pypi: pipeline | Projects | Ecosyste.ms: Papers

10.1186/s12859-017-1847-x

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Cited by: 42
Author(s): Joseph N. Paulson, Cho-Yi Chen, Camila M. Lopes‐Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush
Software Mentions: 10
Published: about 7 years ago

10.1186/1471-2164-16-S6-S3

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application
Cited by: 54
Author(s): Mattia D’Antonio, Paolo D’Onorio De Meo, Matteo Pallocca, Ernesto Picardi, Anna Maria D’Erchia, Raffaele Calogero, Tiziana Castrignanò, Graziano Pesole
Software Mentions: 9
Published: over 9 years ago

10.1111/eva.13035

Demographic history and genomics of local adaptation in blue tit populations
Cited by: 8
Author(s): Charles Perrier, Quentin Rougemont, Anne Charmantier
Software Mentions: 7
Published: over 4 years ago

10.1534/g3.116.038190

Adapting Genotyping-by-Sequencing for Rice F2 Populations
Cited by: 65
Author(s): Tomohisa Furuta, Motoyuki Ashikari, Kshirod K. Jena, Kouki Doi, Stefan Reuscher
Software Mentions: 7
Published: almost 8 years ago

10.7554/eLife.60176

Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus
Cited by: 21
Author(s): Taro Maeda, Shunichi Takahashi, Takao Yoshida, Shigeru Shimamura, Yoshihiro Takaki, Yukiko Nagai, Atsushi Toyoda, Yutaka Suzuki, Asuka Arimoto, Hisaki Ishii, Nori Satoh, Tomoaki Nishiyama, Mitsuyasu Hasebe, Tadashi Maruyama, Jun Minagawa, Junichi Obokata, Shuji Shigenobu
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2018.02137

Traditional Norwegian Kveik Are a Genetically Distinct Group of Domesticated Saccharomyces cerevisiae Brewing Yeasts
Cited by: 36
Author(s): Richard Preiss, Caroline Tyrawa, Kristoffer Krogerus, Lars Marius Garshol, George van der Merwe
Software Mentions: 6
Published: over 6 years ago

10.3835/plantgenome2017.03.0015

Prospects for Genomic Selection in Cassava Breeding
Cited by: 95
Author(s): Marnin D. Wolfe, Dunia Pino Del Carpio, Olumide Alabi, Lydia Ezenwaka, Ugochukwu N. Ikeogu, Siraj Ismail Kayondo, Roberto Lozano, Uche Godfrey Okeke, Alfred Ozimati, Williams Esuma, Chiedozie Egesi, Robert Kawuki, Peter Kulakow, Ismail Rabbi, Jean‐Luc Jannink
Software Mentions: 6
Published: about 7 years ago

10.1038/s41392-020-00263-y

Adaptive immune responses to SARS-CoV-2 infection in severe versus mild individuals
Cited by: 127
Author(s): Fan Zhang, Rui Gan, Ziqi Zhen, Xiaoli Hu, Xiang Li, Fengxia Zhou, Ying Liu, Chuangeng Chen, Shuangyu Xie, Bailing Zhang, Xiaoke Wu, Zhiwei Huang
Software Mentions: 6
Published: over 4 years ago

10.1186/s40168-019-0687-5

Evolution of the gut microbiome following acute HIV-1 infection
Cited by: 61
Author(s): Muntsa Rocafort, Marc Noguera‐Julian, Javier Rivera, Lucía Pastor, Yolanda Guillén, Jost Langhorst, Mariona Parera, Inácio Mandomando, Jorge Carrillo, Víctor Urrea, C. Rodríguez, María Casadellà, M. Luz Calle, Bonaventura Clotet, Julià Blanco, Denise Naniche, Roger Paredes
Software Mentions: 6
Published: over 5 years ago

10.18632/oncotarget.10962

Epigenetic reprogramming and aberrant expression of PRAME are associated with increased metastatic risk in Class 1 and Class 2 uveal melanomas
Cited by: 85
Author(s): Matthew G. Field, Michael A. Durante, Christina L. Decatur, Berçin Tarlan, Kristen M. Oelschlager, John F. Stone, Jeffim N. Kuznetsov, Anne M. Bowcock, Stefan Kurtenbach, J. William Harbour
Software Mentions: 6
Published: over 8 years ago

10.1186/s13059-021-02326-x

AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data
Cited by: 5
Author(s): Kyle Fletcher, Lin Zhang, Juliana Gil, Rongkui Han, Keri Cavanaugh, Richard W. Michelmore
Software Mentions: 6
Published: over 3 years ago

