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: Archive

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

Simple library that provides a common interface for extracting zip and tar archives.
2 versions
Latest release: almost 13 years ago
1 dependent package
458 downloads last month

Papers Mentioning Archive 363

10.1186/s12866-016-0694-7
Influence of periparturient and postpartum diets on rumen methanogen communities in three breeds of primiparous dairy cows
Cited by: 24
Author(s): Laura M. Cersosimo, Melissa L. Bainbridge, Jana Kraft, André Denis G. Wright
Software Mentions: 3
Published: over 8 years ago
10.1186/s12862-014-0233-9
The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive
Cited by: 55
Author(s): Amanda M. Larracuente
Software Mentions: 3
Published: almost 10 years ago
10.1186/s12862-017-1066-0
Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia)
Cited by: 51
Author(s): Jessica A. Goodheart, Adam L. Bazinet, Ángel Valdés, Allen G. Collins, Michael P. Cummings
Software Mentions: 3
Published: about 7 years ago
10.1186/s13059-014-0572-2
De novo assembly of bacterial transcriptomes from RNA-seq data
Cited by: 764
Author(s): Brian Tjaden
Software Mentions: 3
Published: almost 10 years ago
10.1186/s12864-016-3287-9
AnnoLnc: a web server for systematically annotating novel human lncRNAs
Cited by: 43
Author(s): Mei Hou, Xing Tang, Feng Tian, Fang-Yuan Shi, Fenglin Liu, Ge Gao
Software Mentions: 3
Published: about 8 years ago
10.1186/gb-2012-13-4-r31
Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel
Cited by: 33
Author(s): Marieke Simonis, Santosh S. Atanur, Sam E.V. Linsen, Victor Guryev, Frans-Paul Ruzius, Laurence Gamé, Nico Lansu, Ewart de Bruijn, Sebastiaan van Heesch, Steven J.M. Jones, Michal Pravenec, Tim Aitman, Edwin Cuppen
Software Mentions: 3
Published: almost 13 years ago
10.1007/s00018-021-03865-z
Splicing and editing of ionotropic glutamate receptors: a comprehensive analysis based on human RNA-Seq data
Cited by: 14
Author(s): Robin Herbrechter, Nadine Hube, Raoul Buchholz, Andreas Reiner
Software Mentions: 3
Published: over 3 years ago
10.3389/fgene.2019.01128
Transcriptome of Gonads From High Temperature Induced Sex Reversal During Sex Determination and Differentiation in Chinese Tongue Sole, Cynoglossus semilaevis
Cited by: 33
Author(s): Qian Wang, Kaiqiang Liu, Bo Feng, Zhihua Zhang, Renkai Wang, Lili Tang, Wensheng Li, Qiye Li, Francesc Piferrer, Changwei Shao
Software Mentions: 3
Published: about 5 years ago
10.1186/1471-2105-14-S14-S5
A cross disciplinary study of link decay and the effectiveness of mitigation techniques
Cited by: 29
Author(s): Jason Hennessey, Xijin Ge
Software Mentions: 3
Published: about 11 years ago
10.3389/fmicb.2017.02366
Combination of Classifiers Identifies Fungal-Specific Activation of Lysosome Genes in Human Monocytes
Cited by: 3
Author(s): J. Saraiva, Cristina Zubiría-Barrera, Tilman E. Klassert, Maximilian Julius Lautenbach, Markus Blaess, Ralf A. Claus, Hortense Slevogt, Rainer König
Software Mentions: 3
Published: almost 7 years ago
10.1016/j.dib.2019.104172
Data describing the effects of depletion of Myoparr, myogenin, Ddx17, and hnRNPK in differentiating C2C12 cells
Cited by: 3
Author(s): Keisuke Hitachi, Kunihiro Tsuchida
Software Mentions: 3
Published: over 5 years ago
10.1093/gigascience/giaa138
iGenomics: Comprehensive DNA sequence analysis on your Smartphone
Cited by: 17
Author(s): Aspyn Palatnick, Bin Zhou, Elodie Ghedin, Michael C. Schatz
Software Mentions: 3
Published: almost 4 years ago
10.1093/database/bax105
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability
Cited by: 14
Author(s): Randi Vita, James A. Overton, Christopher J. Mungall, Alessandro Sette, Bjoern Peters
Software Mentions: 2
Published: almost 7 years ago
10.1186/1471-2164-15-506
ShrimpGPAT: a gene and protein annotation tool for knowledge sharing and gene discovery in shrimp
