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: bioconductor: goseq

https://packages.ecosyste.ms/registries/bioconductor.org/packages/goseq

Gene Ontology analyser for RNA-seq and other length biased data
1 version
Latest release: 12 months ago
5 dependent packages
204,177 downloads total

Papers Mentioning goseq 132

10.1093/bioinformatics/bty947
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data
Cited by: 19
Author(s): Jamie Soul, Timothy E. Hardingham, Raymond P. Boot-Handford, Jean-Marc Schwartz
Software Mentions: 18
Published: almost 6 years ago
10.1186/s12859-020-03819-5
ideal: an R/Bioconductor package for interactive differential expression analysis
Cited by: 18
Author(s): Fédérico Marini, Jan Linke, Harald Binder
Software Mentions: 17
Published: almost 4 years ago
10.3390/cells8111321
Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding Datasets
Cited by: 16
Author(s): Mahmoud Ahmed, Trang Huyen Lai, Jin Seok Hwang, Sahib Zada, Trang Minh Pham, Deok Ryong Kim
Software Mentions: 15
Published: almost 5 years ago
10.1186/s13072-020-00380-6
Distinctive epigenomic alterations in NF1-deficient cutaneous and plexiform neurofibromas drive differential MKK/p38 signaling
Cited by: 7
Author(s): Jamie Grit, Benjamin K. Johnson, Patrick S. Dischinger, Curt J. Essenburg, Marie Adams, Stacy Campbell, Kai Pollard, Christine A. Pratilas, Tim Triche, Carrie R. Graveel, Matthew R. Steensma
Software Mentions: 13
Published: over 3 years ago
10.3390/ijms22031075
A Novel Epigenetic Machine Learning Model to Define Risk of Progression for Hepatocellular Carcinoma Patients
Cited by: 7
Author(s): Luca Bedon, Michele Dal Bo, Monica Mossenta, Davide Busato, Giuseppe Toffoli, Maurizio Polano
Software Mentions: 13
Published: over 3 years ago
10.1038/s41598-020-69239-w
Neural innervation as a potential trigger of morphological color change and sexual dimorphism in cichlid fish
Cited by: 14
Author(s): Yipeng Liang, Axel Meyer, Claudius F. Kratochwil
Software Mentions: 12
Published: about 4 years ago
10.1186/s12859-016-1260-x
MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
Cited by: 14
Author(s): Bohdan B. Khomtchouk, John L. Hennessy, Claes Wahlestedt
Software Mentions: 12
Published: about 8 years ago
10.1080/21623945.2019.1697563
Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes
Cited by: 6
Author(s): Mahmoud Ahmed, Deok Ryong Kim
Software Mentions: 11
Published: almost 6 years ago
10.1186/s12864-017-3819-y
RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples
Cited by: 67
Author(s): Petr V. Nazarov, Arnaud Muller, Tony Kaoma, Nathalie Nicot, Cristina Máximo, Philippe Birembaut, Nhan L. Tran, Gunnar Dittmar, Laurent Vallar
Software Mentions: 11
Published: over 7 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: almost 4 years ago
10.1007/s00401-020-02187-x
Interleukin-1 promotes autoimmune neuroinflammation by suppressing endothelial heme oxygenase-1 at the blood–brain barrier
Cited by: 44
Author(s): Judith Hauptmann, Lisa Johann, Fédérico Marini, Maja Kitic, E. Colombo, Ilgiz A. Mufazalov, Martin W. Krueger, Khalad Karram, Sonja Moos, Florian Wanke, Florian C. Kurschus, Matthias Klein, Sílvia Cardoso, Johannes Strauß, Subhashini Bolisetty, Fred Lühder, Markus Schwaninger, Harald Binder, Ingo Bechman, Tobias Bopp, Anupam Agarwal, Miguel P. Soares, Tommy Regen, Ari Waisman
Software Mentions: 9
Published: about 4 years ago
10.3390/cancers12030653
Molecular-Clinical Correlation in Pediatric Medulloblastoma: A Cohort Series Study of 52 Cases in Taiwan
Cited by: 6
Author(s): Kuo Sheng Wu, Donald Ming Tak Ho, Shiann-Tarng Jou, Alice L. Yu, Huy Tran, Muh Lii Liang, Hsin Hung Chen, Yi Yen Lee, Yi Wei Chen, Shih Chieh Lin, Feng Chi Chang, Meng‐Li Tsai, Yen‐Lin Liu, Hsin Lun Lee, Kevin Hsieh, Wen Chang Huang, Shian Ying Sung, Che-Chang Chang, Chun A. Changou, Kung‐Hao Liang, Tsung Han Hsieh, Yun Ru Liu, Meng En Chao, Chonghua Wan, Shing Shung Chu, Er Chieh Cho, Tai-Tong Wong
Software Mentions: 9
Published: over 4 years ago
10.1186/1471-2105-11-S12-S11
An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators
Cited by: 10
Author(s): Laurent Gautier
Software Mentions: 9