10.1186/s12882-020-01773-1

The urinary microbiome shows different bacterial genera in renal transplant recipients and non-transplant patients at time of acute kidney injury – a pilot study
Cited by: 10
Author(s): Daniela Gerges, Peter Pichler, Alexander Zimprich, Christoph Hotzy, Wolfgang Barousch, Rita Lang, Elisabeth Lobmeyr, Sabina Baumgartner‐Parzer, Ludwig Wagner, Wolfgang Winnicki
Software Mentions: 6
Published: over 4 years ago

10.1016/j.csbj.2019.04.012

Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts
Cited by: 23
Author(s): Isaac A. Babarinde, Yuhao Li, Andrew P. Hutchins
Software Mentions: 6
Published: almost 6 years ago

10.1155/2020/3165958

Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple
Cited by: 6
Author(s): Qing Liu, Mengnan Chai, Man Zhang, Qing-Yu He, Zhenxia Su, S. V. G. N. Priyadarshani, Liping Liu, Guanxi Dong, Yuan Qin
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0245857

Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation
Cited by: 9
Author(s): Rachel M. Wilson, Ahmed A. Zayed, Kelsey B. Crossen, Ben J. Woodcroft, Malak M. Tfaily, Joanne B. Emerson, Nicole Raab, S. B. Hodgkins, B. A. Verbeke, Gene W. Tyson, Patrick Crill, S. R. Saleska, Jeffrey P. Chanton, V. I. Rich
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.38340

The origin of the odorant receptor gene family in insects
Cited by: 88
Author(s): Philipp Brand, Hugh M. Robertson, Wei Lin, Ratnasri Pothula, William E. Klingeman, Juan Luís Jurat-Fuentes, Brian R. Johnson
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-25022-6

DNAp: A Pipeline for DNA-seq Data Analysis
Cited by: 13
Author(s): Jason Causey, Cody Ashby, Karl Walker, Zhiping Paul Wang, Mary Qu Yang, Yuanfang Guan, Jason H. Moore, Xiuzhen Huang
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-017-1881-8

K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity
Cited by: 14
Author(s): Chang Sik Kim, Martyn Winn, Vipin Sachdeva, Kirk E. Jordan
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-018-37269-0

Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions
Cited by: 67
Author(s): Narinder Singh, Shuangye Wu, W. J. Raupp, Sunish K. Sehgal, Sanu Arora, Vijay K. Tiwari, Prashant Vikram, Sukhwinder Singh, Parveen Chhuneja, Bikram S. Gill, Jesse Poland
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1004660

Widespread Genome Reorganization of an Obligate Virus Mutualist
Cited by: 66
Author(s): Gaelen R. Burke, Kimberly K. O. Walden, James B. Whitfield, Hugh M. Robertson, Michael R. Strand
Software Mentions: 4
Published: over 10 years ago

10.1093/database/baw063

PGD: a pangolin genome hub for the research community
Cited by: 4
Author(s): Tze King Tan, Ka Yun Tan, Riitta Hari, Aini Mohamed Yusoff, George T.F. Wong, Cheuk Chuen Siow, Naresh V.R. Mutha, Mikhail Rayko, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Ian C. Paterson, Wesley C. Warren, Warren E. Johnson, Stephen J. O’Brien, Siew Woh Choo
Software Mentions: 4
Published: almost 9 years ago

10.1002/ece3.3503

Radiation of the polymorphic Little Devil poison frog (Oophaga sylvatica) in Ecuador
Cited by: 16
Author(s): Alexandre B. Roland, Juan Carlos Santos, Bella C. Carriker, Stephanie N. Caty, Elicio Tapia, Luis A. Coloma, Lauren A. O’Connell
Software Mentions: 4
Published: about 7 years ago

10.1186/gb-2014-15-4-r57

Evidence for the biogenesis of more than 1,000 novel human microRNAs
Cited by: 214
Author(s): Marc R. Friedländer, Esther Lizano, Anna J.S. Houben, Daniela Bezdan, Mónica Báñez-Coronel, Grzegorz Kudla, Elisabet Mateu-Huertas, Birgit Kagerbauer, Justo González, Kevin C. Chen, Emily LeProust, Eulàlia Martı́, Xavier Estivill
Software Mentions: 4
Published: almost 11 years ago

10.3389/fmicb.2021.666584

Combined Stochastic and Deterministic Processes Drive Community Assembly of Anaerobic Microbiomes During Granule Flotation
Cited by: 63
Author(s): Anna Christine Trego, Paul G. McAteer, Corine Nzeteu, Thérèse Mahony, Florence Abram, Umer Zeeshan Ijaz, Vincent O’Flaherty
Software Mentions: 4
Published: over 3 years ago

10.3389/fnins.2018.00006

Group Analysis in MNE-Python of Evoked Responses from a Tactile Stimulation Paradigm: A Pipeline for Reproducibility at Every Step of Processing, Going from Individual Sensor Space Representations to an across-Group Source Space Representation
Cited by: 17
Author(s): Lau M. Andersen
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0231083

Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla
Cited by: 4
Author(s): Yakshi Ortiz, Carla Restrepo, Brayan Vilanova-Cuevas, Eugenio Santiago‐Valentín, Susannah G. Tringe, Filipa Godoy-Vitorino
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-018-2485-7

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
Cited by: 590
Author(s): Michael J. Roach, Simon A. Schmidt, Anthony R. Borneman
Software Mentions: 4
Published: about 6 years ago

10.3390/microorganisms8111679

Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants
Cited by: 13
Author(s): Valentina Méndez, Matías A. Valenzuela, Francisco Salvà‐Serra, Daniel Jaén‐Luchoro, Ximena Besoaín, Edward R. B. Moore, Michael Seeger
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-016-3404-9

ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data
Cited by: 25
Author(s): Bernardo Rodríguez-Martín, Emilio Palumbo, Santiago Marco-Sola, Thasso Griebel, Paolo Ribeca, Graciela Alonso, Alberto Rastrojo, Begoña Aguado, Roderic Guigó, Sarah Djebali
Software Mentions: 3
Published: almost 8 years ago

10.3390/brainsci8040050

Connexin 43 Controls the Astrocyte Immunoregulatory Phenotype
Cited by: 14
Author(s): Anne Boulay, Alice Gilbert, Vanessa Oliveira Moreira, Corinne Blugeon, Sandrine Perrin, Juliette Pouch, Stéphane Le Crom, Bertrand Ducos, Martine Cohen-Salmon
Software Mentions: 3
Published: almost 7 years ago

10.1093/bioinformatics/btu595

BigDataScript: a scripting language for data pipelines
Cited by: 29
Author(s): Pablo Cingolani, Robert Sladek, Mathieu Blanchette
Software Mentions: 3
Published: over 10 years ago

10.3390/jof6010007

Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1
Cited by: 5
Author(s): Ling Peng, Liangwei Li, Xiaochuan Liu, Jianwei Chen, Chengcheng Shi, Wenjie Guo, Qiwu Xu, Guangyi Fan, Xin Liu, Dehai Li
Software Mentions: 3
Published: about 5 years ago

10.1186/1756-0500-7-132

STINGRAY: system for integrated genomic resources and analysis
Cited by: 5
Author(s): Glauber Wagner, Rodrigo Jardim, Diogo A. Tschoeke, Daniel R Loureiro, Kary Ocaña, Antonio Ribeiro, Vanessa Erichsen Emmel, Christian M. Probst, André Nóbrega Pitaluga, Edmundo C. Grisard, Maria Cláudia Cavalcanti, María Luiza Machado Campos, Marta Mattoso, Alberto M. R. Dávila
Software Mentions: 3
Published: almost 11 years ago

10.7554/eLife.35066

Bleaching causes loss of disease resistance within the threatened coral species Acropora cervicornis
Cited by: 81
Author(s): Erinn M. Muller, Erich Bartels, Iliana B. Baums
Software Mentions: 3
Published: over 6 years ago

10.3390/microorganisms9010113

Metagenomics and Culture Dependent Insights into the Distribution of Firmicutes across Two Different Sample Types Located in the Black Hills Region of South Dakota, USA
Cited by: 7
Author(s): Tanvi Govil, Manasi Paste, Dipayan Samanta, Aditi David, Kian Mau Goh, Xiangkai Li, David R. Salem, Rajesh K. Sani
Software Mentions: 3
Published: almost 4 years ago

10.1186/s40169-015-0064-3

A proteomic profiling of laser‐microdissected lung adenocarcinoma cells of early lepidic‐types
Cited by: 14
Author(s): Yasufumi Kato, Hiroki Nakamura, Hiromasa Tojo, Masatoshi Nomura, Toshitaka Nagao, Takeshi Kawamura, Tatsuhiko Kodama, Tetsuya Ohira, Norihiko Ikeda, Thomas E. Fehniger, György Markó-Varga, Toshihide Nishimura, Harubumi Kato
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0208406

Extracellular polymeric substances (EPS) producing and oil degrading bacteria isolated from the northern Gulf of Mexico
Cited by: 46
Author(s): Hernando P. Bacosa, Manoj Kamalanathan, Meng Hsuen Chiu, Shih Ming Tsai, Luni Sun, Jessica M. Labonté, Kathleen A. Schwehr, David Hala, Peter H. Santschi, Wei Chun Chin, Antonietta Quigg
Software Mentions: 3
Published: about 6 years ago

