Ecosyste.ms: Papers

10.1038/s41598-018-23931-0

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience
Cited by: 98
Author(s): Dinka Mandaković, Claudia Rojas, Jonathan Maldonado, Mauricio Latorre, Dante Travisany, Erwan Delage, Audrey Bihouée, Géraldine Jean, Francisco Javier Mato Díaz, Beatriz Fernández-Gómez, Pablo J. Cabrera, Alexis Gaete, Claudio Latorre, Rodrigo A. Gutiérrez, Alejandro Maass, Verónica Cambiazo, Sergio A. Navarrete, Damien Eveillard, Maurício González
Software Mentions: 3
Published: over 6 years ago

10.1186/s12915-020-00899-w

Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection
Cited by: 18
Author(s): Peter D. Olson, Alan S. Tracey, Andrew Baillie, Katherine James, Stephen R. Doyle, Sarah Kay Buddenborg, Faye H. Rodgers, Nancy Holroyd, Matthew Berriman
Software Mentions: 3
Published: about 4 years ago

10.1128/mSystems.00179-21

Gut Microbiome Structure and Association with Host Factors in a Korean Population
Cited by: 10
Author(s): Mi Young Lim, Seungpyo Hong, So-Jung Bang, Won‐Hyong Chung, Ji-Hee Shin, Jung-Ha Kim
Software Mentions: 3
Published: about 3 years ago

10.1093/gigascience/giz041

Bioportainer Workbench: a versatile and user-friendly system that integrates implementation, management, and use of bioinformatics resources in Docker environments
Cited by: 6
Author(s): Fabiano Bezerra Menegídio, David Aciole Barbosa, Rafael Dos S Gonçalves, Marcio M Nishime, Daniela Jabés, Regina Costa de Oliveira, Luiz R. Nunes
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0216233

A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set
Cited by: 37
Author(s): Boas Pucker, Daniela Holtgräwe, Kai Bernd Stadermann, Karl Frey, Bruno Huettel, Richard Reinhardt, Bernd Weißhaar
Software Mentions: 3
Published: over 5 years ago

10.1186/s12863-021-00981-4

Transcriptome profiling provides insights into the molecular mechanisms of maize kernel and silk development
Cited by: 0
Author(s): Ting Li, Yapeng Wang, Ying Shi, Xiaonan Gou, Bingpeng Yang, Jianzhou Qu, Xinghua Zhang, Jiquan Xue, Shutu Xu
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.0030022

Transition-Transversion Bias Is Not Universal: A Counter Example from Grasshopper Pseudogenes
Cited by: 138
Author(s): Irene Keller, Douda Bensasson, Richard A. Nichols
Software Mentions: 3
Published: almost 18 years ago

10.3390/ijms22179622

Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties
Cited by: 5
Author(s): Qionghou Li, Xin Qiao, Luting Jia, Yuxin Zhang, Shaoling Zhang
Software Mentions: 3
Published: about 3 years ago

10.3762/bjoc.16.105

Anthelmintic drug discovery: target identification, screening methods and the role of open science
Cited by: 28
Author(s): Frederick A. Partridge, Ruth Forman, Carole J. R. Bataille, Graham M. Wynne, Marina Nick, Angela J. Russell, Kathryn J. Else, David B. Sattelle
Software Mentions: 3
Published: over 4 years ago

10.1186/s41065-017-0043-3

Genotypic and phenotypic evaluation of off-type grasses in hybrid Bermudagrass [Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] putting greens using genotyping-by-sequencing and morphological characterization
Cited by: 6
Author(s): Eric H. Reasor, James T. Brosnan, Margaret Staton, Thomas Lane, Robert N. Trigiano, Phillip A. Wadl, Joann A. Conner, Brian M. Schwartz
Software Mentions: 2
Published: over 7 years ago

10.3390/antiox10071112

Activation of Adenosine A1 Receptor in Ischemic Stroke: Neuroprotection by Tetrahydroxy Stilbene Glycoside as an Agonist
Cited by: 10
Author(s): Ling-Yu Ruan, Guanghui Li, Wenlong Zhao, Huihui Meng, Qi Zheng, Junsong Wang
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-13-103

rCUR: an R package for CUR matrix decomposition
Cited by: 18
Author(s): András Bodor, István Csabai, Michael W. Mahoney, Norbert Solymosi
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2105-12-457

