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: perl

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

Perl as a Python package
2 versions
Latest release: about 5 years ago
1 dependent package
6,426 downloads last month

Papers Mentioning perl 604

10.1186/s13068-015-0246-7
Uniconazole-induced starch accumulation in the bioenergy crop duckweed (Landoltia punctata) I: transcriptome analysis of the effects of uniconazole on chlorophyll and endogenous hormone biosynthesis
Cited by: 37
Author(s): Liuyan Yang, Yang Fang, Mengjun Huang, Yanling Jin, Jiaolong Sun, Tao Xiang, Zhang Guo-hua, Kai He, Yun Zhao, Hai Zhao
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2105-15-266
Natural language processing of radiology reports for the detection of thromboembolic diseases and clinically relevant incidental findings
Cited by: 80
Author(s): Anne-Dominique Pham, Aurélie Névéol, Thomas Lee, D Yasunaga, Olivier Clémеnt, Guy Meyer, Rémy Morello, Anita Burgun
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.ppat.1001037
Spliced Leader Trapping Reveals Widespread Alternative Splicing Patterns in the Highly Dynamic Transcriptome of Trypanosoma brucei
Cited by: 173
Author(s): Daniel Nilsson, Kapila Gunasekera, Jan Mani, Magne Østerås, Laurent Farinelli, Loic Bærlocher, Isabel Roditi, Torsten Ochsenreiter
Software Mentions: 2
Published: over 14 years ago
10.1186/1471-2164-15-1023
Comparative transcriptomic analyses revealed divergences of two agriculturally important aphid species
Cited by: 10
Author(s): Dahai Wang, Qi Liu, Huw Jones, Toby J. A. Bruce, Lanqin Xia
Software Mentions: 2
Published: almost 10 years ago
10.1186/1471-2105-10-160
IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico
Cited by: 27
Author(s): Tzong‐Yuan Wu, Chih‐Wei Hsieh, Jun-Jie Hong, Chung-Yung Chen, Yuh-Show Tsai
Software Mentions: 2
Published: over 15 years ago
10.1186/1745-6150-1-12
Cited by: 10
Author(s): Dimitris Papamichail, Nicholas Delihas
Software Mentions: 2
Published: almost 19 years ago
10.1186/gb-2012-13-10-r94
Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis
Cited by: 21
Author(s): Lidija Berke, Gabino F. Sánchez-Pérez, Berend Snel
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.ppat.1003579
Functional Specialization of the Small Interfering RNA Pathway in Response to Virus Infection
Cited by: 69
Author(s): João Trindade Marques, Ji Ping Wang, Xiaohong Wang, Karla Pollyanna Vieira de Oliveira, Catherine Gao, Eric Roberto Guimarães Rocha Aguiar, Nadereh Jafari, Richard W. Carthew
Software Mentions: 2
Published: about 11 years ago
10.1186/1471-2164-14-355
Phase-defined complete sequencing of the HLA genes by next-generation sequencing
Cited by: 106
Author(s): Kazuyoshi Hosomichi, Timothy A. Jinam, Shigeki Mitsunaga, Hirofumi Nakaoka, Ituro Inoue
Software Mentions: 2
Published: over 11 years ago
10.1534/g3.117.300405
Inter-replicon Gene Flow Contributes to Transcriptional Integration in the <i>Sinorhizobium meliloti</i> Multipartite Genome
Cited by: 14
Author(s): George C. diCenzo, Deelaka Wellappili, G. Brian Golding, Turlough M. Finan
Software Mentions: 2
Published: over 6 years ago
10.1186/1471-2164-15-423
CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data
Cited by: 134
Author(s): Zhifu Sun, Jared M. Evans, Aditya Bhagwate, Sumit Middha, Matthew A. Bockol, Huihuang Yan, Jean Pierre A. Kocher
Software Mentions: 2
Published: almost 11 years ago
10.1534/g3.119.400262
Developing a High-Quality Linkage Map for the Atlantic Killifish<i>Fundulus heteroclitus</i>
Cited by: 10
Author(s): Jeffrey T. Miller, Noah M. Reid, Diane Nacci, Andrew Whitehead
Software Mentions: 2
Published: about 5 years ago
10.1186/s12859-017-1799-1
Using machine learning algorithms to identify genes essential for cell survival
Cited by: 4
Author(s): Santosh Philips, Hui Wu, Lang Li
Software Mentions: 2
Published: about 7 years ago
10.3390/genes12081280
PlantMirP2: An Accurate, Fast and Easy-To-Use Program for Plant Pre-miRNA and miRNA Prediction
