Ecosyste.ms: Papers

10.1186/s12920-017-0261-6

CVE: an R package for interactive variant prioritisation in precision oncology
Cited by: 6
Author(s): Andreas Möck, Suzanne Murphy, James A. Morris, Francesco Marass, Nitzan Rosenfeld, Charles E. Massie
Software Mentions: 14
Published: over 7 years ago

10.1186/s12859-021-04142-3

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
Cited by: 11
Author(s): Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise A Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordóñez, Andrew E. Jaffe, Leonardo Collado‐Torres
Software Mentions: 13
Published: over 3 years ago

10.1186/s12861-018-0163-7

Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells
Cited by: 4
Author(s): Anna Mantsoki, Guillaume Devailly, Anagha Joshi
Software Mentions: 13
Published: almost 7 years ago

10.1534/g3.120.401270

Application of Transcriptional Gene Modules to Analysis of <i>Caenorhabditis elegans</i>’ Gene Expression Data
Cited by: 7
Author(s): Michael Cary, Katie Podshivalova, Cynthia Kenyon
Software Mentions: 11
Published: about 4 years ago

10.3389/fgene.2015.00339

Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X Chromosome
Cited by: 23
Author(s): Emanuele Libertini, Alice Lebreton, Goran Lakisic, Marie‐Agnès Dillies, Stephan Beck, Jean‐Yves Coppée, Pascale Cossart, Hélène Bierne
Software Mentions: 9
Published: about 9 years ago

10.1371/journal.pone.0240895

RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef
Cited by: 9
Author(s): Joel D. Leal-Gutiérrez, Mauricio A. Elzo, Chad Carr, Raluca G. Mateescu
Software Mentions: 9
Published: about 4 years ago

10.1186/s13059-020-02155-4

Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC
Cited by: 51
Author(s): Paul Saary, Alex L. Mitchell, Alex Bateman
Software Mentions: 8
Published: over 4 years ago

10.12688/wellcomeopenres.14306.1

CoverView: a sequence quality evaluation tool for next generation sequencing data
Cited by: 7
Author(s): Márton Münz, Shazia Mahamdallie, Shawn Yost, Andrew Rimmer, Emma Poyastro-Pearson, Ann Strydom, Sheila Seal, Elise Ruark, Nazneen Rahman
Software Mentions: 8
Published: over 6 years ago

10.3389/fgene.2021.732211

A Ferroptosis-Related Prognostic Signature Based on Antitumor Immunity and Tumor Protein p53 Mutation Exploration for Guiding Treatment in Patients With Head and Neck Squamous Cell Carcinoma
Cited by: 13
Author(s): Xin Fan, YangShaobo Ou, Huijie Liu, Liangzhen Zhan, Xiaohui Zhu, Mingyang Cheng, Qun Li, Dongmei Yin, Lan Liao
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pgen.1007784

Maternal and zygotic gene regulatory effects of endogenous RNAi pathways
Cited by: 17
Author(s): Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, René F. Ketting
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12862-015-0499-6

Analysis of 5’ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals
Cited by: 7
Author(s): Nathaniel J. Davies, Peter Krusche, Eran Tauber, Sascha Ott
Software Mentions: 7
Published: about 9 years ago

10.1371/journal.ppat.1006767

Comparative transcriptome profiling of virulent and non-virulent Trypanosoma cruzi underlines the role of surface proteins during infection
Cited by: 50
Author(s): Ashton T. Belew, Caroline Junqueira, Gabriela F. Rodrigues-Luiz, Bruna M. Valente, Antônio Edson Rocha Oliveira, Rafael B. Polidoro, Luciana W. Zuccherato, Daniella Castanheira Bartholomeu, Sérgio Schenkman, Ricardo T. Gazzinelli, Barbara A. Burleigh, Najib M. El-Sayed, Santuza Maria Ribeiro Teixeira
Software Mentions: 7
Published: about 7 years ago

10.1186/s13195-020-00709-z

TREM2 Alzheimer’s variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages
Cited by: 25
Author(s): Hazel Hall‐Roberts, Devika Agarwal, Juliane Obst, Thomas B. Smith, Jimena Monzón‐Sandoval, Elena Di Daniel, Caleb Webber, William James, Emma Mead, John B. Davis, Sally A. Cowley
Software Mentions: 7
Published: about 4 years ago