A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships
Cited by: 12
Author(s): Claire Lemaitre, Aurélien Barré, Christine Citti, Florence Tardy, François Thiaucourt, Pascal Sirand‐Pugnet, Patricia Thébault
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2105-11-556

Assessment and optimisation of normalisation methods for dual-colour antibody microarrays
Cited by: 23
Author(s): Martin Sill, Christoph Schröder, Jörg D. Hoheisel, Axel Benner, Manuela Zucknick
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2105-15-48

LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms
Cited by: 6
Author(s): Peng Yang, Min Wu, Jing Guo, Chee Keong Kwoh, Teresa M. Przytycka, Jie Zheng
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12915-017-0399-x

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution
Cited by: 240
Author(s): Evelyn E. Schwager, Prashant P. Sharma, Thomas H. Clarke, Daniel J. Leite, Torsten Wierschin, Matthias Pechmann, Yasuko Akiyama-Oda, Lauren A. Esposito, Jesper Bechsgaard, Trine Bilde, Alexandra D. Buffry, Hsu Chao, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Cornelius Eibner, Cassandra G. Extavour, Peter Funch, Jessica E. Garb, Luis Baudouin Gonzalez, Vanessa L. González, Sam Griffiths-Jones, Yi Han, Cheryl Y. Hayashi, Maarten Hilbrant, Daniel Hughes, Ralf Janßen, Sandra L. Lee, Ignacio Maeso, Shwetha C. Murali, Donna M. Muzny, Rodrigo Nunes da Fonseca, Christian Louis Bonatto Paese, Jiaxin Qu, Matthew Ronshaugen, Christoph Schomburg, Anna Schönauer, Angelika Stollewerk, Montserrat Torres-Oliva, Natascha Turetzek, Bram Vanthournout, John H. Werren, Carsten Wolff, Kim C. Worley, Gregor Bucher, Richard A. Gibbs, Jonathan A. Coddington, Hiroki Oda, Mario Stanke, Nadia A. Ayoub, Nikola-Michael Prpíc, Jean‐François Flot, Nico Posnien, Stephen Richards, Alistair P. McGregor
Software Mentions: 2
Published: over 7 years ago

10.1186/s12863-015-0222-z

Quantitative high resolution melting: two methods to determine SNP allele frequencies from pooled samples
Cited by: 15
Author(s): Roxana L Capper, Young Koo Jin, Petra Lundgren, Lesa M. Peplow, Mikhail V. Matz, Madeleine J. H. van Oppen
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-12-164

Taxonomically restricted genes are associated with the evolution of sociality in the honey bee
Cited by: 130
Author(s): Brian R. Johnson, Neil D. Tsutsui
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2164-15-545

A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements
Cited by: 106
Author(s): Hong-Seok Ha, Jimin Song, Shuoguo Wang, Aurélie Kapusta, Cédric Feschotte, Kevin C. Chen, Jinchuan Xing
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-018-5244-2

Do environmentally induced DNA variations mediate adaptation in Aspergillus flavus exposed to chromium stress in tannery sludge?
Cited by: 9
Author(s): Akanksha Jaiswar, Deepti Varshney, Alok Adholeya, Priyanka Prasad
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-018-5269-6

Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle
Cited by: 43
Author(s): Xiaoying Li, Yue Ma, Shuqing Liang, Yu Tian, Sanjun Yin, Shuhong Xie, Hua Xie
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-017-4394-y

Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion
Cited by: 23
Author(s): Juan Liu, Anupma Sharma, Marie Jamille Niewiara, Ratnesh Singh, Ray Ming, Qingyi Yu
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-019-6049-7

Combining next-generation sequencing and single-molecule sequencing to explore brown plant hopper responses to contrasting genotypes of japonica rice
Cited by: 13
Author(s): Jing Zhang, Wanqing Guan, Chao Huang, Yinxia Hu, Yu Chen, Jianping Guo, Cong Zhou, Rongzhi Chen, Bo Du, Lili Zhu, Danax Huanhan, Guangcun He
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-14-915

