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: mysql
https://packages.ecosyste.ms/registries/pypi.org/packages/mysql
Virtual package for MySQL-python
3 versions
Latest release: over 3 years ago
13 dependent packages
406,868 downloads last month
Papers Mentioning mysql 59
10.1371/journal.pone.0000737
ADaCGH: A Parallelized Web-Based Application and R Package for the Analysis of aCGH DataCited by: 26
Author(s): Ramón Díaz‐Uriarte, Oscar M. Rueda
Software Mentions: 8
Published: over 17 years ago
10.1038/sdata.2018.148
Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequencesCited by: 5
Author(s): Soo-Yon Rhee, Robert W. Shafer
Software Mentions: 7
Published: over 6 years ago
10.1093/database/baz151
LeukmiR: a database for miRNAs and their targets in acute lymphoblastic leukemiaCited by: 13
Author(s): Abdul Rawoof, Guruprasadh Swaminathan, Shrish Tiwari, Rekha A. Nair, Lekha Dinesh Kumar
Software Mentions: 7
Published: almost 5 years ago
10.1371/journal.pone.0064212
Differential Response of the Cynomolgus Macaque Gut Microbiota to Shigella InfectionCited by: 52
Author(s): Anna M. Seekatz, Aruna Panda, David A. Rasko, Franklin R. Toapanta, Emiley A. Eloe‐Fadrosh, Abdul Qayyum Khan, Zhenqiu Liu, Steven T. Shipley, Louis J. DeTolla, Marcelo B. Sztein, Claire M. Fraser
Software Mentions: 6
Published: over 11 years ago
10.3390/metabo8010016
RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and MetabolitesCited by: 27
Author(s): Bofei Zhang, Senyang Hu, Elizabeth Baskin, Andrew Patt, Jalal K. Siddiqui, Ewy A. Mathé
Software Mentions: 5
Published: over 6 years ago
10.1186/1471-2105-12-S15-S5
Data hosting infrastructure for primary biodiversity dataCited by: 13
Author(s): Anthony Goddard, Nevin Wilson, Phil Cryer, Grant Yamashita
Software Mentions: 5
Published: almost 13 years ago
10.1371/journal.pone.0028634
Gene Discovery in the Threatened Elkhorn Coral: 454 Sequencing of the Acropora palmata TranscriptomeCited by: 52
Author(s): Nicholas R. Polato, J. Cristobal Vera, Iliana B. Baums
Software Mentions: 5
Published: almost 13 years ago
10.1371/journal.pone.0085568
Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis PipelinesCited by: 58
Author(s): Oliver Rupp, J. Ole Becker, Karina Brinkrolf, Christina Timmermann, Nicole Borth, Alfred Pühler, Thomas Noll, Alexander Goesmann
Software Mentions: 5
Published: almost 11 years ago
10.1186/s12918-018-0566-x
KF-finder: identification of key factors from host-microbial networks in cervical cancerCited by: 15
Author(s): Jialu Hu, Yiqun Gao, Yanyan Zheng, Xuequn Shang
Software Mentions: 4
Published: over 6 years ago
10.1186/1471-2105-9-537
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum dataCited by: 28
Author(s): Fan Mo, Hong Xu, Feng Gao, Lin Du, Jun Wang, Gilbert S. Omenn, Biaoyang Lin
Software Mentions: 4
Published: almost 16 years ago
10.1186/1471-2105-10-221
An introduction to scripting in Ruby for biologistsCited by: 15
Author(s): Jan Aerts, Andy Law
Software Mentions: 4
Published: over 15 years ago
10.3390/biology10080790
agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal SpeciesCited by: 5
Author(s): Selina Klees, Felix Heinrich, Armin O. Schmitt, Mehmet Gültaş
Software Mentions: 3
Published: over 3 years ago
10.1186/1471-2407-6-36
Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysisCited by: 12
Author(s): Vladimir N. Babenko, Malay Kumar Basu, Fyodor A. Kondrashov, Igor B. Rogozin, Eugene V. Koonin
Software Mentions: 3
Published: almost 19 years ago
10.1186/gb-2009-10-4-r39
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactionsCited by: 64
Author(s): Jessica Severin, Andrew Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr J. Balwierz, Michiel de Hoon, David Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten O. Daub, Alistair R.R. Forrest
Software Mentions: 3
Published: almost 16 years ago
10.1038/s41598-019-55703-9
Significant effect of HIV/HAART on oral microbiota using multivariate analysisCited by: 20
