pypi: perl | Projects | Ecosyste.ms: Papers

10.1128/JVI.00787-20

Genome Number and Size Polymorphism in Zika Virus Infectious Units
Cited by: 13
Author(s): Nicole R. Sexton, Eric D Bellis, Reyes A. Murrieta, Mark Cole Spangler, Parker J. Cline, James Weger-Lucarelli, Gregory D. Ebel
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-9-203

Stage-specific gene expression during urediniospore germination in Puccinia striiformis f. sp tritici
Cited by: 55
Author(s): Yonghong Zhang, Zhibo Qu, Wenming Zheng, Bo Liu, Xiaojie Wang, Xiao‐Feng Xue, Liangsheng Xu, Lili Huang, Qingmei Han, Jie Zhao, Zhensheng Kang
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pbio.1002078

Numerous Transitions of Sex Chromosomes in Diptera
Cited by: 265
Author(s): Beatriz Vicoso, Doris Bachtrog
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-018-5069-z

Comparative genome analyses reveal sequence features reflecting distinct modes of host-adaptation between dicot and monocot powdery mildew
Cited by: 33
Author(s): Ying Wu, Xiao Ma, Zhiyong Pan, Shiv D. Kale, Yi Song, Harlan King, Qiong Zhang, Christian Presley, Xiuxin Deng, Cheng–I Wei, Shaobo Xiao
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pcbi.0010073

Selective Constraint on Noncoding Regions of Hominid Genomes
Cited by: 25
Author(s): Eliot C. Bush, Bruce T. Lahn
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2156-13-92

Historically low mitochondrial DNA diversity in koalas (Phascolarctos cinereus)
Cited by: 24
Author(s): Kyriakos Tsangaras, María C. Ávila-Arcos, Yasuko Ishida, Kristofer M. Helgen, Alfred L. Roca, Alex D. Greenwood
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pgen.1005681

Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level
Cited by: 101
Author(s): Chandrasekhar Natarajan, Joana Projecto-Garcia, Hideaki Moriyama, Roy E. Weber, Violeta Muñoz-Fuentes, Andy J. Green, Cecilia Kopuchian, Pablo L. Tubaro, Luis Alza, Mariana Bulgarella, Matthew M. Smith, R. E. Wilson, Angela Fago, Kevin G. McCracken, Jay F. Storz
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12859-016-1286-0

Convert your favorite protein modeling program into a mutation predictor: “MODICT”
Cited by: 2
Author(s): Ibrahim Tanyalçin, Katrien Stouffs, Dorien Daneels, Carla Al Assaf, Willy Lissens, Anna Jansen, Alexander Gheldof
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-020-73715-8

Common origin of ornithine–urea cycle in opisthokonts and stramenopiles
Cited by: 9
Author(s): Aleš Horák, Andrew E. Allen, Miroslav Oborník
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pgen.1002512

EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development
Cited by: 113
Author(s): Sang Yeol Kim, Jung-Eun Lee, Leor Eshed Williams, Daniel Zilberman, Z. Renee Sung
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1006862

Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles
Cited by: 116
Author(s): James T. Robinson, Lisbeth A. Guethlein, Nezih Cereb, Soo Young Yang, Paul J. Norman, Steven G.E. Marsh, Peter Parham
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1001030

Tinkering Evolution of Post-Transcriptional RNA Regulons: Puf3p in Fungi as an Example
Cited by: 29
Author(s): Huifeng Jiang, Wenjun Guan, Zhenglong Gu
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1003471

Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona
Cited by: 82
Author(s): Zhemin Zhou, A. McCann, Eva Litrup, Ronan A. Murphy, Martin Cormican, Séamus Fanning, D. J. F. Brown, David S. Guttman, Sylvain Brisse, Mark Achtman
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-6-133

SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms
Cited by: 33
Author(s): Mark L. Crowe
Software Mentions: 1
Published: over 19 years ago