10.18632/oncotarget.14401

Src promotes castration-recurrent prostate cancer through androgen receptor-dependent canonical and non-canonical transcriptional signatures
Cited by: 32
Author(s): Indranil Chattopadhyay, Jianmin Wang, Maochun Qin, Lingqiu Gao, Renae Holtz, Robert L. Vessella, Robert W. Leach, Irwin H. Gelman
Software Mentions: 3
Published: about 8 years ago

10.1016/j.csbj.2020.03.022

Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in Crocus sativus
Cited by: 28
Author(s): Junyang Yue, Ran Wang, Xiaojing Ma, Jiayi Liu, Xiaohui Lu, Sambhaji Balaso Thakar, Ning An, Jia Liu, Enhua Xia, Yongsheng Liu
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.ppat.1005265

The Structure of the RNA-Dependent RNA Polymerase of a Permutotetravirus Suggests a Link between Primer-Dependent and Primer-Independent Polymerases
Cited by: 25
Author(s): D.S. Ferrero, M. Buxaderas, José F. Rodrı́guez, N. Verdaguer
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0165089

Chromosomal Instability Estimation Based on Next Generation Sequencing and Single Cell Genome Wide Copy Number Variation Analysis
Cited by: 29
Author(s): Stephanie Greene, Angel E. Dago, Laura Leitz, Yipeng Wang, Jerry Lee, Shannon L. Werner, Steven Gendreau, Premal H. Patel, Shidong Jia, Liangxuan Zhang, Eric Tucker, Michael Malchiodi, Ryon P. Graf, Ryan Dittamore, Dena Marrinucci, Mark Landers
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-020-73396-3

Loss of bacterial diversity in the sinuses is associated with lower smell discrimination scores
Cited by: 6
Author(s): Kristi Biswas, Brett Wagner Mackenzie, C Ballauf, Julia Draf, Richard Douglas, Thomas Hummel
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-015-1494-4

De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response
Cited by: 41
Author(s): Hai-Bin Zhang, Enhua Xia, Hui Huang, Jianjun Jiang, Benying Liu, Li‐Zhi Gao
Software Mentions: 3
Published: over 9 years ago

10.3389/fgene.2020.00462

Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.)
Cited by: 4
Author(s): Xingwei Zheng, Mengmeng Shi, Jian Wang, Na Yang, Ke Wang, Jilong Xi, Chong Wu, Tianyuan Xi, Jun Zheng, Jiancheng Zhang
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2020.01245

Low IgA Associated With Oropharyngeal Microbiota Changes and Lung Disease in Primary Antibody Deficiency
Cited by: 21
Author(s): Roos-Marijn Berbers, Firdaus A. A. Mohamed Hoesein, Pauline M. Ellerbroek, Joris M. van Montfrans, Virgil A. S. H. Dalm, P. Martin van Hagen, Fernanda L. Paganelli, Marco C. Viveen, Malbert R. C. Rogers, Pim A. de Jong, Hae‐Won Uh, Rob J. L. Willems, Helen L. Leavis
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2018.00344

Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis
Cited by: 11
Author(s): Anne Busch, Prasad Thomas, Eric Zuchantke, Holger Brendebach, Kerstin Neubert, Josephine Gruetzke, Sascha Al Dahouk, Martin C. Peters, Helmut Hotzel, Heinrich Neubauer, Herbert Tomaso
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-017-14998-2

MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation
Cited by: 19
Author(s): Mir Asif Iquebal, Sarika Jaiswal, Ajay Kumar Mahato, Pawan Kumar Jayaswal, U. B. Angadi, Neeraj Kumar, Nimisha Sharma, Anand Kumar Singh, Manish Srivastav, Jai Prakash, Sanjay Kumar Singh, Kasim Khan, Rupesh Kumar Mishra, Shailendra Rajan, Anju Bajpai, B. Sandhya, P. Nischita, K. V. Ravishankar, M. R. Dinesh, Anil Rai, Dinesh Kumar, Tilak Raj Sharma, Nagendra Singh
Software Mentions: 3
Published: about 7 years ago

10.1186/gm461

Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing Charcot-Marie-Tooth neuropathy
Cited by: 134
Author(s): James R. Lupski, Claudia Gonzaga‐Jauregui, Yaping Yang, Matthew N. Bainbridge, Shalini N. Jhangiani, Christian Buhay, Christie Kovar, Min Wang, Alicia Hawes, Jeffrey G. Reid, Christine M. Eng, Donna M. Muzny, Richard A. Gibbs
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-14-895

Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation
Cited by: 52
Author(s): Adam B. Olson, Heather Kent, Christopher D. Sibley, Margot E. Grinwis, Philip Mabon, Claude Ouellette, Shari Tyson, Morag Graham, Shaun Tyler, Gary Van Domselaar, Michael G. Surette, Cindi R. Corbett
Software Mentions: 3
Published: about 11 years ago

