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: topGO

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

Enrichment Analysis for Gene Ontology
1 version
Latest release: about 1 year ago
24 dependent packages
428,733 downloads total

Papers Mentioning topGO 652

10.1371/journal.pone.0143563
RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression
Cited by: 135
Author(s): Adam Labadorf, Andrew G. Hoss, Valentina N. Lagomarsino, Jeanne C. Latourelle, Tiffany C. Hadzi, Joli Bregu, Marcy E. MacDonald, James F. Gusella, Jiang‐Fan Chen, Schahram Akbarian, Zhiping Weng, Richard H. Myers
Software Mentions: 6
Published: almost 9 years ago
10.1038/s41598-020-75998-3
Transcriptomic profiling of feline teeth highlights the role of matrix metalloproteinase 9 (MMP9) in tooth resorption
Cited by: 8
Author(s): S. Lee, Stephen J. Bush, Susan Thorne, Nicola Mawson, Colin Farquharson, Guraa Bergkvist
Software Mentions: 6
Published: about 4 years ago
10.1186/s12915-020-00842-z
Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo
Cited by: 19
Author(s): Jialin Liu, Michael Frochaux, Vincent Gardeux, Bart Deplancke, Marc Robinson‐Rechavi
Software Mentions: 6
Published: about 4 years ago
10.3389/fimmu.2020.628804
Transcriptomic Analysis of Long-Term Protective Immunity Induced by Vaccination With Mycoplasma gallisepticum Strain ts-304
Cited by: 5
Author(s): Sathya N Kulappu Arachchige, Neil D. Young, Anna Kanci Condello, Oluwadamilola S Omotainse, Amir H. Noormohammadi, Nadeeka K. Wawegama, Glenn F. Browning
Software Mentions: 6
Published: almost 4 years ago
10.1371/journal.pone.0164542
IGSA: Individual Gene Sets Analysis, including Enrichment and Clustering
Cited by: 3
Author(s): Lingxiang Wu, Xiujie Chen, Denan Zhang, Wubing Zhang, Lei Liu, Hongzhe Ma, Jingbo Yang, Hongbo Xie, Bo Liu, Qing Jin
Software Mentions: 6
Published: about 8 years ago
10.1016/j.stemcr.2017.09.018
Laser Capture and Deep Sequencing Reveals the Transcriptomic Programmes Regulating the Onset of Pancreas and Liver Differentiation in Human Embryos
Cited by: 33
Author(s): Rachel Jennings, Andrew Berry, Dave T. Gerrard, Stephen J. Wearne, James Strutt, Sarah Withey, Mariya Chhatriwala, Karen Piper Hanley, Ludovic Vallier, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 6
Published: about 7 years ago
10.3390/v11080677
Viral Long-Term Evolutionary Strategies Favor Stability over Proliferation
Cited by: 4
Author(s): Stéphane Aris‐Brosou, Louis Parent, Neke Ibeh
Software Mentions: 6
Published: over 5 years ago
10.1371/journal.pone.0246695
Analysis of lung transcriptome in calves infected with Bovine Respiratory Syncytial Virus and treated with antiviral and/or cyclooxygenase inhibitor
Cited by: 5
Author(s): Maxim Lebedev, Heather McEligot, Victoria Mutua, Paul Walsh, Francisco R. Carvallo Chaigneau, Laurel J. Gershwin
Software Mentions: 6
Published: almost 4 years ago
10.1186/s13072-020-00379-z
DNA methylation differs extensively between strains of the same geographical origin and changes with age in Daphnia magna
Cited by: 15
Author(s): Jack Hearn, Fiona A. Plenderleith, Tom J. Little
Software Mentions: 6
Published: almost 4 years ago
10.1371/journal.pgen.1006619
Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum
Cited by: 46
Author(s): Yi Jin Liew, Yong Li, Sebastian Baumgarten, Christian R. Voolstra, Manuel Aranda
Software Mentions: 5
Published: over 7 years ago
10.3390/curroncol28040214
Targeted Next-Generation Sequencing of Circulating Tumor DNA Mutations among Metastatic Breast Cancer Patients
Cited by: 1
Author(s): Ming Sun, Fangqin Lin, Lu-Jia Chen, Hong Li, Wei‐De Lin, Hongwu Du, Xiaobo Yang, Ming Li
Software Mentions: 5
Published: over 3 years ago
10.1038/s41438-021-00544-9
The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative
Cited by: 18
Author(s): Josué Barrera‐Redondo, Guillermo Sánchez‐de la Vega, Jonás A. Aguirre‐Liguori, Gabriela Castellanos‐Morales, Yocelyn T. Gutiérrez-Guerrero, Xitlali Aguirre-Dugua, Erika Aguirre‐Planter, Maud I. Tenaillon, Rafael Lira‐Saade, Luis E. Eguiarte