10.1186/s12967-018-1566-8

The TGFβ-signaling pathway and colorectal cancer: associations between dysregulated genes and miRNAs
Cited by: 33
Author(s): Andrew J. Pellatt, Lila E. Mullany, Jennifer S. Herrick, Lori C. Sakoda, Roger K. Wolff, Wade S. Samowitz, Martha L. Slattery
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pntd.0003771

Transcriptome Profiling and Genetic Study Reveal Amplified Carboxylesterase Genes Implicated in Temephos Resistance, in the Asian Tiger Mosquito Aedes albopictus
Cited by: 43
Author(s): Linda Grigoraki, Jacques Lagnel, Ilias Kioulos, Anastasia Kampouraki, Evangelia Morou, Pierrick Labbé, Mylène Weill, John Vontas
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-12-107

MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences
Cited by: 162
Author(s): Yonggan Wu, Bo Wei, Haizhou Liu, Tianxian Li, Simon Rayner
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2156-6-S1-S20

Investigation of altering single-nucleotide polymorphism density on the power to detect trait loci and frequency of false positive in nonparametric linkage analyses of qualitative traits
Cited by: 6
Author(s): Alison P. Klein, Ya Yu Tsai, Priya Duggal, Elizabeth M. Gillanders, Michael W. Barnhart, Rasika A. Mathias, Ian P. Dusenberry, Amy Turiff, Peter S. Chines, Janet L. Goldstein, Robert Wojciechowski, Wayne A. Hening, Elizabeth Pugh, Joan E. Bailey-Wilson
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pntd.0000947

Gender-Associated Genes in Filarial Nematodes Are Important for Reproduction and Potential Intervention Targets
Cited by: 27
Author(s): Ben-Wen Li, Amy C. Rush, Daojun Jiang, Makedonka Mitreva, Sahar Abubucker, Gary J. Weil
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0010473

Insights into the Influence of Priors in Posterior Mapping of Discrete Morphological Characters: A Case Study in Annonaceae
Cited by: 9
Author(s): Thomas L. P. Couvreur, Gerrit Gort, James E. Richardson, M.S.M. Sosef, Lars W. Chatrou
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2156-12-70

Molecular characterization of a long range haplotype affecting protein yield and mastitis susceptibility in Norwegian Red cattle
Cited by: 21
Author(s): Marte Sodeland, Harald Grove, Matthew Kent, S. Taylor, Mathias Tiedemann Svendsen, Ben J. Hayes, Sigbjørn Lien
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0010654

Analysis of Gene Order Conservation in Eukaryotes Identifies Transcriptionally and Functionally Linked Genes
Cited by: 48
Author(s): Marcela Dávila López, Juan José Martínez Guerra, Tore Samuelsson
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2156-14-56

High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI
Cited by: 18
Author(s): Xiaojun Huang, Hanlin Lu, Junwen Wang, Liqin Xu, Si Yang Liu, Jihua Sun, Fei Gao
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0018158

Identification of Novel SNPs in Glioblastoma Using Targeted Resequencing
Cited by: 17
Author(s): Andreas Keller, Christian Harz, Mark Matzas, Benjamin Meder, Hugo A. Katus, Nicole Ludwig, Ulrike Fischer, Eckart Meese
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0029435

RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336”
Cited by: 29
Author(s): Ranjit Kumar, Mark L. Lawrence, James Watt, Amanda M. Cooksey, Shane C. Burgess, Bindu Nanduri
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0235054

Insights into aphid prey consumption by ladybirds: Optimising field sampling methods and primer design for high throughput sequencing
Cited by: 7
Author(s): Lolita Ammann, Rosemary J. Moorhouse‐Gann, Jordan P. Cuff, Colette Bertrand, Laia Mestre, Nicolás Pérez Hidalgo, Amy Ellison, Félix Herzog, Martin H. Entling, Matthias Albrecht, William Oliver Christian Symondson
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0013532