Cited by: 7
Author(s): Parpakron Korshkari, Sirintra Vaiwsri, Timothy W. Flegel, Sudsanguan Ngamsuriyaroj, Burachai Sonthayanon, Anuphap Prachumwat
Software Mentions: 2
Published: over 10 years ago
10.1186/1471-2105-7-190
MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation
Cited by: 15
Author(s): Leandro Hermida, Olivier Schaad, Philippe Demougin, Patrick Descombes, Michael Primig
Software Mentions: 2
Published: over 18 years ago
10.12688/f1000research.8548.1
Uptake of dietary milk miRNAs by adult humans: a validation study
Cited by: 68
Author(s): A. Auerbach, Gopi Vyas, Anne Li, Marc K. Halushka, Kenneth W. Witwer
Software Mentions: 2
Published: over 8 years ago
10.3389/fcimb.2021.645951
Leveraging 16S rRNA Microbiome Sequencing Data to Identify Bacterial Signatures for Irritable Bowel Syndrome
Cited by: 17
Author(s): Yuxia Liu, Wenhui Li, Hongxia Yang, Xiaoying Zhang, Wenxiu Wang, Sitong Jia, Xiang Bai, Yi Wang, Lin Miao, Han Zhang, Lin Wang, Yujing Wang, Jinfeng Song, Yingjie Sun, Li‐Juan Chai, Xiaoxuan Tian
Software Mentions: 2
Published: over 3 years ago
10.1093/molbev/msw242
Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication
Cited by: 119
Author(s): Yezi Xiang, Chien-Hua Huang, Yi Hu, Jun Wen, Shisheng Li, Ting‐Shuang Yi, Hongyi Chen, Jun Xiang, Hong Mā
Software Mentions: 2
Published: about 8 years ago
10.1186/s12864-017-3771-x
OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations
Cited by: 22
Author(s): Michael Dunne, Steven Kelly
Software Mentions: 2
Published: over 7 years ago
10.3389/fgene.2020.551495
Systematic Identification of Hub Genes in Placenta Accreta Spectrum Based on Integrated Transcriptomic and Proteomic Analysis
Cited by: 5
Author(s): Bingnan Chen, Di Wang, Yue Bian, Jiapo Li, Tian Yang, Na Li, Chong Qiao
Software Mentions: 2
Published: about 4 years ago
10.12688/wellcomeopenres.16291.2
Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project
Cited by: 34
Author(s): Mark Achtman, Zhemin Zhou, Nabil-Fareed Alikhan, William Tyne, Julian Parkhill, Martin Cormican, Chien-Shun Chiou, Mia Torpdahl, Eva Litrup, Deirdre M. Prendergast, John E. Moore, Sam Strain, Christian Kornschober, Richard J. Meinersmann, Alexandra Uesbeck, François‐Xavier Weill, Aidan Coffey, Helene Andrews‐Polymenis, Roy Curtiss, Séamus Fanning
Software Mentions: 2
Published: almost 4 years ago
10.3389/fmicb.2018.02389
Evaluation of Microbial Communities Associated With the Liquid and Solid Phases of the Rumen of Cattle Offered a Diet of Perennial Ryegrass or White Clover
Cited by: 14
Author(s): J M Bowen, Matthew S. McCabe, S.J. Lister, Paul Cormican, Richard J. Dewhurst
Software Mentions: 2
Published: about 6 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/s12859-020-03928-1
Menoci: lightweight extensible web portal enhancing data management for biomedical research projects
Cited by: 7
Author(s): Markus Suhr, Christoph U. Lehmann, Christian R. Bauer, Theresa Bender, Cornelius Knopp, Luca Freckmann, Björn Öst Hansen, Christian Henke, Georg Aschenbrandt, Lea K Kühlborn, Sophia Rheinländer, Linus Weber, Bartlomiej Marzec, Marcel Hellkamp, Philipp Wieder, Harald Kusch, Ulrich Sax, Sara Y. Nussbeck
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12864-018-4463-x
The aquatic animals’ transcriptome resource for comparative functional analysis
Cited by: 4
Author(s): Chih‐Hung Chou, Hsi‐Yuan Huang, Wei‐Chih Huang, Sheng Da Hsu, Chung-Der Hsiao, Chia-Yu Liu, Yu-Hung Chen, Yuchen Liu, Wei Huang, Meng-Lin Lee, Yi‐Chang Chen, Hsien-Da Huang
Software Mentions: 2
Published: over 6 years ago
10.3389/fonc.2021.653061
Baicalein Induces Apoptosis of Pancreatic Cancer Cells by Regulating the Expression of miR-139-3p and miR-196b-5p
Cited by: 6
Author(s): Danhui Ma, Sinuo Chen, Heming Wang, Jiayi Wei, Hao Wu, Hong Gao, Xinlai Cheng, Taotao Liu, Shihua Luo, Yicheng Zhao, Guangqi Song