Published: almost 14 years ago
10.26508/lsa.202101108
Microglia show differential transcriptomic response to Aβ peptide aggregates ex vivo and in vivo
Cited by: 11
Author(s): Karen N. McFarland, Carolina Wiesner Ceballos, Awilda M. Rosario, Thomas B. Ladd, Brenda D. Moore, Griffin Golde, Xue Wang, Mariet Allen, Nilufer Ertekin‐Taner, Cory C. Funk, Max Robinson, Priyanka Baloni, Noa Rappaport, Paramita Chakrabarty, Todd E. Golde
Software Mentions: 9
Published: over 3 years ago
10.1371/journal.pone.0051609
Comparative Transcriptome Profiling of the Early Response to Magnaporthe oryzae in Durable Resistant vs Susceptible Rice (Oryza sativa L.) Genotypes
Cited by: 129
Author(s): Paolo Bagnaresi, Chiara Biselli, Luigi Orrù, Simona Urso, Laura Crispino, Pamela Abbruscato, Pietro Piffanelli, Elisabetta Lupotto, Luigi Cattivelli, Giampiero Valè
Software Mentions: 8
Published: almost 12 years ago
10.3389/fpls.2018.00108
Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size
Cited by: 61
Author(s): Sophie Lamarre, Pierre Frasse, Mohamed Zouine, Delphine Labourdette, Elise Sainderichin, Guojian Hu, Véronique Le Berre-Anton, Mondher Bouzayen, Élie Maza
Software Mentions: 8
Published: over 6 years ago
10.1371/journal.pone.0246052
Transcriptomic profiling of susceptible and resistant flax seedlings after Fusarium oxysporum lini infection
Cited by: 10
Author(s): Aleksandra Boba, Kamil Kostyń, Bartosz Kozak, Iwan Zalewski, Jan Szopa, Anna Kulma
Software Mentions: 8
Published: over 3 years ago
10.1016/j.heliyon.2019.e01558
Factor Analysis for Bicluster Acquisition (FABIA) revealed vincristine-sensitive transcript pattern of canine transmissible venereal tumors
Cited by: 5
Author(s): Kaj Chokeshaiusaha, Denis Puthier, Cong Tu Nguyen, Pansawut Sudjaidee, Thanida Sananmuang
Software Mentions: 8
Published: over 5 years ago
10.1111/eva.13120
Comparative transcriptomics of ice‐crawlers demonstrates cold specialization constrains niche evolution in a relict lineage
Cited by: 4
Author(s): Sean D. Schoville, Sabrina Simon, Ming Bai, Zachary T. Beethem, R. Yu. Dudko, Monika J. B. Eberhard, Paul B. Frandsen, Simon Küpper, Ryuichiro Machida, Max Verheij, Peter Willadsen, Xin Zhou, Benjamin Wipfler‍
Software Mentions: 8
Published: about 4 years ago
10.1038/s41598-017-05377-y
Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes
Cited by: 33
Author(s): Zupeng Wang, Yifei Liu, Li Li, Dawei Li, Qiong Zhang, Yangtao Guo, Shuaibin Wang, Caihong Zhong, Hongwen Huang
Software Mentions: 7
Published: over 7 years ago
10.1038/s42003-021-01990-w
Multi-omics phenotyping of the gut-liver axis reveals metabolic perturbations from a low-dose pesticide mixture in rats
Cited by: 26
Author(s): Robin Mesnage, Maxime Teixeira, Daniele Mandrioli, Laura Falcioni, Mariam Ibragim, Quinten R Ducarmon, Romy D. Zwittink, Caroline Amiel, Jean-Michel Panoff, Emma Bourne, Emanuel Savage, Charles A. Mein, Fiorella Belpoggi, Michael Antoniou
Software Mentions: 7
Published: over 3 years ago
10.1038/s41419-020-2477-1
Deficiency in the autophagy modulator Dram1 exacerbates pyroptotic cell death of Mycobacteria-infected macrophages
Cited by: 22
Author(s): Rui Zhang, Mónica Varela, Gabriel Forn-Cuní, Vincenzo Torraca, Michiel van der Vaart, Annemarie H. Meijer
Software Mentions: 7
Published: over 4 years ago
10.1186/s12864-021-07509-1
Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, ECM and MCM functions, and iron homeostasis
Cited by: 7
Author(s): Yang Dong, Morgan Newman, Stephen Pederson, Karissa Barthelson, Nhi Hin, Michael Lardelli
Software Mentions: 7
Published: over 3 years ago
10.1186/s13059-020-02098-w
Population variation in miRNAs and isomiRs and their impact on human immunity to infection
Cited by: 11
Author(s): Maxime Rotival, Katherine J. Siddle, Martin Silvert, Julien Pothlichet, Hélène Quach, Lluı́s Quintana-Murci
Software Mentions: 7
Published: about 4 years ago
10.1371/journal.pgen.1004900
An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifolia
Cited by: 41
Author(s): Aashish Ranjan, Brad T. Townsley, Yasunori Ichihashi, Neelima Sinha, Daniel H. Chitwood
Software Mentions: 7
Published: over 9 years ago