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-019-5578-4
Genome-wide methylation is modified by caloric restriction in Daphnia magna
Cited by: 20
Author(s): Jack Hearn, Marianne Pearson, Mark Blaxter, Philip J. Wilson, Tom J. Little
Software Mentions: 5
Published: over 5 years ago
10.1186/s12864-015-2124-x
De novo transcriptome reconstruction and annotation of the Egyptian rousette bat
Cited by: 34
Author(s): Albert Kim Lee, Kirsten A. Kulcsar, Oliver Elliott, Hossein Khiabanian, Elyse R. Nagle, Megan E. B. Jones, Brian R. Amman, Mariano Sánchez-Lockhart, Jonathan S. Towner, Gustavo Palacios, Raúl Rabadán
Software Mentions: 5
Published: almost 9 years ago
10.1371/journal.pgen.1008917
Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites
Cited by: 23
Author(s): Élodie Gazanion, Laurent Lacroix, Patrizia Alberti, Pratima Gurung, Sharon Wein, Ming Cheng, Jean‐Louis Mergny, Ana Gomes, José-Juan Lopez-Rubio
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.pgen.1005952
Evolution of Social Insect Polyphenism Facilitated by the Sex Differentiation Cascade
Cited by: 46
Author(s): Antonia Klein, Eva Schultner, Helena Lowak, Lukas Schrader, Juergen Heinze, Luke Holman, Jan Oettler
Software Mentions: 5
Published: over 8 years ago
10.3389/fpls.2018.01256
Comparative Transcriptomic Analysis of Two Actinorhizal Plants and the Legume Medicagotruncatula Supports the Homology of Root Nodule Symbioses and Is Congruent With a Two-Step Process of Evolution in the Nitrogen-Fixing Clade of Angiosperms
Cited by: 14
Author(s): Kai Battenberg, Daniel Potter, Christine A. Tabuloc, Joanna C. Chiu, Alison M. Berry
Software Mentions: 5
Published: about 6 years ago
10.1186/s12864-019-6024-3
Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods
Cited by: 14
Author(s): Polina Drozdova, Lorena Rivarola-Duarte, Daria Bedulina, Denis V. Axenov-Gribanov, S Schreiber, Anton Gurkov, Z. M. Shatilina, Kseniya Vereshchagina, Yulia Lubyaga, Ekaterina Madyarova, Christian Otto, Frank Jühling, Wibke Busch, Lena Jakob, Magnus Lucassen, Franz-Josef Sartoris, Jörg Hackermüller, Steve Hoffmann, Hans‐Otto Pörtner, Till Luckenbach, Maxim A. Timofeyev, Peter F. Stadler
Software Mentions: 5
Published: about 5 years ago
10.1186/s13059-018-1545-7
Modularity of genes involved in local adaptation to climate despite physical linkage
Cited by: 37
Author(s): Katie E. Lotterhos, Sam Yeaman, Jon C. Degner, Sally N. Aitken, Kathryn A. Hodgins
Software Mentions: 5
Published: about 6 years ago
10.1186/s13059-018-1490-5
A comparative study of endoderm differentiation in humans and chimpanzees
Cited by: 31
Author(s): Lauren E. Blake, Samantha M. Thomas, John Blischak, Chiaowen Joyce Hsiao, Claudia Chavarria, Marsha Myrthil, Yoav Gilad, Bryan J. Pavlovic
Software Mentions: 5
Published: about 6 years ago
10.15252/msb.20145123
Natural genetic variation impacts expression levels of coding, non‐coding, and antisense transcripts in fission yeast
Cited by: 61
Author(s): Mathieu Clément-Ziza, Xavi Marsellach, Sandra Codlin, Manos A. Papadakis, Susanne Reinhardt, María Rodríguez-López, Stuart Martin, Samuel Marguerat, Alexander Schmidt, Eun‐Hye Lee, Christopher T. Workman, Jürg Bähler, Andreas Beyer
Software Mentions: 5
Published: about 10 years ago
10.1002/ece3.6899
Insights into the genetic basis of predator‐induced response in<i>Daphnia galeata</i>
Cited by: 9
Author(s): Verena Tams, Jana Nickel, Anne Ehring, Mathilde Cordellier
Software Mentions: 5
Published: about 4 years ago
10.1093/gigascience/giz071
The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge)
Cited by: 35
Author(s): Liang Qiang, Huayang Li, Shouke Li, Fuling Yuan, Jiantong Sun, Qicheng Duan, Qingyun Li, Rui Zhang, Ya Lin Sang, Nian Wang, Xiangwen Hou, Ke Yang, Jian Ning Liu, Long Yang
Software Mentions: 5
Published: over 5 years ago
10.1186/s12862-019-1572-3
The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish
Cited by: 4
Author(s): Mauricio Losilla, David Luecke, Jason R. Gallant
Software Mentions: 5
Published: almost 5 years ago
10.3389/fpls.2021.636652
