Filiberto Sánchez-López, Andrés Cota-Huízar, Rogerio R. Sotelo‐Mundo, Abraham Guerrero, Alfredo Mendoza-Vargas, Bruno Gómez‐Gil, Adrián Ochoa-Leyva
Software Mentions: 5
Published: over 4 years ago
10.3389/fmicb.2020.587306
An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration Sites
Cited by: 4
Author(s): Nicolas Rosewick, Vincent Hahaut, Keith Durkin, Maria Artesi, Snehal D. Karpe, Jérôme Wayet, Philip Griebel, Natasa Arsic, Ambroise Marçais, Olivier Hermine, Arsène Burny, Michel Georges, Anne Van den Broeke
Software Mentions: 5
Published: almost 4 years ago
10.3389/fmicb.2018.01561
A Single Vibrionales 16S rRNA Oligotype Dominates the Intestinal Microbiome in Two Geographically Separated Atlantic cod Populations
Cited by: 16
Author(s): Even Sannes Riiser, Thomas Haverkamp, Ørnulf Borgan, Kjetill S. Jakobsen, Sissel Jentoft, Bastiaan Star
Software Mentions: 5
Published: about 6 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: over 7 years ago
10.1186/s13059-021-02302-5
ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics
Cited by: 31
Author(s): Helena García-Castro, Nathan J. Kenny, Marta Iglesias, Patricia Álvarez‐Campos, Vincent Mason, Anamaria Elek, Anna Schönauer, Victoria A. Sleight, Jakke Neiro, A. Aziz Aboobaker, Jon Permanyer, Manuel Irimia, Arnau Sebé-Pedrós, Jordi Solana
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-021-07724-w
Transcriptomic and metabolomic characterization of post-hatch metabolic reprogramming during hepatic development in the chicken
Cited by: 4
Author(s): Heidi A. Van Every, Carl J. Schmidt
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-018-4943-z
ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference
Cited by: 19
Author(s): Thomas Pranzatelli, Drew G. Michael, John A. Chiorini
Software Mentions: 5
Published: about 6 years ago
10.3389/fpubh.2019.00241
Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation
Cited by: 28
Author(s): Helena M. B. Seth-Smith, Ferdinando Bonfiglio, Aline Cuénod, Josiane Reist, Adrian Egli, Daniel Wüthrich
Software Mentions: 5
Published: about 5 years ago
10.1186/s13104-017-2616-7
fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data
Cited by: 6
Author(s): Damien M. O’Halloran
Software Mentions: 5
Published: about 7 years ago
10.7554/eLife.52611
Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides
Cited by: 108
Author(s): Jamie R Wangen, Rachel Green
Software Mentions: 5
Published: over 4 years ago
10.1128/mBio.00521-21
Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria
Cited by: 26
Author(s): Alexander L. Jaffe, Alex D. Thomas, Christine He, Ray Keren, Luis E. Valentin-Alvarado, Patrick Munk, Keith Bouma‐Gregson, Ibrahim Farag, Yuki Amano, Rohan Sachdeva, Patrick T. West
Software Mentions: 5
Published: about 3 years ago
10.7717/peerj.1025
GenomePeek—an online tool for prokaryotic genome and metagenome analysis
Cited by: 12
Author(s): Katelyn McNair, Robert A. Edwards
Software Mentions: 4
Published: over 9 years ago
10.1038/s41598-017-13462-5
Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
Cited by: 54
Author(s): Michaela Asp, Fredrik Salmén, Patrik L. Ståhl, Sanja Vicković, Ulrika Felldin, Marie Löfling, José Fernández Navarro, Jonas Maaskola, Maria Eriksson, Bengt Persson, Matthias Corbascio, Hans Persson, Cecilia Linde, Joakim Lundeberg
Software Mentions: 4
Published: almost 7 years ago
10.1186/s12870-019-2193-0
Variation in plastid genomes in the gynodioecious species Silene vulgaris
Cited by: 7
Author(s): Manuela Krüger, Oushadee A. J. Abeyawardana, Miloslav Juříček, Claudia Krüger, Helena Štorchová
Software Mentions: 4
Published: almost 5 years ago
10.3390/v13081424
Application of Oxford Nanopore Technology to Plant Virus Detection
Cited by: 32
Author(s): L. W. Liefting, David W. Waite, Jeremy R. Thompson