Transcriptome-wide profiling and expression analysis of transcription factor families in a liverwort, Marchantia polymorpha
Cited by: 25
Author(s): Niharika Sharma, Prem L. Bhalla, Mohan B. Singh
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-018-5192-x

A genome-scale metabolic model of potato late blight suggests a photosynthesis suppression mechanism
Cited by: 19
Author(s): Kelly Botero, Silvia Restrepo, Andrés Pinzón
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2164-15-626

LTR retroelements are intrinsic components of transcriptional networks in frogs
Cited by: 4
Author(s): José Horacio Grau, Albert J. Poustka, Martin Meixner, Jörg Plötner
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-018-5112-0

Genomic comparison of Trypanosoma conorhini and Trypanosoma rangeli to Trypanosoma cruzi strains of high and low virulence
Cited by: 14
Author(s): Katie R. Bradwell, Vishal N. Kopardé, Andrey V. Matveyev, Myrna G. Serrano, João M. P. Alves, Hardik I. Parikh, Bernice Huang, Vladimir Lee, Oneida Espinosa-Álvarez, Paola A. Ortíz, André G. Costa-Martins, Marta Maria Geraldes Teixeira, Gregory A. Buck
Software Mentions: 2
Published: about 6 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

10.1186/1755-8794-4-53

The functional cancer map: A systems-level synopsis of genetic deregulation in cancer
Cited by: 36
Author(s): Markus Krupp, T Maass, Jens U. Marquardt, Frank Staib, Tobias Bauer, Rainer König, Stefan Biesterfeld, Peter R. Galle, Achim Tresch, Andreas Teufel
Software Mentions: 2
Published: over 13 years ago

10.1186/s12866-021-02215-0

Comprehensive analysis of gut microbiota of a healthy population and covariates affecting microbial variation in two large Japanese cohorts
Cited by: 21
Author(s): Jonguk Park, Koichi Kato, Haruka Murakami, Koji Hosomi, Kumpei Tanisawa, Takashi Nakagata, Harumi Ohno, Kana Konishi, Hitoshi Kawashima, Yi An Chen, Attayeb Mohsen, Jin Xiao, Toshitaka Odamaki, Jun Kunisawa, Kenji Mizuguchi, Motohiko Miyachi
Software Mentions: 2
Published: over 3 years ago

10.1186/1472-6831-11-33

Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis
Cited by: 100
Author(s): Shi Huang, Fang Yang, Xiaowei Zeng, Jie Chen, Rui Li, Ting Wen, Chun Li, Wei Wei, Jiquan Liu, Lan Chen, Catherine Davis, Jian Xu
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2229-13-111

Sequencing-based variant detection in the polyploid crop oilseed rape
Cited by: 12
Author(s): Rachel Wells, Martin Trick, F C Fråser, Eleni Soumpourou, Leah Clissold, Colin Morgan, Jérôme Pauquet, Ian Bancroft
Software Mentions: 2
Published: over 11 years ago

10.1186/1756-0500-4-265

Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio
Cited by: 38
Author(s): Klas Hatje, Oliver Keller, Björn Hammesfahr, Holger Pillmann, Stephan Waack, Martin Kollmar
Software Mentions: 2
Published: over 13 years ago

10.1186/s13040-021-00251-0

Indels in SARS-CoV-2 occur at template-switching hotspots
Cited by: 23
Author(s): Brianna Chrisman, Kelley Paskov, Nate Stockham, Kevin Tabatabaei, Jae-Yoon Jung, Peter Washington, Maya Varma, Min Sun, Sepideh Maleki, Dennis P. Wall
Software Mentions: 2
Published: over 3 years ago

10.1186/s13062-015-0045-x

An atlas of mouse CD4+ T cell transcriptomes
Cited by: 75
Author(s): Michael J. T. Stubbington, Bidesh Mahata, Valentine Svensson, Andrew Deonarine, Jesper K. Nissen, Alexander G. Betz, Sarah A. Teichmann
Software Mentions: 2
Published: over 9 years ago

10.1155/2017/4751780

Identification of Potent Chloride Intracellular Channel Protein 1 Inhibitors from Traditional Chinese Medicine through Structure-Based Virtual Screening and Molecular Dynamics Analysis
Cited by: 7
Author(s): Wei Wang, Ming Wan, Dongjiang Liao, Guilin Peng, Xin Xu, Weiqiang Yin, Guixin Guo, Funeng Jiang, Weijie Zhong, Jianxing He
Software Mentions: 2
Published: almost 8 years ago