Non-target Site Herbicide Resistance Is Conferred by Two Distinct Mechanisms in Black-Grass (Alopecurus myosuroides)
Cited by: 25
Author(s): S. Franco Ortega, Alina Goldberg-Cavalleri, Andrew Walker, Melissa Brazier‐Hicks, Nawaporn Onkokesung, Robert Edwards
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-017-4364-4
Pronounced strain-specific chemosensory receptor gene expression in the mouse vomeronasal organ
Cited by: 16
Author(s): Kyle Duyck, Vasha DuTell, Limei Ma, Ariel Paulson, Chong Yu
Software Mentions: 5
Published: almost 7 years ago
10.3390/genes10030212
RNA Sequencing Reveals Specific Transcriptomic Signatures Distinguishing Effects of the [SWI+] Prion and SWI1 Deletion in Yeast Saccharomyces cerevisiae
Cited by: 11
Author(s): Yury V. Malovichko, Kirill S. Antonets, Anna R. Maslova, Е. А. Андреева, Sergey G. Inge-Vechtomov, Anton A. Nizhnikov
Software Mentions: 5
Published: over 5 years ago
10.1111/j.1365-294X.2012.05756.x
Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome‐wide digital gene expression analysis
Cited by: 83
Author(s): Tobias L. Lenz, Christophe Eizaguirre, Björn Rotter, Martin Kalbe, Manfred Milinski
Software Mentions: 5
Published: about 12 years ago
10.15252/msb.20199270
Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance
Cited by: 22
Author(s): Stephan Kamrad, Jan Großbach, María Rodríguez-López, Michael Mülleder, StJohn Townsend, Valentina Cappelletti, Gorjan Stojanovski, Clara Correia‐Melo, Paola Picotti, Andreas Beyer, Markus Ralser, Jürg Bähler
Software Mentions: 5
Published: over 4 years ago
10.1186/s12864-019-6314-9
Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause
Cited by: 32
Author(s): Thomas J. Colgan, Sive Finlay, Mark J. F. Brown, James C. Carolan
Software Mentions: 5
Published: almost 5 years ago
10.1371/journal.pone.0160925
The 4p16.3 Parkinson Disease Risk Locus Is Associated with GAK Expression and Genes Involved with the Synaptic Vesicle Membrane
Cited by: 16
Author(s): Michael W. Nagle, Jeanne C. Latourelle, Adam Labadorf, Alexandra Dumitriu, Tiffany C. Hadzi, Thomas G. Beach, Richard H. Myers
Software Mentions: 5
Published: over 8 years ago
10.3390/ijms221910297
Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development
Cited by: 10
Author(s): Saeid Babaei, Mohan B. Singh, Prem L. Bhalla
Software Mentions: 5
Published: about 3 years ago
10.7717/peerj.10818
Cytochrome P450 monooxygenase genes in the wild silkworm, <i>Bombyx mandarina</i>
Cited by: 5
Author(s): Linrong Wan, Zhou Anlian, Wen‐Fu Xiao, Bangxing Zou, Yaming Jiang, Jing Xiao, Cao Deng, Youhong Zhang, Mengjia Liu
Software Mentions: 5
Published: almost 4 years ago
10.3390/ijms22179146
Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses
Cited by: 5
Author(s): Mirosław Tyrka, Beata Bakera, Magdalena Szeliga, Magdalena Święcicka, Paweł Krajewski, Monika Mokrzycka, Monika Rakoczy-Trojanowska
Software Mentions: 5
Published: about 3 years ago
10.7554/eLife.35471
Genetics of trans-regulatory variation in gene expression
Cited by: 133
Author(s): Frank W. Albert, Joshua S. Bloom, Jake J. Siegel, Laura Day, Leonid Kruglyak
Software Mentions: 5
Published: over 6 years ago
10.7554/eLife.21049
Proliferation-independent regulation of organ size by Fgf/Notch signaling
Cited by: 36
Author(s): Agnė Kozlovskaja-Gumbrienė, Yi Ren, Alexander Richard, Andy Aman, Ryan Jiskra, Danielle Nagelberg, Holger Knaut, Melainia McClain, Tatjana Piotrowski
Software Mentions: 5
Published: almost 8 years ago
10.7554/eLife.07103
A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics
Cited by: 103
Author(s): Irene Gallego Romero, Bryan J. Pavlovic, Irene Hernando-Herraez, Xiang Zhou, Michelle C. Ward, Nicholas E. Banovich, Courtney L Kagan, Jonathan E. Burnett, Constance H Huang, Amy Mitrano, Claudia Chavarria, Inbar Friedrich Ben-Nun, Yingchun Li, Karen Sabatini, Trevor R. Leonardo, Mana M. Parast, Tomàs Marquès‐Bonet, Louise C. Laurent, Jeanne F. Loring, Yoav Gilad
Software Mentions: 5
Published: over 9 years ago
10.1186/s12864-017-3660-3