Software Mentions: 2
Published: over 3 years ago
10.3389/fonc.2021.737152
A Systematic Analysis Identifies Key Regulators Involved in Cell Proliferation and Potential Drugs for the Treatment of Human Lung Adenocarcinoma
Cited by: 3
Author(s): Kai Wang, Man Zhang, Jiao Wang, Ping Sun, Jizhuang Luo, Haizhen Jin, Rong Li, Changqing Pan, Liming Lu
Software Mentions: 2
Published: about 3 years ago
10.1186/s12920-019-0509-4
Alternative cleavage and polyadenylation of genes associated with protein turnover and mitochondrial function are deregulated in Parkinson’s, Alzheimer’s and ALS disease
Cited by: 24
Author(s): Radhika Patel, Cillian Brophy, Mark Hickling, Jonathan Neve, André Furger
Software Mentions: 2
Published: over 5 years ago
10.3389/fpls.2021.646025
Novel Effects of Leonardite-Based Applications on Sugar Beet
Cited by: 11
Author(s): Maria Cristina Della Lucia, Giovanni Bertoldo, Chiara Broccanello, Laura Maretto, Samathmika Ravi, Francesco Marinello, Luigi Sartori, Giovanni Marsilio, Andrea Baglieri, Alessandro Romano, M. Colombo, Francesco Magro, G. Campagna, Giuseppe Concheri, Andrea Squartini, Piergiorgio Stevanato
Software Mentions: 2
Published: over 3 years ago
10.1186/1755-8794-7-45
Functional characterization of breast cancer using pathway profiles
Cited by: 10
Author(s): Feng Tian, Yajie Wang, Michael Seiler, Zhenjun Hu
Software Mentions: 2
Published: over 10 years ago
10.1186/s12911-015-0213-z
Development of a decision analytic model to support decision making and risk communication about thrombolytic treatment
Cited by: 13
Author(s): Peter McMeekin, Darren Flynn, Gary A. Ford, Helen Rodgers, Joanne Gray, Richard Thomson
Software Mentions: 2
Published: about 9 years ago
10.3389/fpls.2016.00488
Genetic Adaptation of Giant Lobelias (Lobelia aberdarica and Lobelia telekii) to Different Altitudes in East African Mountains
Cited by: 8
Author(s): Shu Ying Zhao, Ling Yun Chen, John K. Muchuku, Guang Hu, Qing Feng Wang
Software Mentions: 2
Published: over 8 years ago
10.1186/s12859-016-0938-4
Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators
Cited by: 12
Author(s): Marcin Piechota, Michał Korostyński, Joanna Ficek, Andrzej Tomski, Ryszard Przewłocki
Software Mentions: 2
Published: almost 9 years ago
10.3389/fpubh.2021.526286
The National Children's Study Archive Model: A 3-Tier Framework for Dissemination of Data and Specimens for General Use and Secondary Analysis
Cited by: 1
Author(s): Peter K. Gilbertson, Susan Forrester, Linda Wasmer Andrews, Kathleen McCann, Lydia Rogers, Christina Park, Jack Moye
Software Mentions: 2
Published: over 3 years ago
10.1534/g3.112.004473
Evidence for Population-Specific Positive Selection on Immune Genes of<i>Anopheles gambiae</i>
Cited by: 16
Author(s): Jacob E. Crawford, Emmanuel Bischoff, Thierry Garnier, Awa Gnémé, Karin Eiglmeier, Inge Holm, Michelle M. Riehle, Wamdaogo M. Guelbeogo, N’Falé Sagnon, Brian P. Lazzaro, Kenneth D. Vernick
Software Mentions: 2
Published: almost 12 years ago
10.1186/s12870-016-0770-z
Identification of miRNAs and their targets through high-throughput sequencing and degradome analysis in male and female Asparagus officinalis
Cited by: 31
Author(s): Jingli Chen, Yi Zheng, Qin Li, Yan Wang, Lifei Chen, Yanjun He, Zhangjun Fei, Gang Lü
Software Mentions: 2
Published: over 8 years ago
10.1534/g3.119.400959
Whole Genome Sequences of 23 Species from the <i>Drosophila montium</i> Species Group (Diptera: Drosophilidae): A Resource for Testing Evolutionary Hypotheses
Cited by: 15
Author(s): Michael J. Bronski, Ciera C. Martinez, Holli A. Weld, Michael B. Eisen
Software Mentions: 2
Published: over 4 years ago
10.3390/genes8040106
Differences in the Bacteriome of Smokeless Tobacco Products with Different Oral Carcinogenicity: Compositional and Predicted Functional Analysis
Cited by: 41