Cited by: 4
Author(s): Dashuai Fan, Yuangen Yao, Ming Yi
Software Mentions: 2
Published: over 3 years ago
10.1186/gb-2011-12-1-r7
Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi
Cited by: 182
Author(s): Anke Burmester, Ekaterina Shelest, Gernot Glöckner, Christoph Heddergott, Susann Schindler, Peter Staib, Andrew J. Heidel, Marius Felder, A. Petzold, Karol Szafranski, Marc Feuermann, Ivo Pedruzzi, Stefan Priebe, Marco Groth, Robert Winkler, Wenjun Li, Olaf Kniemeyer, Volker Schroeckh, Christian Hertweck, Bernhard Hube, Theodore C. White, Matthias Platzer, Reinhard Guthke, Joseph Heitman, Johannes Wöstemeyer, Peter F. Zipfel, Michel Monod, Axel A. Brakhage
Software Mentions: 2
Published: almost 14 years ago
10.1186/1756-0500-4-227
CANGS DB: a stand-alone web-based database tool for processing, managing and analyzing 454 data in biodiversity studies
Cited by: 5
Author(s): Ram Vinay Pandey, Viola Nolte, Jens Boenigk, Christian Schlötterer
Software Mentions: 2
Published: over 13 years ago
10.1186/1475-2875-8-88
WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures
Cited by: 36
Author(s): Vinod Kasam, Jean Salzemann, Marli Botha, Ana Dacosta, Gianluca Degliesposti, Raúl Isea, Doman Kim, Astrid Maaß, Colin Kenyon, Giulio Rastelli, Martin Hofmann‐Apitius, Vincent Breton
Software Mentions: 2
Published: over 15 years ago
10.1093/gbe/evz092
Ancient Polyploidy and Genome Evolution in Palms
Cited by: 24
Author(s): Craig F. Barrett, Michael R. McKain, Brandon T. Sinn, Xue Jun Ge, Yu‐Qu Zhang, Alexandre Antonelli, Christine D. Bacon
Software Mentions: 2
Published: over 5 years ago
10.3389/fpls.2017.01985
Transcriptomic Profiling and Physiological Responses of Halophyte Kochia sieversiana Provide Insights into Salt Tolerance
Cited by: 17
Author(s): Lijie Zhao, Zongze Yang, Qiaobing Guo, Shun Mao, Shaoqiang Li, Fasheng Sun, Huan Wang, Chunwu Yang
Software Mentions: 2
Published: almost 7 years ago
10.3389/fpls.2017.01519
Identification and Expression Profile of CYPome in Perennial Ryegrass and Tall Fescue in Response to Temperature Stress
Cited by: 29
Author(s): Tao Xiang, Mingxiu Wang, Yan Dai, Yan Wang, Yan-Fen Fan, Ping Mao, Xinrong Ma
Software Mentions: 2
Published: about 7 years ago
10.1186/s12864-015-1858-9
Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae)
Cited by: 25
Author(s): Francesco Lamanna, Frank Kirschbaum, Isabelle Waurick, Christoph Dieterich, Ralph Tiedemann
Software Mentions: 2
Published: about 9 years ago
10.1186/1756-0500-6-109
Cloud-based solution to identify statistically significant MS peaks differentiating sample categories
Cited by: 5
Author(s): Jun Ji, Jeffrey Ling, Helen Jiang, Qiaojun Wen, John C. Whitin, Lu Tian, Harvey J. Cohen, Xuefeng B. Ling
Software Mentions: 2
Published: over 11 years ago
10.1186/s12915-015-0132-6
snoRNAs are a novel class of biologically relevant Myc targets
Cited by: 44
Author(s): Eva K. Herter, Maria Stauch, Maria Gallant, Elmar Wolf, Thomas Raabe, Peter Gallant
Software Mentions: 2
Published: over 9 years ago
10.1038/s41598-018-30515-5
Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics
Cited by: 75
Author(s): Alejandra Escobar‐Zepeda, Elizabeth Ernestina Godoy-Lozano, Luciana Raggi, Lorenzo Segovia, Enrique Merino, Rosa Marı́a Gutièrrez-Rı́os, Katy Juarez, Alexei F. Licea-Navarro, Liliana Pardo-López, Alejandro Sánchez-Flores
Software Mentions: 2
Published: over 6 years ago
10.1186/1471-2229-8-66
A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance
Cited by: 57
Author(s): Marco Moroldo, Sophie Paillard, Raffaella Marconi, Fabrice Legeai, Aurélie Canaguier, Corinne Cruaud, Véronique de Berardinis, Cécile Guichard, Véronique Brunaud, Isabelle Le Clainche, Simone Scalabrin, R. Testolin, Gabriele Di Gaspero, Michèle Morgante, Anne-Françoise Adam-Blondon
Software Mentions: 2
Published: over 16 years ago
10.3390/ani10010053
Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes
Cited by: 13