Highly localized divergence within supergenes in Atlantic cod (Gadus morhua) within the Gulf of Maine
Cited by: 37
Author(s): Bryan T. Barney, Christiane Munkholm, David R. Walt, Stephen R. Palumbi
Software Mentions: 5
Published: over 7 years ago
10.1093/bib/bbz018
CAFU: a Galaxy framework for exploring unmapped RNA-Seq data
Cited by: 11
Author(s): Siyuan Chen, Chengzhi Ren, Jingjing Zhai, Jinxin Yu, Xuyang Zhao, Zelong Li, Ting Zhang, Wenlong Ma, Zhaoxue Han, Chuang Ma
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pone.0022176
Time-Resolved Human Kinome RNAi Screen Identifies a Network Regulating Mitotic-Events as Early Regulators of Cell Proliferation
Cited by: 9
Author(s): Jitao David Zhang, Cindy Körner, Stephanie Bechtel, Christian Bender, Ioanna Keklikoglou, Christian Schmidt, Anja Irsigler, Ute Ernst, Özgür Şahin, Stefan Wiemann, Ulrich Tschulena
Software Mentions: 5
Published: over 13 years ago
10.7554/eLife.51243
Global genome diversity of the Leishmania donovani complex
Cited by: 77
Author(s): Susanne U. Franssen, Caroline Durrant, Olivia Stark, Bettina A. Moser, Tim Downing, Hideo Imamura, Jean Claude Dujardin, Mandy Sanders, Isabel Maurício, Michael A. Miles, Lionel F. Schnur, Charles L. Jaffe, Abedelmajeed Nasereddin, Henk D. F. H. Schallig, Matthew Yeo, Tapan Bhattacharyya, Mohammad Zahangir Alam, Matthew Berriman, Thierry Wirth, Gabriele Schönian, James A. Cotton
Software Mentions: 5
Published: over 4 years ago
10.1186/s13068-021-01915-z
Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species
Cited by: 10
Author(s): Jose J De Vega, Abel Teshome, Manfred Klaas, Jim Grant, John Finnan, Susanne Barth
Software Mentions: 5
Published: over 3 years ago
10.3389/fmicb.2020.01943
Commonalities and Differences in the Transcriptional Response of the Model Fungus Saccharomyces cerevisiae to Different Commercial Graphene Oxide Materials
Cited by: 4
Author(s): Felix Laguna-Teno, María Suárez-Diez, Juan Antonio Tamayo-Ramos
Software Mentions: 5
Published: over 4 years ago
10.1128/mBio.01093-21
Inhibitory Concentrations of Ciprofloxacin Induce an Adaptive Response Promoting the Intracellular Survival of Salmonella enterica Serovar Typhimurium
Cited by: 5
Author(s): Sushmita Sridhar, Sally Forrest, Derek Pickard, Claire Cormie, Emily A. Lees, Nicholas R. Thomson, Gordon Dougan, Stephen Baker
Software Mentions: 5
Published: over 3 years ago
10.3389/fmicb.2017.00773
The 25–26 nt Small RNAs in Phytophthora parasitica Are Associated with Efficient Silencing of Homologous Endogenous Genes
Cited by: 28
Author(s): Jinbu Jia, Wenqin Lu, Chengcheng Zhong, Ran Zhou, Junjie Xu, Wei Liu, Xiuhong Gou, Qinhu Wang, Junliang Yin, Changwu Xu, Weixing Shan
Software Mentions: 5
Published: over 7 years ago
10.1371/journal.pone.0024351
Molecular Insights into Reprogramming-Initiation Events Mediated by the OSKM Gene Regulatory Network
Cited by: 63
Author(s): Nancy Mah, Ying Wang, Mei-Chih Liao, Alessandro Prigione, Justyna Józefczuk, Björn Lichtner, Katharina Wolfrum, Manuela Haltmeier, Max Flöttmann, Martin H. Schaefer, Alexander Hahn, Ralf Mrowka, Edda Klipp, Miguel A. Andrade‐Navarro, James Adjaye
Software Mentions: 5
Published: about 13 years ago
10.1371/journal.pone.0118731
Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis
Cited by: 77
Author(s): Katherine C. H. Amrine, Bárbara Blanco-Ulate, Dario Cantu
Software Mentions: 5
Published: over 9 years ago
10.1093/bioinformatics/btx179
<i>Fuento</i>: functional enrichment for bioinformatics
Cited by: 5
Author(s): David Tobias Weichselbaum, Bojan Žagrović, Anton A. Polyansky
Software Mentions: 5
Published: over 7 years ago
10.1371/journal.pone.0115692
HPOSim: An R Package for Phenotypic Similarity Measure and Enrichment Analysis Based on the Human Phenotype Ontology
Cited by: 49
Author(s): Yue Deng, Lin Gao, Bingbo Wang, Guo Xia-zhen
Software Mentions: 5
Published: almost 10 years ago
10.1186/1756-0381-5-19
Visualising associations between paired ‘omics’ data sets
Cited by: 211
Author(s): Ignacio González, Kim‐Anh Lê Cao, Melissa J. Davis, Sébastien Déjean