Author(s): Nezar N. Al-Hebshi, Fahd Alharbi, Mohammed Mahri, Tsute Chen
Software Mentions: 2
Published: over 7 years ago
10.3390/genes9030130
De Novo Transcriptome Assembly and Characterization of the Synthesis Genes of Bioactive Constituents in Abelmoschus esculentus (L.) Moench
Cited by: 14
Author(s): Chenghao Zhang, Dong Wang, Gen Wei, Baoyu Xu, Chenjia Shen, Chenliang Yu
Software Mentions: 2
Published: over 6 years ago
10.3390/genes10040280
The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1
Cited by: 11
Author(s): João Fernando Lourenço de Almeida, Ricardo Zorzetto Nicoliello Vêncio, Alan Péricles Rodrigues Lorenzetti, Felipe Ten Caten, José Vicente Gomes-Filho, Tie Koide
Software Mentions: 2
Published: over 5 years ago
10.3390/genes12030389
Filling the Gaps in the Cyanobacterial Tree of Life—Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014
Cited by: 5
Author(s): Pia Marter, Sixing Huang, Henner Brinkmann, Silke Pradella, Michael Jarek, Manfred Rohde, Boyke Bunk, Jörn Petersen
Software Mentions: 2
Published: over 3 years ago
10.1186/s12870-021-03080-9
The report of anthocyanins in the betalain-pigmented genus Hylocereus is not well evidenced and is not a strong basis to refute the mutual exclusion paradigm
Cited by: 5
Author(s): Boas Pucker, Hidam Bishworjit Singh, Monika Kumari, Mohammad Imtiyaj Khan, Samuel F. Brockington
Software Mentions: 2
Published: over 3 years ago
10.1128/genomeA.00237-16
Draft Genome Sequence of <i>Mycobacterium brumae</i> ATCC 51384
Cited by: 4
Author(s): Giuseppe D’Auria, Eduard Torrents, Marina Luquin, Iñaki Comas, Esther Julián
Software Mentions: 2
Published: over 8 years ago
10.1186/gb-2010-11-1-r1
Genomic characterization of the Yersinia genus
Cited by: 94
Author(s): Peter E. Chen, Constance E. Cook, Andrew C. Stewart, Niranjan Nagarajan, Dan Sommer, Mihai Pop, Brendan Thomason, Maureen P. Kiley Thomason, Shannon M. Lentz, Nichole Nolan, Shanmuga Sozhamannan, Alexander Sulakvelidze, Alfred Mateczun, Lei Du, Michael E. Zwick, Timothy D. Read
Software Mentions: 2
Published: almost 15 years ago
10.1186/s13059-015-0690-5
Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development
Cited by: 470
Author(s): Linda Szabo, Robert Morey, Nathan J. Palpant, Peter L. Wang, Nastaran Afari, Chuan Jiang, Mana M. Parast, Charles E. Murry, Louise C. Laurent, Julia Salzman
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2229-10-96
Uncovering the evolutionary origin of plant molecular processes: comparison of Coleochaete (Coleochaetales) and Spirogyra (Zygnematales) transcriptomes
Cited by: 83
Author(s): Ruth Timme, Charles F. Delwiche
Software Mentions: 2
Published: almost 15 years ago
10.1186/s13073-018-0537-2
Sensitivity to sequencing depth in single-cell cancer genomics
Cited by: 13
Author(s): João M. Alves, David Posada
Software Mentions: 2
Published: over 6 years ago
10.1186/s12870-015-0692-1
WheatExp: an RNA-seq expression database for polyploid wheat
Cited by: 100
Author(s): Stephen Pearce, Hans Vazquez-Gross, Sayer Y. Herin, David L. Hane, Yi Wang, Yong Gu, Jorge Dubcovsky
Software Mentions: 2
Published: almost 9 years ago
10.1093/gigascience/giz104
Comparison of single-nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga toxin–producing Escherichia coli
Cited by: 28
Author(s): David R. Greig, Claire Jenkins, Saheer E. Gharbia, Timothy J. Dallman
Software Mentions: 2
Published: over 5 years ago
10.1093/gigascience/giz100
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
Cited by: 376
Author(s): Elena Bushmanova, Dmitry Antipov, Alla Lapidus, Andrey D. Prjibelski
Software Mentions: 2
Published: about 5 years ago
10.1093/gigascience/giab021
Torix <i>Rickettsia</i> are widespread in arthropods and reflect a neglected symbiosis
Cited by: 24
Author(s): Jack Pilgrim, Panupong Thongprem, Helen Rebecca Davison, Stefanos Siozios, Matthew Baylis, Evgeny Zakharov, Sujeevan Ratnasingham, Jeremy R deWaard, Craig R. Macadam, M. Alex Smith, Gregory D. D. Hurst
