pypi: biomart | Projects | Ecosyste.ms: Papers

10.3389/fgene.2021.559998

Gene Size Matters: An Analysis of Gene Length in the Human Genome
Cited by: 55
Author(s): Inês Lopes, Gulam Altab, Priyanka Raina, João Pedro de Magalhães
Software Mentions: 15
Published: almost 4 years ago

10.1186/s12859-018-2254-7

Netpredictor: R and Shiny package to perform drug-target network analysis and prediction of missing links
Cited by: 12
Author(s): Abhik Seal, David Wild
Software Mentions: 9
Published: over 6 years ago

10.3390/ijms22179426

Gravitational Force—Induced 3D Chromosomal Conformational Changes Are Associated with Rapid Transcriptional Response in Human T Cells
Cited by: 14
Author(s): Christian Vahlensieck, Cora S. Thiel, Ye Zhang, Andreas Huge, Oliver Ullrich
Software Mentions: 8
Published: over 3 years ago

10.1002/1873-3468.14180

Genome‐scale metabolic modelling of SARS‐CoV‐2 in cancer cells reveals an increased shift to glycolytic energy production
Cited by: 13
Author(s): Elisabeth Yaneske, Guido Zampieri, Loris Bertoldi, Giuseppe Benvenuto, Claudio Angione
Software Mentions: 7
Published: over 3 years ago

10.1186/s13073-020-00788-5

Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation
Cited by: 10
Author(s): Shi Yang Liu, Nathan Harmston, Trudy Lee Glaser, Yunka Wong, Zheng Zhong, Babita Madan, David M. Virshup, Enrico Petretto
Software Mentions: 7
Published: about 4 years ago

10.1093/database/baaa082

Siberian sturgeon multi-tissue reference transcriptome database
Cited by: 2
Author(s): Christophe Klopp, Cédric Cabau, Gonzalo Greif, André Lasalle, Santiago Di Landro, Denise Vizziano-Cantonnet
Software Mentions: 6
Published: almost 5 years ago

10.1111/age.12873

Genomic regions influencing intramuscular fat in divergently selected rabbit lines
Cited by: 15
Author(s): Bolívar Samuel Sosa-Madrid, Pilar Hernández, A. Blasco, Chris Haley, Luca Fontanesi, M. A. Santacreu, Ramona N. Pena, Pau Navarro, Noelia Ibáñez‐Escriche
Software Mentions: 6
Published: about 5 years ago

10.3390/cancers12082261

MiR-302b as a Combinatorial Therapeutic Approach to Improve Cisplatin Chemotherapy Efficacy in Human Triple-Negative Breast Cancer
Cited by: 12
Author(s): Alessandra Cataldo, Sandra Romero-Córdoba, Ilaria Plantamura, Giulia Cosentino, Alfredo Hidalgo‐Miranda, Elda Tagliabue, Marilena V. Iorio
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2021.698033

ACE2 Netlas: In silico Functional Characterization and Drug-Gene Interactions of ACE2 Gene Network to Understand Its Potential Involvement in COVID-19 Susceptibility
Cited by: 4
Author(s): Gita A. Pathak, Frank R. Wendt, Aranyak Goswami, Dóra Koller, Flavio De Angelis, Covid Host Genetics Initiative, Renato Polimanti
Software Mentions: 5
Published: over 3 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

10.1371/journal.pcbi.1006937

Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder
Cited by: 9
Author(s): Abrar E. Al‐Shaer, George R. Flentke, Mark E. Berres, Ana Garic, Susan Smith
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-66630-5

Single-cell RNA sequencing reveals that lung mesenchymal progenitor cells in IPF exhibit pathological features early in their differentiation trajectory
Cited by: 23
Author(s): Daniel Beisang, Karen Smith, Libang Yang, Alexey O. Benyumov, Adam Gilbertsen, Jeremy Herrera, Eric F. Lock, Emilian Racila, Colleen L. Forster, Brian J Sandri, Craig A. Henke, Peter B. Bitterman
Software Mentions: 4
Published: over 4 years ago

