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
10.1093/molbev/msx199
Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in VertebratesCited by: 40
Author(s): Julien Roux, Jialin Liu, Marc Robinson‐Rechavi
Software Mentions: 1
Published: over 7 years ago
10.3389/fonc.2020.614067
Solasonine Suppresses the Proliferation of Acute Monocytic Leukemia Through the Activation of the AMPK/FOXO3A AxisCited by: 6
Author(s): Hong Zhang, Fang Tian, Pengjun Jiang, Shushu Qian, Xianglin Dai, Bangyun Ma, Mengya Wang, Huibo Dai, Xiaocao Sha, Zhaohui Yang, Xuejun Zhu, Sun Xianlin
Software Mentions: 1
Published: almost 4 years ago
10.3389/fmolb.2021.654465
Alteration of N6-Methyladenosine RNA Profiles in Cisplatin-Induced Acute Kidney Injury in MiceCited by: 8
Author(s): Canming Li, Ming Li, Wenbo Zhao, Zengchun Ye, Hui Peng
Software Mentions: 1
Published: over 3 years ago
10.1093/aob/mcv006
Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae)Cited by: 18
Author(s): Andrew Tedder, Matthias Helling, John R. Pannell, Rie Shimizu‐Inatsugi, Tetsuhiro Kawagoe, Julia van Campen, Jun Sese, Kentaro Shimizu
Software Mentions: 1
Published: over 9 years ago
10.1186/s12864-019-6210-3
Comparative transcriptional analysis of Capsicum flower buds between a sterile flower pool and a restorer flower pool provides insight into the regulation of fertility restorationCited by: 13
Author(s): Bingqiang Wei, Lanlan Wang, Paul W. Bosland, Gaoyuan Zhang, Ru Zhang
Software Mentions: 1
Published: about 5 years ago
10.3389/fimmu.2020.01729
Differently Expression Analysis and Function Prediction of Long Non-coding RNAs in Duck Embryo Fibroblast Cells Infected by Duck Tembusu VirusCited by: 10
Author(s): Yun Lin, Jing Yang, Dalin He, Xudong Li, Jing Li, Yi Tang, Youxiang Diao
Software Mentions: 1
Published: over 4 years ago
10.1093/molbev/msab028
Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular EvolutionCited by: 22
Author(s): Joshua H.T. Potter, Kalina T. J. Davies, Laurel Yohe, Miluska K.R. Sánchez, Edgardo M. Rengifo, Monika Struebig, Kim Warren, Georgia Tsagkogeorga, Burton K. Lim, Mario dos Reis, Liliana M. Dávalos, Stephen J. Rossiter
Software Mentions: 1
Published: over 3 years ago
10.1136/annrheumdis-2016-209428
The intervertebral disc contains intrinsic circadian clocks that are regulated by age and cytokines and linked to degenerationCited by: 113
Author(s): Michal Dudek, Nan Yang, Jayalath P.D. Ruckshanthi, Jack Williams, Elzbieta Borysiewicz, Ping Wang, Antony Adamson, Jian Li, John F. Bateman, Michael R White, Raymond P. Boot-Handford, Judith A. Hoyland, Qing‐Jun Meng
Software Mentions: 1
Published: over 8 years ago
10.3390/molecules200610734
Transcriptomic Analysis of Flower Blooming in Jasminum sambac through De Novo RNA SequencingCited by: 14
Author(s): Yonghua Li, Wei Zhang, Yong Li
Software Mentions: 1
Published: over 9 years ago
10.1093/gbe/evaa204
From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall WaspsCited by: 4
Author(s): Erik Gobbo, Nicolas Lartillot, Jack Hearn, Graham Stone, Yoshihisa Abe, Christopher W. Wheat, Tatsuya Ide, Fredirik Ronquist
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pone.0218029
Comprehensive analysis of Ogura cytoplasmic male sterility-related genes in turnip (Brassica rapa ssp. rapifera) using RNA sequencing analysis and bioinformaticsCited by: 14