Aging of Xenopus tropicalis Eggs Leads to Deadenylation of a Specific Set of Maternal mRNAs and Loss of Developmental Potential
Cited by: 18
Author(s): Anna Kosubek, Ludger Klein-Hitpaß, Katrin Rademacher, Bernhard Horsthemke, Gerhart U. Ryffel
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2148-6-77

Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids
Cited by: 135
Author(s): Zhengqiu Cai, Cynthia Peñaflor, Jennifer V. Kuehl, James H. Leebens‐Mack, John E. Carlson, Claude W. dePamphilis, Jeffrey L. Boore, Robert K. Jansen
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0090447

The Whole Set of Constitutive Promoters Recognized by RNA Polymerase RpoD Holoenzyme of Escherichia coli
Cited by: 90
Author(s): Tomohiro Shimada, Yukiko Yamazaki, Kan Tanaka, Akira Ishihama
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0078054

Transcriptome Analysis of Nautilus and Pygmy Squid Developing Eye Provides Insights in Lens and Eye Evolution
Cited by: 5
Author(s): Konstantinos Sousounis, Atsushi Ogura, Panagiotis A. Tsonis
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0067908

Targeted Enrichment: Maximizing Orthologous Gene Comparisons across Deep Evolutionary Time
Cited by: 61
Author(s): Shannon M. Hedtke, Matthew J. Morgan, David C. Cannatella, David M. Hillis
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0000650

Complete Mitochondrial Genome Sequence of Three Tetrahymena Species Reveals Mutation Hot Spots and Accelerated Nonsynonymous Substitutions in Ymf Genes
Cited by: 30
Author(s): Mike M. Moradian, Denis Beglaryan, Jill M. Skozylas, Varand Kerikorian
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0083177

Sequence Divergence and Conservation in Genomes of Helicobacter cetorum Strains from a Dolphin and a Whale
Cited by: 24
Author(s): Dangeruta Kersulyte, Mirko Rossi, Douglas E. Berg
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0134246

A Comprehensive Analysis of the Transcriptomes of Marssonina brunnea and Infected Poplar Leaves to Capture Vital Events in Host-Pathogen Interactions
Cited by: 13
Author(s): Cheng-Wen Chen, Ye Yao, Liang Zhang, Minjie Xu, Jianping Jiang, Tonghai Dou, Wei Lin, Guoping Zhao, Minren Huang, Yan Zhou
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0047450

Resolving Discrepancy between Nucleotides and Amino Acids in Deep-Level Arthropod Phylogenomics: Differentiating Serine Codons in 21-Amino-Acid Models
Cited by: 98
Author(s): Andreas Zwick, Jerome C. Regier, Derrick J. Zwickl
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0044031

Deep Insight into the Ganoderma lucidum by Comprehensive Analysis of Its Transcriptome
Cited by: 56
Author(s): Guojun Yu, Man Wang, Jinfeng Huang, Yalin Yin, Yijie Chen, Shuai Jiang, Yifei Jin, Xianqing Lan, Barry Hon Cheung Wong, Yi Liang, Hui Sun
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0128808

Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants
Cited by: 14
Author(s): Johannes A. Hofberger, Aldana M. Ramirez, Erik van den Bergh, Xin‐Guang Zhu, Harro J. Bouwmeester, Robert C. Schuurink, M. Eric Schranz
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0012725

Comparative Genome Analysis Reveals an Absence of Leucine-Rich Repeat Pattern-Recognition Receptor Proteins in the Kingdom Fungi
Cited by: 32
Author(s): Darren M. Soanes, Nicholas J. Talbot
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0024442

A Systematic Analysis of Eluted Fraction of Plasma Post Immunoaffinity Depletion: Implications in Biomarker Discovery
Cited by: 84
Author(s): Amit Kumar Yadav, Gourav Bhardwaj, Trayambak Basak, Dhirendra Kumar, Shadab Ahmad, Ruby Priyadarshini, Ashish Kumar Singh, Debasis Dash, Shantanu Sengupta
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0145365

Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci
Cited by: 47
Author(s): Robert S. Cornman, Clint R. V. Otto, Deborah D. Iwanowicz, Jeffery S. Pettis
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0133635

HPV Infection and Cervical Screening in Socially Isolated Indigenous Women Inhabitants of the Amazonian Rainforest
Cited by: 35
Author(s): Allex Jardim da Fonseca, Daniela Taeko, Thiciane Araújo Chaves, Lucia Dayanny da Costa Amorim, Raisa Saron Wanderley Murari, Angélica Espinosa Miranda, Zigui Chen, Robert D. Burk, Luíz Carlos Lima Ferreira
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0179545

Hypoxia Inducible Factor (HIF) transcription factor family expansion, diversification, divergence and selection in eukaryotes
Cited by: 66
Author(s): Allie M Graham, Jason S. Presnell
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0154279

Characterization of the Small RNA Transcriptome of the Marine Coccolithophorid, Emiliania huxleyi
Cited by: 11
Author(s): Xiaoyu Zhang, Jaime Gamarra, Steven Castro, Estela Carrasco, Aaron E Hernandez, Thomas Möck, Ahmad Hadaegh, Betsy Read
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0006659

Detection of Genomic Variation by Selection of a 9 Mb DNA Region and High Throughput Sequencing
Cited by: 11
Author(s): Sergey I. Nikolaev, Christian Iseli, Andrew J. Sharp, Daniel Robyr, Jacques Rougemont, Corinne Gehrig, Laurent Farinelli, Stylianos E. Antonarakis
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0155258

Comparative Genomics of Pathogens Causing Brown Spot Disease of Tobacco: Alternaria longipes and Alternaria alternata
Cited by: 34
Author(s): Yujie Hou, Xiao Ma, Wenting Wan, Ni Long, Jing Zhang, Yuntao Tan, Shengchang Duan, Yan Zeng, Yang Dong
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0246573

Recombinase polymerase amplification assay combined with a dipstick-readout for rapid detection of Mycoplasma ovipneumoniae infections
Cited by: 7
Author(s): Sandeep Gupta, Qing Deng, Tanushree B. Gupta, Paul Maclean, Joerg Jores, Axel Heiser, D. Neil Wedlock
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0059361

Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral Cavity
Cited by: 36
Author(s): Alisha G. Campbell, James H. Campbell, Patrick Schwientek, Tanja Woyke, Alexander Sczyrba, S. L. Allman, Clifford J. Beall, Ann L. Griffen, Eugene J. Leys, Mircea Podar
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0006263

Polyphasic Taxonomic Analysis Establishes Mycobacterium indicus pranii as a Distinct Species
Cited by: 78
Author(s): Vikram Saini, Saurabh Raghuvanshi, G.P. Talwar, Niyaz Ahmed, Jitendra P. Khurana, Seyed E. Hasnain, Akhilesh K. Tyagi, Anil K. Tyagi
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0001271

Analysis of the Neurotoxin Complex Genes in Clostridium botulinum A1-A4 and B1 Strains: BoNT/A3, /Ba4 and /B1 Clusters Are Located within Plasmids
Cited by: 150
Author(s): Theresa J. Smith, Karen K. Hill, Brian Foley, John C. Detter, A. Christine Munk, David Bruce, Norman A. Doggett, Leonard A. Smith, James D. Marks, Gary Xie, Thomas Brettin
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0169923

Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes
Cited by: 19
Author(s): Gregory J. Boyle, Kerstin Richter, Henry D. Priest, David Traver, Todd C. Mockler, Jeffrey T. Chang, Steve A. Kay, Ghislaı̀n Breton
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0157908

Dissecting the Root Nodule Transcriptome of Chickpea (Cicer arietinum L.)
Cited by: 20
Author(s): Chandra Kant, Seema Pradhan, Sabhyata Bhatia
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0165366

Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse
Cited by: 42
Author(s): Deborah D. Iwanowicz, Amy G. Vandergast, Robert S. Cornman, Cynthia R. Adams, Joshua R. Kohn, Robert N. Fisher, Cheryl S. Brehme
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0111893

