pypi: mysql | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0000737

ADaCGH: A Parallelized Web-Based Application and R Package for the Analysis of aCGH Data
Cited by: 26
Author(s): Ramón Díaz‐Uriarte, Oscar M. Rueda
Software Mentions: 8
Published: about 17 years ago

10.1038/sdata.2018.148

Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences
Cited by: 5
Author(s): Soo-Yon Rhee, Robert W. Shafer
Software Mentions: 7
Published: about 6 years ago

LeukmiR: a database for miRNAs and their targets in acute lymphoblastic leukemia
Cited by: 13
Author(s): Abdul Rawoof, Guruprasadh Swaminathan, Shrish Tiwari, Rekha A. Nair, Lekha Dinesh Kumar
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0064212

Differential Response of the Cynomolgus Macaque Gut Microbiota to Shigella Infection
Cited 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 Metabolites
Cited 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 data
Cited 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 Transcriptome
Cited by: 52
Author(s): Nicholas R. Polato, J. Cristobal Vera, Iliana B. Baums
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pone.0085568

Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis Pipelines
Cited 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: over 10 years ago

10.1186/s12918-018-0566-x

KF-finder: identification of key factors from host-microbial networks in cervical cancer
Cited 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 data
Cited 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 biologists
Cited by: 15
Author(s): Jan Aerts, Andy Law
Software Mentions: 4
Published: about 15 years ago

10.3390/biology10080790

agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal Species
Cited by: 5
Author(s): Selina Klees, Felix Heinrich, Armin O. Schmitt, Mehmet Gültaş
Software Mentions: 3
Published: about 3 years ago

10.1186/1471-2407-6-36

Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis
Cited by: 12
Author(s): Vladimir N. Babenko, Malay Kumar Basu, Fyodor A. Kondrashov, Igor B. Rogozin, Eugene V. Koonin
Software Mentions: 3
Published: over 18 years ago

10.1186/gb-2009-10-4-r39

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions
Cited 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: over 15 years ago

10.1038/s41598-019-55703-9

Significant effect of HIV/HAART on oral microbiota using multivariate analysis
Cited 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: over 4 years ago

10.1093/database/bau111

CBMAR: a comprehensive β-lactamase molecular annotation resource
Cited by: 35
Author(s): Abhishikha Srivastava, Neelja Singhal, Manisha Goel, Jugsharan Singh Virdi, Manish Kumar
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-021-90799-y

KAUST Metagenomic Analysis Platform (KMAP), enabling access to massive analytics of re-annotated metagenomic data
Cited 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 manuscript
Cited by: 1
Author(s): Stéphane Télétchéa, Fabrice Teletchea
Software Mentions: 3
Published: over 4 years ago

10.1093/database/bat069

Nencki Genomics Database—Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs
Cited by: 20
Author(s): Izabella Krystkowiak, Jakub Lenart, Konrad J. Dębski, Piotr Kuterba, Michal Petas, Bożena Kamińska, Michał Dąbrowski
Software Mentions: 3
Published: over 11 years ago

10.1186/s12859-018-2047-z

Oasis 2: improved online analysis of small RNA-seq data
Cited 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: over 6 years ago

10.1371/journal.pone.0111187

MitProNet: A Knowledgebase and Analysis Platform of Proteome, Interactome and Diseases for Mammalian Mitochondria
Cited 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: almost 10 years ago

10.1177/2472555218818053

Unbiased Phenotype Detection Using Negative Controls
Cited 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 complex
Cited 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 spectrometry
Cited 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 data
Cited 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 Pipeline
Cited 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-numbers
Cited by: 22
Author(s): Charlotte Gustafsson, Annick De Paepe, Christian Schmidl, Robert Månsson
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-10-316

Genomic Resources of Magnaporthe oryzae (GROMO): A comprehensive and integrated database on rice blast fungus
Cited by: 8
Author(s): Shalabh Thakur, Sanjay Jha, Subhankar Roy-Barman, Bharat B. Chattoo
Software Mentions: 2
Published: about 15 years ago

10.1186/1471-2164-8-388

EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome
Cited by: 6
Author(s): Françoise Thibaud‐Nissen, Matthew A. Campbell, John Hamilton, Wei Zhu, C. Robin Buell
Software Mentions: 2
Published: almost 17 years ago

10.1186/s12909-018-1136-z

A searchable database of medical education objectives – creating a comparable gold standard
Cited 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 Sequencing
Cited by: 2
Author(s): Xiaohong Wang, Yaw A. Afrane, Guiyun Yan, Jun Li
Software Mentions: 2
Published: over 9 years ago