Author(s): Siavash Salek Ardestani, Mehdi Aminafshar, Mohammad Bagher Zandi Baghche Maryam, Mohammad Hossein Banabazi, Mehdi Sargolzaei, Younes Miar
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12859-018-2576-5
iRODS metadata management for a cancer genome analysis workflow
Cited by: 3
Author(s): Lech Nieroda, Lukas Maas, Scott Thiebes, Ulrich Lang, Ali Sunyaev, Viktor Achter, Martin Peifer
Software Mentions: 2
Published: almost 6 years ago
10.3389/fmicb.2018.02524
Expression Patterns, Genomic Conservation and Input Into Developmental Regulation of the GGDEF/EAL/HD-GYP Domain Proteins in Streptomyces
Cited by: 31
Author(s): Mahmoud M. Al‐Bassam, Julian Haist, Sara Alina Neumann, Sandra Lindenberg, Natalia Tschowri
Software Mentions: 2
Published: about 6 years ago
10.3389/fmolb.2020.599142
Identification of Tumor Mutation Burden and Immune Infiltrates in Hepatocellular Carcinoma Based on Multi-Omics Analysis
Cited by: 17
Author(s): Yin Li, Liuzhi Zhou, Ruochen Xu
Software Mentions: 2
Published: almost 4 years ago
10.1186/1477-5956-5-4
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ TM
Cited by: 22
Author(s): Jennifer A. Siepen, Neil Swainston, Andrew R. Jones, Sarah R. Hart, Henning Hermjakob, Philip Jones, Simon J. Hubbard
Software Mentions: 2
Published: almost 18 years ago
10.1186/1471-2164-11-398
Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training
Cited by: 78
Author(s): Beatrice A. McGivney, Paul A. McGettigan, John A. Browne, A.C.O. Evans, R. Fonseca, Brendan J. Loftus, Amanda J. Lohan, David E. MacHugh, Barbara A. Murphy, Lisa Katz, E. W. Hill
Software Mentions: 2
Published: over 14 years ago
10.1186/s12870-017-1195-z
Comparative analysis of inverted repeats of polypod fern (Polypodiales) plastomes reveals two hypervariable regions
Cited by: 20
Author(s): Maria D. Logacheva, A.A. Krinitsina, Maxim S. Belenikin, K. Khafizov, Е. А. Коноров, С.В. Купцов, Anna S. Speranskaya
Software Mentions: 2
Published: almost 7 years ago
10.3389/fmolb.2021.659058
Phenotypic and Multi-Omics Characterization of Escherichia coli K-12 Adapted to Chlorhexidine Identifies the Role of MlaA and Other Cell Envelope Alterations Regulated by Stress Inducible Pathways in CHX Resistance
Cited by: 7
Author(s): Branden S. J. Gregorchuk, Shelby L Reimer, Kari A. C. Green, Nicola Helen Cartwright, Daniel R. Beniac, Shannon L Hiebert, Timothy F. Booth, Patrick Chong, Garrett Westmacott, George G. Zhanel, Denice C. Bay
Software Mentions: 2
Published: over 3 years ago
10.3390/v12070717
The Diversity and Distribution of Viruses Associated with Culex annulirostris Mosquitoes from the Kimberley Region of Western Australia
Cited by: 13
Author(s): Simon H. Williams, Avram Levy, Rachel A. Yates, Nilusha Somaweera, Peter J. Neville, Jay Nicholson, M.D. Lindsay, John S. Mackenzie, Komal Jain, Allison Imrie, David W. Smith, W. Ian Lipkin
Software Mentions: 2
Published: over 4 years ago
10.1186/1472-6793-9-23
Transcriptional profile of isoproterenol-induced cardiomyopathy and comparison to exercise-induced cardiac hypertrophy and human cardiac failure
Cited by: 90
Author(s): Cristi L. Galindo, Michael A. Skinner, Mounir Errami, Lyle Olson, David A. Watson, Jing Li, John McCormick, Lauren J. McIver, Neil M. Kumar, Thinh Q. Pham, Harold R. Garner
Software Mentions: 2
Published: almost 15 years ago
10.1186/1471-2164-14-54
Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction
Cited by: 72
Author(s): Miguel Redondo‐Nieto, Matthieu Barret, John P. Morrissey, Kieran J. Germaine, Francisco Martínez‐Granero, Emma Barahona, Ana Navazo, María Sánchez-Contreras, Jennifer A. Moynihan, Candela Muriel, David N. Dowling, Fergal O’Gara, Marta Martín, Rafael Rivilla
Software Mentions: 2
Published: almost 12 years ago
10.1186/1471-2164-12-142
Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis
Cited by: 13
Author(s): Zhixi Tian, Yong Yu, Feng Lin, Yeisoo Yu, Phillip SanMiguel, Rod A. Wing, Susan R. McCouch, Jianxin Ma, Scott A. Jackson
Software Mentions: 2