Author(s): Sue Lin, Yingjing Miao, Shiwen Su, Jian Xu, Libo Jin, Da Sun, Renyi Peng, Li Huang, Jiashu Cao
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pone.0077192
Functional Analyses of NSF1 in Wine Yeast Using Interconnected Correlation Clustering and Molecular AnalysesCited by: 5
Author(s): Kyrylo Bessonov, Christopher J. Walkey, Barry J. Shelp, H. J. J. Van Vuuren, David Chiu, George van der Merwe
Software Mentions: 1
Published: about 11 years ago
10.1186/s13024-020-0357-x
VGF-derived peptide TLQP-21 modulates microglial function through C3aR1 signaling pathways and reduces neuropathology in 5xFAD miceCited by: 45
Author(s): Farida El Gaamouch, Mickaël Audrain, Wei-Jye Lin, Noam D. Beckmann, Cheng Jiang, Siddharth Hariharan, Peter S. Heeger, Eric E. Schadt, Sam Gandy, Michelle E. Ehrlich, Stephen R. Salton
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.pone.0069513
Integrated Analysis of Drug-Induced Gene Expression Profiles Predicts Novel hERG InhibitorsCited by: 20
Author(s): Joseph J. Babcock, Fang Du, Kaiping Xu, Sarah J. Wheelan, Min Li
Software Mentions: 1
Published: over 11 years ago
10.1155/2016/2086346
Transcriptomic Analysis of Resistant and Susceptible<i>Bombyx mori</i>Strains Following BmNPV Infection Provides Insights into the Antiviral MechanismsCited by: 20
Author(s): Gang Li, Heying Qian, Luo Xufang, Peng Xu, Jianhua Yang, Mingzhu Liu, Anying Xu
Software Mentions: 1
Published: almost 9 years ago
10.3389/fimmu.2019.00997
Immune Differentiation Regulator p100 Tunes NF-κB Responses to TNFCited by: 8
Author(s): B. B. Chatterjee, Payel Roy, Uday Aditya Sarkar, Mingming Zhao, Yashika Ratra, Amit Singh, M. L. Chawla, Supriyo De, James Gomes, Ranjan Sen, Soumen Basak
Software Mentions: 1
Published: over 5 years ago
10.18632/aging.103408
Blood DNA methylation sites predict death risk in a longitudinal study of 12, 300 individualsCited by: 11
Author(s): Elena Colicino, Riccardo E. Marioni, Cavin Ward‐Caviness, Rahul Gondalia, Weihua Guan, Brian Chen, Pei Chien Tsai, Tianxiao Huan, Xu Gao, Golareh Agha, Joel Schwartz, Pantel Vokonas, Allan C. Just, John M. Starr, Allan F. McRae, Naomi R. Wray, Peter M. Visscher, Jan Bressler, Wen Zhang, Toshiko Tanaka, Ann Zenobia Moore, Luke C. Pilling, Guosheng Zhang, James D. Stewart, Yun Li, Lifang Hou, Juan Castillo-Fernandez, Tim D. Spector, Douglas P. Kiel, Joanne M. Murabito, Chunyu Liu, Mike Mendelson, Tim Assimes, Devin Absher, Phil S. Tsaho, Ake T. Lu, Luigi Ferrucci, Rory Wilson, Mélanie Waldenberger, Holger Prokisch, Stefania Bandinelli, Jordana T. Bell, Daniel Levy, Ian J. Deary, Steve Horvath, James S. Pankow, Annette Peters, Eric A. Whitsel, Andrea A. Baccarelli
Software Mentions: 1
Published: over 4 years ago
10.3389/fcell.2020.592573
Tm7sf2 Disruption Alters Radial Gene Positioning in Mouse Liver Leading to Metabolic Defects and Diabetes CharacteristicsCited by: 4
Author(s): Leonardo Gatticchi, Jose I. de las Heras, Aishwarya Sivakumar, Nikolaj Zuleger, Rita Roberti, Eric C. Schirmer
Software Mentions: 1
Published: almost 4 years ago
10.3389/fcell.2019.00222
Dissecting the Shared and Context-Dependent Pathways Mediated by the p140Cap Adaptor Protein in Cancer and in NeuronsCited by: 6