10.3390/cells10071690

Characterisation of Neurospheres-Derived Cells from Human Olfactory Epithelium
Cited by: 1
Author(s): E. A. Zelenova, Nikolay Kondratyev, Т. В. Лежейко, G. Yu. Tsarapkin, A. I. Kryukov, Alexander E Kishinevsky, A.S. Tovmasyan, Ekaterina Momotyuk, Э. Б. Дашинимаев, В. Е. Голимбет
Software Mentions: 7
Published: over 3 years ago

10.1186/s12944-019-1165-6

Sequence analysis and variant identification at the APOC3 gene locus indicates association of rs5218 with BMI in a sample of Kuwaiti’s
Cited by: 0
Author(s): Zainab H. Malalla, Ahmad Al-Serri, Huda Alaskar, Wafaa Y. Al-Kandari, Suzanne A. Al-Bustan
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0092111

Transcriptome Analysis Reveals Differential Splicing Events in IPF Lung Tissue
Cited by: 69
Author(s): Tracy Nance, Kevin S. Smith, Vanessa Anaya, Rhea Richardson, Lawrence Ho, Mauro Pala, Sara Mostafavi, Alexis Battle, Carol Feghali‐Bostwick, Glenn D. Rosen, Stephen B. Montgomery
Software Mentions: 6
Published: almost 11 years ago

10.1093/g3journal/jkab274

Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland
Cited by: 1
Author(s): S. Eryn McFarlane, Josephine M. Pemberton
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-017-3568-y

Conserved expression of transposon-derived non-coding transcripts in primate stem cells
Cited by: 41
Author(s): LeeAnn Ramsay, Maria C. Marchetto, Maxime Caron, Shu-Huang Chen, Stephan Busche, Tony Kwan, Tomi Pastinen, Fred H. Gage, Guillaume Bourque
Software Mentions: 6
Published: almost 8 years ago

10.1186/s13073-021-00931-w

Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma
Cited by: 25
Author(s): Clément Meiller, François Montagne, Théo Z. Hirsch, Stefano Caruso, Julien De Wolf, Quentin Bayard, Jean-Baptiste Assié, Léa Meunier, Yuna Blum, Lisa Quetel, Laure Gibault, Ecaterina Pintilie, Cécile Badoual, Sarah Humez, Françoise Galateau-Sallé, Marie‐Christine Copin, Éric Letouzé, Arnaud Scherpereel, Jessica Zucman–Rossi, Françoise Le Pimpec‐Barthes, Marie-Claude Jaurand, Didier Jean
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1008546

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation
Cited by: 53
Author(s): Máté Pálfy, G Schulze, Eivind Valen, Nadine L. Vastenhouw
Software Mentions: 6
Published: almost 5 years ago

10.7554/eLife.02535

High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species
Cited by: 111
Author(s): Molly Schumer, Rongfeng Cui, Daniel L. Powell, Rebecca Dresner, Gil G. Rosenthal, Peter Andolfatto
Software Mentions: 6
Published: over 10 years ago

10.1111/eva.12047

A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals
Cited by: 14
Author(s): John D. Kirwan, Michaël Bekaert, Jennifer M. Commins, Kalina T. J. Davies, Stephen J. Rossiter, Emma C. Teeling
Software Mentions: 6
Published: almost 12 years ago

10.1186/s12864-016-2849-1

Deciphering transcriptome profiles of peripheral blood mononuclear cells in response to PRRSV vaccination in pigs
Cited by: 26
Author(s): M. S. Islam, Christine Große‐Brinkhaus, Maren Pröll, Muhammad Jasim Uddin, Sharmin Aqter Rony, Dawit Tesfaye, Ernst Tholen, Michael Hölker, K. Schellander, Christiane Neuhoff
Software Mentions: 6
Published: over 8 years ago

10.1038/s42003-020-0916-2

Tankyrase inhibition sensitizes melanoma to PD-1 immune checkpoint blockade in syngeneic mouse models
Cited by: 23
Author(s): Jo Waaler, Line Mygland, Anders Aune Tveita, Martin Frank Strand, Nina Solberg, Petter Olsen, Aleksandra Aizenshtadt, Marte Fauskanger, Kaja Lund, Jo Waaler, Max Lycke, Elisabeth Dybing, Vegard Nygaard, Sigurd Leinæs Bøe, Karen‐Marie Heintz, Eivind Hovig, Clara Hammarström, Alexandre Corthay, Stefan Krauß
Software Mentions: 6
Published: over 4 years ago