10.1038/s41598-019-43935-8

GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data
Cited by: 105
Author(s): Naim Al Mahi, Mehdi Fazel Najafabadi, Marcin Pilarczyk, Michal Kouril, Mario Medvedovic
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0084482

Cdk5 Phosphorylates Dopamine D2 Receptor and Attenuates Downstream Signaling
Cited by: 20
Author(s): Jong Ju Jeong, Young-Un Park, Dae-Kyum Kim, Saebom Lee, Yongdo Kwak, Seol-Ae Lee, Haeryun Lee, Yoo-Hun Suh, Yong Song Gho, Daehee Hwang, Sang Ki Park
Software Mentions: 3
Published: about 11 years ago

10.1002/jmd2.12209

A novel homozygous variant in <scp> C1QBP </scp> causes severe <scp>IUGR</scp> , edema, and cardiomyopathy in two fetuses
Cited by: 3
Author(s): Morten Alstrup, Ida Vogel, Puk Sandager, Jenny Blechingberg, Naja Becher, Elsebet Østergaard
Software Mentions: 2
Published: almost 4 years ago

10.3389/fninf.2017.00035

ATPP: A Pipeline for Automatic Tractography-Based Brain Parcellation
Cited by: 17
Author(s): Hai Li, Lingzhong Fan, Junjie Zhuo, Jiaojian Wang, Yu Zhang, Zhengyi Yang, Tianzi Jiang
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.10485

Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers
Cited by: 6
Author(s): Zhixin Wang, Yalin Sun, Xinfang Huang, Li Feng, Yuping Liu, Haishan Zhu, Zhengwei Liu, Weidong Ke
Software Mentions: 2
Published: about 4 years ago

10.1186/s12870-019-2217-9

Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato
Cited by: 18
Author(s): Astère Bararyenya, Bode A. Olukolu, Phinehas Tukamuhabwa, Wolfgang J. Grüneberg, WN Ekaya, Jan Low, Mildred Ochwo-Ssemakula, Thomas Odong, Herbert Talwana, Arfang Badji, Martina Kyalo, Nasser Yao, Dorcus C. Gemenet, Mercy Kitavi, R.O.M. Mwanga
Software Mentions: 2
Published: almost 5 years ago

10.3389/fpls.2021.621276

Linking Plant Secondary Metabolites and Plant Microbiomes: A Review
Cited by: 215
Author(s): Zhiqiang Pang, Jia Chen, Tuhong Wang, Chunsheng Gao, Zhimin Li, Long Guo, Jianping Xu, Yi Cheng
Software Mentions: 2
Published: almost 4 years ago

10.3389/fpls.2013.00362

Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines
Cited by: 30
Author(s): Robert S. Allen, Kenlee Nakasugi, Rachel L. Doran, Anthony A. Millar, Peter M. Waterhouse
Software Mentions: 2
Published: almost 12 years ago

10.1111/pbi.13171

Strong temporal dynamics of QTL action on plant growth progression revealed through high‐throughput phenotyping in canola
Cited by: 42
Author(s): Dominic Knoch, Amine Abbadi, Fabian Grandke, Rhonda C. Meyer, Birgit Samans, Christian R. Werner, Rod J. Snowdon, Thomas Altmann
Software Mentions: 2
Published: over 5 years ago

10.1186/s13104-017-2886-0

Array comparative genomic hybridization of 18 pancreatic ductal adenocarcinomas and their autologous metastases
Cited by: 7
Author(s): Valentin Rausch, Andreas Krieg, Jordi Camps, Bianca Behrens, Manfred Beier, Darawalee Wangsa, Kerstin Heselmeyer‐Haddad, Stephan Baldus, Wolfram Trudo Knoefel, Thomas Ried, Nikolas H. Stoecklein
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1003986

Alcohol-Induced Histone Acetylation Reveals a Gene Network Involved in Alcohol Tolerance
Cited by: 48
Author(s): Alfredo Ghezzi, Harish R. Krishnan, Linda Lew, Francisco J. Prado, Darryl S. Ong, Nigel S. Atkinson
Software Mentions: 2
Published: about 11 years ago

10.1534/g3.114.012567

Genome Sequence of Candidatus Riesia pediculischaeffi, Endosymbiont of Chimpanzee Lice, and Genomic Comparison of Recently Acquired Endosymbionts from Human and Chimpanzee Lice
Cited by: 28
Author(s): Bret M. Boyd, Julie M. Allen, Valérie de Crécy‐Lagard, David L. Reed
Software Mentions: 2
Published: about 10 years ago

10.1534/g3.118.200613

Prediction of Subgenome Additive and Interaction Effects in Allohexaploid Wheat
Cited by: 9
Author(s): Nicholas Santantonio, Jean‐Luc Jannink, Mark E. Sorrells
Software Mentions: 2
Published: almost 6 years ago