10.1002/evl3.245
Widespread cryptic variation in genetic architecture between the sexes
Cited by: 11
Author(s): Wouter van der Bijl, Judith E. Mank
Software Mentions: 7
Published: about 3 years ago
10.1186/1756-8935-8-6
De novo identification of differentially methylated regions in the human genome
Cited by: 639
Author(s): Timothy J. Peters, Michael Buckley, Aaron L. Statham, Ruth Pidsley, Katherine Samaras, Reginald V. Lord, Susan J. Clark, Peter L. Molloy
Software Mentions: 7
Published: over 9 years ago
10.1186/s13068-018-1116-x
Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032
Cited by: 54
Author(s): Shihui Yang, Jessica M. Vera, Jeff Grass, Giannis Savvakis, Oleg V. Moskvin, Yongqiang Yang, Sean J. McIlwain, Yucai Lyu, Irene Zinonos, Alexander S. Hebert, Joshua J. Coon, Donna M. Bates, Trey K. Sato, Steven D. Brown, Michael E. Himmel, Min Zhang, Robert Landick, Katherine M. Pappas, Yaoping Zhang
Software Mentions: 6
Published: over 6 years ago
10.1038/s41598-020-64929-x
Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity
Cited by: 29
Author(s): Maxime Caron, Pascal St-Onge, Thomas Sontag, Yu Chang Wang, Chantal Richer, Jiannis Ragoussis, Daniel Sinnett, Guillaume Bourque
Software Mentions: 6
Published: over 4 years ago
10.1186/s12284-016-0098-1
Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress
Cited by: 32
Author(s): Elena Baldoni, Paolo Bagnaresi, Franca Locatelli, Monica Mattana, Annamaria Genga
Software Mentions: 6
Published: over 8 years ago
10.1038/s41598-021-81933-x
Cell type-specific changes in transcriptomic profiles of endothelial cells, iPSC-derived neurons and astrocytes cultured on microfluidic chips
Cited by: 15
Author(s): Heleen H.T. Middelkamp, Anouk H.A. Verboven, Aisen Vivas, Chantal Schoenmaker, Teun Klein Gunnewiek, Robert Passier, Cornelis A. Albers, Peter-Bram A.C. ’t Hoen, Nael Nadif Kasri, Andries D. van der Meer
Software Mentions: 6
Published: over 3 years ago
10.1074/jbc.RA120.014598
The nuclear factor CECR2 promotes somatic cell reprogramming by reorganizing the chromatin structure
Cited by: 2
Author(s): Linlin Wu, Guoqing Zhao, Xu Shou, Jinqiang Kuang, Ming Jin, Guiying Wu, Tao Wang, Bo Wang, Ping Zhu, Duanqing Pei, Jing Liu
Software Mentions: 6
Published: almost 4 years ago
10.1016/j.immuni.2021.08.011
Adenosine-to-inosine editing of endogenous Z-form RNA by the deaminase ADAR1 prevents spontaneous MAVS-dependent type I interferon responses
Cited by: 58
Author(s): Qingli Tang, Rachel E. Rigby, George R. Young, Astrid Korning Hvidt, Tanja Davis, Tiong Kit Tan, Anne Bridgeman, Alain Townsend, George Kassiotis, Jan Rehwinkel
Software Mentions: 6
Published: about 3 years ago
10.1002/ece3.5516
Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs
Cited by: 18
Author(s): Jóhannes Guðbrandsson, Kalina H. Kapralova, Sigríður Rut Franzdóttir, Þóra Margrét Bergsveinsdóttir, Völundur Hafstað, Zophonı́as O. Jónsson, Sigurður S. Snorrason, Arnar Pálsson
Software Mentions: 6
Published: about 5 years ago
10.1371/journal.pgen.1006750
TCF21 and the environmental sensor aryl-hydrocarbon receptor cooperate to activate a pro-inflammatory gene expression program in coronary artery smooth muscle cells
Cited by: 50
Author(s): Juyong Brian Kim, Milos Pjanic, Trieu Nguyen, Clint L. Miller, Dharini Iyer, Boxiang Liu, Ting Wang, Olga V. Sazonova, Iván Cárcamo-Orive, Ljubica Matic, Lars Maegdefessel, Ulf Hedin, Thomas Quertermous
Software Mentions: 6
Published: over 7 years ago
10.1038/s41598-021-90093-x
Prematurity alters the progenitor cell program of the upper respiratory tract of neonates
Cited by: 6
Author(s): Jessica E. Shui, Wei Wang, Helu Liu, Анна Степанова, Grace Liao, Jun Qian, Xingbin Ai, Vadim S. Ten, Jining Lü, Wellington V. Cardoso
Software Mentions: 6
Published: over 3 years ago
10.1186/s12864-019-6076-4
Transcriptome analysis of the effect of C-C chemokine receptor 5 deficiency on cell response to Toxoplasma gondii in brain cells
Cited by: 7
Author(s): Kaoru Kobayashi, Kousuke Umeda, Fumie Ihara, Sadao Tanaka, Junya Yamagishi, Yutaka Suzuki, Yoshifumi Nishikawa
Software Mentions: 6
Published: about 5 years ago
10.1038/s41598-019-57214-z