10.3390/biom11071040

Systematic Structure-Based Search for Ochratoxin-Degrading Enzymes in Proteomes from Filamentous Fungi
Cited by: 9
Author(s): Ana Lúcia Leitão, Francisco J. Enguita
Software Mentions: 2
Published: over 3 years ago

10.1111/bjop.12471

The cultural dimension of intergroup conspiracy theories
Cited by: 39
Author(s): Jan‐Willem van Prooijen, Mengdi Song
Software Mentions: 2
Published: over 4 years ago

10.1007/s10985-018-9423-x

The wild bootstrap for multivariate Nelson–Aalen estimators
Cited by: 11
Author(s): Tobias Bluhmki, Dennis Dobler, Jan Beyersmann, Markus Pauly
Software Mentions: 2
Published: over 6 years ago

10.1002/lno.11157

Ecology of a polymetallic nodule occurrence gradient: Implications for deep‐sea mining
Cited by: 61
Author(s): Erik Simon-Lledó, Brian J. Bett, Veerle Huvenne, Timm Schoening, Noëlie M.A. Benoist, Daniel O. B. Jones
Software Mentions: 2
Published: over 5 years ago

10.1007/s11306-014-0662-x

Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach
Cited by: 22
Author(s): Lucille Stuani, Christophe Lechaplais, Aaro V. Salminen, Béatrice Segurens, Maxime Durot, Vanina Castelli, Agnès Pinet, Karine Labadie, Stéphane Cruveiller, Jean Weissenbach, Véronique de Berardinis, Marcel Salanoubat, Alain Perret
Software Mentions: 2
Published: over 10 years ago

10.1186/s12934-018-1039-z

One-step affinity purification of fusion proteins with optimal monodispersity and biological activity: application to aggregation-prone HPV E6 proteins
Cited by: 3
Author(s): Anna Bonhoure, Auguste Demenge, Camille Kostmann, Leticia San José, Eva De la Cal, Pilar Armisén, Yves Nominé, Gilles Travé
Software Mentions: 2
Published: almost 6 years ago

10.3390/microorganisms8091391

A New Method for Next-Generation Sequencing of the Full Hepatitis B Virus Genome from A Clinical Specimen: Impact for Virus Genotyping
Cited by: 5
Author(s): Flávia Hebeler-Barbosa, Ivan Rodrigo Wolf, Guilherme Targino Valente, Francisco Campello do Amaral Mello, Elisabeth Lampe, Maria Inês de Moura Campos Pardini, Rejane Maria Tommasini Grotto
Software Mentions: 2
Published: about 4 years ago

10.1186/s43556-021-00050-3

Computationally repurposed drugs and natural products against RNA dependent RNA polymerase as potential COVID-19 therapies
Cited by: 9
Author(s): Sakshi Piplani, Puneet Kumar Singh, David A. Winkler, Nikolai Petrovsky
Software Mentions: 2
Published: about 3 years ago

10.1111/mec.13434

A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual
Cited by: 22
Author(s): Sebastian Eves‐van den Akker, Catherine J. Lilley, A. Reid, J. Pickup, Eric Anderson, Peter J. A. Cock, Mark Blaxter, Peter E. Urwin, John T. Jones, Vivian C. Blok
Software Mentions: 2
Published: almost 9 years ago

10.3390/molecules23071688

Theoretical Model of EphA2-Ephrin A1 Inhibition
Cited by: 4
Author(s): Wiktoria Jedwabny, Alessio Lodola, Edyta Dyguda-Kazimierowicz
Software Mentions: 2
Published: over 6 years ago

10.15252/msb.20209584

<scp>P</scp> recision design of stable genetic circuits carried in highly‐insulated <i>E. coli</i> genomic landing pads
Cited by: 31
Author(s): Yong‐Jin Park, Amin Espah Borujeni, Thomas E. Gorochowski, Jinwoo Shin, Christopher A. Voigt
Software Mentions: 2
Published: over 4 years ago