Published: over 13 years ago
10.3389/fmicb.2018.01577
Related Endogenous Retrovirus-K Elements Harbor Distinct Protease Active Site Motifs
Cited by: 6
Author(s): Matthew Turnbull, Renée N. Douville
Software Mentions: 2
Published: over 6 years ago
10.1186/1471-2105-7-S2-S19
An Automated Method for Rapid Identification of Putative Gene Family Members in Plants
Cited by: 6
Author(s): Ronald Frank, Ajay Mane, Fikret Erçal
Software Mentions: 2
Published: about 18 years ago
10.1186/1471-2180-13-252
Disturbance induced decoupling between host genetics and composition of the associated microbiome
Cited by: 104
Author(s): K. Mathias Wegner, Nils Volkenborn, Hannes Peter, Alexander Eiler
Software Mentions: 2
Published: almost 12 years ago
10.3389/fimmu.2020.618687
Integrated Analysis of circRNA-miRNA-mRNA Regulatory Networks in the Intestine of Sebastes schlegelii Following Edwardsiella tarda Challenge
Cited by: 15
Author(s): Min Cao, Yan Xu, Baofeng Su, Ning Yang, Qiang Fu, Ting Xue, Lin Song, Qi Li, Chao Li
Software Mentions: 2
Published: almost 4 years ago
10.3389/fmicb.2021.594075
Domestication Shapes the Community Structure and Functional Metagenomic Content of the Yak Fecal Microbiota
Cited by: 7
Author(s): Haibo Fu, Liangzhi Zhang, Chao Fan, Chuanfa Liu, Wenjing Li, Jiye Li, Xinquan Zhao, Shangang Jia, Yanming Zhang
Software Mentions: 2
Published: over 3 years ago
10.1186/s12864-020-6582-4
Evolution of PHAS loci in the young spike of Allohexaploid wheat
Cited by: 12
Author(s): Rongzhi Zhang, Siyuan Huang, Shiming Li, Guang Song, Yulian Li, Wei Li, Jihu Li, Jie Gao, Tiantian Gu, Dandan Li, Shujuan Zhang, Genying Li
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2164-13-249
IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes
Cited by: 29
Author(s): Alejandro Reyes, Andrea Sandoval, Andrés Cubillos-Ruiz, Katherine E. Varley, Iván Hernandez-Neuta, Sofía Samper, Carlos Martı́n, María Jesús García García, Viviana Ritacco, Lucelly López, Jaime Robledo, María Mercedes Zambrano, Robi D. Mitra, Patricia Del Portillo
Software Mentions: 2
Published: over 12 years ago
10.1186/1755-8794-3-1
Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information
Cited by: 104
Author(s): Yonqing Zhang, Supriyo De, John Garner, Kirstin Smith, S Alex Wang, Kevin G. Becker
Software Mentions: 2
Published: almost 15 years ago
10.1186/1755-8794-7-36
Whole genome sequencing reveals potential targets for therapy in patients with refractory KRASmutated metastatic colorectal cancer
Cited by: 17
Author(s): Vijayalakshmi Shanmugam, Ramesh K. Ramanathan, Nicole A. Lavender, Shripad Sinari, Manpreet K. Chadha, Winnie S. Liang, Ahmet Kurdoglu, Tyler Izatt, Alexis Christoforides, Hollie Benson, L Taylor Phillips, Angela Baker, Christopher W. Murray, Galen Hostetter, Daniel D. Von Hoff, David W. Craig, John D. Carpten
Software Mentions: 2
Published: over 10 years ago
10.1186/s12864-017-3948-3
Expansion and evolutionary patterns of cysteine-rich peptides in plants
Cited by: 17
Author(s): Lianxi Xing, Huping Zhang, Huijun Jiao, Leiting Li, Xin Qiao, Fabrice Musana Rwalinda, Juyou Wu, Shaoling Zhang
Software Mentions: 2
Published: over 7 years ago
10.1186/1471-2164-11-221
LEAPdb: a database for the late embryogenesis abundant proteins
Cited by: 78
Author(s): Gilles Hunault, Emmanuel Jaspard
Software Mentions: 2
Published: almost 15 years ago
10.3389/fgene.2014.00190
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome
Cited by: 34
Author(s): Joanna Moreton, Stephen Dunham, Richard D. Emes
Software Mentions: 2
Published: over 10 years ago
10.3389/fgene.2013.00199
The spliced leader trans-splicing mechanism in different organisms: molecular details and possible biological roles
Cited by: 28
Author(s): Mainá Bitar, Mariana Boroni, Andréa Mara Macedo, Carlos Renato Machado, Glória Regina Franco
Software Mentions: 2
Published: almost 12 years ago
10.1186/1471-2164-12-279
Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions
Cited by: 25
Author(s): Sota Fujii, Takushi Toda, Shunsuke Kikuchi, Rikako Suzuki, Koji Yokoyama, Hiroko Tsuchida, Kentarô Yano, Kinya Toriyama
Software Mentions: 2
Published: over 13 years ago
10.3389/fgene.2019.00251
Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish (Ictalurus punctatus)
Cited by: 35
Author(s): Shiyong Zhang, Xinhui Zhang, Xiaohui Chen, Tengfei Xu, Minghua Wang, Qin Qin, Liqiang Zhong, Hucheng Jiang, Xiaohua Zhu, Hongyan Liu, Junjie Shao, Zhiyuan Zhu, Qiong Shi, Wenji Bian, Xinxin You
Software Mentions: 2
Published: over 5 years ago
10.3389/fgene.2021.741858
Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed
Cited by: 4
Author(s): Pengfei Xu, Yujie Zhu, Yanfeng Zhang, Jianxia Jiang, Liyong Yang, Jianxin Mu, Xiang Yu, Yuqing He
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pbio.0050077
The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
Cited by: 1,787
Author(s): Douglas B. Rusch, Aaron L. Halpern, Granger Sutton, Karla B. Heidelberg, Shannon J. Williamson, Shibu Yooseph, Dongying Wu, Jonathan A. Eisen, Jeff Hoffman, Karin Remington, Karen Beeson, Benjamin Tran, Hamilton O. Smith, Holly Baden-Tillson, Clare Stewart, Joyce Thorpe, Jason Freeman, Cynthia Andrews-Pfannkoch, Joseph E. Venter, Kelvin Li, Saul Kravitz, John F. Heidelberg, Terry Utterback, Yu-Hui Rogers, Luisa I. Falcón, Valeria Souza, Germán Bonilla-Rosso, Luis E. Eguiarte, David M. Karl, Shubha Sathyendranath, Trevor Platt, Eldredge Bermingham, Víctor A. Gallardo, Giselle Tamayo‐Castillo, Michael R. Ferrari, Robert L. Strausberg, Kenneth H. Nealson, Robert M. Friedman, M.E. Frazier, J. Craig Venter
Software Mentions: 2
Published: over 17 years ago
10.1186/1471-2164-7-206
A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits
Cited by: 333
Author(s): Peter Wenzl, Haobing Li, Jason Carling, Meixue Zhou, Harsh Raman, E. M. Paul, P. Hearnden, Christina Maier, Xiujin Lan, Vanessa Caig, Jaroslava Ovesná, M. Çakır, David Me Poulsen, Junping Wang, Rosy Raman, Kevin P. Smith, Gary J. Muehlbauer, K. J. Chalmers, A. Kleinhofs, Eric Huttner, Andrzej Kilian
Software Mentions: 2
Published: over 18 years ago
10.3389/fbioe.2014.00048
Protein Network Signatures Associated with Exogenous Biofuels Treatments in Cyanobacterium Synechocystis sp. PCC 6803
Cited by: 11
Author(s): Guangsheng Pei, Lei Chen, Jiangxin Wang, Jianjun Qiao, Weiwen Zhang
Software Mentions: 2
Published: about 10 years ago
10.3389/fgene.2019.00105
Using Pan RNA-Seq Analysis to Reveal the Ubiquitous Existence of 5′ and 3′ End Small RNAs
Cited by: 14
Author(s): Xiao Xu, Haishuo Ji, Xiufeng Jin, Zhi Cheng, Xuemei Yao, Yanqiang Liu, Qiang Zhao, Tao Zhang, Jishou Ruan, Wenjun Bu, Ze Chen, Shan Gao
Software Mentions: 2
Published: almost 6 years ago
10.1155/2012/913709
In Silico RAPD Priming Sites in Expressed Sequences and iSCAR Markers for Oil Palm
Cited by: 9
Author(s): Balakrishnan Vasanthakumari Premkrishnan, V. Arunachalam
Software Mentions: 2
Published: almost 13 years ago
10.1093/database/baw041
The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development
Cited by: 20
Author(s): Meik Kunz, Chunguang Liang, Santosh Nilla, Alexander Cecil, Thomas Dandekar
Software Mentions: 2
Published: almost 9 years ago
10.1186/1471-2164-14-849
The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum
Cited by: 50
Author(s): Keerthi P. Venkataramanan, Shawn W. Jones, Kevin McCormick, Sridhara G. Kunjeti, Matthew T. Ralston, Blake C. Meyers, Eleftherios T. Papoutsakis
Software Mentions: 2
Published: almost 11 years ago
10.1186/1471-2105-6-S4-S14
Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control
Cited by: 20
Author(s): Giacomo Finocchiaro, Francesco Mancuso, Heiko Müller
Software Mentions: 2
Published: almost 19 years ago
10.1186/s12864-015-1566-5
Mitochondrial phylogenomics and genetic relationships of closely related pine moth (Lasiocampidae: Dendrolimus) species in China, using whole mitochondrial genomes
Cited by: 40