5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation
Cited by: 14
Author(s): Santiago Uribe-Lewis, Thomas Carroll, Suraj Menon, Anna M. Nicholson, Piotr J. Manasterski, Douglas J. Winton, Simon Buczacki, Adele Murrell
Software Mentions: 6
Published: over 4 years ago
10.1016/j.celrep.2021.108735
Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage
Cited by: 38
Author(s): Qifan Zhu, Fei Sang, Sarah Withey, Walfred W.C. Tang, Sabine Dietmann, Doris Klisch, Priscila Ramos‐Ibeas, Haixin Zhang, Cristina E. Requena, Petra Hájková, Matt Loose, M. Azim Surani, Ramiro Alberio
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: over 6 years ago
10.18632/aging.102822
Transcriptomic and metabolomic profiling of long-lived growth hormone releasing hormone knock-out mice: evidence for altered mitochondrial function and amino acid metabolism
Cited by: 13
Author(s): Jessica M. Hoffman, Aliza Poonawalla, Mert Icyuz, William R. Swindell, Landon Wilson, Stephen Barnes, Liou Y. Sun
Software Mentions: 5
Published: over 4 years ago
10.1016/j.tcsw.2020.100039
A seven-membered cell wall related transglycosylase gene family in Aspergillus niger is relevant for cell wall integrity in cell wall mutants with reduced α-glucan or galactomannan
Cited by: 13
Author(s): Tim M. van Leeuwe, Jasper Wattjes, Anna Niehues, Gabriel Forn-Cuní, Nicholas Geoffrion, Hugo Mélida, Mark Arentshorst, Antonio Molina, Adrian Tsang, Annemarie H. Meijer, Bruno M. Moerschbacher, Peter J. Punt, Arthur F. J. Ram
Software Mentions: 5
Published: almost 4 years ago
10.1038/s41598-019-39318-8
Identifying Windows of Susceptibility by Temporal Gene Analysis
Cited by: 9
Author(s): Kristin P. Bennett, Elisabeth M. Brown, Hannah De los Santos, Matthew Poegel, Thomas R. Kiehl, Evan W. Patton, Spencer Norris, Sally Temple, John S. Erickson, Deborah L. McGuinness, Nathan C. Boles
Software Mentions: 5
Published: over 5 years ago
10.3389/fnmol.2018.00481
Common CHD8 Genomic Targets Contrast With Model-Specific Transcriptional Impacts of CHD8 Haploinsufficiency
Cited by: 30
Author(s): A. Ayanna Wade, Kenneth J. Lim, Rinaldo Catta-Preta, Alexander Nord
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pntd.0002905
Dual RNA-seq of Parasite and Host Reveals Gene Expression Dynamics during Filarial Worm–Mosquito Interactions
Cited by: 59
Author(s): Young Jun Choi, Matthew T. Aliota, George F. Mayhew, Sara M. Erickson, Bruce M. Christensen
Software Mentions: 5
Published: over 10 years ago
10.1186/s40168-020-00850-9
The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts
Cited by: 24
Author(s): Avihai Zolti, Stefan J. Green, Noa Sela, Yitzhak Hadar, Dror Minz
Software Mentions: 5
Published: over 4 years ago
10.1038/s41598-018-23366-7
Glucose Levels Alter the Mga Virulence Regulon in the Group A Streptococcus
Cited by: 25
Author(s): Kayla M. Valdes, Ganesh S. Sundar, Ashton T. Belew, Emrul Islam, Najib M. El-Sayed, Yoann Le Breton, Kevin S. McIver
Software Mentions: 5
Published: over 6 years ago
10.1038/s41598-021-81349-7
Inhibition of mitochondrial function by metformin increases glucose uptake, glycolysis and GDF-15 release from intestinal cells
Cited by: 46
Author(s): Ming Yang, Tamana Darwish, Pierre Larraufie, Debra Rimmington, Irène Cimino, Deborah A. Goldspink, Benjamin Jenkins, Albert Koulman, Cheryl A. Brighton, Marcella Ma, Brian Lam, Anthony P. Coll, Stephen O’Rahilly, Frank Reimann, Fiona M. Gribble
Software Mentions: 5
Published: over 3 years ago
10.1074/mcp.RA120.001964
Flow-induced Reorganization of Laminin-integrin Networks Within the Endothelial Basement Membrane Uncovered by Proteomics
Cited by: 13
Author(s): Eelke P. Béguin, Esmée F.J. Janssen, Mark Hoogenboezem, Alexander B. Meijer, Arie J. Hoogendijk, Maartje van den Biggelaar
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.ppat.1007050
Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses
Cited by: 48
Author(s): William H. Palmer, Nathan Medd, Philippa M. Beard, Darren J. Obbard
Software Mentions: 5
Published: over 6 years ago
10.1016/j.stemcr.2019.04.012
Human iPSC-Derived Retinal Pigment Epithelium: A Model System for Prioritizing and Functionally Characterizing Causal Variants at AMD Risk Loci