Gun Possession among American Youth: A Discovery-Based Approach to Understand Gun Violence
Cited by: 31
Author(s): Kelly V. Ruggles, Sonali Rajan
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0032833

UniDrug-Target: A Computational Tool to Identify Unique Drug Targets in Pathogenic Bacteria
Cited by: 18
Author(s): Sree Krishna Chanumolu, Chittaranjan Rout, Rajinder Singh Chauhan
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0055741

Intravenous Glial Growth Factor 2 (GGF2) Isoform of Neuregulin-1β Improves Left Ventricular Function, Gene and Protein Expression in Rats after Myocardial Infarction
Cited by: 34
Author(s): Michael Hill, Amish V. Patel, A. Murphy, Holly Smith, Cristi L. Galindo, Laura Pentassuglia, Xiao Peng, Carrie Geisberg Lenneman, Oghenerukevwe Odiete, David Friedman, Marvin W. Kronenberg, Siyuen Zheng, Zhongming Zhao, Yanna Song, Frank E. Harrell, Maya Srinivas, Anindita Ganguly, Jennifer F. Iaci, Tom J. Parry, Anthony O. Caggiano, Douglas B. Sawyer
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0100448

sgRNAcas9: A Software Package for Designing CRISPR sgRNA and Evaluating Potential Off-Target Cleavage Sites
Cited by: 285
Author(s): Shengsong Xie, Bin Shen, Chaobao Zhang, Xingxu Huang, Yonglian Zhang
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0075149

Development and Characterization of Genomic and Expressed SSRs in Citrus by Genome-Wide Analysis
Cited by: 63
Author(s): Shengrui Liu, Wenyang Li, Dang Long, Chun-Gen Hu, Jin‐Zhi Zhang
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0131800

Comparative Population Genomics of African Montane Forest Mammals Support Population Persistence across a Climatic Gradient and Quaternary Climatic Cycles
Cited by: 25
Author(s): Terrence C. Demos, Julian C. Kerbis Peterhans, Tyler Joseph, John D. Robinson, Bernard Agwanda, Michael J. Hickerson
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0007539

Deep Sequencing of the Small RNAs Derived from Two Symptomatic Variants of a Chloroplastic Viroid: Implications for Their Genesis and for Pathogenesis
Cited by: 83
Author(s): Francesco Di Serio, Andreas Gisel, Beatriz Navarro, Sonia Delgado, Ángel Emilio Martínez de Alba, Giacinto Donvito, Ricardo Flores
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0021298

Genome-Wide Distribution and Organization of Microsatellites in Plants: An Insight into Marker Development in Brachypodium
Cited by: 184
Author(s): Humira Sonah, Rupesh Deshmukh, Anshul Sharma, V. P. Singh, Deepak Kumar Gupta, Raju N. Gacche, Jai Chand Rana, Nagendra Singh, Tilak Raj Sharma
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0058419

Endometrial Receptivity: A Revisit to Functional Genomics Studies on Human Endometrium and Creation of HGEx-ERdb
Cited by: 58
Author(s): Sonali R. Bhagwat, Darshan S. Chandrashekar, Ruchi Kakar, Sravanthi Davuluri, Akhilesh Kumar Bajpai, Sumeet Nayak, Sumit Bhutada, Kshitish K. Acharya, Geetanjali Sachdeva
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0002300

Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis
Cited by: 168
Author(s): Darren M. Soanes, Intikhab Álam, Mike Cornell, Han Min Wong, Cornelia Hedeler, Norman W. Paton, Magnus Rattray, Simon J. Hubbard, Stephen G. Oliver, Nicholas J. Talbot
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0048650

De Novo Origin of Protein-Coding Genes in Murine Rodents
Cited by: 45
Author(s): Daniel N. Murphy, Aoife McLysaght
Software Mentions: 1
Published: about 12 years ago