Author(s): Jie Qin, Yanzhou Zhang, Xin Zhou, Xiangbo Kong, Shu‐Jun Wei, Robert Ward, Aibing Zhang
Software Mentions: 2
Published: over 9 years ago
10.1155/2012/695827
Mutator-Like Elements with Multiple Long Terminal Inverted Repeats in Plants
Cited by: 9
Author(s): Ann A. Ferguson, Ning Jiang
Software Mentions: 2
Published: almost 13 years ago
10.1002/ece3.3924
Ancient pathogen DNA in human teeth and petrous bones
Cited by: 35
Author(s): Ashot Margaryan, Henrik Hansen, Simon Rasmussen, Martin Sikora, Vyacheslav Moiseyev, Alexandr Khoklov, Andrey Epimakhov, Levon Yepiskoposyan, Айвар Крийска, Liivi Varul, Lehti Saag, Niels Lynnerup, Eske Willerslev, Morten E. Allentoft
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0135978
Transcriptome Analysis of Liangshan Pig Muscle Development at the Growth Curve Inflection Point and Asymptotic Stages Using Digital Gene Expression Profiling
Cited by: 16
Author(s): Linyuan Shen, Jia Luo, Jing Du, Chendong Liu, Xiaoqian Wu, Qiang Pu, Yuhua Fu, Qianzi Tang, Yuanrui Liu, Qiang Li, Ronghua Yang, Xuewei Li, Guoqing Tang, Yanzhi Jiang, Mingzhou Li, Shunhua Zhang, Li Zhu
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0018561
Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads
Cited by: 194
Author(s): Paul D. Etter, Jessica L. Preston, Susan Bassham, William A. Cresko, Eric A. Johnson
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0000110
Unusually Long Palindromes Are Abundant in Mitochondrial Control Regions of Insects and Nematodes
Cited by: 33
Author(s): Kallare P. Arunkumar, Javaregowda Nagaraju
Software Mentions: 2
Published: almost 18 years ago
10.1186/s13148-017-0386-7
CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13-gene panel
Cited by: 44
Author(s): Luca Morandi, Davide Bartolomeo Gissi, Achille Tarsitano, Sofia Asioli, Andrea Gabusi, Claudio Marchetti, Lucio Montebugnoli, Maria Pia Foschini
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0066476
The Composition of Microbiome in Larynx and the Throat Biodiversity between Laryngeal Squamous Cell Carcinoma Patients and Control Population
Cited by: 66
Author(s): Hongli Gong, Yi Shi, Liang Zhou, Chunping Wu, Pengyu Cao, Lei Tao, Chen Xu, Dongsheng Hou, Yuezhu Wang
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0125989
Dicer-Dependent Biogenesis of Small RNAs and Evidence for MicroRNA-Like RNAs in the Penicillin Producing Fungus Penicillium chrysogenum
Cited by: 33
Author(s): Tim A. Dahlmann, Ulrich Kück
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0151673
Comparative Genomic Analysis of Escherichia coli O157:H7 Isolated from Super-Shedder and Low-Shedder Cattle
Cited by: 14
Author(s): Krysty Munns, Rahat Zaheer, Yong Xu, Kim Stanford, Chad R. Laing, Victor P. J. Gannon, L.B. Selinger, Tim A. McAllister
Software Mentions: 2
Published: over 8 years ago
10.1186/s12864-015-1534-0
Genome-wide identification of SSR and SNP markers from the non-heading Chinese cabbage for comparative genomic analyses
Cited by: 45
Author(s): Xiaoming Song, Tingting Ge, Ying Li, Xilin Hou
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0083383
New rRNA Gene-Based Phylogenies of the Alphaproteobacteria Provide Perspective on Major Groups, Mitochondrial Ancestry and Phylogenetic Instability
Cited by: 99
Author(s): Matteo P. Ferla, J. Cameron Thrash, Stephen J. Giovannoni, Wayne M. Patrick
Software Mentions: 2
Published: almost 11 years ago
10.1186/1471-2105-14-259
MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment
Cited by: 21
Author(s): Shuying Sun, Aaron Noviski, Xiaoqing Yu
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pone.0089673
SnapShot-Seq: A Method for Extracting Genome-Wide, In Vivo mRNA Dynamics from a Single Total RNA Sample
Cited by: 51
Author(s): Jesse Gray, David A. Harmin, Sarah A. Boswell, Nicole Cloonan, Thomas E. Mullen, Joseph J. Ling, Nimrod Miller, Scott Kuersten, Chao Yin, Steven A. McCarroll, Sean M. Grimmond, Michael Springer
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0180135