Author(s): Jennifer Chapelle, Oksana Sorokina, Colin McLean, Vincenzo Salemme, Annalisa Alfieri, Costanza Angelini, Alessandro Morellato, Annie Adrait, Elisabetta Menna, Michela Matteoli, Yohann Couté, Ugo Ala, Emilia Turco, Paola Defilippi, J. Douglas Armstrong
Software Mentions: 1
Published: about 5 years ago
10.1371/journal.pgen.1001044
Genome-Wide Analysis Reveals Novel Genes Essential for Heme Homeostasis in Caenorhabditis elegansCited by: 34
Author(s): Scott Severance, Abbhirami Rajagopal, Anita U. Rao, Gustavo C. Cerqueira, Makedonka Mitreva, Najib M. El-Sayed, Michael Krause, Iqbal Hamza
Software Mentions: 1
Published: over 14 years ago
10.1093/molbev/msu141
Patterns of Positive Selection in Seven Ant GenomesCited by: 134
Author(s): Julien Roux, Eyal Privman, Sébastien Moretti, Joséphine T. Daub, Marc Robinson‐Rechavi, Laurent Keller
Software Mentions: 1
Published: over 10 years ago
10.3389/fbioe.2021.709488
Mechanotransduction Regulates Reprogramming Enhancement in Adherent 3D Keratocyte CulturesCited by: 2
Author(s): Shenyang Li, Chengcheng Ding, Yanjie Guo, Yanan Zhang, Hao Wang, Xihao Sun, Jun Zhang, Zekai Cui, Jiansu Chen
Software Mentions: 1
Published: about 3 years ago
10.1080/19336934.2015.1114694
Insights into ALS pathomechanisms: from flies to humansCited by: 6
Author(s): Andrea Chai, Giuseppa Pennetta
Software Mentions: 1
Published: over 9 years ago
10.1186/1471-2164-12-502
Transcriptional signatures of regulatory and toxic responses to benzo-[a]-pyrene exposureCited by: 26
Author(s): Jacob J. Michaelson, Saskia Trump, Susanne Rudzok, Carolin Gräbsch, Danielle Jannuzzi Madureira, Franziska Dautel, Juliane Mai, Sabine Attinger, Kristin Schirmer, Martin von Bergen, Irina Lehmann, Andreas Beyer
Software Mentions: 1
Published: about 13 years ago
10.1186/1471-2164-15-970
Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic originCited by: 38
Author(s): James R. Doroghazi, Daniel H. Buckley
Software Mentions: 1
Published: almost 11 years ago
10.1172/jci.insight.148881
T-bet+CD27+CD21– B cells poised for plasma cell differentiation during antibody-mediated rejection of kidney transplantsCited by: 15
Author(s): Kévin Louis, Élodie Bailly, Camila Macedo, Louis Lau, Bala Ramaswami, Alexander Chang, Uma Chandran, Douglas Landsittel, Xinyan Gu, Geetha Chalasani, Adriana Zeevi, Parmjeet Randhawa, Harinder Singh, Carmen Lefaucheur, Diana Metes
Software Mentions: 1
Published: over 3 years ago
10.3390/plants9050573
The Consequences of a Disruption in Cyto-Nuclear Coadaptation on the Molecular Response to a Nitrate Starvation in ArabidopsisCited by: 0
Author(s): Fabien Chardon, Gwendal Cueff, Étienne Delannoy, Fabien Aubé, Aurélia Lornac, Magali Bedu, Françoise Gilard, Stéphanie Pateyron, Hélène Rogniaux, Audrey Gargaros, Hakim Mireau, Loïc Rajjou, Marie‐Laure Martin‐Magniette, Françoise Budar
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0187760
Identification and characterization of intestine microRNAs and targets in red swamp crayfish, Procambarus clarkii infected with white spot syndrome virusCited by: 5
Author(s): Zhiqiang Du, Kai Wang, Xiu-li Shen, Yanhui Jin, Haixia Jin, Xin-Cang Li
Software Mentions: 1
Published: about 7 years ago
10.1186/2043-9113-2-8
Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteomeCited by: 11
Author(s): Khader Shameer, Ramanathan Sowdhamini
Software Mentions: 1
Published: almost 13 years ago