Cited by: 31
Author(s): Erin N. Smith, Agnieszka D’Antonio‐Chronowska, William W. Greenwald, Victor Borja, Lana Ribeiro Aguiar, Robert Pogue, Hiroko Matsui, Paola Benaglio, Shyamanga Borooah, Matteo D’Antonio, Radha Ayyagari, Kelly A. Frazer
Software Mentions: 5
Published: over 5 years ago
10.3389/fgene.2021.625466
Zebrafish Chromosome 14 Gene Differential Expression in the fmr1hu2787 Model of Fragile X Syndrome
Cited by: 1
Author(s): Karissa Barthelson, Lachlan Baer, Yang Dong, Melanie L. Hand, Zac Pujic, Morgan Newman, Geoffrey J. Goodhill, Robert I. Richards, Stephen Pederson, Michael Lardelli
Software Mentions: 5
Published: over 3 years ago
10.7554/eLife.07295
Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100
Cited by: 179
Author(s): Shouan Liu, Barbara Kracher, J. Ziegler, Rainer P. Birkenbihl, Imre E. Somssich
Software Mentions: 5
Published: over 9 years ago
10.1016/j.molcel.2019.03.010
A Secreted RNA Binding Protein Forms RNA-Stabilizing Granules in the Honeybee Royal Jelly
Cited by: 35
Author(s): Eyal Maori, Isabela Cunha Navarro, Humberto Boncristiani, David J. Seilly, Konrad L. M. Rudolph, Alexandra Sapetschnig, Chi-Chuan Lin, John E. Ladbury, Jay D. Evans, Jonathan L. Heeney, Eric A. Miska
Software Mentions: 4
Published: over 5 years ago
10.1186/s12864-015-2321-7
Deep sequencing transcriptional fingerprinting of rice kernels for dissecting grain quality traits
Cited by: 16
Author(s): Chiara Biselli, Paolo Bagnaresi, Daniela Cavalluzzo, Simona Urso, Francesca Desiderio, G. Orasen, Alberto Gianinetti, Federico Righettini, M. C. Gennaro, Rosaria Perrini, Manel Ben Hassen, Gian Attilio Sacchi, Luigi Cattivelli, Giampiero Valè
Software Mentions: 4
Published: almost 9 years ago
10.1186/s12864-020-07091-y
Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning
Cited by: 10
Author(s): Fernando Henrique Correr, Guilherme Kenichi Hosaka, Fernando Barreto, Isabella Barros Valadão, Thiago Willian Almeida Balsalobre, Agnelo Furtado, Robert J. Henry, Monalisa Sampaio Carneiro, Gabriel Rodrigues Alves Margarido
Software Mentions: 4
Published: about 4 years ago
10.1186/s12864-019-5775-1
Translation of upstream open reading frames in a model of neuronal differentiation
Cited by: 25
Author(s): Caitlin M. Rodriguez, Sang-Young Chun, Ryan E. Mills, Peter K. Todd
Software Mentions: 4
Published: over 5 years ago
10.1186/s12864-021-07710-2
Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China
Cited by: 11
Author(s): Peishi Feng, Tao Zeng, Hua Yang, Guohong Chen, Junzheng Du, Li Chen, Junda Shen, Zhenrong Tao, Ping Wang, Lin Yang, Lizhi Liu
Software Mentions: 4
Published: over 3 years ago
10.1186/s12864-016-2925-6
Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi
Cited by: 74
Author(s): S. Matić, Paolo Bagnaresi, Chiara Biselli, Luigi Orrù, Greice Amaral Carneiro, Ilenia Siciliano, Giampiero Valè, M. L. Gullino, D. Spadaro
Software Mentions: 4
Published: about 8 years ago
10.1186/s13229-021-00432-y
Neuroanatomy and behavior in mice with a haploinsufficiency of AT-rich interactive domain 1B (ARID1B) throughout development
Cited by: 17
Author(s): Jacob Ellegood, Stela P. Petkova, Adrienne Kinman, Lily R. Qiu, Anna Adhikari, A. Ayanna Wade, Darren Fernandes, Zsuzsa Lindenmaier, Amie Creighton, Lauryl M. J. Nutter, Alexander Nord, Jill L. Silverman, Jason P. Lerch
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pntd.0001409
A Deep Sequencing Approach to Comparatively Analyze the Transcriptome of Lifecycle Stages of the Filarial Worm, Brugia malayi
Cited by: 86
Author(s): Young Jun Choi, Elodie Ghedin, Matthew Berriman, Jacqueline A. McQuillan, Nancy Holroyd, George F. Mayhew, Bruce M. Christensen, Michelle L. Michalski
Software Mentions: 4
Published: almost 13 years ago
10.1111/eva.12463
Plasticity in gene transcription explains the differential performance of two invasive fish species
Cited by: 47
Author(s): Kyle Wellband, Daniel D. Heath
Software Mentions: 4
Published: over 7 years ago
10.3389/fpls.2021.643137
Nepenthes × ventrata Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs
Cited by: 4