Author(s): Ann L. Griffen, Zachary A. Thompson, Clifford J. Beall, Elizabeth A. Lilly, Carolina Granada, Kelly Treas, Kenneth R. DuBois, Shahr B. Hashmi, Chiranjit Mukherjee, Aubrey Gilliland, José Antonio Vázquez, Michael E. Hagensee, Eugene J. Leys, Paul L. Fidel
Software Mentions: 3
Published: almost 5 years ago
10.1093/database/bau111
CBMAR: a comprehensive β-lactamase molecular annotation resourceCited by: 35
Author(s): Abhishikha Srivastava, Neelja Singhal, Manisha Goel, Jugsharan Singh Virdi, Manish Kumar
Software Mentions: 3
Published: almost 11 years ago
10.1038/s41598-021-90799-y
KAUST Metagenomic Analysis Platform (KMAP), enabling access to massive analytics of re-annotated metagenomic dataCited by: 1
Author(s): Intikhab Álam, Allan Kamau, David Kamanda Ngugi, Takashi Gojobori, Carlos M. Duarte, Vladimir B. Bajić
Software Mentions: 3
Published: over 3 years ago
10.1093/database/baaa095
OUP accepted manuscriptCited by: 1
Author(s): Stéphane Télétchéa, Fabrice Teletchea
Software Mentions: 3
Published: almost 5 years ago
10.1093/database/bat069
Nencki Genomics Database—Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifsCited by: 20
Author(s): Izabella Krystkowiak, Jakub Lenart, Konrad J. Dębski, Piotr Kuterba, Michal Petas, Bożena Kamińska, Michał Dąbrowski
Software Mentions: 3
Published: almost 12 years ago
10.1186/s12859-018-2047-z
Oasis 2: improved online analysis of small RNA-seq dataCited by: 58
Author(s): Raza-Ur Rahman, Abhivyakti Gautam, Joern Bethune, Abdul Sattar, Maksims Fiošins, Daniel Sumner Magruder, Vincenzo Capece, Orr Shomroni, Stefan Bonn
Software Mentions: 3
Published: almost 7 years ago
10.1371/journal.pone.0111187
MitProNet: A Knowledgebase and Analysis Platform of Proteome, Interactome and Diseases for Mammalian MitochondriaCited by: 5
Author(s): Jiabin Wang, Jian Yang, Song Mao, Xiaoqiang Chai, Yang‐Gen Hu, Xugang Hou, Yiheng Tang, Cheng Bi, Xiao Li
Software Mentions: 3
Published: about 10 years ago
10.1177/2472555218818053
Unbiased Phenotype Detection Using Negative ControlsCited by: 2
Author(s): Antje Janosch, Carolin Kaffka, Marc Bickle
Software Mentions: 3
Published: over 5 years ago
10.7554/eLife.02866
Characterization of TSET, an ancient and widespread membrane trafficking complexCited by: 110
Author(s): Jennifer Hirst, Alexander Schlacht, J. P. Norcott, David Traynor, Gareth Bloomfield, Robin Antrobus, Robert R. Kay, Joel B. Dacks, Margaret S. Robinson
Software Mentions: 2
Published: over 10 years ago
10.1186/1471-2105-12-78
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometryCited by: 62
Author(s): Mi-Youn Brusniak, Sung-Tat Kwok, Mark Christiansen, D. S. Campbell, Lukas Reiter, Paola Picotti, Ulrike Kusebauch, Hector Ramos, Eric W. Deutsch, Jingchun Chen, Robert L. Moritz, Ruedi Aebersold
Software Mentions: 2
Published: over 13 years ago
10.1186/1471-2105-14-S7-S11
WEP: a high-performance analysis pipeline for whole-exome dataCited by: 42
Author(s): Mattia D’Antonio, Paolo D’Onorio De Meo, Daniele Paoletti, B Elmi, Matteo Pallocca, Nico Sanna, Ernesto Picardi, Graziano Pesole, Tiziana Castrignanò
Software Mentions: 2
Published: over 11 years ago
10.1186/1471-2105-11-269
Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification PipelineCited by: 16
Author(s): Joachim M. De Schrijver, Kim De Leeneer, Steve Lefever, Nick Sabbe, Filip Pattyn, Filip Van Nieuwerburgh, Paul Coucke, Dieter Deforce, Jo Vandesompele, Sofie Bekaert, Jan Hellemans, Wim Van Criekinge
Software Mentions: 2
Published: over 14 years ago
10.1186/s12864-018-5299-0
High-throughput ChIPmentation: freely scalable, single day ChIPseq data generation from very low cell-numbersCited by: 22
Author(s): Charlotte Gustafsson, Annick De Paepe, Christian Schmidl, Robert Månsson
Software Mentions: 2
Published: almost 6 years ago
10.1186/1471-2164-10-316