Software Mentions: 2
Published: over 3 years ago
10.3390/plants10081517
The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)
Cited by: 6
Author(s): Se-Hwan Cheon, Min-Ah Woo, Sangjin Jo, Young-Kee Kim, Ki Joong Kim
Software Mentions: 2
Published: over 3 years ago
10.1007/s11104-017-3324-8
Chemical changes in organic matter after fungal colonization in a nitrogen fertilized and unfertilized Norway spruce forest
Cited by: 10
Author(s): César Nicolás, Juan Pablo Almeida, Magnus Ellström, Adam Bahr, Sharon E. Bone, Nicholas P. Rosenstock, John R. Bargar, Anders Tunlid, Per Persson, Håkan Wallander
Software Mentions: 2
Published: over 7 years ago
10.1186/s40621-021-00330-0
The role of domestic violence in fatal mass shootings in the United States, 2014–2019
Cited by: 17
Author(s): L Geller, Marisa D. Booty, Cassandra K. Crifasi
Software Mentions: 2
Published: over 3 years ago
10.1093/jamia/ocaa228
The technology behind TB DEPOT: a novel public analytics platform integrating tuberculosis clinical, genomic, and radiological data for visual and statistical exploration
Cited by: 3
Author(s): Alyssa Long, Alexander Glogowski, Matthew Meppiel, Lisa De Vito, Eric Engle, Michael A. Harris, Grace K Ha, Darren Schneider, Andrei Gabrielian, Darrell E. Hurt, Alex Rosenthal
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pcbi.1007633
The impact of news exposure on collective attention in the United States during the 2016 Zika epidemic
Cited by: 23
Author(s): Michele Tizzoni, André Panisson, Daniela Paolotti, Ciro Cattuto
Software Mentions: 2
Published: over 4 years ago
10.3390/jcm9061672
Association Analysis of TP53 rs1042522, MDM2 rs2279744, rs3730485, MDM4 rs4245739 Variants and Acute Myeloid Leukemia Susceptibility, Risk Stratification Scores, and Clinical Features: An Exploratory Study
Cited by: 6
Author(s): Florin Tripon, Mihaela Iancu, Adrian P. Trifa, George Andrei Crauciuc, Alina Bogliş, Beáta Balla, Adriana S Cosma, Delia Dima, Marcela Cândea, Erzsébet Lázár, Laura Jimbu, Claudia Bănescu
Software Mentions: 2
Published: over 4 years ago
10.1128/JCM.02070-19
Genomic Epidemiology and Evolution of Diverse Lineages of Clinical Campylobacter jejuni Cocirculating in New Hampshire, USA, 2017
Cited by: 5
Author(s): Cooper J. Park, Jinfeng Li, Xinglu Zhang, Fei Gao, Christopher S. Benton, Cheryl P. Andam
Software Mentions: 2
Published: over 4 years ago
10.5888/pcd17.200096
Exploring Spatial Differences Between 2 US Firearm Mortality Data Sets in 2017
Cited by: 3
Author(s): Meghan K Herring, Cassandra A. Kersten
Software Mentions: 2
Published: about 4 years ago
10.1186/1471-2105-10-421
BLAST+: architecture and applications
Cited by: 12,922
Author(s): Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason S. Papadopoulos, Kevin Bealer, Thomas Madden
Software Mentions: 2
Published: almost 15 years ago
10.3390/proteomes1010003
Protein-Protein Interactions: Gene Acronym Redundancies and Current Limitations Precluding Automated Data Integration
Cited by: 1
Author(s): Juan Casado‐Vela, Rune Matthiesen, Susana Sellés, José Ramón Naranjo
Software Mentions: 2
Published: over 11 years ago
10.1038/sdata.2015.11
Sequence variants from whole genome sequencing a large group of Icelanders
Cited by: 60
Author(s): Daníel F. Guðbjartsson, Patrick Sulem, Hannes Helgason, Arnaldur Gylfason, Sigurjon A. Gudjonsson, Florian Zink, Asmundur Oddson, Gísli Magnússon, Bjarni V. Halldórsson, Eirikur Hjartarson, Gunnar Sigurðsson, Augustine Kong, Agnar Helgason, Gísli Másson, Ólafur Þ. Magnússon, Unnur Þorsteinsdóttir, Kāri Stefánsson
Software Mentions: 2
Published: over 9 years ago
10.1038/sdata.2018.72
The electronic Rothamsted Archive (e-RA), an online resource for data from the Rothamsted long-term experiments
Cited by: 54