Software Mentions: 4
Published: about 3 years ago
10.3390/v12111255
Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION
Cited by: 22
Author(s): Crystal M. Gigante, Gowri Yale, Rene Edgar Condori, Niceta Cunha Costa, Nguyen Van Duc Long, Phạm Quang Minh, Vo Dinh Chuong, Nguyen Dang Tho, Nguyen Tat Thanh, Nguyen Xuan Thin, Nguyễn Thị Hồng Hạnh, Gati Wambura, Frederick Ade, Oscar Mito, Veronicah Chuchu, Mathew Muturi, Athman Mwatondo, Katie Hampson, Samuel M. Thumbi, Byron G Thomae, Victor Hugo de Paz, Sergio Meneses, Peninah Munyua, David Morán, Loren Cadena, Andrew D Gibson, Crystal M. Gigante, Emily G. Pieracci, Li Yu
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41598-019-52832-z
New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies
Cited by: 14
Author(s): Weihong Qi, Andrea Colarusso, Miriam Olombrada, Ermenegilda Parrilli, Andrea Patrignani, Maria Luisa Tutino, Macarena Toll‐Riera
Software Mentions: 4
Published: almost 5 years ago
10.1186/s13100-019-0166-3
Horizontal transfer of a retrotransposon between parasitic nematodes and the common shrew
Cited by: 17
Author(s): Sonja M. Dunemann, James D. Wasmuth
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-020-77218-4
Accuracy and efficiency of germline variant calling pipelines for human genome data
Cited by: 49
Author(s): Sen Zhao, Oleg Agafonov, Abdulrahman Azab, Tomasz Stokowy, Eivind Hovig
Software Mentions: 4
Published: almost 4 years ago
10.1038/s42003-020-0896-2
Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis
Cited by: 10
Author(s): Maeve O’Huallachain, Felice-Alessio Bava, Mary Shen, Carolina Dallett, Sri Paladugu, Nikolay Samusik, Shichao Yu, Razika Hussein, Grantland Hillman, Samuel G. Higgins, Melanie Lou, Angelica Trejo, Laura Qin, Yu Chuan Tai, Shigemi Kinoshita, Astraea Jager, Deval Lashkari, Yury Goltsev, Sedide B. Ozturk, Garry P. Nolan
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0225834
Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken
Cited by: 5
Author(s): Rooksana E. Noorai, Vijay Shankar, Nowlan H. Freese, Christopher M. Gregorski, Steve Chapman
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pone.0198773
When old metagenomic data meet newly sequenced genomes, a case study
Cited by: 9
Author(s): Xin Li, Saleh A. Naser, Annette R. Khaled, Haiyan Hu, Xiaoman Li
Software Mentions: 4
Published: over 6 years ago
10.1534/genetics.118.301482
Diverse Lineages of <i>Candida albicans</i> Live on Old Oaks
Cited by: 54
Author(s): Douda Bensasson, Jo Dicks, John M. Ludwig, Christopher J. Bond, Adam Elliston, Ian N. Roberts, Stephen A. James
Software Mentions: 4
Published: almost 6 years ago
10.1371/journal.pone.0217600
Exploration of antibiotic resistance risks in a veterinary teaching hospital with Oxford Nanopore long read sequencing
Cited by: 15
Author(s): Kanishka Indiwari Kamathewatta, Rhys N. Bushell, Neil D. Young, Mark Stevenson, Helen Billman‐Jacobe, Glenn F. Browning, Marc S. Marenda
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pone.0081760
When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes
Cited by: 205
Author(s): Shea N. Gardner, Barry G. Hall
Software Mentions: 4
Published: almost 11 years ago
10.1371/journal.pone.0124671
From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows
Cited by: 158
Author(s): Dáithí C. Murray, Megan L. Coghlan, Michael Bunce
Software Mentions: 4
Published: over 9 years ago
10.1186/s12940-018-0394-x
The Ramazzini Institute 13-week pilot study on glyphosate and Roundup administered at human-equivalent dose to Sprague Dawley rats: effects on the microbiome
Cited by: 78
Author(s): Qixing Mao, Fabiana Manservisi, Simona Panzacchi, Daniele Mandrioli, I Menghetti, Andrea Vornoli, Luciano Bua, Laura Falcioni, Corina Lesseur, Jia Chen, Fiorella Belpoggi, Jianzhong Hu