Genomic Resources of Magnaporthe oryzae (GROMO): A comprehensive and integrated database on rice blast fungusCited by: 8
Author(s): Shalabh Thakur, Sanjay Jha, Subhankar Roy-Barman, Bharat B. Chattoo
Software Mentions: 2
Published: over 15 years ago
10.1186/1471-2164-8-388
EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genomeCited by: 6
Author(s): Françoise Thibaud‐Nissen, Matthew A. Campbell, John Hamilton, Wei Zhu, C. Robin Buell
Software Mentions: 2
Published: about 17 years ago
10.1186/s12909-018-1136-z
A searchable database of medical education objectives – creating a comparable gold standardCited by: 2
Author(s): Sam Brooks, Namita Biala, Sage Arbor
Software Mentions: 2
Published: over 6 years ago
10.1155/2015/238139
Constructing a Genome-Wide LD Map of Wild<i>A. gambiae</i>Using Next-Generation SequencingCited by: 2
Author(s): Xiaohong Wang, Yaw A. Afrane, Guiyun Yan, Jun Li
Software Mentions: 2
Published: almost 10 years ago
10.1186/s13100-018-0142-3
Variation in proviral content among human genomes mediated by LTR recombinationCited by: 63
Author(s): Jainy Thomas, Hervé Perron, Cédric Feschotte
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0028436
Plantagora: Modeling Whole Genome Sequencing and Assembly of Plant GenomesCited by: 28
Author(s): Roger A. Barthelson, Adam J. McFarlin, Steven D. Rounsley, Sarah Young
Software Mentions: 2
Published: almost 13 years ago
10.1155/2016/1281379
ATIPS: Automatic Travel Itinerary Planning System for Domestic AreasCited by: 13
Author(s): Hsien-Tsung Chang, Yi-Ming Chang, Meng-Tze Tsai
Software Mentions: 2
Published: almost 9 years ago
10.3389/fmicb.2018.01591
Study the Features of 57 Confirmed CRISPR Loci in 38 Strains of Staphylococcus aureusCited by: 34
Author(s): Xihong Zhao, Zhixue Yu, Zhenbo Xu
Software Mentions: 2
Published: over 6 years ago
10.1155/2014/237243
Network-Based Analysis of Software Change PropagationCited by: 7
Author(s): Rongcun Wang, Rubing Huang, Binbin Qu
Software Mentions: 2
Published: almost 11 years ago
10.3390/s16111884
Internet of Things Platform for Smart Farming: Experiences and Lessons LearntCited by: 241
Author(s): Prem Prakash Jayaraman, Ali Yavari, Dimitrios Georgakopoulos, Ahsan Morshed, Arkady Zaslavsky
Software Mentions: 2
Published: about 8 years ago
10.1186/s12879-019-3934-2
Retention in care and virological failure among adult HIV+ patients on second-line ART in Rwanda: a national representative studyCited by: 12
Author(s): Sabin Nsanzimana, Muhammed Semakula, Vedaste Ndahindwa, Eric Remera, Dieudonné Sebuhoro, Jean Paul Uwizihiwe, Nathan Ford, Marcel Tanner, Steve Kanters, Edward J. Mills, Heiner C. Bucher
Software Mentions: 1
Published: over 5 years ago
10.1186/1471-2164-9-368
SoyXpress: A database for exploring the soybean transcriptomeCited by: 25
Author(s): Kei Chin Christine Cheng, Martina V. Strömvik
Software Mentions: 1
Published: almost 17 years ago
10.1002/ece3.3492
Patterns of genomic variation in Coho salmon following reintroduction to the interior Columbia RiverCited by: 8
Author(s): Nathan R. Campbell, Cory M. Kamphaus, Keely Murdoch, Shawn R. Narum
Software Mentions: 1
Published: about 7 years ago
10.3390/s21144871
Cognitive Accessibility and Support in Special EducationCited by: 4
Author(s): Miguel Angel Guillomía, J.I. Artigas, Jorge L. Falcó
Software Mentions: 1
Published: over 3 years ago
10.1534/g3.118.200503
The Sleep Inbred Panel, a Collection of Inbred <i>Drosophila melanogaster</i> with Extreme Long and Short Sleep DurationCited by: 13
Author(s): Yazmin L. Serrano Negron, Nancy F. Hansen, Susan T Harbison
Software Mentions: 1
Published: about 6 years ago
10.1186/gb-2005-6-4-r34
Cited by: 80Author(s): Charleen Moreau, N. V. Aksenov, Maribel García Lorenzo, Bo Segerman, Christiane Funk, Peter Nilsson, Stefan Jansson, Hannele Tuominen
Software Mentions: 1
Published: almost 20 years ago
10.1186/gb-2005-6-11-r90