Author(s): А. В. Щенникова, Alexey V. Beletsky, M. A. Filyushin, М. А. Слугина, Eugeny V. Gruzdev, Andrey V. Mardanov, Е. З. Кочиева, Н. В. Равин
Software Mentions: 4
Published: over 3 years ago
10.1186/s13059-020-02198-7
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements
Cited by: 17
Author(s): Pingli Liu, Xi Zhang, Jian‐Feng Mao, Yan-Ming Hong, Rengang Zhang, E Yilan, Shuai Nie, Kai‐Hua Jia, Chen-Kun Jiang, Jian He, Weiwei Shen, Qizouhong He, Wenqing Zheng, Samar H. Abbas, Pawan Kumar Jewaria, Xue Tian, Changjun Liu, Xueyu Jiang, Yafang Yin, Bo Liu, Li Wang, Biao Jin, Yongpeng Ma, Zongbo Qiu, Frantǐsek Baluška, Jozef Šamaj, Xin-Qiang He, Shihui Niu, Jianbo Xie, Lei Xie, Huimin Xu, Hongzhi Kong, Song Ge, Richard A. Dixon, Yuannian Jiao, Jinxing Lin
Software Mentions: 4
Published: almost 4 years ago
10.1186/s13059-021-02438-4
CoCoA-diff: counterfactual inference for single-cell gene expression analysis
Cited by: 6
Author(s): Yongjin Park, M Kellis
Software Mentions: 4
Published: about 3 years ago
10.1186/s13073-021-00884-0
Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice
Cited by: 14
Author(s): Jessica L Haigh, Anna Adhikari, Nycole A Copping, Tyler W. Stradleigh, A. Ayanna Wade, Rinaldo Catta-Preta, Linda Su-Feher, Iva Zdilar, Sarah Morse, Timothy A. Fenton, Anh B Nguyen, Diana Quintero, Samrawit Agezew, Michael Sramek, Ellie J Kreun, Jasmine Carter, Andrea Gompers, Jason T. Lambert, Cesar P Canales, L Pennacchio, Axel Visel, Diane E. Dickel, Jill L. Silverman, A. Nord
Software Mentions: 4
Published: over 3 years ago
10.1097/MIB.0000000000001131
Azathioprine with Allopurinol
Cited by: 7
Author(s): Sally A. Coulthard, Phil Berry, Sarah McGarrity, Simon D. McLaughlin, Azhar Ansari, Christopher P.F. Redfern
Software Mentions: 4
Published: over 7 years ago
10.1093/jxb/erw006
Evidence for maternal control of seed size in maize from phenotypic and transcriptional analysis
Cited by: 32
Author(s): Xia Zhang, Candice N. Hirsch, Rajandeep S. Sekhon, Natalia de León, Shawn M. Kaeppler
Software Mentions: 4
Published: over 8 years ago
10.1038/s41598-018-31618-9
Comparative transcriptome analysis to identify putative genes involved in thymol biosynthesis pathway in medicinal plant Trachyspermum ammi L.
Cited by: 21
Author(s): Mehdi Soltani Howyzeh, Seyed Ahmad Sadat Noori, Vahid Shariati J, Mahboubeh Amiripour
Software Mentions: 4
Published: about 6 years ago
10.1038/s41398-017-0058-6
Enriched expression of genes associated with autism spectrum disorders in human inhibitory neurons
Cited by: 43
Author(s): Ping Wang, Dejian Zhao, Herbert M. Lachman, Deyou Zheng
Software Mentions: 4
Published: over 6 years ago
10.1128/mBio.02500-18
Determination of the Global Pattern of Gene Expression in Yeast Cells by Intracellular Levels of Guanine Nucleotides
Cited by: 8
Author(s): Andrew Hesketh, Marta Vergnano, Stephen G. Oliver
Software Mentions: 4
Published: over 5 years ago
10.7554/eLife.60546
Acquisition of innate odor preference depends on spontaneous and experiential activities during critical period
Cited by: 13
Author(s): Qiang Qiu, Yunming Wu, Limei Ma, Wenjing Xu, Max Hills, Vivekanandan Ramalingam, Chong Yu
Software Mentions: 4
Published: over 3 years ago
10.3389/fmicb.2020.613532
CopR, a Global Regulator of Transcription to Maintain Copper Homeostasis in Pyrococcus furiosus
Cited by: 7
Author(s): Felix Grünberger, Robert Reichelt, Ingrid Waege, Verena Ned, Korbinian Bronner, Marcell Kaljanac, Nina Weber, Zubeir El Ahmad, Lena Knauss, M. Gregor Madej, Christine Ziegler, Dina Grohmann, Winfried Hausner
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0229513
The RNA-seq transcriptomic analysis reveals genes mediating salt tolerance through rapid triggering of ion transporters in a mutant barley
Cited by: 24
Author(s): Sareh Yousefirad, Hassan Soltanloo, Seyedeh Sanaz Ramezanpour, Khalil Zaynali Nezhad, Vahid Shariati
Software Mentions: 3
Published: over 4 years ago
10.1242/bio.039917
Characterization and comparative analyses of transcriptomes of cloned and <i>in vivo</i> fertilized porcine pre-implantation embryos
Cited by: 7
Author(s): Xiaoyan He, Cheng Tan, Zicong Li, Chengfa Zhao, Junsong Shi, Rong Zhou, Xingwang Wang, Gelong Jiang, Guangyan Cai, Dewu Liu, Zhenfang Wu