Software Mentions: 5
Published: about 12 years ago
10.1186/1752-0509-6-2
Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control
Cited by: 15
Author(s): Kevin M. D’Auria, Gina M. Donato, Mary C. Gray, Glynis L. Kolling, Cirle A. Warren, Lauren M Cave, Michael D. Solga, Joanne Lannigan, Jason A. Papin, Erik L. Hewlett
Software Mentions: 5
Published: almost 13 years ago
10.1038/s41598-018-19984-w
Comparative transcriptome analysis reveals molecular response to salinity stress of salt-tolerant and sensitive genotypes of indica rice at seedling stage
Cited by: 51
Author(s): Jun Wang, Zhu Jun, Yadong Zhang, Fangjun Fan, Wenqi Li, Fangquan Wang, Zhong WeiGong, Cailin Wang, Jie Yang
Software Mentions: 5
Published: almost 7 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
10.1186/s12870-021-03042-1
Transcriptome and proteome analysis of walnut (Juglans regia L.) fruit in response to infection by Colletotrichum gloeosporioides
Cited by: 12
Author(s): Hongcheng Fang, Xia Liu, Yixin Dong, Shan Feng, Rui Zhou, Changxi Wang, Xinmei Ma, Jianning Liu, Ke Yang
Software Mentions: 5
Published: over 3 years ago
10.1186/s12885-020-07088-6
Overexpression of HOXA10 is associated with unfavorable prognosis of acute myeloid leukemia
Cited by: 17
Author(s): Chao Guo, Qianqian Ju, Chunxia Zhang, Ming Gong, Zhenling Li, Ya-yue Gao
Software Mentions: 5
Published: over 4 years ago
10.1038/s41598-018-33718-y
A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat
Cited by: 40
Author(s): Yongpeng Li, Xing Fu, Meicheng Zhao, Wei Zhang, Bo Li, Diaoguo An, Junming Li, Aimin Zhang, Renyi Liu, Xigang Liu
Software Mentions: 5
Published: about 6 years ago
10.1038/s41598-019-48435-3
Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction
Cited by: 22
Author(s): Junbo Zou, Herzl Chai, Xiaofei Zhang, Deliang Guo, Jia Tai, Yu Wang, Yulin Liang, Fang Wang, Jiangxue Cheng, Jing Wang, Yajun Shi
Software Mentions: 5
Published: over 5 years ago
10.1186/s13071-020-04424-4
Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae)
Cited by: 3
Author(s): Maksim A. Nesterenko, Viktor V. Starunov, Sergei V. Shchenkov, Anna R. Maslova, Sofia Denisova, Andrey I. Granovich, Andrej A. Dobrovolskij, Konstantin Khalturin
Software Mentions: 5
Published: about 4 years ago
10.1002/evl3.166
Artificial selection reveals the role of transcriptional constraints in the maintenance of life history variation
Cited by: 6
Author(s): Joel L. Pick, Masaomi Hatakeyama, Kate E. Ihle, Julien Gasparini, Claudy Haussy, Satoshi Ishishita, Yoichi Matsuda, Takashi Yoshimura, Masahiro M. Kanaoka, Rie Shimizu‐Inatsugi, Kentaro Shimizu, Barbara Tschirren
Software Mentions: 5
Published: over 4 years ago
10.3389/fimmu.2019.00330
Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression
Cited by: 37
Author(s): Florian Kirchner, Katharina Littringer, Simon Altmeier, Van Du T. Tran, Franziska Annett Schönherr, Christina Braunsdorf, Marco Pagni, Dominique Sanglard, Nicole Joller, Salomé LeibundGut‐Landmann
Software Mentions: 5
Published: over 5 years ago
10.1038/s41598-020-68949-5
Capsidiol-related genes are highly expressed in response to Colletotrichum scovillei during Capsicum annuum fruit development stages
Cited by: 10
Author(s): Viviane Yumi Baba, Adrian F. Powell, Suzana Tiemi Ivamoto, Luiz Filipe Protásio Pereira, André Luís Laforga Vanzela, Renata Mussoi Giacomin, Susan R. Strickler, Lukas A. Mueller, Rosana Rodrigues, Leandro Simões Azeredo Gonçalves
Software Mentions: 5
Published: over 4 years ago
10.7554/eLife.47980
Controlling gene activation by enhancers through a drug-inducible topological insulator
Cited by: 5
Author(s): Taro Tsujimura, Osamu Takase, Masahide Yoshikawa, Etsuko Sano, Matsuhiko Hayashi, Kazuto Hoshi, Tsuyoshi Takato, Atsushi Toyoda, Hideyuki Okano, Keiichi Hishikawa
Software Mentions: 5
Published: over 4 years ago
10.1111/jcmm.15569
LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity
Cited by: 8
Author(s): Amandine Guérin, Delphine Martire, Eva Trenquier, Tom Lesluyes, Sébastien Sagnol, Marine Pratlong, Elise Lefebvre, Frédéric Chibon, Pascal de Santa Barbara, Sandrine Faure