10.3389/fbioe.2020.00266

Characterization of lncRNA-Associated ceRNA Network to Reveal Potential Prognostic Biomarkers in Lung Adenocarcinoma
Cited by: 8
Author(s): Yang Wang, Ruyi He, Lixin Ma
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2164-14-862

De novo characterization of the gene-rich transcriptomes of two color-polymorphic spiders, Theridion grallator and T. californicum (Araneae: Theridiidae), with special reference to pigment genes
Cited by: 51
Author(s): Peter J.P. Croucher, Michael S. Brewer, Christopher J. Winchell, Geoff Oxford, Rosemary G. Gillespie
Software Mentions: 4
Published: almost 12 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

10.7554/eLife.58597

The leukocyte non-coding RNA landscape in critically ill patients with sepsis
Cited by: 28
Author(s): Brendon P. Scicluna, Fabrice Uhel, Lonneke A. van Vught, Maryse A. Wiewel, Arie J. Hoogendijk, Ingelore Baessman, Marek Franitza, Peter Nürnberg, Janneke Horn, Olaf L. Cremer, Marc J. M. Bonten, Marcus J. Schultz, Tom van der Poll
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.50770

YAP1 and TAZ negatively control bone angiogenesis by limiting hypoxia-inducible factor signaling in endothelial cells
Cited by: 43
Author(s): Kishor K. Sivaraj, Backialakshmi Dharmalingam, Vishal Mohanakrishnan, Hyun‐Woo Jeong, Katsuhiro Kato, Silke Schröder, Susanne Adams, Gou Young Koh, Ralf H. Adams
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0130413

A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes
Cited by: 11
Author(s): J. Watson Grice, Boris Noyvert, Laura Doglio, Greg Elgar
Software Mentions: 3
Published: over 9 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

10.3389/fpls.2016.01347

A Primary Sequence Analysis of the ARGONAUTE Protein Family in Plants
Cited by: 22
Author(s): Daniel Rodríguez-Leal, Amanda Castillo-Cobián, Isaac Rodríguez‐Arévalo, Jean‐Philippe Vielle‐Calzada
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.ppat.1008781

Gene expression network analyses during infection with virulent and avirulent Trypanosoma cruzi strains unveil a role for fibroblasts in neutrophil recruitment and activation
Cited by: 8
Author(s): Antônio Edson Rocha Oliveira, Milton Pereira, Ashton T. Belew, Ludmila Rodrigues Pinto Ferreira, Larissa M. N. Pereira, Eula G. A. Neves, Maria do Carmo Pereira Nunes, Barbara A. Burleigh, Walderez Ornelas Dutra, Najib M. El-Sayed, Ricardo T. Gazzinelli, Santuza Maria Ribeiro Teixeira
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-021-04207-3

Lantern: an integrative repository of functional annotations for lncRNAs in the human genome
Cited by: 2
Author(s): Swapna Vidhur Daulatabad, Rajneesh Srivastava, Sarath Chandra Janga
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-13-459

Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae
Cited by: 52
Author(s): Agnieszka Podolska, Christian Anthon, Mads Bak, Niels Tommerup, Kerstin Skovgaard, Peter M. H. Heegaard, Jan Gorodkin, Susanna Cirera, Merete Fredholm
Software Mentions: 3
Published: over 12 years ago

10.1093/bioinformatics/bts525

JEnsembl: a version-aware Java API to Ensembl data systems
Cited by: 3
Author(s): Trevor Paterson, Andy Law
Software Mentions: 3
Published: over 12 years ago

10.1186/s40462-016-0069-6

Gene expression in the brain of a migratory songbird during breeding and migration
Cited by: 19
Author(s): John Boss, Miriam Liedvogel, Max Lundberg, Peter Olsson, Nils Reischke, Sara Naurin, Susanne Åkesson, Dennis Hasselquist, Anthony P. H. Wright, Mats Grahn, Staffan Bensch
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pbio.3000152

Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development
Cited by: 113
Author(s): Mazène Hochane, Patrick R. van den Berg, Xueying Fan, Noémie M. L. P. Bérenger-Currias, Esmée Adegeest, Monika Bialecka, Maaike Nieveen, Maarten Menschaart, Susana M. Chuva de Sousa Lopes, Stefan Semrau
Software Mentions: 3
Published: almost 6 years ago

10.18632/oncotarget.26272

Nasal administration of mesenchymal stem cells restores cisplatin-induced cognitive impairment and brain damage in mice
Cited by: 48
Author(s): Gabriel Sean-Hang Chiu, Nabila Boukelmoune, Angie C.A. Chiang, Bo Peng, Vikram Rao, Charles V. Kingsley, Ho Ling Liu, Annemieke Kavelaars, Shelli R. Kesler, Cobi J. Heijnen
Software Mentions: 3
Published: about 6 years ago

10.1534/g3.116.031120

Genome-Wide Analysis of Polyadenylation Events in <i>Schmidtea mediterranea</i>
Cited by: 12
Author(s): Vairavan Lakshmanan, Dhiru Bansal, Jahnavi Kulkarni, Deepak Poduval, Srikar Krishna, Vidyanand Sasidharan, Praveen Anand, Aswin Sai Narain Seshasayee
Software Mentions: 3
Published: about 8 years ago

10.4049/jimmunol.1600624

Network Analysis Identifies Proinflammatory Plasma Cell Polarization for Secretion of ISG15 in Human Autoimmunity
Cited by: 45
Author(s): Matthew A. Care, Sophie Stephenson, Nicholas A. Barnes, Im Fan, Alexandre Zougman, Yasser M. El-Sherbiny, Edward M Vital, David R. Westhead, Reuben Tooze, Gina M. Doody
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-019-5874-z

Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation
Cited by: 6
Author(s): Anja Striberny, Even H. Jørgensen, Christophe Klopp, Élodie Magnanou
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-11-68

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing
Cited by: 57
Author(s): Heiner Kuhl, Alfred Beck, Grzegorz Woźniak, Adelino V.M. Canário, Filip Volckaert, Richard Reinhardt
Software Mentions: 2
Published: almost 15 years ago

10.1186/1755-8794-4-64

Identification of candidate genes linking systemic inflammation to atherosclerosis; results of a human in vivoLPS infusion study
Cited by: 24
Author(s): Suthesh Sivapalaratnam, Rosienne Farrugia, Max Nieuwdorp, Cordelia Langford, Rachel T. van Beem, Stephanie Maiwald, Jaap Jan Zwaginga, Arief Gusnanto, Nicholas A. Watkins, Mieke D. Trip, Willem H. Ouwehand
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1002316

Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping
Cited by: 330
Author(s): Amaury Vaysse, Abhirami Ratnakumar, Thomas Derrien, Erik Axelsson, Gerli Pielberg, Snaevar Sigurðsson, Tove Fall, Eija H. Seppälä, Mark Hansen, Cindy Lawley, Elinor K. Karlsson, Danika Bannasch, Carles Vilà, Hannes Lohi, Francis Galibert, Merete Fredholm, Jens Häggström, Åke Hedhammar, Catherine André, Kerstin Lindblad‐Toh, Christophe Hitte, Matthew T. Webster
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0239143

Genetic variations (eQTLs) in muscle transcriptome and mitochondrial genes, and trans-eQTL molecular pathways in feed efficiency from Danish breeding pigs
Cited by: 2
Author(s): Victor Adriano Okstoft Carmelo, Haja N. Kadarmideen
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0096821

RNAbrowse: RNA-Seq De Novo Assembly Results Browser
Cited by: 19
Author(s): Jérôme Mariette, Céline Noirot, Ibounyamine Nabihoudine, Philippe Bardou, Claire Hoede, Anis Djari, Cédric Cabau, Christophe Klopp
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0010709

A Data Integration Approach to Mapping OCT4 Gene Regulatory Networks Operative in Embryonic Stem Cells and Embryonal Carcinoma Cells
Cited by: 80
Author(s): Myung-Hwan Jung, Hedi Peterson, Lukas Chávez, Pascal Kahlem, Hans Lehrach, Jaak Vilo, James Adjaye
Software Mentions: 2
Published: over 14 years ago