Software Mentions: 3
Published: almost 6 years ago
10.1038/s41598-017-14905-9
Sex differentiation in grayling (Salmonidae) goes through an all-male stage and is delayed in genetic males who instead grow faster
Cited by: 13
Author(s): Diane Maitre, Oliver Selmoni, Anshu Uppal, Lucas Marques da Cunha, Laetitia G. E. Wilkins, Julien Roux, Kenyon B. Mobley, Isabelle Castro, Susanne Knörr, Marc Robinson‐Rechavi, Claus Wedekind
Software Mentions: 3
Published: almost 7 years ago
10.1186/1753-6561-5-S7-P20
Detection of genes involved in bud phenology in sessile oak (Quercus petraeaMatt. Liebl) combining digital expression analysis and Q-PCR
Cited by: 3
Author(s): S. Ueno, Christophe Klopp, Céline Noirot, Valérie Léger, Elodie Prince, Antoine Kremer, Christophe Plomion, Grégoire Le Provost
Software Mentions: 3
Published: about 13 years ago
10.1128/mBio.00029-17
The Transcriptome of<i>Leishmania major</i>Developmental Stages in Their Natural Sand Fly Vector
Cited by: 72
Author(s): Ehud Inbar, V. K. Hughitt, Laura A. L. Dillon, Kashinath Ghosh, Najib M. El-Sayed, David L. Sacks
Software Mentions: 3
Published: over 7 years ago
10.1038/s41396-017-0039-z
Identifying metabolic pathways for production of extracellular polymeric substances by the diatom Fragilariopsis cylindrus inhabiting sea ice
Cited by: 34
Author(s): Shazia Aslam, Jan Strauss, David N. Thomas, Thomas Möck, Graham J. C. Underwood
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0256319
Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening
Cited by: 4
Author(s): Fernando G. Razo-Mendivil, Fernando Hernández-Godínez, Corina Hayano-Kanashiro, Octavio Martínez
Software Mentions: 3
Published: about 3 years ago
10.1038/s41398-018-0223-6
Common and differential transcriptional responses to different models of traumatic stress exposure in rats
Cited by: 2
Author(s): Moriah L. Jacobson, Lydia A. Kim, Rob Patro, Barbara Rosati, David McKinnon
Software Mentions: 3
Published: about 6 years ago
10.1186/s12864-016-2863-3
Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes
Cited by: 12
Author(s): Gabriel Santpere, Maria Lopez-Valenzuela, Natalia Petit-Marty, Arcadi Navarro, Yolanda Espinosa‐Parrilla
Software Mentions: 3
Published: about 8 years ago
10.1038/s41598-019-53032-5
The β-oxidation pathway is downregulated during diapause termination in Calanus copepods
Cited by: 12
Author(s): Elise Skottene, Ann M. Tarrant, Anders J. Olsen, Dag Altin, Mari‐Ann Östensen, Bjørn Henrik Hansen, Marvin Choquet, Bjørn Munro Jenssen, Rolf Erik Olsen
Software Mentions: 3
Published: almost 5 years ago
10.7554/eLife.37182
A selective gut bacterial bile salt hydrolase alters host metabolism
Cited by: 156
Author(s): Lina Yao, Sarah C. Seaton, Sula Ndousse-Fetter, Arijit A. Adhikari, Nicholas DiBenedetto, Amir I. Mina, Alexander S. Banks, Lynn Bry, A. Sloan Devlin
Software Mentions: 3
Published: about 6 years ago
10.1186/1471-2164-14-236
Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing
Cited by: 73
Author(s): S. Ueno, Christophe Klopp, Jean‐Charles Leplé, Jérémy Derory, Céline Noirot, Valérie Leger, Elodie Prince, Antoine Kremer, Christophe Plomion, Grégoire Le Provost
Software Mentions: 3
Published: over 11 years ago
10.1038/s41598-020-65947-5
De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress
Cited by: 13
Author(s): Elham Younesi-Melerdi, Ghorbanali Nematzadeh, Ali Pakdin Parizi, Mohammad Reza Bakhtiarizadeh, Seyed Abolfazl Motahari
Software Mentions: 3
Published: over 4 years ago
10.3389/fpls.2019.01325
A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization
Cited by: 23
Author(s): Abdul Kader Alabdullah, Philippa Borrill, Azahara C. Martín, Ricardo H. Ramírez-González, Keywan Hassani‐Pak, Cristóbal Uauy, Peter Shaw, Graham Moore
Software Mentions: 3
Published: almost 5 years ago
10.1371/journal.pbio.3000046
Fine-tuned adaptation of embryo–endometrium pairs at implantation revealed by transcriptome analyses in Bos taurus
Cited by: 14
Author(s): Fernando H. Biase, Isabelle Hue, Sarah Dickinson, Florence Jaffrézic, Dénis Laloë, Harris A. Lewin, Olivier Sandra