Software Mentions: 4
Published: over 4 years ago
10.1093/jxb/ery147
Genomic comparison of two independent seagrass lineages reveals habitat-driven convergent evolution
Cited by: 24
Author(s): HueyTyng Lee, Agnieszka A. Golicz, Philipp E. Bayer, Anita A. Severn‐Ellis, Chon‐Kit Kenneth Chan, Jacqueline Batley, Gary A. Kendrick, David Edwards
Software Mentions: 4
Published: over 6 years ago
10.15252/embj.2019103894
<scp>SCHENGEN</scp> receptor module drives localized <scp>ROS</scp> production and lignification in plant roots
Cited by: 67
Author(s): Satoshi Fujita, Damien De Bellis, Kai H. Edel, Philipp Köster, Tonni Grube Andersen, Emanuel Schmid‐Siegert, Valérie Dénervaud Tendon, Alexandre Pfister, Peter Marhavý, Robertas Ursache, Verónica G. Doblas, Marie Barberon, Jean Daraspe, Audrey Creff, Gwyneth Ingram, Jörg Kudla, Niko Geldner
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pgen.1009390
Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition
Cited by: 11
Author(s): Luis Enrique Cabrera-Quio, Alexander Schleiffer, Karl Mechtler, Andrea Pauli
Software Mentions: 4
Published: almost 4 years ago
10.1186/1471-2164-14-266
Characterization of differential transcript abundance through time during Nematostella vectensis development
Cited by: 73
Author(s): Rebecca R. Helm, Stefan Siebert, Sarah Tulin, Joel Smith, Casey W. Dunn
Software Mentions: 4
Published: almost 12 years ago
10.1002/ece3.7664
Alternative migratory tactics in brown trout (<i>Salmo trutta</i>) are underpinned by divergent regulation of metabolic but not neurological genes
Cited by: 3
Author(s): Robert Wynne, Louise C. Archer, Stephen A. Hutton, Luke Harman, Patrick Gargan, Peter Moran, Eileen Dillane, Jamie Coughlan, T. Cross, Philip McGinnity, Thomas J. Colgan, Thomas E. Reed
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pgen.1008189
Host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia
Cited by: 66
Author(s): Guoxin Cui, Yi Jin Liew, Yong Li, Najeh M. Kharbatia, Noura Ibrahim Omar Zahran, Abdul‐Hamid Emwas, Vı́ctor M. Eguı́luz, Manuel Aranda
Software Mentions: 4
Published: over 5 years ago
10.1089/hum.2020.213
Genetic Rescue of X-Linked Retinoschisis Mouse (<i>Rs1</i><sup>−/y</sup>) Retina Induces Quiescence of the Retinal Microglial Inflammatory State Following AAV8-<i>RS1</i> Gene Transfer and Identifies Gene Networks Underlying Retinal Recovery
Cited by: 16
Author(s): Camasamudram Vijayasarathy, Yong Zeng, Matthew Brooks, Robert N Fariss, Paul A. Sieving
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pcbi.1004809
QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks
Cited by: 11
Author(s): Asa Thibodeau, Eladio J. Márquez, Oscar Junhong Luo, Yijun Ruan, Francesca Menghi, Dong-Guk Shin, Michael L. Stitzel, Paola Vera-Licona, Duygu Ucar
Software Mentions: 4
Published: over 8 years ago
10.1186/s12864-018-5146-3
Cell-type specific RNA-Seq reveals novel roles and regulatory programs for terminally differentiated Dictyostelium cells
Cited by: 18
Author(s): Koryu Kin, Gillian Forbes, Andrew Cassidy, Pauline Schaap
Software Mentions: 4
Published: about 6 years ago
10.1186/gm122
Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia
Cited by: 105
Author(s): Nathan Stephens, Iain J. Gallagher, Olav Rooyackers, Richard J.E. Skipworth, Ben Tan, Troels Marstrand, James A. Ross, Denis C. Guttridge, Lars Lundell, Kenneth C. H. Fearon, James A. Timmons
Software Mentions: 4
Published: almost 15 years ago
10.1371/journal.pgen.1006959
Loss of the chromatin modifier Kdm2aa causes BrafV600E-independent spontaneous melanoma in zebrafish
Cited by: 12
Author(s): Catherine Scahill, Zsofia Digby, Ian Sealy, Sonia Wojciechowska, Richard White, John Collins, Derek L. Stemple, Till Bartke, Marie E. Mathers, E. Elizabeth Patton, Elisabeth M Busch-Nentwich
Software Mentions: 4
Published: over 7 years ago
10.1186/s12864-019-5669-2
Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships
Cited by: 39