10.1186/s13148-020-00881-x

Gene–methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk
Cited by: 7
Author(s): Julia Romanowska, Øystein Ariansen Haaland, Astanand Jugessur, Miriam Gjerdevik, Zongli Xu, Jack A. Taylor, Allen J. Wilcox, Inge Jonassen, Rolv Terje Lie, Håkon K. Gjessing
Software Mentions: 6
Published: over 4 years ago

10.1111/mec.13550

Bs<scp>RAD</scp>seq: screening <scp>DNA</scp> methylation in natural populations of non‐model species
Cited by: 95
Author(s): Emiliano Trucchi, Anna B. Mazzarella, Gregor D. Gilfillan, María Teresa Cáceres Lorenzo, Peter Schönswetter, Ovidiu Paun
Software Mentions: 5
Published: almost 9 years ago

10.1111/mec.12833

Fine-scale population epigenetic structure in relation to gastrointestinal parasite load in red grouse (<i>Lagopus lagopus scotica</i>)
Cited by: 52
Author(s): Marius Wenzel, Stuart B. Piertney
Software Mentions: 5
Published: over 10 years ago

10.1186/s12864-015-1820-x

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications
Cited by: 19
Author(s): Rima Chaudhuri, Arash Sadrieh, Nolan J. Hoffman, Benjamin L. Parker, Sean J. Humphrey, Jacqueline Stöckli, Adam P. Hill, David E. James, Jean Yee Hwa Yang
Software Mentions: 5
Published: over 9 years ago

10.1038/s42003-021-02320-w

A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels
Cited by: 13
Author(s): Guste Urbonaite, Jimmy Tsz Hang Lee, Ping Liu, Guillermo E. Parada, Martin Hemberg, Murat Açar
Software Mentions: 5
Published: over 3 years ago

10.12688/wellcomeopenres.14735.2

Mapping targets for small nucleolar RNAs in yeast
Cited by: 16
Author(s): Tatiana Dudnakova, Hywel Dunn-Davies, Rosie Peters, David Tollervey
Software Mentions: 5
Published: about 6 years ago

10.7554/eLife.62270

The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline
Cited by: 66
Author(s): Danielle Janosevic, Jered Myslinski, Thomas McCarthy, Amy Zollman, Farooq Syed, Xiaoling Xuei, Hongyu Gao, Yunlong Liu, Kimberly S. Collins, Ying‐Hua Cheng, Seth Winfree, Tarek M. El‐Achkar, Bernhard Maier, Ricardo Melo Ferreira, Michael T. Eadon, Takashi Hato, Pierre C. Dagher
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0075578

Role of Alternative Polyadenylation during Adipogenic Differentiation: An In Silico Approach
Cited by: 7
Author(s): Lucía Spangenberg, Alejandro Correa, Bruno Dallagiovanna, Hugo Naya
Software Mentions: 5
Published: about 11 years ago

10.1038/s41598-019-51379-3

Tissue- and Species-Specific Patterns of RNA metabolism in Post-Mortem Mammalian Retina and Retinal Pigment Epithelium
Cited by: 9
Author(s): Les Kallestad, Seth Blackshaw, Ahmad M. Khalil, Krzysztof Palczewski
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.64669

Detecting adaptive introgression in human evolution using convolutional neural networks
Cited by: 52
Author(s): Graham Gower, Pablo Iáñez Picazo, Matteo Fumagalli, Fernando Racimo
Software Mentions: 5
Published: over 3 years ago

10.3389/fpls.2018.00037

Comparative Transcriptome Profiles of Near-Isogenic Hexaploid Wheat Lines Differing for Effective Alleles at the 2DL FHB Resistance QTL
Cited by: 37
Author(s): Chiara Biselli, Paolo Bagnaresi, Primetta Faccioli, Xinkun Hu, Margaret Balcerzak, M. Gabriela Mattera, Zehong Yan, Thérèse Ouellet, Luigi Cattivelli, Giampiero Valè
Software Mentions: 5
Published: almost 7 years ago

10.1111/mec.13113

Variation in promiscuity and sexual selection drives avian rate of Faster‐Z evolution
Cited by: 74
Author(s): Alison E. Wright, Peter W. Harrison, Fabian Zimmer, Stephen H. Montgomery, Marie A. Pointer, Judith E. Mank
Software Mentions: 5
Published: almost 10 years ago