Author(s): S. A. M. Perryman, Nathalie Castells-Brooke, M. J. Glendining, Keith Goulding, Malcolm J. Hawkesford, A. J. Macdonald, Richard Ostler, P. R. Poulton, Christopher J. Rawlings, T. Scott, P. J. Verrier
Software Mentions: 2
Published: over 6 years ago
10.1038/sdata.2018.202
A radiogenomic dataset of non-small cell lung cancer
Cited by: 146
Author(s): Shaimaa Bakr, Olivier Gevaert, Sebastian Echegaray, Kelsey Ayers, Mu Zhou, Mājid Shafiq, Hong Zheng, Jalen Benson, Weiruo Zhang, Ann N. Leung, Michel Kadoch, Chuong D. Hoang, Joseph B. Shrager, Andrew Quon, Daniel L. Rubin, Sylvia K. Plevritis, Sandy Napel
Software Mentions: 2
Published: about 6 years ago
10.1186/s12859-018-2579-2
NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors
Cited by: 119
Author(s): John Gaspar
Software Mentions: 2
Published: almost 6 years ago
10.1038/s41597-019-0043-4
Atlas of RNA sequencing profiles for normal human tissues
Cited by: 69
Author(s): Maria Suntsova, Нуршат Гайфуллин, Daria Allina, Alexey Reshetun, Xinmin Li, Л. П. Менделеева, В. Л. Сурин, Anna Sergeeva, Pavel Spirin, Vladimir Prassolov, Alexander Morgan, Andrew Garazha, Maxim Sorokin, Anton Buzdin
Software Mentions: 2
Published: over 5 years ago
10.1186/1471-2105-15-257
The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web
Cited by: 10
Author(s): Brian J. Stucky, John Deck, Tom Conlin, Lukasz Ziemba, Nico Cellinese, Robert Guralnick
Software Mentions: 2
Published: over 10 years ago
10.1038/s41597-019-0130-6
The genome assembly of asparagus bean, Vigna unguiculata ssp. sesquipedialis
Cited by: 17
Author(s): Qiuju Xia, Lei Pan, Ru Zhang, Xiliang Ni, Yangzi Wang, Dong Xiao, Yun Gao, Zhe Zhang, Ling Kui, Yong Li, Wen Wang, Huanming Yang, Chen Chanyou, Miao Jin, Wei Chen, Yang Dong
Software Mentions: 2
Published: over 5 years ago
10.1038/s41597-019-0229-9
Tracking vegetation phenology across diverse biomes using Version 2.0 of the PhenoCam Dataset
Cited by: 76
Author(s): Bijan Seyednasrollah, Adam M. Young, Koen Hufkens, Tom Milliman, M. A. Friedl, Steve Frolking, Andrew D. Richardson
Software Mentions: 2
Published: about 5 years ago
10.1038/s41597-021-00934-7
The Upworthy Research Archive, a time series of 32,487 experiments in U.S. media
Cited by: 10
Author(s): J. Nathan Matias, Kevin Munger, Marianne Aubin Le Quere, Charles R. Ebersole
Software Mentions: 2
Published: over 3 years ago
10.1038/srep10814
Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome
Cited by: 52
Author(s): Li R, Chia‐Ling Hsieh, Amanda Young, Zhihong Zhang, Xiaoliang Ren, Zhongying Zhao
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0085024
An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis
Cited by: 325
Author(s): Cristian Del Fabbro, Simone Scalabrin, Michèle Morgante, Federico M. Giorgi
Software Mentions: 2
Published: almost 11 years ago
10.1093/bioinformatics/btab315
Practical selection of representative sets of RNA-seq samples using a hierarchical approach
Cited by: 0
Author(s): Laura H. Tung, Carl Kingsford
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0250579
Five genetic variants explain over 70% of hair coat pheomelanin intensity variation in purebred and mixed breed domestic dogs
Cited by: 6
Author(s): Andrea Slavney, Takeshi Kawakami, Meghan K. Jensen, Thomas C. Nelson, Aaron J. Sams, Adam R. Boyko
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-017-03631-x
Insights into enterotoxigenic Escherichia coli diversity in Bangladesh utilizing genomic epidemiology
Cited by: 29
Author(s): Jason W. Sahl, Jeticia R. Sistrunk, Nabilah Ibnat Baby, Yasmin Begum, Qingwei Luo, Alaullah Sheikh, Firdausi Qadri, James M. Fleckenstein, David A. Rasko
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0016410
Abundant Human DNA Contamination Identified in Non-Primate Genome Databases
Cited by: 108
Author(s): Mark S. Longo, Michael O’Neill, Rachel J. O’Neill
Software Mentions: 2