Author(s): Afshin Soltani, Sarathi M. Weraduwage, Thomas D. Sharkey, David B. Lowry
Software Mentions: 4
Published: over 5 years ago
10.1186/s12864-021-07889-4
Experimental Babesia rossi infection induces hemolytic, metabolic, and viral response pathways in the canine host
Cited by: 6
Author(s): Rachel Smith, Amelia Goddard, Arun K. Boddapati, Steven Brooks, Johan P. Schoeman, Justin Lack, Andrew L. Leisewitz, Hans Ackerman
Software Mentions: 4
Published: over 3 years ago
10.3390/cells7120275
Activation of Polyamine Catabolism by N1,N11-Diethylnorspermine in Hepatic HepaRG Cells Induces Dedifferentiation and Mesenchymal-Like Phenotype
Cited by: 12
Author(s): О. Н. Иванова, Anastasiya V. Snezhkina, George S. Krasnov, Vladimir T. Valuev-Elliston, Olga A. Khomich, Alexey Khomutov, Tuomo A. Keinänen, Leena Alhonen, Birke Bartosch, Anna V. Kudryavtseva, Sergey N. Kochetkov, Alexander Ivanov
Software Mentions: 4
Published: almost 6 years ago
10.1016/j.stem.2017.03.003
H3K4 Methylation-Dependent Memory of Somatic Cell Identity Inhibits Reprogramming and Development of Nuclear Transfer Embryos
Cited by: 85
Author(s): Eva Hörmanseder, Angela Simeone, George E. Allen, Charles R. Bradshaw, Magdalena Figlmüller, J. B. Gurdon, Jérôme Jullien
Software Mentions: 4
Published: over 7 years ago
10.3390/cells9071745
Ribosomal Protein uL11 as a Regulator of Metabolic Circuits Related to Aging and Cell Cycle
Cited by: 7
Author(s): Mateusz Mołoń, Eliza Molestak, Monika Kula-Maximenko, Przemysław Grela, Marek Tchórzewski
Software Mentions: 4
Published: over 4 years ago
10.1186/s13059-016-1014-0
The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum
Cited by: 83
Author(s): Evelien M. Bunnik, Gayani Batugedara, Anita Saraf, Jacques Prudhomme, Laurence Florens, Karine G. Le Roch
Software Mentions: 4
Published: over 8 years ago
10.1371/journal.pcbi.1006091
Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse
Cited by: 1
Author(s): R. Buckley, R. Daniel Kortschak, David L. Adelson
Software Mentions: 4
Published: over 6 years ago
10.1186/s13059-016-0947-7
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
Cited by: 858
Author(s): Aaron T. L. Lun, Karsten Bach, John C. Marioni
Software Mentions: 4
Published: over 8 years ago
10.1186/s13059-016-1146-2
Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts
Cited by: 148
Author(s): Jonas Paulsen, Monika Sekelja, Anja R. Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L. Sørensen, Corinne Vigouroux, Brigitte Buendia, Philippe Collas
Software Mentions: 4
Published: almost 8 years ago
10.1186/s10020-020-00266-z
The transcriptome-wide association search for genes and genetic variants which associate with BMI and gestational weight gain in women with type 1 diabetes
Cited by: 2
Author(s): Agnieszka H. Ludwig-Słomczyńska, Michał Seweryn, Przemysław Kapusta, Ewelina Pitera, Urszula Mantaj, Katarzyna Cyganek, Paweł Gutaj, Łucja Dobrucka, Ewa Wender-Ożegowska, Maciej Małecki, Paweł Wołkow
Software Mentions: 4
Published: almost 4 years ago
10.3390/genes10020089
A 24 h Age Difference Causes Twice as Much Gene Expression Divergence as 100 Generations of Adaptation to a Novel Environment
Cited by: 12
Author(s): Sheng‐Kai Hsu, Ana Marija Jakšić, Viola Nolte, Neda Barghi, François Mallard, Kerstin Otte, Christian Schlötterer
Software Mentions: 4
Published: almost 6 years ago
10.3390/genes11010031
Transcriptome-Wide Analysis Reveals Key DEGs in Flower Color Regulation of Hosta plantaginea (Lam.) Aschers
Cited by: 7
Author(s): Jingying Zhang, Changhai Sui, Yanli Wang, Shuying Liu, Huimin Liu, Zhengren Zhang, Liu Hong-zhang
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pbio.2005359
Comparative genomics and the nature of placozoan species
Cited by: 63
Author(s): Michael Eitel, Warren R. Francis, Frédérique Varoqueaux, Jean Daraspe, Hans-Jürgen Osigus, Stefan Krebs, Sergio Vargas, Helmut Blum, Gray A. Williams, Bernd Schierwater, Gert Wörheide
Software Mentions: 4
Published: over 6 years ago
10.1186/1471-2164-14-728
Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivumL.)