10.1186/1751-0473-2-5

OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences
Cited by: 12
Author(s): Guozhen Liu, Monica Uddin, Munirul Islam, Morris Goodman, Lawrence I. Grossman, Roberto Romero, Derek E. Wildman
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0018634

Discretization Provides a Conceptually Simple Tool to Build Expression Networks
Cited by: 6
Author(s): J. Keith Vass, Desmond J. Higham, Manikhandan Mudaliar, Xuerong Mao, Daniel Crowther
Software Mentions: 1
Published: over 13 years ago

10.1186/s13029-014-0031-1

AdmixKJump: identifying population structure in recently diverged groups
Cited by: 0
Author(s): Timothy D. O’Connor
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0024106

Genetic Evidence Supporting the Association of Protease and Protease Inhibitor Genes with Inflammatory Bowel Disease: A Systematic Review
Cited by: 31
Author(s): Isabelle Cleynen, Peter Jüni, Geertruida E Bekkering, Eveline Nüesch, Camila T. Mendes, Stéfanie Schmied, Stefan Wyder, Eliane Kellen, Peter M. Villiger, Paul Rutgeerts, Séverine Vermeire, Daniel Lottaz
Software Mentions: 1
Published: about 13 years ago

10.1186/s13029-016-0055-9

Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines
Cited by: 2
Author(s): John M. MacDonald, Paul C. Boutros
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0077423

Quantitative Phosphoproteome Analysis Unveils LAT as a Modulator of CD3ζ and ZAP-70 Tyrosine Phosphorylation
Cited by: 26
Author(s): Mogjiborahman Salek, Simon J. McGowan, David C. Trudgian, Omer Dushek, Ben de Wet, Georgios Efstathiou, Oreste Acuto
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0023289

Comparison of the ‘Ca. Liberibacter asiaticus’ Genome Adapted for an Intracellular Lifestyle with Other Members of the Rhizobiales
Cited by: 38
Author(s): John Hartung, Jonathan Shao, L. D. Kuykendall
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0071118

Genome-Wide Survey and Comparative Analysis of LTR Retrotransposons and Their Captured Genes in Rice and Sorghum
Cited by: 31
Author(s): Shu‐Ye Jiang, Srinivasan Ramachandran
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0201763

A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal
Cited by: 23
Author(s): Oliver Hawlitschek, Ángel Fernández‐González, Alfonso Balmori‐de la Puente, José Castresana
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0151780

Discovery of piRNAs Pathway Associated with Early-Stage Spermatogenesis in Chicken
Cited by: 7
Author(s): Liping Xu, Lingling Qiu, Guobin Chang, Qixin Guo, Xiangping Liu, Yue Bi, Yu Zhang, Hongzhi Wang, Zhiteng Li, Xiaoming Gao, Fang Wan, Yang Zhang, Qi Xu
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0011630

Polyploidy Did Not Predate the Evolution of Nodulation in All Legumes
Cited by: 70
Author(s): Steven B. Cannon, Daniel C. Ilut, Andrew Farmer, Sonja L. Maki, Gregory D. May, Susan R. Singer, Jeff J. Doyle
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0045777

Transcriptomic and Proteomic Analyses of a Wolbachia-Free Filarial Parasite Provide Evidence of Trans-Kingdom Horizontal Gene Transfer
Cited by: 21
Author(s): Samantha N. McNulty, Sahar Abubucker, Gabriel Simón, Makedonka Mitreva, Nathan P. McNulty, Kerstin Fischer, Kurt C. Curtis, Norbert W. Brattig, Gary J. Weil, Peter U. Fischer
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0066007

Characterization of Rice Black-Streaked Dwarf Virus- and Rice Stripe Virus-Derived siRNAs in Singly and Doubly Infected Insect Vector Laodelphax striatellus
Cited by: 49
Author(s): Junmin Li, Ida Bagus Andika, Jiangfeng Shen, Yuanda Lv, Yongqiang Ji, Liying Sun, Jianping Chen
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0104998