10.1534/g3.120.401372

Genome-Wide Characterization and Comparative Analysis of MYB Transcription Factors in Ganoderma Species
Cited by: 8
Author(s): Lining Wang, Qinghua Huang, Liulian Zhang, Qingfu Wang, Lei Liang, Baosheng Liao
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pntd.0009428

Deep amplicon sequencing highlights low intra-host genetic variability of Echinococcus multilocularis and high prevalence of the European-type haplotypes in coyotes and red foxes in Alberta, Canada
Cited by: 6
Author(s): Maria A Santa, Andrew M. Rezansoff, Rebecca Chen, John S. Gilleard, Marco Musiani, Kathreen E. Ruckstuhl, Alessandro Massolo
Software Mentions: 2
Published: over 3 years ago

10.1128/genomeA.00235-16

Draft Genome Sequence of Bacillus clausii UBBC07, a Spore-Forming Probiotic Strain
Cited by: 5
Author(s): Aditya Upadrasta, Swetha Pitta, Ratna Sudha Madempudi
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0025263

Analysis of 16S rRNA Amplicon Sequencing Options on the Roche/454 Next-Generation Titanium Sequencing Platform
Cited by: 191
Author(s): Hideyuki Tamaki, Chris Wright, Xiangzhen Li, Qiaoyan Lin, Chao‐Lung Hwang, Shiping Wang, Jyothi Thimmapuram, Yoichi Kamagata, Wen Tso Liu
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0226106

Flax rust infection transcriptomics reveals a transcriptional profile that may be indicative for rust Avr genes
Cited by: 13
Author(s): Wen-Rong Wu, Adnane Nemri, Leila M. Blackman, Ann‐Maree Catanzariti, Jana Sperschneider, Gregory J. Lawrence, Peter N. Dodds, David A. Jones, Adrienne R. Hardham
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0021088

A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing
Cited by: 14
Author(s): Georges Natsoulis, John Bell, Hua Xu, Jason D. Buenrostro, Heather Ordonez, Susan M. Grimes, Daniel E. Newburger, Michael A. Jensen, Jacob M. Zahn, Nancy R. Zhang, Hanlee P. Ji
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0212586

Apple consumption is associated with a distinctive microbiota, proteomics and metabolomics profile in the gut of Dawley Sprague rats fed a high-fat diet
Cited by: 13
Author(s): José F. García-Mazcorro, Romina Pedreschi, Jialing Yuan, Jorge R. Kawas, Boon P. Chew, Scot E. Dowd, Giuliana Noratto
Software Mentions: 2
Published: almost 6 years ago

10.1001/jamanetworkopen.2019.5394

Prevalence of Periodontal Disease and Periodontopathic Bacteria in Anti–Cyclic Citrullinated Protein Antibody–Positive At-Risk Adults Without Arthritis
Cited by: 69
Author(s): Kulveer Mankia, Ziyang Cheng, Thuy Do, Laura Hunt, Josephine L. Meade, Jing Kang, V. Clerehugh, A F Speirs, Aradhna Tugnait, Elizabeth M A Hensor, Jackie Nam, Deirdre DeVine, Paul Emery
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-14-415

Global transcriptome profiles of Camellia sinensis during cold acclimation
Cited by: 239
Author(s): Xinchao Wang, Qiongyi Zhao, Chun-Lei Ma, Zong Hong Zhang, Hongli Cao, Yawei Kong, Chuan Yue, Xinyuan Hao, Liang Chen, Jianqiang Ma, Jiye Jin, Xuan Li, Yajun Yang
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0192898

Identification of fungi in shotgun metagenomics datasets
Cited by: 66
Author(s): Paul D. Donovan, Gabriel González, Desmond G. Higgins, Geraldine Butler, Kimihito Ito
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12284-017-0147-4

Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm
Cited by: 48
Author(s): Christine Jade Dilla-Ermita, Erwin Tandayu, Venice Margarette Juanillas, Jeffrey Detras, Dennis N. Lozada, Maria Stefanie Dwiyanti, Casiana Vera Cruz, Edwige Gaby Nkouaya Mbanjo, E. Y. Ardales, Maria Genaleen Q. Diaz, Merlyn S. Mendioro, Michael J. Thomson, Tobias Kretzschmar
Software Mentions: 2
Published: almost 8 years ago

10.1007/s00430-018-0542-5

Gut microbiome of Moroccan colorectal cancer patients
Cited by: 52
Author(s): Imane Allali, Noureddine Benkeblia, Leila Bouguenouch, Hanaa Hardi, Hanae Abir Boudouaya, María Belén Cadenas, Karim Ouldim, Saaïd Amzazi, M. Andrea Azcarate‐Peril, Hassan Ghazal
Software Mentions: 2
Published: over 6 years ago