Cited by: 80
Author(s): Karl G. Kugler, Gerald Siegwart, Thomas Nußbaumer, Christian Ametz, Manuel Spannagl, Barbara Steiner, Marc Lemmens, Klaus Mayer, Hermann Buerstmayr, Wolfgang Schweiger
Software Mentions: 4
Published: about 11 years ago
10.1093/g3journal/jkab072
Photoperiod-dependent developmental reprogramming of the transcriptional response to seawater entry in Atlantic salmon (Salmo salar)
Cited by: 2
Author(s): Marianne Iversen, Teshome Dagne Mulugeta, Alexander C. West, Even H. Jørgensen, Samuel Martín, Simen Rød Sandve, David G. Hazlerigg
Software Mentions: 4
Published: over 3 years ago
10.1111/mec.12521
Population genomic footprints of selection and associations with climate in natural populations of <i>Arabidopsis halleri</i> from the Alps
Cited by: 89
Author(s): Martin C. Fischer, Christian Rellstab, Andrew Tedder, Stefan Zoller, Félix Gugerli, Kentaro Shimizu, Rolf Holderegger, Alex Widmer
Software Mentions: 4
Published: about 11 years ago
10.1093/molbev/msz048
Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection
Cited by: 26
Author(s): Iakov I. Davydov, Nicolas Salamin, Marc Robinson‐Rechavi
Software Mentions: 4
Published: over 5 years ago
10.1534/g3.118.200810
Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression
Cited by: 13
Author(s): Stephen J. Bush, Mary E. B. McCulloch, Charity Muriuki, Mazdak Salavati, Gemma M. Davis, Iseabail L. Farquhar, Zofia M. Lisowski, Alan Archibald, David Hume, Emily L. Clark
Software Mentions: 4
Published: almost 6 years ago
10.3390/cancers12092433
Oncogenic Orphan Nuclear Receptor NR4A3 Interacts and Cooperates with MYB in Acinic Cell Carcinoma
Cited by: 11
Author(s): David Y. Lee, Kathryn J. Brayer, Yoshitsugu Mitani, Eric A Burns, Pulivarthi H. Rao, Diana Bell, Michelle D. Williams, Renata Ferrarotto, Kristen B. Pytynia, Adel K. El‐Naggar, Scott A. Ness
Software Mentions: 4
Published: about 4 years ago
10.1534/g3.119.400729
Regeneration Rosetta: An Interactive Web Application To Explore Regeneration-Associated Gene Expression and Chromatin Accessibility
Cited by: 2
Author(s): Andrea Rau, Sumona P. Dhara, Ava J. Udvadia, Paul L. Auer
Software Mentions: 4
Published: almost 5 years ago
10.3390/genes11070789
Transcriptional Profiling of Normal, Stenotic, and Regurgitant Human Aortic Valves
Cited by: 13
Author(s): Christina L. Greene, Kevin J Jaatinen, Hanjay Wang, Tiffany Koyano, Mary Sheridan Bilbao, Y. Joseph Woo
Software Mentions: 4
Published: over 4 years ago
10.3390/microorganisms9010149
Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species
Cited by: 21
Author(s): Niranjan P. Sahu, Zsolt Merényi, Balázs Bálint, Brigitta Kiss, György Sipos, Rebecca A. Owens, László G. Nagy
Software Mentions: 4
Published: almost 4 years ago
10.1099/mgen.0.000393
Evaluation of methods for detecting human reads in microbial sequencing datasets
Cited by: 10
Author(s): Stephen J. Bush, Thomas R. Connor, Tim Peto, Derrick W. Crook, A Sarah Walker
Software Mentions: 4
Published: over 4 years ago
10.1186/s12864-016-3291-0
Liver transcriptome response to hyperthermic stress in three distinct chicken lines
Cited by: 40
Author(s): Xi Lan, John Hsieh, Carl J. Schmidt, Qing Zhu, Susan J. Lamont
Software Mentions: 4
Published: almost 8 years ago
10.1371/journal.pone.0235763
Comparative transcriptome analysis uncovers different heat stress responses in heat-resistant and heat-sensitive jujube cultivars
Cited by: 17
Author(s): Juan Jin, Lei Yang, Dingyu Fan, Xuxin Liu, Qing Hao
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pone.0255738
Adenomatous Polyposis Coli loss controls cell cycle regulators and response to paclitaxel in MDA-MB-157 metaplastic breast cancer cells
Cited by: 3
Author(s): Emily Astarita, Sara Maloney, Camden A. Hoover, Bronwyn J. Berkeley, Monica K. VanKlompenberg, T. Murlidharan Nair, Jenifer R. Prosperi
Software Mentions: 4
Published: over 3 years ago