10.3389/fimmu.2015.00380

An Introduction to Automated Flow Cytometry Gating Tools and Their Implementation
Cited by: 56
Author(s): Chris P. Verschoor, Alina Lelic, Jonathan L. Bramson, Dawn M. E. Bowdish
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-015-1716-9

Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system
Cited by: 66
Author(s): Rodrigo Pulgar, Christian Hödar, Dante Travisany, Alejandro Zúñiga, Cristina Ruesca Domínguez, Alejandro Maass, Maurício González, Verónica Cambiazo
Software Mentions: 4
Published: over 9 years ago

10.3389/fnbeh.2017.00069

Persistent Effects of Developmental Exposure to 17α-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior
Cited by: 26
Author(s): Tove Porseryd, Kristina Volkova, Nasim Reyhanian Caspillo, Thomas Källman, Patrik Dinnétz, Inger Porsch Hällström
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms21228749

Dysregulation of Transcription Factor Activity during Formation of Cancer-Associated Fibroblasts
Cited by: 6
Author(s): Przemysław Kapusta, Joanna Dulińska-Litewka, Justyna Totoń‐Żurańska, A. Borys, Paweł Konieczny, Paweł Wołkow, Michał Seweryn
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-016-3227-8

Blood miRNomes and transcriptomes reveal novel longevity mechanisms in the long-lived bat, Myotis myotis
Cited by: 43
Author(s): Zixia Huang, David Jebb, Emma C. Teeling
Software Mentions: 4
Published: about 8 years ago

10.1186/s12917-020-02373-9

Transcriptome profiling of porcine testis tissue reveals genes related to sperm hyperactive motility
Cited by: 5
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Dag Inge Våge, Teklu Tewoldebrhan Zeremichael, Frøydis Deinboll Myromslien, Eli Grindflek
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2164-6-169

The EH1 motif in metazoan transcription factors
Cited by: 67
Author(s): Richard R. Copley
Software Mentions: 4
Published: about 19 years ago

10.1093/database/bax039

GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species
Cited by: 14
Author(s): Richard Challis, Sujai Kumar, Lewis Stevens, Mark Blaxter
Software Mentions: 4
Published: almost 8 years ago

10.1016/j.celrep.2013.08.012

In Vivo T-Box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuromesodermal Bipotency
Cited by: 95
Author(s): George E. Gentsch, Nick Owens, Stephen R. Martin, Paul Piccinelli, Tiago Faial, Matthew Trotter, Michael J. Gilchrist, James C. Smith
Software Mentions: 4
Published: over 11 years ago

10.1038/s41598-020-58711-2

Nucleus accumbens pathways control cell-specific gene expression in the medial prefrontal cortex
Cited by: 5
Author(s): Takatoshi Hikida, Shuhei Yao, Tom Macpherson, Ayumi Fukakusa, Maki Morita, Haruhide Kimura, Keisuke Hirai, Tatsuya Ando, Hiroyoshi Toyoshiba, Akira Sawa
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-9-110

Search for the genes involved in oocyte maturation and early embryo development in the hen
Cited by: 47
Author(s): Sébastien Elis, Florence Batellier, Isabelle Couty, Sandrine Balzergue, Marie‐Laure Martin‐Magniette, Philippe Monget, Élisabeth Blesbois, Marina Govoroun
Software Mentions: 4
Published: almost 17 years ago

10.1038/s41598-017-16603-y

RNA-seq of serial kidney biopsies obtained during progression of chronic kidney disease from dogs with X-linked hereditary nephropathy
Cited by: 11
Author(s): Candice P. Chu, Jessica A. Hokamp, Rachel E. Cianciolo, Alan R. Dabney, Candice Brinkmeyer-Langford, George E. Lees, Mary B. Nabity
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0210859

Synthetic lethality guiding selection of drug combinations in ovarian cancer
Cited by: 16
Author(s): Andreas Heinzel, Maximilian Marhold, Paul M. Mayer, Michael Schwarz, Erwin Tomasich, Arno Lukas, Michael Krainer, Paul Perco
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0186435

Identification of cis-regulatory sequences reveals potential participation of lola and Deaf1 transcription factors in Anopheles gambiae innate immune response
Cited by: 14
Author(s): Bernardo Pérez-Zamorano, Sandra Rosas‐Madrigal, Oscar Arturo Migueles Lozano, Manuel Castillo Méndez, Verónica Valverde-Garduño
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0022022