10.1186/s13100-018-0142-3

Variation in proviral content among human genomes mediated by LTR recombination
Cited 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 Genomes
Cited 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 Areas
Cited by: 13
Author(s): Hsien-Tsung Chang, Yi-Ming Chang, Meng-Tze Tsai
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2018.01591

Study the Features of 57 Confirmed CRISPR Loci in 38 Strains of Staphylococcus aureus
Cited by: 34
Author(s): Xihong Zhao, Zhixue Yu, Zhenbo Xu
Software Mentions: 2
Published: about 6 years ago

10.1155/2014/237243

Network-Based Analysis of Software Change Propagation
Cited by: 7
Author(s): Rongcun Wang, Rubing Huang, Binbin Qu
Software Mentions: 2
Published: over 10 years ago

10.3390/s16111884

Internet of Things Platform for Smart Farming: Experiences and Lessons Learnt
Cited by: 241
Author(s): Prem Prakash Jayaraman, Ali Yavari, Dimitrios Georgakopoulos, Ahsan Morshed, Arkady Zaslavsky
Software Mentions: 2
Published: almost 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 study
Cited 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 transcriptome
Cited by: 25
Author(s): Kei Chin Christine Cheng, Martina V. Strömvik
Software Mentions: 1
Published: over 16 years ago

10.1002/ece3.3492

Patterns of genomic variation in Coho salmon following reintroduction to the interior Columbia River
Cited by: 8
Author(s): Nathan R. Campbell, Cory M. Kamphaus, Keely Murdoch, Shawn R. Narum
Software Mentions: 1
Published: almost 7 years ago

10.3390/s21144871

Cognitive Accessibility and Support in Special Education
Cited by: 4
Author(s): Miguel Angel Guillomía, J.I. Artigas, Jorge L. Falcó
Software Mentions: 1
Published: about 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 Duration
Cited 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: 80
Author(s): Charleen Moreau, N. V. Aksenov, Maribel García Lorenzo, Bo Segerman, Christiane Funk, Peter Nilsson, Stefan Jansson, Hannele Tuominen
Software Mentions: 1
Published: over 19 years ago

10.1186/gb-2005-6-11-r90

Cited by: 107
Author(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: over 19 years ago

10.1186/gb-2006-7-11-r111

Cited by: 18
Author(s): Shannon D. Schlueter, Matthew D. Wilkerson, Qunfeng Dong, Volker Brendel
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-9-277

Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes
Cited by: 4
Author(s): Flavio Mignone, Anna Anselmo, Giacinto Donvito, G. Mäggi, Giorgio Grillo, Graziano Pesole
Software Mentions: 1
Published: over 16 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: about 5 years ago

10.1186/1471-2105-11-12

SKPDB: a structural database of shikimate pathway enzymes
Cited 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: over 14 years ago

10.1186/1471-2105-8-172

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
Cited 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-regulon
Cited 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: about 3 years ago

10.1186/s12859-018-2237-8

Proteome-wide analysis of human motif-domain interactions mapped on influenza A virus
Cited 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: about 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, Mozambique
Cited 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 Control
Cited 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 Mosquitoes
Cited 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: 17
Author(s): SA Kirov, Xinxia Peng, Erich J. Baker, Denise D. Schmoyer, B Zhang, Jay Snoddy
Software Mentions: 1
Published: over 19 years ago

10.3390/s17102273

Empowerment of Patients with Hypertension through BPM, IoT and Remote Sensing
Cited by: 33
Author(s): Daniel Ruiz-Fernández, Diego Marcos-Jorquera, Virgilio Gilart-Iglesias, Víctor Vives-Boix, Javier Ramírez-Navarro
Software Mentions: 1
Published: almost 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 origin
Cited by: 3
Author(s): Jimmy F. Zhang, F. Zachary James, Anju Shukla, Philippe M. Campeau, Alex R. Paciorkowski
Software Mentions: 1
Published: about 7 years ago

10.1186/s12909-019-1917-z

New doctor-patient communication learning software to help interns succeed in communication skills
Cited by: 11
Author(s): Chao Sun, Junkai Zou, Lanbo Zhao, Qing Wang, Shaozhi Zhang, Qurat Ulain, Qing Song, Qiling Li
Software Mentions: 1
Published: over 4 years ago

Projects: pypi: mysql

Papers Mentioning mysql 59