In-Cell Intrabody Selection from a Diverse Human Library Identifies C12orf4 Protein as a New Player in Rodent Mast Cell Degranulation
Cited by: 13
Author(s): Elsa Mazuc, Laurence Guglielmi, Nicole Bec, Vincent Perreten, Chang S. Hahn, Caroline Mollévi, Hugues Parrinello, Jean-Pierre Desvignes, Christian Larroque, Jupp Ray, Piona Dariavach, Pierre Martineau
Software Mentions: 1
Published: over 10 years ago

10.1186/s40793-015-0019-8

High-quality genome sequence and description of Bacillus dielmoensis strain FF4T sp. nov.
Cited by: 17
Author(s): Cheikh Ibrahima Lo, Roshan Padhmanabhan, Oleg Mediannikov, Jérôme Terras, Caroline Robert, N. Faye, Didier Raoult, Pierre‐Edouard Fournier, Florence Fénollar
Software Mentions: 1
Published: over 9 years ago

10.1186/s40793-015-0083-0

Genome sequence and description of Pantoea septica strain FF5
Cited by: 4
Author(s): Cheikh Ibrahima Lo, Roshan Padhmanabhan, Oleg Mediannikov, Thi Tien Nguyen, Didier Raoult, Pierre‐Edouard Fournier, Florence Fénollar
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0040430

Metagenomic Insights into the Fibrolytic Microbiome in Yak Rumen
Cited by: 83
Author(s): Xin Dai, Yaxin Zhu, Yingfeng Luo, Lei Song, Di Liu, Li Liu, Fu‐Rong Chen, Min Wang, Jiabao Li, Xiaowei Zeng, Zhiyang Dong, Songnian Hu, Lingyan Li, Jian Xu, Li Huang, Xiuzhu Dong
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0159648

An Optimized Method for Accurate Fetal Sex Prediction and Sex Chromosome Aneuploidy Detection in Non-Invasive Prenatal Testing
Cited by: 19
Author(s): Ting Wang, Quanze He, Haibo Li, Jie Ding, Ping Wen, Qin Zhang, Jingjing Xiang, Qiong Li, Xuan Liu, Lingyin Kong, Yan Mao, Yijun Zhu, Jin Shen, Bo Liang, Hong Li
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0059779

Sodium Laurate, a Novel Protease- and Mass Spectrometry-Compatible Detergent for Mass Spectrometry-Based Membrane Proteomics
Cited by: 42
Author(s): Yong Lin, Linju Huo, Liu Z, Jianglin Li, Yi Liu, Quanze He, Xianchun Wang, Songping Liang
Software Mentions: 1
Published: over 11 years ago

10.1186/s12862-015-0393-2

Horizontal gene transfer and genome evolution in Methanosarcina
Cited by: 13
Author(s): Sofya K. Garushyants, Marat D. Kazanov, Mikhail S. Gelfand
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0047310

Identification of an Abbreviated Test Battery for Detection of HIV-Associated Neurocognitive Impairment in an Early-Managed HIV-Infected Cohort
Cited by: 28
Author(s): David J. Moore, Mollie Roediger, Lynn E. Eberly, Kaitlin Blackstone, Braden Hale, Amy Weintrob, Anuradha Ganesan, Brian K. Agan, Scott Letendre, Nancy F. Crum-Cianflone
Software Mentions: 1
Published: about 12 years ago

10.1186/s12862-019-1563-4

A genome-skimmed phylogeny of a widespread bryozoan family, Adeonidae
Cited by: 8
Author(s): Russell J. S. Orr, Marianne Nilsen Haugen, Björn Berning, Philip E. Bock, Robyn L. Cumming, Wayne K. Florence, Masataka Hirose, Emanuela Di Martino, Mali H. Ramsfjell, Maja M. Sannum, Abigail M. Smith, Leandro M. Vieira, Andrea Waeschenbach, Lee Hsiang Liow
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0002442