Origin and Evolution of TRIM Proteins: New Insights from the Complete TRIM Repertoire of Zebrafish and Pufferfish
Cited by: 94
Author(s): Pierre Boudinot, Lieke M. van der Aa, Luc Jouneau, Louis Du Pasquier, Pierre Pontarotti, Valérie Briolat, Abdenour Benmansour, Jean‐Pierre Levraud
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pcbi.1007737

SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures
Cited by: 0
Author(s): Kunal Kathuria, Aakrosh Ratan
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0100250

Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion
Cited by: 8
Author(s): Tzintzuni Garcia, Isa Matos, Yingjia Shen, Vagmita Pabuwal, M. M. Coelho, Yuko Wakamatsu, Manfred Schartl, Ronald B. Walter
Software Mentions: 4
Published: over 10 years ago

10.7717/peerj.7107

Characterization of bidirectional gene pairs in The Cancer Genome Atlas (TCGA) dataset
Cited by: 8
Author(s): Juchuanli Tu, Xiaolu Li, Jianjun Wang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-015-1308-8

A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification
Cited by: 109
Author(s): Shanrong Zhao, Baohong Zhang
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0225392

Evidence in support of chromosomal sex influencing plasma based metabolome vs APOE genotype influencing brain metabolome profile in humanized APOE male and female mice
Cited by: 22
Author(s): Yuan Shang, Aarti Mishra, Tian Wang, Yiwei Wang, Maunil K. Desai, Shuhua Chen, Zisu Mao, Loi Do, Adam Bernstein, Theodore P. Trouard, Roberta Dı́az Brinton
Software Mentions: 4
Published: almost 5 years ago

10.1002/1878-0261.12651

Genetic alterations of malignant pleural mesothelioma: association with tumor heterogeneity and overall survival
Cited by: 66
Author(s): Lisa Quetel, Clément Meiller, Jean-Baptiste Assié, Yuna Blum, Sandrine Imbeaud, François Montagne, Robin Tranchant, Julien De Wolf, Stefano Caruso, Marie‐Christine Copin, Véronique Hofman, Laure Gibault, Cécile Badoual, Ecaterina Pintilie, Paul Hofman, I. Monnet, Arnaud Scherpereel, Françoise Le Pimpec‐Barthes, Jessica Zucman‐Rossi, Marie‐Claude Jaurand, Didier Jean
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-019-5947-z

Small RNA discovery in the interaction between barley and the powdery mildew pathogen
Cited by: 26
Author(s): Matt Hunt, Sagnik Banerjee, Priyanka Surana, Meiling Liu, Greg Fuerst, Sandra M. Mathioni, Blake C. Meyers, Dan Nettleton, Roger P. Wise
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2148-14-139

Molecular evolution of NASP and conserved histone H3/H4 transport pathway
Cited by: 30
Author(s): Syed Nabeel‐Shah, Kanwal Ashraf, Ronald E. Pearlman, Jeffrey Fillingham
Software Mentions: 4
Published: over 10 years ago

10.3389/fcell.2021.666303

Lgr4 Regulates Oviductal Epithelial Secretion Through the WNT Signaling Pathway
Cited by: 3
Author(s): Xue Tan, Lingling Zhang, Tianqi Li, Jia Zhan, Kun Qiao, Haili Wu, Shenfei Sun, Meina Huang, Fangxi Zhang, Meixing Zhang, Changwei Li, Li R, Hongjie Pan
Software Mentions: 3
Published: over 3 years ago

10.1111/mec.13596

Divergence in gene expression within and between two closely related flycatcher species
Cited by: 56
Author(s): Severin Uebbing, Axel Künstner, Hannu Mäkinen, Niclas Backström, Paulina Bolívar, Reto Burri, Ludovic Dutoit, Carina F. Mugal, Alexander Nater, Bronwen Aken, Paul Flicek, Fergal J. Martin, Stephen M. J. Searle, Hans Ellegren
Software Mentions: 3
Published: over 8 years ago

10.3389/fcell.2021.727183

A Novel Pyroptosis-Associated Long Non-coding RNA Signature Predicts Prognosis and Tumor Immune Microenvironment of Patients With Breast Cancer
Cited by: 29
Author(s): Liqin Ping, Kaiming Zhang, Xueqi Ou, Xingsheng Qiu, Xia Xiao
Software Mentions: 3
Published: over 3 years ago