Published: almost 14 years ago
10.1186/s13062-018-0206-9
Prevalence of loss-of-function alleles does not correlate with lifetime fecundity and other life-history traits in metazoans
Cited by: 0
Author(s): Aleksandra V. Bezmenova, Georgii A. Bazykin, Alexey S. Kondrashov
Software Mentions: 2
Published: over 6 years ago
10.1186/s12859-021-04038-2
ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
Cited by: 8
Author(s): Zachary Deng, Eric Delwart
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0150908
Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains
Cited by: 30
Author(s): Taryn Athey, Sarah Teatero, Daisuke Takamatsu, Jessica Wasserscheid, Ken Dewar, Marcelo Gottschalk, Nahuel Fittipaldi
Software Mentions: 2
Published: over 8 years ago
10.1128/mBio.00846-16
The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers
Cited by: 45
Author(s): Jason W. Sahl, Adam J. Vazquez, Carina M. Hall, Joseph D. Busch, Apichai Tuanyok, Mark Mayo, James M. Schupp, Madeline Lummis, Talima Pearson, Kenzie Shippy, Rebecca E. Colman, Christopher John Allender, Vanessa Theobald, Derek S. Sarovich, Erin P. Price, Alex Hutcheson, Jonas Korlach, John J. LiPuma, Jason T. Ladner, Sean Lovett, G. I. Koroleva, Gustavo Palacios, Direk Limmathurotsakul, Vanaporn Wuthiekanun, Gumphol Wongsuwan, Bart J. Currie, Paul Keim, David M. Wagner
Software Mentions: 2
Published: about 8 years ago
10.1093/cvr/cvab094
Cardiovascular RNA markers and artificial intelligence may improve COVID-19 outcome: a position paper from the EU-CardioRNA COST Action CA17129
Cited by: 14
Author(s): Lina Badimon, Emma Robinson, Amela Jusić, Irina Carpusca, Leon J. deWindt, Costanza Emanueli, Péter Ferdinándy, Wei Gu, Mariann Gyöngyösi, Matthias Hackl, Kanita Karađuzović-Hadžiabdić, Mitja Luštrek, Fabio Martelli, Eric Nham, Ines Potočnjak, Venkata Satagopam, Reinhard Schneider, Thomas Thum, Yvan Devaux
Software Mentions: 2
Published: over 3 years ago
10.1128/mSystems.00202-17
SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control
Cited by: 59
Author(s): Gabriel A. Al‐Ghalith, Benjamin Hillmann, Kaiwei Ang, Robin R. Shields-Cutler, Dan Knights
Software Mentions: 2
Published: over 6 years ago
10.1128/mSystems.00134-21
Multilevel Genome Typing Describes Short- and Long-Term Vibrio cholerae Molecular Epidemiology
Cited by: 6
Author(s): Liam Cheney, Michael Payne, Sandeep Kaur, Ruiting Lan
Software Mentions: 2
Published: about 3 years ago
10.26508/lsa.202000902
A novel <i>canis lupus familiaris</i> reference genome improves variant resolution for use in breed-specific GWAS
Cited by: 8
Author(s): Robert A. Player, Ellen R. Forsyth, Kathleen Verratti, David Mohr, Alan F. Scott, Christopher Bradburne
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0170701
Coalescence computations for large samples drawn from populations of time-varying sizes
Cited by: 7
Author(s): Andrzej Polański, Agnieszka Szczęsna, Mateusz Garbulowski, Marek Kimmel
Software Mentions: 2
Published: almost 8 years ago
10.1186/s12906-019-2428-5
Validation of the anti-infective potential of a polyherbal ‘Panchvalkal’ preparation, and elucidation of the molecular basis underlining its efficacy against Pseudomonas aeruginosa
Cited by: 16
Author(s): Chinmayi Joshi, Pooja Patel, Hanmanthrao Palep, Vijay Kothari
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0245316
Mitochondrial introgression by ancient admixture between two distant lacustrine fishes in Sulawesi Island
Cited by: 17
Author(s): Mizuki Horoiwa, Ixchel F. Mandagi, Nobu Sutra, Javier Montenegro, Fadly Y. Tantu, Kawilarang W. A. Masengi, Atsushi J. Nagano, Junko Kusumi, Nina Yasuda, Kazunori Yamahira
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0213300
Technological improvements or climate change? Bayesian modeling of time-varying conformance to Benford’s Law
Cited by: 2
Author(s): Junho Lee, Miguel de Carvalho