Estimation of Isolation Times of the Island Species in the Drosophila simulans Complex from Multilocus DNA Sequence Data
Cited by: 57
Author(s): Shannon R. McDermott, Richard M. Kliman
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0146759

Comprehensive Map of Molecules Implicated in Obesity
Cited by: 17
Author(s): Jaisri Jagannadham, Hitesh Kumar Jaiswal, Stuti Agrawal, Kamal Rawal
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0091347

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics
Cited by: 4
Author(s): Bhaskar DasGupta, Kota Kasahara, Narutoshi Kamiya, Haruki Nakamura, Akira R. Kinjo
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0092166

Quantitative Proteomic Analysis of Gene Regulation by miR-34a and miR-34c
Cited by: 24
Author(s): Olivia A. Ebner, Matthias Selbach
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2148-8-260

Ultraconserved coding regions outside the homeobox of mammalian Hox genes
Cited by: 18
Author(s): Zhenguo Lin, Hong Mā, Masatoshi Nei
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0007686

Deep Sequencing of Viroid-Derived Small RNAs from Grapevine Provides New Insights on the Role of RNA Silencing in Plant-Viroid Interaction
Cited by: 129
Author(s): Beatriz Navarro, Vitantonio Pantaleo, Andreas Gisel, Simon Moxon, Tamás Dalmay, György Dénes Bisztray, Francesco Di Serio, József Burgyán
Software Mentions: 1
Published: about 15 years ago

10.1007/s13199-012-0154-6

Simultaneous genome sequencing of symbionts and their hosts
Cited by: 37
Author(s): Sujai Kumar, Mark Blaxter
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2148-11-122

Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways
Cited by: 60
Author(s): Yang Li, Chaoqun Li, Guohui Ding, Youxin Jin
Software Mentions: 1
Published: over 13 years ago

10.1016/j.dib.2015.10.042

“Controlled, cross-species dataset for exploring biases in genome annotation and modification profiles”
Cited by: 0
Author(s): Alison McAfee, Sarah Michaud, Leonard J. Foster
Software Mentions: 1
Published: almost 9 years ago

10.1016/j.dib.2018.08.011

New WGS data and annotation of the heterosomal vs. autosomal localization of Ostrinia scapulalis (Lepidoptera, Crambidae) nuclear genomic scaffolds
Cited by: 4
Author(s): Louise Brousseau, Sabine Nidelet, Réjane Streiff
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2148-5-39

Conservation of pregnancy-specific glycoprotein (PSG) N domains following independent expansions of the gene families in rodents and primates
Cited by: 32
Author(s): Andrew McLellan, Wolfgang Zimmermann, Tom Moore
Software Mentions: 1
Published: over 19 years ago

10.1093/database/bax013

GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii)
Cited by: 7
Author(s): Zhenzhen Xu, Jing Liu, NI Wan-chao, Zhen Peng, Yue Guo, Wuwei Ye, Fang Huang, Xianggui Zhang, Peng Xu, Qi Guo, Xinlian Shen, Jing Du
Software Mentions: 1
Published: almost 8 years ago

10.1093/database/bax005

The HIV oligonucleotide database (HIVoligoDB)
Cited by: 3
Author(s): João Carneiro, Adriana Resende, Filipe Pereira
Software Mentions: 1
Published: almost 8 years ago

10.1093/database/bav111

SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications
Cited by: 7
Author(s): Mir Asif Iquebal, Sarika Jaiswal, U. B. Angadi, Gaurav Sablok, Vasu Arora, Sunil Kumar, Anil Rai, Dinesh Kumar
Software Mentions: 1
Published: almost 10 years ago

10.1016/j.devcel.2014.01.030

Dedifferentiation of Neurons Precedes Tumor Formation in lola Mutants
Cited by: 68
Author(s): Tony D. Southall, Catherine M. Davidson, Claire Miller, Adrian R. Carr, Andrea H. Brand
Software Mentions: 1
Published: over 10 years ago

Projects: pypi: perl

Papers Mentioning perl 604