10.1111/j.1742-4658.2009.06893.x

Talin 2 is a large and complex gene encoding multiple transcripts and protein isoforms
Cited by: 58
Author(s): Emmanuel Debrand, Yasmine El Jai, Lorraine Spence, Neil Bate, Uta Praekelt, Catrin Pritchard, Susan J. Monkley, David R. Critchley
Software Mentions: 3
Published: almost 16 years ago

10.1186/1471-2164-13-31

Sequencing and comparative genomic analysis of 1227 Felis catus cDNA sequences enriched for developmental, clinical and nutritional phenotypes
Cited by: 8
Author(s): Kristopher J. L. Irizarry, S. B. Malladi, Xiangming Gao, Katherine Mitsouras, Lynda Melendez, Patricia A Burris, Jeffrey A. Brockman, Samer Al-Murrani
Software Mentions: 3
Published: almost 13 years ago

10.1186/1475-2875-12-345

Variations in ncRNA gene LOC284889 and MIF-794CATT repeats are associated with malaria susceptibility in Indian populations
Cited by: 6
Author(s): Aditya Nath Jha, Pandarisamy Sundaravadivel, Sudhanshu S. Pati, Pradeep Kumar Patra, Kumarasamy Thangaraj
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-017-3858-4

Identification and characterization of long intergenic noncoding RNAs in bovine mammary glands
Cited by: 51
Author(s): Chao Tong, Qiaoling Chen, Lili Zhao, Junfei Ma, Eveline M. Ibeagha‐Awemu, Xin Zhao
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms21020547

Open Data for Differential Network Analysis in Glioma
Cited by: 8
Author(s): Claire Jean-Quartier, Fleur Jeanquartier, Andreas Holzinger
Software Mentions: 3
Published: almost 5 years ago

10.1002/ece3.484

Cis‐regulatory sequence variation and association with <i>Mycoplasma</i> load in natural populations of the house finch ( <i>Carpodacus mexicanus</i> )
Cited by: 11
Author(s): Niclas Backström, Daria Shipilina, Mozes P. K. Blom, Scott V. Edwards
Software Mentions: 3
Published: almost 12 years ago

10.1186/1471-2164-14-148

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs
Cited by: 47
Author(s): Anna Esteve‐Codina, Yogesh Paudel, Luca Ferretti, Emanuele Raineri, Hendrik‐Jan Megens, L. Silío, M. C. Rodríguez, Martien A. M. Groenen, Sebastián E. Ramos-Onsins, Miguel Pérez‐Enciso
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12920-018-0452-9

Comparison of different functional prediction scores using a gene-based permutation model for identifying cancer driver genes
Cited by: 6
Author(s): Alice Djotsa Nono, Ken Chen, Xiaoming Liu
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0254189

Transcriptome analysis of bread wheat leaves in response to salt stress
Cited by: 19
Author(s): Nazanin Amirbakhtiar, Ahmad Ismaili, Mohammad Reza Ghaffari, Raheleh Mirdar Mansuri, Sepideh Sanjari, Zahra‐Sadat Shobbar
Software Mentions: 3
Published: over 3 years ago

10.1093/database/bax049

Benchmarking distributed data warehouse solutions for storing genomic variant information
Cited by: 9
Author(s): Marek Wiewiórka, Dawid P Wysakowicz, Michał Okoniewski, Tomasz Gambin
Software Mentions: 3
Published: almost 8 years ago

10.1099/jgv.0.000744

Differentially expressed genes during spontaneous lytic switch of Marek's disease virus in lymphoblastoid cell lines determined by global gene expression profiling
Cited by: 9
Author(s): William Mwangi, Deepali Vasoya, Lydia Kgosana, Michael Watson, Venugopal Nair
Software Mentions: 3
Published: almost 8 years ago

10.1523/ENEURO.0103-19.2019

Concentration-Dependent Recruitment of Mammalian Odorant Receptors
Cited by: 12
Author(s): Xiaoyang Serene Hu, Kentaro Ikegami, Aashutosh Vihani, Kevin Zhu, M Camila Fernández Zapata, Claire A. de March, Matthew Do, Natasha Vaidya, Gary Kucera, Cheryl B. Bock, Yue Jiang, Masafumi Yohda, Hiroaki Matsunami
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-40659-7