10.1080/21505594.2019.1593776

A unique aspartyl protease gene expansion in <i>Talaromyces marneffei</i> plays a role in growth inside host phagocytes
Cited by: 8
Author(s): Michael Payne, Harshini Weerasinghe, Irma Tedja, Alex Andrianopoulos
Software Mentions: 2
Published: almost 6 years ago

10.3390/v12101187

A Systematic Evaluation of High-Throughput Sequencing Approaches to Identify Low-Frequency Single Nucleotide Variants in Viral Populations
Cited by: 7
Author(s): David J. King, Graham Freimanis, Lidia Lasecka-Dykes, Amin S. Asfor, Paolo Ribeca, Ryan Waters, Donald P. King, Emma Laing
Software Mentions: 2
Published: about 4 years ago

10.7717/peerj.4842

Selective constraint acting on TLR2 and TLR4 genes of Japanese<i>Rana</i>frogs
Cited by: 7
Author(s): Quintin Lau, Takeshi Igawa, Tiffany A. Kosch, Yoko Satta
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.333

A cross-ocean comparison of responses to settlement cues in reef-building corals
Cited by: 22
Author(s): Sarah W. Davies, Eli Meyer, Sarah Guermond, Mikhail V. Matz
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.2074

DeepSNVMiner: a sequence analysis tool to detect emergent, rare mutations in subsets of cell populations
Cited by: 19
Author(s): Thomas D. Andrews, Yogesh Jeelall, Dipti Talaulikar, Christopher C. Goodnow, Matthew A. Field
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.4806

Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining
Cited by: 3
Author(s): Sanna M Kreula, Suwisa Kaewphan, Filip Ginter, Patrik R. Jones
Software Mentions: 2
Published: over 6 years ago

10.1098/rstb.2013.0379

Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing
Cited by: 52
Author(s): Matthew D. Teasdale, NL van Doorn, Sarah Fiddyment, Webb Cc, T. P. O'Connor, Michael Hofreiter, Matthew J. Collins, Daniel G. Bradley
Software Mentions: 2
Published: almost 10 years ago

10.3390/plants8100375

A Novel Stay-Green Mutant of Rice with Delayed Leaf Senescence and Better Harvest Index Confers Drought Tolerance
Cited by: 20
Author(s): M. K. Ramkumar, S. Kumar, Kishor Gaikwad, Ravi P. Pandey, Viswanathan Chinnusamy, Nagendra Singh, Ashok Kumar Singh, Trilochan Mohapatra, Amitha Mithra Sevanthi
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pcbi.1006256

Proteome-scale relationships between local amino acid composition and protein fates and functions
Cited by: 26
Author(s): Sean M. Cascarina, Eric D. Ross
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1008678

One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads
Cited by: 37
Author(s): Carlos Valiente-Mullor, Beatriz Beamud, Iván Ansari, Carlos Francés‐Cuesta, Neris García-González, Lorena Mejía, Paula Ruiz-Hueso, Fernando González‐Candelas
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pcbi.1006315

Irrelevance by inhibition: Learning, computation, and implications for schizophrenia
Cited by: 3
Author(s): Nathan Insel, Jordan Guerguiev, Blake A Richards
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1005631

GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data
Cited by: 28
Author(s): Thomas F. Cooke, Muh-Ching Yee, Marina Muzzio, Alexandra Sockell, Ryan T. Bell, Omar E. Cornejo, Joanna L. Kelley, Graciela Bailliet, Cláudio M. Bravi, Carlos D. Bustamante, Eimear E. Kenny
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pgen.1003915

FliZ Is a Global Regulatory Protein Affecting the Expression of Flagellar and Virulence Genes in Individual Xenorhabdus nematophila Bacterial Cells
Cited by: 24
Author(s): Grégory Jubelin, Anne Lanois, Dany Séverac, Stéphanie Rialle, C. F. H. Longin, Sophie Gaudriault, Alain Givaudan
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pgen.1001157

Balancing Selection Maintains a Form of ERAP2 that Undergoes Nonsense-Mediated Decay and Affects Antigen Presentation
Cited by: 209
Author(s): Aida M. Andrés, Megan Y. Dennis, Warren W. Kretzschmar, Jennifer L. Cannons, Shih-Queen Lee-Lin, Belén Hurlé, Nisc Comparative Sequencing Program, Pamela L. Schwartzberg, Scott Williamson, Carlos D. Bustamante, Rasmus Nielsen, Andrew G. Clark, Eric D. Green
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pgen.1005626