10.1038/srep42483

The secondary resistome of multidrug-resistant Klebsiella pneumoniae
Cited by: 61
Author(s): Bimal Jana, Amy K. Cain, William T. Doerrler, Christine J. Boinett, María Fookes, Julian Parkhill, Luca Guardabassi
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-017-05656-8

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)-elicited effects on bile acid homeostasis: Alterations in biosynthesis, enterohepatic circulation, and microbial metabolism
Cited by: 60
Author(s): Kelly A. Fader, Rance Nault, Chen Zhang, Kazuyoshi Kumagai, Jack R. Harkema, Timothy R. Zacharewski
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-13905-z

Hypoxia tolerance, longevity and cancer-resistance in the mole rat Spalax – a liver transcriptomics approach
Cited by: 36
Author(s): Hanno Schmidt, Assaf Malik, Anne Bicker, Gesa Poetzsch, Aaron Avivi, Imad Shams, Thomas Hankeln
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-018-5015-0

Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation)
Cited by: 29
Author(s): Erik A. Visser, Jill L. Wegrzyn, Alexander Andrew Myburg, Sanushka Naidoo
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-74843-x

Point mutation bias in SARS-CoV-2 variants results in increased ability to stimulate inflammatory responses
Cited by: 42
Author(s): Masao Kosuge, Emi Furusawa-Nishii, Koyu Ito, Yoshiro Saito, Kunio Ogasawara
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-021-84373-9

A SPRY1 domain cardiac ryanodine receptor variant associated with short-coupled torsade de pointes
Cited by: 8
Author(s): Zahia Touat-Hamici, Malorie Blancard, Ruijing Ma, Lei Lin, Yasmine Iddir, Isabelle Denjoy, Antoine Leenhardt, Zhiguang Yuchi, Pascale Guicheney
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41421-020-0168-9

Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing
Cited by: 559
Author(s): Wen Wen, Wenru Su, Hao Tang, Wenqing Le, Xiaopeng Zhang, Yingfeng Zheng, Xiuxing Liu, Lihui Xie, Jianmin Li, Jinguo Ye, Liwei Dong, Xiuliang Cui, Yushan Miao, Depeng Wang, Jie Dong, Chuan-Le Xiao, Wei Chen, Hongyang Wang
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.02032-18

Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans
Cited by: 30
Author(s): Jennifer R. Bratburd, Caitlin Keller, Eugenio I. Vivas, Erin Gemperline, Lingjun Li, Federico E. Rey, Cameron R. Currie
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.8102

The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strainStenotrophomonas sp. Pemsol isolated from Mexico
Cited by: 23
Author(s): Temidayo Oluyomi Elufisan, Isabel Cristina Rodríguez-Luna, Omotayo Opemipo Oyedara, Alejandro Sánchez-Varela, Armando Hernández-Mendoza, Edgar Dantán-González, Alma D. Paz-González, Kashif Muhammad, Gildardo Rivera, Miguel Ángel Villalobos-López, Xianwu Guo
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms21207453

Proteome Analysis of Walnut Bacterial Blight Disease
Cited by: 10
Author(s): Cíntia Helena Duarte Sagawa, Renata de Almeida Barbosa Assis, Paulo A. Zaini, Phillip A. Wilmarth, Brett S. Phinney, Leandro Márcio Moreira, Abhaya M. Dandekar
Software Mentions: 2
Published: about 4 years ago

10.1038/s42003-021-02339-z

Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus
Cited by: 15
Author(s): Henrique Machado, Yara Seif, George Sakoulas, Connor A. Olson, Ying Hefner, Amitesh Anand, Ying Jones, Richard Szubin, Jaehyung Kim, Victor Nizet, Adam M. Feist
Software Mentions: 2
Published: over 3 years ago

10.3390/nu9040393

Differential Effect of Sucrose and Fructose in Combination with a High Fat Diet on Intestinal Microbiota and Kidney Oxidative Stress
Cited by: 64
Author(s): Adriana Rosas-Villegas, Mónica Sánchez‐Tapia, Azalia Ávila-Nava, V Mercy Ramírez, Armando R. Tovar, Nimbe Torres
Software Mentions: 2
Published: over 7 years ago

10.3390/nu13051496

Effects of Whole-Grain and Sugar Content in Infant Cereals on Gut Microbiota at Weaning: A Randomized Trial
Cited by: 8
Author(s): Julio Plaza‐Díaz, María Luisa Bernal, Sophie Schutte, Empar Chenoll, Salvador Genovés, Francisco M. Codoñer, Ángel Gil, Luis Manuel Sánchez-Siles
Software Mentions: 2
Published: over 3 years ago