Genome-wide Analysis of bZIP Transcription Factors in wheat and Functional Characterization of a TabZIP under Abiotic Stress
Cited by: 70
Author(s): Pragya Agarwal, Vinay Kumar Baranwal, Paramjit Khurana
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0194036

Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease
Cited by: 11
Author(s): Hirofumi Chiba, Yoichi Kakuta, Yoshitaka Kinouchi, Yosuke Kawai, Kazuhiro Watanabe, Munenori Nagao, Takeo Naito, Motoyuki Onodera, Rintaro Moroi, Masatake Kuroha, Yoshitake Kanazawa, Tsutomu Kimura, Hisashi Shiga, Katsuya Endo, Kenichi Negoro, Masao Nagasaki, Michiaki Unno, Tooru Shimosegawa
Software Mentions: 3
Published: almost 7 years ago

10.3390/cancers11030284

Gliosarcoma Is Driven by Alterations in PI3K/Akt, RAS/MAPK Pathways and Characterized by Collagen Gene Expression Signature
Cited by: 15
Author(s): Bartosz Wojtaś, Bartłomiej Gielniewski, Kamil Wojnicki, Marta Maleszewska, Shamba S. Mondal, Paweł Nauman, Wiesława Grajkowska, Rainer Glaß, Ulrich Schüller, Christel Herold‐Mende, Bożena Kamińska
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0234782

Ab initio GO-based mining for non-tandem-duplicated functional clusters in three model plant diploid genomes
Cited by: 0
Author(s): Paolo Bagnaresi, Luigi Cattivelli
Software Mentions: 3
Published: over 4 years ago

10.1186/s13015-018-0133-4

Coordinate systems for supergenomes
Cited by: 10
Author(s): Fabian Gärtner, Christian Höner zu Siederdissen, Lydia Müller, Peter F. Stadler
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-51141-9

Divergence in Transcriptional and Regulatory Responses to Mating in Male and Female Fruitflies
Cited by: 21
Author(s): Emily K. Fowler, Thomas Bradley, Simon Moxon, Tracey Chapman
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0060588

Identification of a Novel Gig2 Gene Family Specific to Non-Amniote Vertebrates
Cited by: 17
Author(s): Yibing Zhang, Ting-Kai Liu, Jun Jiang, Jun Shi, Ying Liu, Shun Li, Jian‐Fang Gui
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0071775

Postgwas: Advanced GWAS Interpretation in R
Cited by: 23
Author(s): Milan Hiersche, Frank Rühle, Monika Stoll
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pgen.1004223

Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species
Cited by: 87
Author(s): Kohta Yoshida, Takashi Makino, Katsushi Yamaguchi, Shuji Shigenobu, Mitsuyasu Hasebe, Masakado Kawata, Manabu Kume, Seiichi Mori, Catherine L. Peichel, Atsushi Toyoda, Asao Fujiyama, Jun Kitano
Software Mentions: 3
Published: almost 11 years ago

10.1186/1741-7007-7-7

A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish
Cited by: 136
Author(s): Lieke M. van der Aa, Jean‐Pierre Levraud, Malika Yahmi, Emilie Lauret, Valérie Briolat, Philippe Herbomel, Abdenour Benmansour, Pierre Boudinot
Software Mentions: 3
Published: almost 16 years ago

10.1371/journal.pone.0242211

Ikaros antagonizes DNA binding by STAT5 in pre-B cells
Cited by: 7
Author(s): Beate Heizmann, Stéphanie Le Gras, Célestine Simand, Patricia Marchal, Susan Chan, Philippe Kastner
Software Mentions: 3
Published: about 4 years ago

10.1172/jci.insight.141618

Loss of Fas signaling in fibroblasts impairs homeostatic fibrosis resolution and promotes persistent pulmonary fibrosis
Cited by: 25
Author(s): Elizabeth F. Redente, Sangeeta Chakraborty, Satria Sajuthi, Bart P. Black, Benjamin Edelman, Max A. Seibold, David W. H. Riches
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0085104

On the Origin and Evolutionary History of NANOG
Cited by: 21
Author(s): Pierluigi Scerbo, Gabriel V. Markov, Céline Vivien, Laurent Kodjabachian, Barbara Demeneix, Laurent Coen, Fabrice Girardot
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pcbi.1001138

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
Cited by: 495
Author(s): Andrew McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark Sun, Malachi Griffith, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk, Marina Pacheco, Marco A. Marra, Martin Hirst, Torsten O. Nielsen, S. Cenk Şahinalp, David G. Huntsman, Sohrab P. Shah
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0094646