The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis
Cited by: 91
Author(s): Leszek P. Pryszcz, Tibor Németh, Ester Saus, Ewa Księżopolska, Eva Hegedűsová, Jozef Nosek, Kenneth H. Wolfe, Attila Gácser, Toni Gabaldón
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pgen.1004800

ATPase-Independent Type-III Protein Secretion in Salmonella enterica
Cited by: 75
Author(s): Marc Erhardt, Max E. Mertens, Florian Fabiani, Kelly T. Hughes
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pgen.1003464

Breakpoint Analysis of Transcriptional and Genomic Profiles Uncovers Novel Gene Fusions Spanning Multiple Human Cancer Types
Cited by: 101
Author(s): Craig P. Giacomini, Steven Sun, Sushama Varma, A. Hunter Shain, Marilyn M. Giacomini, Jay Michael S. Balagtas, Robert T. Sweeney, Everett Lai, Catherine A. Del Vecchio, Andrew D. Forster, Nicole Clarke, Kelli Montgomery, Shirley Zhu, Albert J. Wong, Matt van de Rijn, Robert B. West, Jonathan R. Pollack
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0189654

Facultative parthenogenesis validated by DNA analyses in the green anaconda (Eunectes murinus)
Cited by: 13
Author(s): Hiroki Shibata, Shuichi Sakata, Yuzo Hirano, Eiji Nitasaka, Ai Sakabe
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0252066

G protein-coupled receptors as candidates for modulation and activation of the chemical senses in decapod crustaceans
Cited by: 7
Author(s): Matthew T. Rump, Mihika T. Kozma, Shrikant Pawar, Charles D. Derby
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0165176

The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family
Cited by: 44
Author(s): Saura R. Silva, Yani C. A. Diaz, Helen Alves Penha, Daniel Guariz Pinheiro, Camila Cesário Fernandes, Vitor F. O. Miranda, Todd P. Michael, Alessandro M. Varani
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0173525

Neural correlates of conflict between gestures and words: A domain-specific role for a temporal-parietal complex
Cited by: 17
Author(s): J. Adam Noah, Swethasri Dravida, Xian Zhou, Shaul Yahil, Joy Hirsch
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0041709

Brain Transcriptional Responses to High-Fat Diet in Acads-Deficient Mice Reveal Energy Sensing Pathways
Cited by: 9
Author(s): Claudia Krüger, K. Ganesh Kumar, Randall L. Mynatt, Júlia Vólaufová, Brenda Richards
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0197123

Anti-angiogenic VEGFAxxxb transcripts are not expressed in the medio-basal hypothalamus of the seasonal sheep
Cited by: 10
Author(s): Didier Lomet, Benoît Piégu, Shona H. Wood, Hugues Dardente
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0123261

ClusTrack: Feature Extraction and Similarity Measures for Clustering of Genome-Wide Data Sets
Cited by: 3
Author(s): Halfdan Rydbeck, Geir Kjetil Sandve, Egil Ferkingstad, Boris Simovski, Morten Rye, Eivind Hovig
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0101631

Genetic Organization of Interphase Chromosome Bands and Interbands in Drosophila melanogaster
Cited by: 57
Author(s): И. Ф. Жимулев, Tatyana Yu Zykova, Fyodor P. Goncharov, V. A. Khoroshko, Olga V. Demakova, V. F. Semeshin, Galina V. Pokholkova, Lidiya V. Boldyreva, D S Demidova, Vladimir N. Babenko, С. А. Демаков, E. S. Belyaeva
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0177553

Characterization of the whole chloroplast genome of Chikusichloa mutica and its comparison with other rice tribe (Oryzeae) species
Cited by: 10
Author(s): Zhiqiang Wu, Cuihua Gu, Luke R. Tembrock, Dong Zhang, Song Ge
Software Mentions: 2
Published: over 7 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.0211919