10.1016/j.gdata.2015.11.013

In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data
Cited by: 5
Author(s): Suyash Agarwal, N. S. Nagpure, Prachi Srivastava, Basdeo Kushwaha, Ravindra Kumar, Manmohan Pandey, Shreya Srivastava
Software Mentions: 2
Published: almost 9 years ago

10.1186/gb-2006-7-7-r66

Cited by: 277
Author(s): Michael Boutros, Lı́gia P. Brás, Wolfgang Huber
Software Mentions: 2
Published: almost 19 years ago

10.7554/eLife.26876

The DREAM complex through its subunit Lin37 cooperates with Rb to initiate quiescence
Cited by: 38
Author(s): Christina Fs Mages, Axel Wintsche, Stephan H. Bernhart, G Müller
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0097535

Epigenetic Characterization of the Growth Hormone Gene Identifies SmcHD1 as a Regulator of Autosomal Gene Clusters
Cited by: 24
Author(s): Shabnam Massah, Robert E. Hollebakken, Mark P. Labrecque, Addie Kolybaba, Timothy V. Beischlag, Gratien G. Préfontaine
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0028213

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells
Cited by: 60
Author(s): Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix, Christelle Borel, Jonathan M. Mudge, Cédric Howald, Sylvain Foissac, Catherine Ucla, Jacqueline Chrast, Paolo Ribeca, David L. Martin, Ryan R. Murray, Xinping Yang, Lila Ghamsari, Chenwei Lin, Ian Bell, Erica Dumais, Jörg Drenkow, Michael L. Tress, Josep Lluís Gelpí, Modesto Orozco, Alfonso Valencia, Nynke L. van Berkum, Bryan R. Lajoie, Marc Vidal, J Stamatoyannopoulos, Philippe Batut, Alexander Dobin, Jennifer Harrow, Tim Hubbard, Job Dekker, Adam Frankish, Kourosh Salehi‐Ashtiani, Alexandre Reymond, Stylianos E. Antonarakis, Roderic Guigó, T Gingeras
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0048336

Insights into the Evolutionary Features of Human Neurodegenerative Diseases
Cited by: 10
Author(s): Arup Panda, Tina Begum, Tapash Chandra Ghosh
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2105-12-S1-S29

Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models
Cited by: 29
Author(s): Ivan G. Costa, Helge G. Roider, Thaís Gaudencio do Rêgo, Francisco de A. T. de Carvalho
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-15-486

The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown
Cited by: 84
Author(s): Anthony Levasseur, Anne Lomascolo, Olivier Chabrol, Francisco J. Ruíz-Dueñas, Eva Boukhris-Uzan, François Piumi, Ursula Kües, Arthur F. J. Ram, Claude Murat, Mireille Haon, Isabelle Benoit, Yonathan Arfi, Didier Chevret, Élodie Drula, Min Jin Kwon, Philippe Gouret, Laurence Lesage‐Meessen, Vincent Lombard, Jérôme Mariette, Céline Noirot, Joohae Park, Aleksandrina Patyshakuliyeva, Jean‐Claude Sigoillot, Ad Wiebenga, Han A. B. Wösten, Francis Martin, Pedro M. Coutinho, Ronald P. de Vries, Ángel T. Martínez, Christophe Klopp, Pierre Pontarotti, Bernard Henrissat, Éric Record
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12859-021-04105-8

Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations
Cited by: 11
Author(s): Yi Chen, Fons J. Verbeek, Katy Wolstencroft
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0021832

HelmCoP: An Online Resource for Helminth Functional Genomics and Drug and Vaccine Targets Prioritization
Cited by: 18
Author(s): Sahar Abubucker, Thomas Martın, Christina Taylor, Makedonka Mitreva
Software Mentions: 1
Published: over 13 years ago

Projects: pypi: biomart

Papers Mentioning biomart 46