Post-Translational Decrease in Respiratory Chain Proteins in the Polg Mutator Mouse Brain
Cited by: 12
Author(s): David N. Hauser, Allissa Dillman, Jinhui Ding, Li Yan, Mark Cookson
Software Mentions: 3
Published: over 10 years ago

10.3389/fmolb.2021.678877

A Ferroptosis-Related lncRNAs Signature Predicts Prognosis and Immune Microenvironment for Breast Cancer
Cited by: 42
Author(s): Kaiming Zhang, Liqin Ping, Tian Du, Gehao Liang, Yun Huang, Zhiling Li, Rong Deng, Jun Tang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1004293

Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma
Cited by: 22
Author(s): Julia C. Engelmann, Thomas Amann, Birgitta Ott-Rötzer, Margit Nützel, Yvonne Reinders, Jörg Reinders, Wolfgang E. Thasler, Theresa Kristl, Andreas Teufel, Christian G. Huber, Peter J. Oefner, Rainer Spang, Claus Hellerbrand
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-015-2336-0

Sex-specific gene expression in the mosquito Culex pipiens f. molestus in response to artificial light at night
Cited by: 25
Author(s): Ann‐Christin Honnen, Paul R. Johnston, Michael T. Monaghan
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12859-020-03864-0

Deep learning based DNA:RNA triplex forming potential prediction
Cited by: 20
Author(s): Yu Zhang, Yahui Long, Chee Keong Kwoh
Software Mentions: 3
Published: about 4 years ago

10.3389/fgene.2020.00876

Chromosome Genome Assembly of the Leopard Coral Grouper (Plectropomus leopardus) With Nanopore and Hi-C Sequencing Data
Cited by: 4
Author(s): Yongbo Wang, Xintian Wen, Xinhui Zhang, Shuyuan Fu, Jinye Liu, Wei Tan, Ming Luo, Longlong Liu, Hai Huang, Xinxin You, Jian Luo, Fuxiao Chen
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2021.636061

Human β-Defensin 2 Mutations Are Associated With Asthma and Atopy in Children and Its Application Prevents Atopic Asthma in a Mouse Model
Cited by: 10
Author(s): Natascha Borchers, Elisangela Santos-Valente, Antoaneta A. Toncheva, Jan Wehkamp, André Franke, Vincent D. Gaertner, Peter Nordkild, Jon Genuneit, Benjamin Anderschou Holbech Jensen, Michael Kabesch
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13024-021-00475-y

SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis
Cited by: 11
Author(s): Lydia M. Castelli, Luisa Cutillo, Catiane Souza, Álvaro Sánchez-Martínez, Ilaria Granata, Ya-Hui Lin, Monika A. Myszczynska, Paul R. Heath, Matthew R. Livesey, Ke Ning, Mimoun Azzouz, Pamela J. Shaw, Mario Rosario Guarracino, Alexander J. Whitworth, Laura Ferraiuolo, Marta Milo, Guillaume M. Hautbergue
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2019.00907

Epigenetic Delay in the Neurodevelopmental Trajectory of DNA Methylation States in Autism Spectrum Disorders
Cited by: 28
Author(s): Michael J. Corley, Naurú Idalia Vargas-Maya, Alina P.S. Pang, Annette Lum-Jones, Dongmei Li, Vedbar S. Khadka, Răzvan Sultana, D. Caroline Blanchard, Alika K. Maunakea
Software Mentions: 3
Published: about 5 years ago

10.1186/s40694-020-00103-2

Extracellular vesicles from the apoplastic fungal wheat pathogen Zymoseptoria tritici
Cited by: 30
Author(s): Erin Hill, Peter S. Solomon
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-62637-0

A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples
Cited by: 8
Author(s): Florian Uellendahl-Werth, Markus Wolfien, André Franke, Olaf Wolkenhauer, David Ellinghaus
Software Mentions: 3
Published: almost 5 years ago

10.1093/molbev/msy243

Influence of Recombination and GC-biased Gene Conversion on the Adaptive and Nonadaptive Substitution Rate in Mammals versus Birds
Cited by: 36
Author(s): Marjolaine Rousselle, Alexandre Laverré, Emeric Figuet, Benoît Nabholz, Nicolas Galtier
Software Mentions: 2
Published: about 6 years ago