Reversible perturbations of gene regulation after genome editing in Drosophila cells
Cited by: 5
Author(s): Stefan Kunzelmann, Klaus Förstemann
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0075485
Genome Aberrations in Canine Mammary Carcinomas and Their Detection in Cell-Free Plasma DNA
Cited by: 45
Author(s): Julia Beck, Silvia Hennecke, Kirsten Bornemann-Kolatzki, Howard B. Urnovitz, Stephan Neumann, Philipp Ströbel, Franz‐Josef Kaup, Bertram Brenig, Ekkehard Schütz
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pone.0043350
Strand-Specific RNA-Seq Reveals Ordered Patterns of Sense and Antisense Transcription in Bacillus anthracis
Cited by: 23
Author(s): Karla D. Passalacqua, Anjana Varadarajan, Charlotte Weist, Brian D. Ondov, Benjamin Byrd, Timothy D. Read, Nicholas H. Bergman
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0054603
An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping
Cited by: 385
Author(s): Humira Sonah, Maxime Bastien, Elmer Iquira, Aurélie Tardivel, Gaétan Légaré, Brian Boyle, Éric Normandeau, Jérôme Laroche, Stéphane Larose, Martine Jean, François Belzile
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0255523
Finding inhibitors for PCSK9 using computational methods
Cited by: 12
Author(s): Rida Zainab, Afshan Kaleem, Michał B. Ponczek, Roheena Abdullah, Mehwish Iqtedar, Daniel C. Hoessli
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0079011
Genome-Wide Computational Prediction and Analysis of Core Promoter Elements across Plant Monocots and Dicots
Cited by: 45
Author(s): Sunita Kumari, Doreen Ware
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pntd.0001966
Temporal Dynamics of the Transcriptional Response to Dengue Virus Infection in Nicaraguan Children
Cited by: 51
Author(s): Stephen J. Popper, Aubree Gordon, Minghsun Liu, Ángel Balmaseda, Eva Harris, David A. Relman
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0027297
Pseudomonas syringae pv. actinidiae Draft Genomes Comparison Reveal Strain-Specific Features Involved in Adaptation and Virulence to Actinidia Species
Cited by: 118
Author(s): Simone Marcelletti, Patrizia Ferrante, Milena Petriccione, Giuseppe Firrao, M. Scortichini
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0035152
Characterization of Common Carp Transcriptome: Sequencing, De Novo Assembly, Annotation and Comparative Genomics
Cited by: 119
Author(s): Peifeng Ji, Guiming Liu, Jian Xu, Xumin Wang, Jiong-Tang Li, Zixia Zhao, Xiaofeng Zhang, Yan Zhang, Peng Xu, Xin Sun
Software Mentions: 2
Published: over 12 years ago
10.1186/1471-2164-13-481
Genome wide identification of chilling responsive microRNAs in Prunus persica
Cited by: 110
Author(s): Abdelali Bara­kat, Aditya Sriram, Joseph Park, Tetyana Zhebentyayeva, Dorrie Main, Albert Abbott
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0007853
The Peculiarities of Large Intron Splicing in Animals
Cited by: 62
Author(s): Samuel S. Shepard, Mark McCreary, Alexei Fedorov
Software Mentions: 2
Published: about 15 years ago
10.1371/journal.pgen.1004593
The Olfactory Transcriptomes of Mice
Cited by: 121
Author(s): Ximena Ibarra-Soria, Maria O. Levitin, Luís R. Saraiva, Darren W. Logan
Software Mentions: 2
Published: about 10 years ago
10.1186/1471-2164-15-929
Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents
Cited by: 2
Author(s): Nicholas J. Marra, J. Andrew DeWoody
Software Mentions: 2
Published: almost 11 years ago
10.1186/1471-2105-6-S4-S24
Web services and workflow management for biological resources
Cited by: 20
Author(s): Paolo Romano, Domenico Marra, Luciano Milanesi
Software Mentions: 2
Published: almost 19 years ago
10.1371/journal.pgen.1007298
Human local adaptation of the TRPM8 cold receptor along a latitudinal cline
Cited by: 66
Author(s): Felix M. Key, Muslihudeen A. Abdul-Aziz, Roger Mundry, Benjamin M. Peter, Aarthi Sekar, Mauro D’Amato, Megan Y. Dennis, Joshua M. Schmidt, Aida M. Andrés