10.3390/ijms21239093
Integrated Analysis of Seed microRNA and mRNA Transcriptome Reveals Important Functional Genes and microRNA-Targets in the Process of Walnut (Juglans regia) Seed Oil AccumulationCited by: 23
Author(s): Xinchi Zhao, Guiyan Yang, Xiaoqiang Liu, Zhiqiang Yu, Shaobing Peng
Software Mentions: 1
Published: almost 4 years ago
10.1186/1471-2164-15-658
A network-based approach to dissect the cilia/centrosome complex interactomeCited by: 19
Author(s): Roberto Amato, Manuela Morleo, Laura Giaquinto, Diego di Bernardo, Franco Bazzoli
Software Mentions: 1
Published: over 10 years ago
10.15252/msb.20166890
Parallel reverse genetic screening in mutant human cells using transcriptomicsCited by: 14
Author(s): Bianca V. Gapp, Tomasz Konopka, Thomas Penz, Vineet Dalal, Tilmann Bürckstümmer, Christoph Bock, Sebastian M. Nijman
Software Mentions: 1
Published: over 8 years ago
10.1098/rsos.150156
A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammalsCited by: 32
Author(s): Georgia Tsagkogeorga, Michael R. McGowen, Kalina T. J. Davies, Simon Jarman, Andrea M. Polanowski, Mads F. Bertelsen, Stephen J. Rossiter
Software Mentions: 1
Published: about 9 years ago
10.1155/2018/6725728
Comparative Transcriptome Analysis of Temperature-Induced Green Discoloration in GarlicCited by: 4
Author(s): Ningyang Li, Zhichang Qiu, Xiaoming Lu, Bingchao Shi, Xiaohui Sun, Xiaozhen Tang, Xuguang Qiao
Software Mentions: 1
Published: almost 6 years ago
10.1155/2020/5196302
A Systems Pharmacology Approach for Identifying the Multiple Mechanisms of Action for the Rougui-Fuzi Herb Pair in the Treatment of Cardiocerebral Vascular DiseasesCited by: 19
Author(s): Chun Li, Xia Du, Yang Liu, Qiqi Liu, Wen Bing Zhi, Chun Liu Wang, Jiansong Zhou, Ye Li, Hong Zhang
Software Mentions: 1
Published: almost 5 years ago
10.1186/s13072-016-0086-0
Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3Cited by: 61
Author(s): Peggy Prickaerts, Michiel E. Adriaens, Twan van den Beucken, Elizabeth Koch, Ludwig Dubois, V.E.H. Dahlmans, Caroline Gits, Chris T. Evelo, Michelle Chan-Seng-Yue, Bradly G. Wouters, Jan Willem Voncken
Software Mentions: 1
Published: about 8 years ago
10.1038/sdata.2017.195
Assembly of an early-matured japonica (Geng) rice genome, Suijing18, based on PacBio and Illumina sequencingCited by: 8
Author(s): Shou-Jun Nie, Yuqiang Liu, Chunchao Wang, Shiwei Gao, Tian-Tian Xu, Qing Liu, Huilin Chang, Yubao Chen, Peiyao Yan, Peng Wei, Tianqing Zheng, Jianlong Xu, Zhikang Li
Software Mentions: 1
Published: almost 7 years ago
10.1186/s12864-018-5247-z
A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies)Cited by: 20
Author(s): Aïda Azaiez, Nathalie Pavy, Sébastien Gérardi, Jérôme Laroche, Brian Boyle, Marie‐Josée Mottet, Jean Beaulieu, Jean Bousquet
Software Mentions: 1
Published: almost 6 years ago
10.1186/1471-2164-15-616
Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideumCited by: 4
Author(s): Si. I. Li, Neil J. Buttery, Christopher Thompson, Michael D. Purugganan
Software Mentions: 1
Published: over 10 years ago
10.1038/srep23195
Transcriptome analysis of different developmental stages of amphioxus reveals dynamic changes of distinct classes of genes during developmentCited by: 15
Author(s): Kevin Yi Yang, Yuan Chen, Zuming Zhang, Patrick Kwok Shing Ng, Wayne Jun-Wei Zhou, Yinfeng Zhang, Minghua Liu, Jun-Yuan Chen, Bingyu Mao, Stephen Kwok‐Wing Tsui