Software Mentions: 4
Published: over 6 years ago
10.1186/s12920-020-00820-y
Mutational profiling of micro-dissected pre-malignant lesions from archived specimens
Cited by: 4
Author(s): Daniela Nachmanson, J. S. Steward, Huazhen Yao, Adam Officer, Eliza Jeong, Thomas J. O’Keefe, Farnaz Hasteh, Kristen Jepsen, Gillian L. Hirst, Laura J. Esserman, Alexander D. Borowsky, Olivier Harismendy
Software Mentions: 4
Published: almost 4 years ago
10.1155/2020/7061972
Electroacupuncture Alleviates Experimental Chronic Inflammatory Pain by Inhibiting Calcium Voltage-Gated Channel-Mediated Inflammation
Cited by: 5
Author(s): Jie Zhou, Jiang Ying, Ruijie Ma, Hongyun Song, Qin Chen, Yueyang Chai, Yi Liang, You Zhou, Jianqiao Fang
Software Mentions: 4
Published: over 4 years ago
10.1016/j.mex.2019.01.009
RppH can faithfully replace TAP to allow cloning of 5′-triphosphate carrying small RNAs
Cited by: 18
Author(s): Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, Hanna Lukas, María Méndez-Lago, René F. Ketting
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pbio.3000166
Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival
Cited by: 32
Author(s): Oliver Smith, Glenn Dunshea, Mikkel‐Holger S. Sinding, Sergey Fedorov, Mietje Germonpré, Hervé Bocherens, M. Thomas P. Gilbert
Software Mentions: 4
Published: about 5 years ago
10.1002/ece3.7146
NGSpeciesID: DNA barcode and amplicon consensus generation from long‐read sequencing data
Cited by: 22
Author(s): Kristoffer Sahlin, Marisa Lim, Stefan Prost
Software Mentions: 4
Published: over 3 years ago
10.1038/s41598-020-78773-6
Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome
Cited by: 28
Author(s): Min Yap, Conor Feehily, Calum J. Walsh, Mark A. Fenelon, Eileen F. Murphy, Fionnuala M. McAuliffe, Douwe van Sinderen, Paul W. O’Toole, Órla O’Sullivan, Paul D. Cotter
Software Mentions: 4
Published: almost 4 years ago
10.7717/peerj.2571
The single-species metagenome: subtyping<i>Staphylococcus aureus</i>core genome sequences from shotgun metagenomic data
Cited by: 8
Author(s): Sandeep J. Joseph, Ben Li, Robert A. Petit, Zhaohui S. Qin, Lyndsey A. Darrow, Timothy D. Read
Software Mentions: 4
Published: almost 8 years ago
10.1186/s12859-019-3031-y
Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data
Cited by: 14
Author(s): Emiliano Pereira-Flores, Frank Oliver Glöckner, Antonio Fernández-Guerra
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.pgen.1006464
Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages
Cited by: 52
Author(s): Lauren Gibilisco, Qi Zhou, Shivani Mahajan, Doris Bachtrog
Software Mentions: 4
Published: almost 8 years ago
10.1093/gigascience/giy140
NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform
Cited by: 79
Author(s): Szymon T. Calus, Umer Zeeshan Ijaz, Ameet J. Pinto
Software Mentions: 4
Published: almost 6 years ago
10.7717/peerj.11842
Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type
Cited by: 2
Author(s): Yen‐Yi Liu, Bo-Han Chen, Chih-Chieh Chen, Chien-Shun Chiou
Software Mentions: 3
Published: about 3 years ago
10.1038/srep46395
Complex multifractal nature in Mycobacterium tuberculosis genome
Cited by: 8
Author(s): Suvra Mandal, Tanmoy Roychowdhury, Keilash Chirom, Alok Bhattacharya, R. K. Brojen Singh
Software Mentions: 3
Published: over 7 years ago
10.3389/fmicb.2021.643682
Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome
Cited by: 18
Author(s): Donovan H. Parks, Fabio Rigato, Patricia Vera-Wolf, Lutz Krause, Philip Hugenholtz, Gene W. Tyson, David Wood
Software Mentions: 3
Published: over 3 years ago
10.1186/s12859-019-3091-z
doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows
Cited by: 2
Author(s): Daniel Svensson, Rickard Sjögren, David Sundell, Andreas Sjödin, Johan Trygg
Software Mentions: 3