Evolution of international collaborative research efforts to develop non-Cochrane systematic reviews
Cited by: 5
Author(s): Isabel Viguera-Guerra, Juan Ruano, Macarena Aguilar-Luque, Jesús Gay-Mimbrera, Ana Montilla, José Luis Fernández-Rueda, José Fernández-Chaichio, Juan Luís Sanz-Cabanillas, Pedro Jesús Gómez-Arias, Antonio Vélez García-Nieto, Francisco Gómez-García, Beatriz Isla-Tejera
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0029814

SNP Discovery and Development of a High-Density Genotyping Array for Sunflower
Cited by: 99
Author(s): Eleni Bachlava, Christopher A. Taylor, Shunxue Tang, John E. Bowers, Jennifer R. Mandel, John M. Burke, Steven J. Knapp
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0227513

Filtered beauty in Oslo and Tokyo: A spatial frequency analysis of facial attractiveness
Cited by: 1
Author(s): Morten Øvervoll, Ilaria Schettino, Hikaru Suzuki, Matia Okubo, Bruno Laeng
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0210928

High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow
Cited by: 64
Author(s): Stijn Vanderzande, Nicholas P. Howard, Lichun Cai, Cássia da Silva Linge, Laima Antanaviciute, M.C.A.M. Bink, Johannes W. Kruisselbrink, Nahla V. Bassil, Ksenija Gašić, Amy Iezzoni, Eric van de Weg, Cameron Peace
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0178519

How do SMA-linked mutations of SMN1 lead to structural/functional deficiency of the SMA protein?
Cited by: 14
Author(s): Wei Li
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0214543

Copy number variation study in Japanese quail associated with stress related traits using whole genome re-sequencing data
Cited by: 4
Author(s): Bhuwan Khatri, Seong Wook Kang, Stephanie Shouse, Nicholas B. Anthony, Wayne J. Kuenzel, Byung-Whi Kong
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0236483

Classification of Takifugu rubripes, T. chinensis and T. pseudommus by genotyping-by-sequencing
Cited by: 2
Author(s): Yeon Jung Park, Mi Nan Lee, Jae Koo Noh, Eun Soo Noh, Jung Ha Kang, Jung Youn Park, Eun Mi Kim
Software Mentions: 2
Published: about 4 years ago

10.1093/database/bax051

The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations
Cited by: 12
Author(s): Yaxin Chen, Minjun Shi, Wanting Zhang, Yingyin Cheng, Yaping Wang, Xiao-Qin Xia
Software Mentions: 2
Published: almost 8 years ago

10.1093/database/bax022

TMPL: a database of experimental and theoretical transmembrane protein models positioned in the lipid bilayer
Cited by: 2
Author(s): Guillaume Postic, Yassine Ghouzam, Catherine Etchebest, Jean‐Christophe Gelly
Software Mentions: 2
Published: almost 8 years ago

10.1002/ece3.4960

Application of a SSR‐GBS marker system on investigation of European Hedgehog species and their hybrid zone dynamics
Cited by: 41
Author(s): Manuel Curto, Silvia Winter, Anna Seiter, Lukas Schmid, Klaus Scheicher, Leon M. F. Barthel, Jürgen Plass, Harald Meimberg
Software Mentions: 2
Published: almost 6 years ago

10.1002/ece3.3144

Upstream trophic structure modulates downstream community dynamics via resource subsidies
Cited by: 10
Author(s): Éric Harvey, Isabelle Gounand, Chelsea J. Little, Emanuel A. Fronhofer, Florian Altermatt
Software Mentions: 2
Published: over 7 years ago

10.1002/ece3.2444

<scp>SNP</scp> s across time and space: population genomic signatures of founder events and epizootics in the House Finch ( <i>Haemorhous mexicanus</i> )
Cited by: 39
Author(s): Allison J. Shultz, Allan J. Baker, Geoffrey E. Hill, Paul M. Nolan, Scott V. Edwards
Software Mentions: 2
Published: about 8 years ago

10.3390/e21070630

Stationary-State Statistics of a Binary Neural Network Model with Quenched Disorder
Cited by: 2
Author(s): Diego Fasoli, Stefano Panzeri
Software Mentions: 2
Published: over 5 years ago

10.1186/s13072-021-00416-5

Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure
Cited by: 8
Author(s): Weitian Chen, Zhe Weng, Zhe Xie, Yeming Xie, Chen Zhang, Zhichao Chen, Fengying Ruan, Juan Wang, Yuxin Sun, Yitong Fang, Mei Guo, Y. Tong, Yaning Li, Chong Tang
Software Mentions: 2
Published: over 3 years ago