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0034791
The Escherichia coli SOS Gene dinF Protects against Oxidative Stress and Bile Salts
Cited by: 36
Author(s): Jerónimo Rodríguez-Beltrán, Alexandro Rodríguez‐Rojas, Javier R. Guelfo, Alejandro Couce, Jesús Blázquez
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0215504
Arsenite malignantly transforms human prostate epithelial cells in vitro by gene amplification of mutated KRAS
Cited by: 17
Author(s): B. Alex Merrick, Dhiral Phadke, Meredith A. Bostrom, Ruchir Shah, Garron M. Wright, Xinguo Wang, Oksana Gordon, Katherine E. Pelch, Scott S. Auerbach, Richard S. Paules, Michael J. DeVito, Michael P. Waalkes, Erik J. Tokar
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0041283
Metagenomic Annotation Networks: Construction and Applications
Cited by: 15
Author(s): Gregory Vey, Gabriel Moreno‐Hagelsieb
Software Mentions: 2
Published: over 12 years ago
10.1186/1471-2164-13-599
Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening
Cited by: 49
Author(s): Carla S. Santos, Miguel Pinheiro, Ana Isabel Silva, Conceição Egas, Marta W. Vasconcelos
Software Mentions: 2
Published: about 12 years ago
10.1093/database/baaa114
CorkOakDB—The Cork Oak Genome Database Portal
Cited by: 8
Author(s): Cirenia Arias-Baldrich, Marta Contreiras Silva, Filippo Bergeretti, Inês Chaves, Celia María Gonzalo Miguel, Nelson J. M. Saibo, Daniel Sobral, Daniel Faria, Pedro M. Barros
Software Mentions: 2
Published: almost 5 years ago
10.1242/dmm.025239
Genomic profiling of murine mammary tumors identifies potential personalized drug targets for p53 deficient mammary cancers
Cited by: 27
Author(s): Adam D. Pfefferle, Yash N. Agrawal, Daniel C. Koboldt, Krishna L. Kanchi, Jason I. Herschkowitz, Elaine R. Mardis, Jeffrey M. Rosen, Charles M. Perou
Software Mentions: 2
Published: almost 9 years ago
10.1186/s13023-016-0462-7
The rare and undiagnosed diseases diagnostic service – application of massively parallel sequencing in a state-wide clinical service
Cited by: 44
Author(s): Gareth Baynam, Nicholas Pachter, Fiona McKenzie, Sharon Townshend, Jennie Slee, Cathy Kiraly-Borri, Anand Vasudevan, Anne Hunsaker Hawkins, Stephanie Broley, Lyn Schofield, Hedwig Verhoef, Caroline E. Walker, Caron Molster, Jenefer M. Blackwell, Sarra E. Jamieson, Dave Tang, Timo Lassmann, Kym Mina, John Beilby, Mark Davis, Nigel G. Laing, Lesley Murphy, Tarun Weeramanthri, Hugh Dawkins, Jack Goldblatt
Software Mentions: 1
Published: over 8 years ago
10.1155/2016/6040124
FullSSR: Microsatellite Finder and Primer Designer
Cited by: 13
Author(s): Sebastián Metz, Juan Manuel Cabrera, Eva Carolina Rueda, Federico Giri, Patricia Susana Amavet
Software Mentions: 1
Published: over 8 years ago
10.3390/ani10081297
Population Genetic Analysis of Ten Geographically Isolated Tibetan Pig Populations
Cited by: 12
Author(s): Peng Shang, Wenting Li, Zhankun Tan, Jian Zhang, Shixiong Dong, Kejun Wang, Yangzom Chamba
Software Mentions: 1
Published: over 4 years ago
10.3390/ani9121123
Effects of Dietary Energy on Growth Performance, Rumen Fermentation and Bacterial Community, and Meat Quality of Holstein-Friesians Bulls Slaughtered at Different Ages
Cited by: 17
Author(s): Haibo Wang, Hang Li, Fei Wu, Xiaobing Qiu, Zhantao Yu, Wen-jing Niu, Yang He, Huawei Su, Binghai Cao
Software Mentions: 1
Published: almost 5 years ago
10.1093/aob/mcab102
The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights
Cited by: 15
Author(s): Hannes Becher, Robyn F. Powell, Brown Mr, Chris Metherell, Jaume Pellicer, Ilia J. Leitch, Alex D. Twyford
Software Mentions: 1
Published: over 3 years ago
10.3390/antibiotics9060339
The Basis for Natural Multiresistance to Phage in Pseudomonas aeruginosa
Cited by: 10
Author(s): Christine Pourcel, Cédric Midoux, Gilles Vergnaud, Libera Latino
Software Mentions: 1
Published: over 4 years ago