Published: almost 5 years ago
10.3389/fmicb.2021.682356
Comparative Transcriptome and Endophytic Bacterial Community Analysis of Morchella conica SH
Cited by: 3
Author(s): Bei Lü, Guo Wu, Yu Sun, Liang S. Zhang, Xiao Wu, Wei Jiang, Peng Li, Yan Huang, Jin B. Wang, Yong Zhao, Hua Liu, Li Song, Qin Mo, Ai H. Pan, Yan Yang, Xuan Long, Wei Cui, Chao Zhang, Xu Wang, Xue Tang
Software Mentions: 3
Published: about 3 years ago
10.1038/srep41498
Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells
Cited by: 46
Author(s): Jean‐François Mangot, Ramiro Logares, Pablo Sánchez, Fran Latorre, Yoann Seeleuthner, Samuel Mondy, Michael E. Sieracki, Olivier Jaillon, Patrick Wincker, Colomban de Vargas, Ramón Massana
Software Mentions: 3
Published: over 7 years ago
10.1093/gigascience/giz043
Ultra-deep, long-read nanopore sequencing of mock microbial community standards
Cited by: 199
Author(s): Samuel M. Nicholls, Joshua Quick, Siu Wa Tang, Nicholas J. Loman
Software Mentions: 3
Published: over 5 years ago
10.1093/molbev/msy217
Repeated Evolution of Asexuality Involves Convergent Gene Expression Changes
Cited by: 24
Author(s): Darren J. Parker, Jens Bast, Kirsten M. Jalvingh, Zoé Dumas, Marc Robinson‐Rechavi, Tanja Schwander
Software Mentions: 3
Published: almost 6 years ago
10.1128/AEM.02788-19
Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes
Cited by: 19
Author(s): Even Sannes Riiser, Thomas Haverkamp, Srinidhi Varadharajan, Ørnulf Borgan, Kjetill S. Jakobsen, Sissel Jentoft, Bastiaan Star
Software Mentions: 3
Published: over 4 years ago
10.1093/gigascience/giab063
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment
Cited by: 12
Author(s): Yilei Fu, Medhat Mahmoud, Viginesh Vaibhav Muraliraman, Fritz J. Sedlazeck, Todd J. Treangen
Software Mentions: 3
Published: about 3 years ago
10.1002/ece3.5181
Differential gene expression in relation to mating system in Peromyscine rodents
Cited by: 2
Author(s): Jesyka Meléndez‐Rosa, Ke Bi, Eileen A. Lacey
Software Mentions: 3
Published: over 5 years ago
10.1186/s12864-015-1859-8
Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing
Cited by: 8
Author(s): Ting-Wen Chen, Ruei Chi Gan, Ian Yi‐Feng Chang, Wei Liao, Timothy Wu, Chi-Ching Lee, Po-Jung Huang, Cheng Yang Lee, Yi-Ywan M. Chen, Cheng Hsun Chiu, Petrus Tang
Software Mentions: 3
Published: about 9 years ago
10.1038/s42003-020-1096-9
Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution
Cited by: 27
Author(s): Austin B. Mudd, Jessen V. Bredeson, Rachel Baum, Dirk Hockemeyer, Daniel S. Rokhsar
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.ppat.1008623
The endosymbiont Wolbachia rebounds following antibiotic treatment
Cited by: 14
Author(s): Emma L. Gunderson, Ian Vogel, Laura Chappell, Christina Bulman, K. C. Lim, Mona Luo, Jeffrey D. Whitman, Chris Franklin, Young Jun Choi, Emilie Lefoulon, Travis A. Clark, Brenda T. Beerntsen, Barton E. Slatko, Makedonka Mitreva, William Sullivan, Judy Sakanari
Software Mentions: 3
Published: about 4 years ago
10.1186/s40168-020-00937-3
High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method
Cited by: 25
Author(s): Lei Liu, Yulin Wang, Ying Che, Yiqiang Chen, Yu Xia, Ruibang Luo, Suk Hang Cheng, Kewei Chen, Tong Zhang
Software Mentions: 3
Published: almost 4 years ago
10.1186/s13073-016-0335-7
Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq
Cited by: 104
Author(s): David Redmond, Asaf Poran, Olivier Elemento
Software Mentions: 3
Published: about 8 years ago
10.3389/fmicb.2017.02434
Strong Genomic and Phenotypic Heterogeneity in the Aeromonas sobria Species Complex
Cited by: 16
Author(s): Jeff Gauthier, Antony T. Vincent, Steve J. Charette, Nicolas Derôme
Software Mentions: 3
Published: almost 7 years ago
10.1371/journal.pone.0101271