10.3390/nu9121361

Prebiotic Dietary Fiber and Gut Health: Comparing the in Vitro Fermentations of Beta-Glucan, Inulin and Xylooligosaccharide
Cited by: 144
Author(s): Justin Carlson, Jennifer Erickson, Julie Hess, Trevor Gould, Joanne L. Slavin
Software Mentions: 2
Published: about 7 years ago

10.3390/ani11061561

Ruminal Protozoal Populations of Angus Steers Differing in Feed Efficiency
Cited by: 2
Author(s): Brooke A. Clemmons, Sung Bong Shin, Timothy P. L. Smith, Mallory Embree, Brynn H. Voy, Liesel G Schneider, Dallas R. Donohoe, Kyle J McLean, Phillip R. Myer
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2015.00045

Identification of copy number variants in whole-genome data using Reference Coverage Profiles
Cited by: 18
Author(s): Gustavo Glusman, Alissa L. Severson, Varsha Dhankani, Max Robinson, Terry Farrah, Denise E. Mauldin, Anna Barbara Stittrich, Seth A. Ament, Jared C. Roach, Mary E. Brunkow, Dale L. Bodian, Joseph G. Vockley, Ilya Shmulevich, John E. Niederhuber, Leroy Hood
Software Mentions: 2
Published: almost 10 years ago

10.1002/1878-0261.12354

A patient‐derived explant ( <scp>PDE</scp> ) model of hormone‐dependent cancer
Cited by: 81
Author(s): Margaret M. Centenera, Theresa E. Hickey, Shalini Jindal, Natalie K. Ryan, Preethi Ravindranathan, Hisham Mohammed, James C. Robinson, Matthew J. Schiewer, Shihong Ma, Payal Kapur, Peter Sutherland, Clive E. Hoffmann, Claus G. Roehrborn, Leonard G. Gomella, Jason S. Carroll, Stephen N. Birrell, Karen E. Knudsen, Ganesh V. Raj, Lisa M. Butler, Wayne D. Tilley
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2019.00107

Survival Mechanisms of Campylobacter hepaticus Identified by Genomic Analysis and Comparative Transcriptomic Analysis of in vivo and in vitro Derived Bacteria
Cited by: 19
Author(s): Thi Thu Hao Van, Jake A. Lacey, Ben Vezina, Canh Phung, Arif Anwar, Peter C. Scott, Robert J. Moore
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2021.662966

Effects of Gallic Acid on Fermentation Parameters, Protein Fraction, and Bacterial Community of Whole Plant Soybean Silage
Cited by: 19
Author(s): Cheng Wang, Mingyang Zheng, Shuo Wu, Xuan Zhou, Xiaoyang Chen, Liangfa Ge, Qing Zhang
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.00012

The Role of Microbial Mats in the Removal of Hexavalent Chromium and Associated Shifts in Their Bacterial Community Composition
Cited by: 11
Author(s): Raeid M. M. Abed, Mary Shanti, T. S. Muthukrishnan, Zayana Al-Riyami, Bernhard Pracejus, Daniel Moraetis
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2018.00914

Variation in Bat Guano Bacterial Community Composition With Depth
Cited by: 17
Author(s): Molli M. Newman, Laura N. Kloepper, Makenzie B. Duncan, John A. McInroy, Joseph W. Kloepper
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2021.571212

Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation
Cited by: 5
Author(s): Xiugen Fu, Li Gong, Yang Liu, Qiliang Lai, Guangyu Li, Zongze Shao
Software Mentions: 2
Published: over 3 years ago

10.1186/s12976-015-0013-2

In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour
Cited by: 16
Author(s): Imen Rekik, Zayneb Chaâbene, C. Douglas Grubb, Noureddine Drira, Foued Chéour, Amine Elleuch
Software Mentions: 1
Published: about 9 years ago

10.1186/s12862-021-01862-1

Dispersal ability, habitat characteristics, and sea-surface circulation shape population structure of Cingula trifasciata (Gastropoda: Rissoidae) in the remote Azores Archipelago
Cited by: 4
Author(s): Lara Baptista, Harald Meimberg, Sérgio P. Ávila, A.M. Santos, Manuel Curto
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-018-4753-3

Muver, a computational framework for accurately calling accumulated mutations
Cited by: 12
Author(s): Adam Burkholder, Scott A. Lujan, Christopher A. Lavender, Sara A. Grimm, Thomas A. Kunkel, David C. Fargo
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-10-61

Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger
Cited by: 36
Author(s): James C. Wright, Deana Sugden, Sue Francis-McIntyre, Isabel Riba-Garcia, Simon J. Gaskell, Igor V. Grigoriev, Scott E. Baker, Robert J. Beynon, Simon J. Hubbard
Software Mentions: 1
Published: almost 16 years ago

Projects: pypi: pipeline

Papers Mentioning pipeline 175