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0094098
De Novo Transcriptome Hybrid Assembly and Validation in the European Earwig (Dermaptera, Forficula auricularia)
Cited by: 15
Author(s): Anne Roulin, Min Wu, Samuel Pichon, Roberto Arbore, Simone Kühn-Bühlmann, Mathias Kölliker, Jean‐Claude Walser
Software Mentions: 2
Published: over 10 years ago
10.1186/s12864-018-4775-x
TSVdb: a web-tool for TCGA splicing variants analysis
Cited by: 70
Author(s): Wenjie Sun, Ting Duan, Panmeng Ye, Kelie Chen, Guanling Zhang, Maode Lai, Honghe Zhang
Software Mentions: 2
Published: over 6 years ago
10.1186/1471-2164-7-171
Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species
Cited by: 127
Author(s): Boris A Legault, Arantxa López‐López, Jose Carlos Alba-Casado, W. Ford Doolittle, Henk Bolhuis, Francisco Rodríguez‐Valera, R. Thane Papke
Software Mentions: 2
Published: over 18 years ago
10.1371/journal.pgen.1002070
Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis
Cited by: 492
Author(s): Stephen B. Goodwin, Sarrah Ben M’Barek, Braham Dhillon, Alexander H. J. Wittenberg, Charles F. Crane, James K. Hane, Andrew J. Foster, Theo A. J. van der Lee, Jane Grimwood, Andrea Aerts, J. F. Antoniw, Andy M. Bailey, Burt H. Bluhm, Judith Bowler, Jim Bristow, Ate van der Burgt, Blondy Canto-Canché, Alice C. L. Churchill, Laura Conde-Ferráez, H. J. Cools, Pedro M. Coutinho, Michael Csukai, Paramvir Dehal, P.J.G.M. de Wit, Bruno Giuliano Garisto Donzelli, H.C. van de Geest, Roeland C. H. J. van Ham, K. E. Hammond‐Kosack, Bernard Henrissat, Andrzej Kilian, Adilson Kenji Kobayashi, Edda Koopmann, Yiannis A. I. Kourmpetis, Arnold Kuzniar, Erika Lindquist, Vincent Lombard, Chris Maliepaard, N. F. Martins, Rahim Mehrabi, Jan Peter Nap, A. Ponomarenko, J. J. Rudd, Asaf Salamov, Jeremy Schmutz, Henk J. Schouten, Harris Shapiro, Ioannis Stergiopoulos, Stefano F. F. Torriani, Hank Tu, Ronald P. de Vries, C. Waalwijk, S.B. Ware, Ad Wiebenga, L.H. Zwiers, Richard P. Oliver, Igor V. Grigoriev, G.H.J. Kema
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0002103
The Mosaic Genome of Anaeromyxobacter dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta-Proteobacteria
Cited by: 128
Author(s): Sara H. Thomas, Ryan D. Wagner, Adrián K. Arakaki, Jeffrey Skolnick, John R. Kirby, Lawrence J. Shimkets, Robert A. Sanford, Frank E. Löffler
Software Mentions: 2
Published: over 16 years ago
10.1371/journal.pone.0006447
Mining Biological Pathways Using WikiPathways Web Services
Cited by: 107
Author(s): Thomas Kelder, Alexander R. Pico, Kristina Hanspers, Martijn P. van Iersel, Chris T. Evelo, Bruce R. Conklin
Software Mentions: 2
Published: over 15 years ago
10.1371/journal.pone.0116696
Infection and Inflammation in Schizophrenia and Bipolar Disorder: A Genome Wide Study for Interactions with Genetic Variation
Cited by: 90
Author(s): Dimitrios Avramopoulos, Brad D. Pearce, John A. McGrath, Paula Wolyniec, Ruihua Wang, Nicole Eckart, Alexandros Hatzimanolis, Fernando S. Goes, Gerald Nestadt, Jennifer G. Mullé, Karen Coneely, Myfanwy Hopkins, Ingo Ruczinski, Robert H. Yolken, Ann E. Pulver
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0076502
Improved Detection of Rare HIV-1 Variants using 454 Pyrosequencing
Cited by: 11
Author(s): Brendan B. Larsen, Lennie Chen, Brandon S. Maust, Moon J. Kim, Hong Zhao, Wenjie Deng, Dylan H. Westfall, Ingrid Beck, Lisa M. Frenkel, James I. Mullins
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pone.0079501
Neuropsychological Deficits in Mice Depleted of the Schizophrenia Susceptibility Gene CSMD1
Cited by: 62
Author(s): Vidar M. Steen, Chirag Nepal, Kari Merete Ersland, Rita Holdhus, Marianne Nævdal, Siri M. Ratvik, Sverre Skrede, Bjarte Håvik
Software Mentions: 2
Published: about 11 years ago
10.1186/1471-2164-9-612
Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites
Cited by: 59
Author(s): Robert Kofler, Christian Schlötterer, Evita Luschützky, T. Lelley
Software Mentions: 2
Published: almost 17 years ago