Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: ensembl
https://packages.ecosyste.ms/registries/pypi.org/packages/ensembl
Ensembl REST API Client
1 version
Latest release: over 1 year ago
Papers Mentioning ensembl 212
10.1186/s12920-017-0261-6
CVE: an R package for interactive variant prioritisation in precision oncologyCited 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 analysesCited 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 cellsCited 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 DataCited 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 ChromosomeCited 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: almost 9 years ago
10.1371/journal.pone.0240895
RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beefCited 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 EukCCCited by: 51
Author(s): Paul Saary, Alex L. Mitchell, Alex Bateman
Software Mentions: 8
Published: about 4 years ago
10.12688/wellcomeopenres.14306.1
CoverView: a sequence quality evaluation tool for next generation sequencing dataCited 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 CarcinomaCited 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: about 3 years ago
10.1371/journal.pgen.1007784
Maternal and zygotic gene regulatory effects of endogenous RNAi pathwaysCited 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 animalsCited 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 infectionCited 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: almost 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 macrophagesCited 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 EpitheliumCited 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’sCited by: 0
Author(s): Zainab H. Malalla, Ahmad Al-Serri, Huda Alaskar, Wafaa Y. Al-Kandari, Suzanne A. Al-Bustan
Software Mentions: 6
Published: almost 5 years ago
10.1371/journal.pone.0092111
Transcriptome Analysis Reveals Differential Splicing Events in IPF Lung TissueCited 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: over 10 years ago
10.1093/g3journal/jkab274
Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, ScotlandCited 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 cellsCited 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: over 7 years ago
10.1186/s13073-021-00931-w
Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesotheliomaCited 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 activationCited 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 speciesCited 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 mammalsCited 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: over 11 years ago
10.1186/s12864-016-2849-1
Deciphering transcriptome profiles of peripheral blood mononuclear cells in response to PRRSV vaccination in pigsCited 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 modelsCited 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 riskCited 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 speciesCited by: 95
Author(s): Emiliano Trucchi, Anna B. Mazzarella, Gregor D. Gilfillan, María Teresa Cáceres Lorenzo, Peter Schönswetter, Ovidiu Paun
Software Mentions: 5
Published: over 8 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 modificationsCited 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 levelsCited 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 yeastCited 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 timelineCited 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 ApproachCited 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 EpitheliumCited 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 networksCited 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 QTLCited 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 evolutionCited 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: over 9 years ago
10.3389/fimmu.2015.00380
An Introduction to Automated Flow Cytometry Gating Tools and Their ImplementationCited 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 systemCited 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 BehaviorCited 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 FibroblastsCited 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 myotisCited 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 motilityCited 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 factorsCited by: 67
Author(s): Richard R. Copley
Software Mentions: 4
Published: almost 19 years ago
10.1093/database/bax039
GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any speciesCited 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 BipotencyCited 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: about 11 years ago
10.1038/s41598-020-58711-2
Nucleus accumbens pathways control cell-specific gene expression in the medial prefrontal cortexCited 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 henCited 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: over 16 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 nephropathyCited 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: almost 7 years ago
10.1371/journal.pone.0210859
Synthetic lethality guiding selection of drug combinations in ovarian cancerCited 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 responseCited 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 PufferfishCited 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 signaturesCited by: 0
Author(s): Kunal Kathuria, Aakrosh Ratan
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0100250
Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele ExclusionCited 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) datasetCited 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 quantificationCited 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 miceCited 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 survivalCited 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: over 4 years ago
10.1186/s12864-019-5947-z
Small RNA discovery in the interaction between barley and the powdery mildew pathogenCited 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 pathwayCited 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 PathwayCited 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: about 3 years ago
10.1111/mec.13596
Divergence in gene expression within and between two closely related flycatcher speciesCited 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 CancerCited by: 29
Author(s): Liqin Ping, Kaiming Zhang, Xueqi Ou, Xingsheng Qiu, Xia Xiao
Software Mentions: 3
Published: about 3 years ago
10.1111/j.1742-4658.2009.06893.x
Talin 2 is a large and complex gene encoding multiple transcripts and protein isoformsCited 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: over 15 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 phenotypesCited 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 populationsCited by: 6
Author(s): Aditya Nath Jha, Pandarisamy Sundaravadivel, Sudhanshu S. Pati, Pradeep Kumar Patra, Kumarasamy Thangaraj
Software Mentions: 3
Published: about 11 years ago
10.1186/s12864-017-3858-4
Identification and characterization of long intergenic noncoding RNAs in bovine mammary glandsCited 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 GliomaCited 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 pigsCited 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 genesCited 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 stressCited 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 informationCited 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 profilingCited by: 9
Author(s): William Mwangi, Deepali Vasoya, Lydia Kgosana, Michael Watson, Venugopal Nair
Software Mentions: 3
Published: over 7 years ago
10.1523/ENEURO.0103-19.2019
Concentration-Dependent Recruitment of Mammalian Odorant ReceptorsCited 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 StressCited by: 70
Author(s): Pragya Agarwal, Vinay Kumar Baranwal, Paramjit Khurana
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0194036
Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel diseaseCited 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: over 6 years ago
10.3390/cancers11030284
Gliosarcoma Is Driven by Alterations in PI3K/Akt, RAS/MAPK Pathways and Characterized by Collagen Gene Expression SignatureCited 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: over 5 years ago
10.1371/journal.pone.0234782
Ab initio GO-based mining for non-tandem-duplicated functional clusters in three model plant diploid genomesCited 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 supergenomesCited by: 10
Author(s): Fabian Gärtner, Christian Höner zu Siederdissen, Lydia Müller, Peter F. Stadler
Software Mentions: 3
Published: about 6 years ago
10.1038/s41598-019-51141-9
Divergence in Transcriptional and Regulatory Responses to Mating in Male and Female FruitfliesCited 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 VertebratesCited 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 RCited 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 SpeciesCited 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: over 10 years ago
10.1186/1741-7007-7-7
A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fishCited 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 cellsCited 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 fibrosisCited 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: almost 4 years ago
10.1371/journal.pone.0085104
On the Origin and Evolutionary History of NANOGCited 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 DataCited 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 BrainCited 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 CancerCited 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 CarcinomaCited 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 nightCited 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 predictionCited 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 DataCited 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: about 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 ModelCited 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: over 3 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 sclerosisCited 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 DisordersCited 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 triticiCited by: 30
Author(s): Erin Hill, Peter S. Solomon
Software Mentions: 3
Published: about 4 years ago
10.1038/s41598-020-62637-0
A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samplesCited by: 8
Author(s): Florian Uellendahl-Werth, Markus Wolfien, André Franke, Olaf Wolkenhauer, David Ellinghaus
Software Mentions: 3
Published: over 4 years ago
10.1093/molbev/msy243
Influence of Recombination and GC-biased Gene Conversion on the Adaptive and Nonadaptive Substitution Rate in Mammals versus BirdsCited by: 36
Author(s): Marjolaine Rousselle, Alexandre Laverré, Emeric Figuet, Benoît Nabholz, Nicolas Galtier
Software Mentions: 2
Published: almost 6 years ago