Cited by: 107Author(s): Robert K. Tran, Daniel Zilberman, Cecilia Bustos, Renata Fava Ditt, Steven Henikoff, Anders M. Lindroth, Jeffrey J. Delrow, Tom Boyle, Samson Kwong, Terri D. Bryson, Steven E. Jacobsen, Steven Henikoff
Software Mentions: 1
Published: almost 20 years ago
10.1186/gb-2006-7-11-r111
Cited by: 18Author(s): Shannon D. Schlueter, Matthew D. Wilkerson, Qunfeng Dong, Volker Brendel
Software Mentions: 1
Published: almost 19 years ago
10.1186/1471-2164-9-277
Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomesCited by: 4
Author(s): Flavio Mignone, Anna Anselmo, Giacinto Donvito, G. Mäggi, Giorgio Grillo, Graziano Pesole
Software Mentions: 1
Published: almost 17 years ago
10.1186/s13326-019-0205-5
Phenotype annotation with the ontology of microbial phenotypes (OMP)Cited by: 9
Author(s): Deborah A. Siegele, Sandra LaBonte, Peter I-Fan Wu, Marcus C. Chibucos, Suvarna Nandendla, Michelle Giglio, James C. Hu
Software Mentions: 1
Published: over 5 years ago
10.1186/1471-2105-11-12
SKPDB: a structural database of shikimate pathway enzymesCited by: 29
Author(s): Helen Andrade Arcuri, Geraldo Francisco Donegá Zafalon, Evandro A. Marucci, Carlos Eduardo Bonalumi, Nelson José Freitas da Silveira, J.M. Machado, Walter Filgueira de Azevedo, Mário Sérgio Palma
Software Mentions: 1
Published: almost 15 years ago
10.1186/1471-2105-8-172
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeatsCited by: 862
Author(s): Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel
Software Mentions: 1
Published: over 17 years ago
10.1186/s12859-021-04312-3
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulonCited by: 4
Author(s): José Santos Oliveira, Miguel Antunes, Cláudia P. Godinho, Miguel C. Teixeira, Isabel Sá‐Correia, Pedro T. Monteiro
Software Mentions: 1
Published: over 3 years ago
10.1186/s12859-018-2237-8
Proteome-wide analysis of human motif-domain interactions mapped on influenza A virusCited by: 8
Author(s): Carlos A. García-Pérez, Xianwu Guo, Juan García Navarro, Diego Alonso Gómez Aguilar, Edgar E. Lara-Ramírez
Software Mentions: 1
Published: over 6 years ago
10.7189/jogh.11.04021
Social determinants and behaviors associated with overweight and obesity among youth and adults in a peri-urban area of Maputo City, MozambiqueCited by: 1
Author(s): Ivalda Macicame, António Prista, Klaus G. Parhofer, Nílzio Cavele, Cremildo Manhiça, Sheila Nhachungue, Elmar Saathoff, Eva Rehfuess
Software Mentions: 1
Published: over 3 years ago
10.3390/s101210752
Study of the Ubiquitous Hog Farm System Using Wireless Sensor Networks for Environmental Monitoring and Facilities ControlCited by: 32
Author(s): Jeong‐Hwan Hwang, Hyun Yoe
Software Mentions: 1
Published: almost 14 years ago
10.1371/journal.pone.0010699
Allelic Gene Structure Variations in Anopheles gambiae MosquitoesCited by: 7
Author(s): Jun Li, José M. C. Ribeiro, Guiyun Yan
Software Mentions: 1
Published: over 14 years ago
10.1186/1471-2105-6-72
Cited by: 17Author(s): SA Kirov, Xinxia Peng, Erich J. Baker, Denise D. Schmoyer, B Zhang, Jay Snoddy
Software Mentions: 1
Published: almost 20 years ago
10.3390/s17102273
Empowerment of Patients with Hypertension through BPM, IoT and Remote SensingCited by: 33
Author(s): Daniel Ruiz-Fernández, Diego Marcos-Jorquera, Virgilio Gilart-Iglesias, Víctor Vives-Boix, Javier Ramírez-Navarro
Software Mentions: 1
Published: about 7 years ago
10.1186/s13104-017-2556-2
India Allele Finder: a web-based annotation tool for identifying common alleles in next-generation sequencing data of Indian originCited by: 3
Author(s): Jimmy F. Zhang, F. Zachary James, Anju Shukla, Philippe M. Campeau, Alex R. Paciorkowski
Software Mentions: 1
Published: over 7 years ago
10.1186/s12909-019-1917-z
New doctor-patient communication learning software to help interns succeed in communication skillsCited by: 11
Author(s): Chao Sun, Junkai Zou, Lanbo Zhao, Qing Wang, Shaozhi Zhang, Qurat Ulain, Qing Song, Qiling Li
Software Mentions: 1
Published: almost 5 years ago