Software Mentions: 1
Published: over 8 years ago
10.1016/j.omtn.2020.02.008
Aberrant Expression Profiles of lncRNAs and Their Associated Nearby Coding Genes in the Hippocampus of the SAMP8 Mouse Model with ADCited by: 9
Author(s): Honghai Hong, Yousheng Mo, Dongli Li, Zhiheng Xu, Yanfang Liao, Ping Yin, Xinning Liu, Yong Xia, Jiansong Fang, Qi Wang, Shuhuan Fang
Software Mentions: 1
Published: over 4 years ago
10.1038/srep31472
A Novel Nitrobenzoate Microtubule Inhibitor that Overcomes Multidrug Resistance Exhibits Antitumor ActivityCited by: 23
Author(s): Yanbo Zheng, Jianhua Gong, Xiujun Liu, Shengxi Wu, Yang Li, Xian-Dong Xu, Bo-Yang Shang, Jinming Zhou, Zhiling Zhu, Shuyi Si, Yong‐Su Zhen
Software Mentions: 1
Published: over 8 years ago
10.1186/1471-2350-14-32
Mutation spectrum in human colorectal cancers and potential functional relevanceCited by: 9
Author(s): Han Yin, Liang Yue, Zhaopeng Yan, Baolin Liu, Shijie Qi
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0235444
Changes in gene expression in potato meristems treated with the sprout suppressor 1,4-dimethylnaphthalene are dependent on tuber age and dormancy statusCited by: 3
Author(s): Michael A. Campbell, Carley Gwin, Helen H. Tai, Rachael Adams
Software Mentions: 1
Published: over 4 years ago
10.1080/21505594.2018.1438025
Both live and dead <i>Enterococci</i> activate <i>Caenorhabditis elegans</i> host defense via immune and stress pathwaysCited by: 47
Author(s): Grace J. Yuen, Frederick M. Ausubel
Software Mentions: 1
Published: over 6 years ago
10.1186/s12920-015-0125-x
Harmful somatic amino acid substitutions affect key pathways in cancersCited by: 16
Author(s): Abhishek Niroula, Mauno Vihinen
Software Mentions: 1
Published: over 9 years ago
10.1038/s41598-017-11724-w
DNA methylation profiling reveals common signatures of tumorigenesis and defines epigenetic prognostic subtypes of canine Diffuse Large B-cell LymphomaCited by: 25
Author(s): Serena Ferraresso, Arianna Aricò, Tiziana Sanavia, Silvia Da Ros, Massimo Milan, Luciano Cascione, S. Comazzi, Valeria Martini, Mery Giantin, Barbara Di Camillo, Sandro Mazzariol, Diana Giannuzzi, Laura Marconato, Luca Aresu
Software Mentions: 1
Published: about 7 years ago
10.1155/2014/867235
The Domain Landscape of Virus-Host InteractomesCited by: 25
Author(s): Lulu Zheng, Chunyan Li, Jie Ping, Yanhong Zhou, Yixue Li, Pei Hao
Software Mentions: 1
Published: almost 11 years ago
10.1186/1755-8794-7-15
The global landscape of intron retentions in lung adenocarcinomaCited by: 31
Author(s): Zhilin Qu, Hua Li, Hong Jin, Huibiao Tan, Jun Zhang, Sitong Sheng
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pone.0131455
De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic DataCited by: 26
Author(s): Xinjie Tian, Yan Long, Jiao Wang, Jingwen Zhang, Yanyan Wang, Weimin Liu, Yufa Peng, Qianhua Yuan, Xinwu Pei
Software Mentions: 1
Published: over 9 years ago
10.1002/ece3.5074
Transcriptomics and differential gene expression in<i>Whitmania pigra</i>(Annelida: Clitellata: Hirudinida: Hirudinidae): Contrasting feeding and fasting modesCited by: 10
Author(s): Muhammad Salabat Khan, De‐Long Guan, Sebastian Kvist, Li Ma, Jun Xie, Sheng‐Quan Xu
Software Mentions: 1
Published: over 5 years ago