These Are Not the K-mers You Are Looking For: Efficient Online K-mer Counting Using a Probabilistic Data Structure
Cited by: 88
Author(s): Zhang Qingpeng, Jason Pell, Rosangela Canino-Koning, Adina Howe, C. Titus Brown
Software Mentions: 3
Published: about 10 years ago
10.1186/s13059-019-1849-2
Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis
Cited by: 13
Author(s): Se-Young Jo, Eun Young Kim, Sang Woo Kim
Software Mentions: 3
Published: almost 5 years ago
10.12688/f1000research.16804.4
Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies
Cited by: 10
Author(s): Federica Cattonaro, Alessandro Spadotto, Slobodanka Radović, Fabio Marroni
Software Mentions: 3
Published: over 4 years ago
10.3389/fmicb.2020.585374
Phylogenomic Analysis of Campylobacter fetus Reveals a Clonal Structure of Insertion Element ISCfe1 Positive Genomes
Cited by: 4
Author(s): Mostafa Y. Abdel-Glil, Helmut Hotzel, Herbert Tomaso, Jörg Linde
Software Mentions: 3
Published: almost 4 years ago
10.1534/g3.120.401149
The Genome Sequence of the Jean-Talon Strain, an Archeological Beer Yeast from Québec, Reveals Traces of Adaptation to Specific Brewing Conditions
Cited by: 2
Author(s): Anna Fijarczyk, Mathieu Hénault, Souhir Marsit, Guillaume Charron, Tobias Fischborn, Luc Nicole-Labrie, Christian R. Landry
Software Mentions: 3
Published: about 4 years ago
10.3389/fgene.2021.630542
Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions
Cited by: 10
Author(s): Chandni Radhakrishnan, Mohit Kumar Divakar, Abhinav Jain, Prasanth Viswanathan, Rahul C. Bhoyar, Bani Jolly, Mohamed Imran, Disha Sharma, Mercy Rophina, Gyan Ranjan, Paras Sehgal, Beena Philomina Jose, R. Raman, Thulaseedharan Nallaveettil Kesavan, Kalpana George, Sheela Mathew, Jayesh Kumar Poovullathil, Sajeev Chakanalil Govindan, Priyanka Raveendranadhan Nair, Shameer Vadekkandiyil, Vineeth Gladson, Midhun Mohan, Fairoz Cheriyalingal Parambath, Mohit Mangla, Afra Shamnath, Sridhar Sivasubbu, Vinod Scaria
Software Mentions: 3
Published: over 3 years ago
10.1186/s13756-018-0356-7
Dynamics of colistin and tobramycin resistance among Enterobacter cloacae during prolonged use of selective decontamination of the digestive tract
Cited by: 5
Author(s): Mirjam J. D. Dautzenberg, Jumamurat R. Bayjanov, Maurine A. Leverstein–van Hall, Anouk E. Muller, L. B. S. Gelinck, C. L. Jansen, Eliane M. S. Leyten, Thomas Ruys, Jelle Scharringa, R. E. van der Starre, Ad C. Fluit, Marc J. M. Bonten
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0255663
Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak
Cited by: 2
Author(s): Efrat Bucris, Victoria Indenbaum, Roberto Azar, Oran Erster, Eric J. Haas, Ella Mendelson, Neta S. Zuckerman
Software Mentions: 3
Published: about 3 years ago
10.3390/genes11111312
Assessment of Imputation from Low-Pass Sequencing to Predict Merit of Beef Steers
Cited by: 50
Author(s): W. M. Snelling, Jesse L. Hoff, Jeremiah H. Li, L. A. Kuehn, Brittney N Keel, A. K. Lindholm‐Perry, Joseph K. Pickrell
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pgen.1007279
Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens
Cited by: 74
Author(s): Lyndal Henden, Stuart Lee, Ivo Müeller, Alyssa E. Barry, Melanie Bahlo
Software Mentions: 3
Published: over 6 years ago
10.1155/2018/2465481
RNA Sequencing for Gene Expression Profiles in a Rat Model of Middle Cerebral Artery Occlusion
Cited by: 7
Author(s): Xianchun Duan, Jianghua Gan, Fan Xu, Lili Li, Lei Han, Can Peng, Qiuyu Bao, Ling Xiao, Daiyin Peng
Software Mentions: 3
Published: almost 6 years ago
10.1186/s12864-016-2704-4
Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
Cited by: 30
Author(s): Nikol Voutsina, Adrienne Payne, Robert D. Hancock, Graham J. J. Clarkson, Steve D. Rothwell, Mark A. Chapman, Gail Taylor
Software Mentions: 3
Published: over 8 years ago