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0118424
Non-Viral Generation of Marmoset Monkey iPS Cells by a Six-Factor-in-One-Vector Approach
Cited by: 38
Author(s): Katharina Debowski, Rita Warthemann, Jana Lentes, Gabriela Salinas-Riester, Ralf Dressel, Daniel Langenstroth, Jörg Gromoll, Erika Sasaki, Rüdiger Behr
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pone.0232559
Transcriptome analysis indicates dominant effects on ribosome and mitochondrial function of a premature termination codon mutation in the zebrafish gene psen2
Cited by: 9
Author(s): Haowei Jiang, Stephen Pederson, Morgan Newman, Yang Dong, Karissa Barthelson, Michael Lardelli
Software Mentions: 3
Published: about 4 years ago
10.1017/S0031182020002176
A <i>Trypanosoma cruzi</i> zinc finger protein that is implicated in the control of epimastigote-specific gene expression and metacyclogenesis
Cited by: 9
Author(s): Thais S. Tavares, Fernanda L. B. Mügge, Viviane Grazielle-Silva, Bruna M. Valente, Wanessa Moreira Goes, Antônio Edson Rocha Oliveira, Ashton T. Belew, Alessandra A. Guarneri, Fabiano Sviatopolk-Mirsky Pais, Najib M. El-Sayed, Santuza Maria Ribeiro Teixeira
Software Mentions: 3
Published: almost 4 years ago
10.1186/s12864-019-5763-5
Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006
Cited by: 27
Author(s): Rocío M. Gamez, Fernando Rodríguez, Newton Medeiros Vidal, Sandra Ramírez, Roberto Vera Alvarez, David Landsman, Leonardo Mariño-Ramírez
Software Mentions: 3
Published: over 5 years ago
10.1002/2211-5463.12512
Circular <scp>RNA</scp> expression profile of spleen in a <i>Clostridium perfringens</i> type C‐induced piglet model of necrotizing enteritis
Cited by: 13
Author(s): Zunqiang Yan, Tiantuan Jiang, Pengfei Wang, Xiaoyu Huang, Qiaoli Yang, Weibo Sun, Shuangbao Gun
Software Mentions: 3
Published: about 6 years ago
10.3390/ijms22031484
Novel Transcript Discovery Expands the Repertoire of Pathologically-Associated, Long Non-Coding RNAs in Vascular Smooth Muscle Cells
Cited by: 5
Author(s): Matthew Bennett, Igor Ulitsky, Iraide Alloza, Koen Vandenbroeck, Vladislav Miscianinov, Amira D. Mahmoud, Margaret D. Ballantyne, Julie Rodor, Andrew H. Baker
Software Mentions: 3
Published: over 3 years ago
10.1016/j.stem.2018.10.023
Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes
Cited by: 111
Author(s): Charmaine Lang, Kieran R Campbell, Brent J. Ryan, Phillippa J. Carling, Moustafa Attar, Jane Vowles, Olga V. Perestenko, Rory Bowden, Fahd Baig, Meike Kasten, Michele T.M. Hu, Sally A. Cowley, Caleb Webber, Richard Wade‐Martins
Software Mentions: 3
Published: almost 6 years ago
10.1371/journal.pone.0164964
Morphological and Molecular Characterization of Human Dermal Lymphatic Collectors
Cited by: 22
Author(s): Viktoria Hasselhof, Anastasia Sperling, Kerstin Buttler, Philipp Ströbel, Jürgen Becker, Tin Aung, Gunther Felmerer, Jörg Wilting
Software Mentions: 3
Published: almost 8 years ago
10.1093/jxb/erw096
<i>SLTAB2</i>is the paramutated<i>SULFUREA</i>locus in tomato
Cited by: 19
Author(s): Quentin Gouil, Ondřej Novák, David C. Baulcombe
Software Mentions: 3
Published: over 8 years ago
10.3390/vaccines8010114
Advanced Safety and Genetic Stability in Mice of a Novel DNA-Launched Venezuelan Equine Encephalitis Virus Vaccine with Rearranged Structural Genes
Cited by: 8
Author(s): Dylan M. Johnson, Kevin J. Sokoloski, Jenny D. Jokinen, Tia L. Pfeffer, Yong Kyu Chu, Robert S. Adcock, Donghoon Chung, Irina Tretyakova, Peter Pushko, Igor S. Lukashevich
Software Mentions: 3
Published: over 4 years ago
10.3389/fmicb.2018.01739
The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli
Cited by: 37
Author(s): Ashley Smith, Agnieszka Kaczmar, Rosemary A. Bamford, Christopher Smith, Simona Frustaci, Andrea Kovacs-Simon, Paul O’Neill, Karen Moore, Konrad Paszkiewicz, Richard W. Titball, Stefano Pagliara
Software Mentions: 3
Published: about 6 years ago
10.1186/s12864-018-5072-4
Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize
Cited by: 23
Author(s): Yang Yu, Jianyang Shi, Xiyang Li, Jian Liu, Qi Geng, Shi Haichun, KE Yong-pei, Qun Sun
Software Mentions: 2
Published: almost 6 years ago