10.1007/s00259-013-2656-8

Comparison between PET template-based method and MRI-based method for cortical quantification of florbetapir (AV-45) uptake in vivo
Cited by: 35
Author(s): Laure Saint‐Aubert, Federico Nemmi, Patrice Péran, Emmanuel J. Barbeau, Pierre Payoux, François Chollet, Jérémie Pariente
Software Mentions: 2
Published: almost 11 years ago

10.1111/eva.12754

Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (<i>Accipiter gentilis laingi</i>) in Haida Gwaii
Cited by: 14
Author(s): Armando Geraldes, Kenneth K. Askelson, Ellen Nikelski, Frank I. Doyle, William L. Harrower, Kevin Winker, Darren E. Irwin
Software Mentions: 2
Published: almost 6 years ago

10.3389/fcimb.2021.633817

Molecular Epidemiology and Clone Transmission of Carbapenem-Resistant Acinetobacter baumannii in ICU Rooms
Cited by: 14
Author(s): Xiufeng Zhang, Fangping Li, Furqan Awan, Hongye Jiang, Zhenling Zeng, Weibiao Lv
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2019.00333

Noonan Syndrome in South Africa: Clinical and Molecular Profiles
Cited by: 13
Author(s): Cedrik Tekendo‐Ngongang, Gloudi Agenbag, Christian Domilongo Bope, Alina Esterhuizen, Ambroise Wonkam
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2021.671686

Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds
Cited by: 2
Author(s): Guangqi Lyu, Chunyu Feng, Shiyu Zhu, Shuang Ren, Wanyi Dang, David M. Irwin, Zhe Wang
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2019.00024

Conservation, Extensive Heterozygosity, and Convergence of Signaling Potential All Indicate a Critical Role for KIR3DL3 in Higher Primates
Cited by: 20
Author(s): Laura Ann Leaton, Jonathan A. Shortt, Katherine M Kichula, Sudan Tao, Neda Nemat-Gorgani, Alexander J. Mentzer, Stephen Oppenheimer, Zhihui Deng, Jill A. Hollenbach, Christopher R. Gignoux, Lisbeth A. Guethlein, Peter Parham, Mary Carrington, Paul J. Norman
Software Mentions: 2
Published: almost 6 years ago

10.3389/fimmu.2015.00023

Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq
Cited by: 31
Author(s): Maura E. Casey, Kieran G. Meade, Nicolas C. Nalpas, Maria Taraktsoglou, John A. Browne, Kate E. Killick, Stephen D. E. Park, Eamonn Gormley, Karsten Hokamp, David A. Magee, David E. MacHugh
Software Mentions: 2
Published: almost 10 years ago

10.3389/fmed.2021.625487

Development and Validation of Automated Visual Field Report Extraction Platform Using Computer Vision Tools
Cited by: 7
Author(s): Murtaza Saifee, Jian Wu, Yingna Liu, Ping Ma, Jutima Patlidanon, Yinxi Yu, Gui‐Shuang Ying, Ying Han
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2015.01540

Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat
Cited by: 14
Author(s): Melanie C. Melendrez, Eric D. Becraft, Jason M. Wood, Millie T. Olsen, Donald A. Bryant, John F. Heidelberg, Douglas B. Rusch, Frederick M. Cohan, David M. Ward
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2019.00835

In silico Identification of Serovar-Specific Genes for Salmonella Serotyping
Cited by: 13
Author(s): Xiaomei Zhang, Michael Payne, Ruiting Lan
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2020.00646

Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin
Cited by: 7
Author(s): Kairi Raime, Kaarel Krjutškov, Maido Remm
Software Mentions: 2
Published: over 4 years ago

10.3389/fpls.2016.02063

A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A
Cited by: 10
Author(s): Barbora Balcárková, Zeev Frenkel, Monika Škopová, Michaël Abrouk, Ajay Kumar, Shiaoman Chao, Shahryar F. Kianian, Eduard Akhunov, Abraham B. Korol, Jaroslav Doležel, Miroslav Valárik
Software Mentions: 2
Published: almost 8 years ago