bioconductor: GOstats | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0151127

MiRComb: An R Package to Analyse miRNA-mRNA Interactions. Examples across Five Digestive Cancers
Cited by: 35
Author(s): María Vila-Casadesús, Meritxell Gironella, Juan José Lozano
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pgen.1005385

MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) Regulates Global Gene Expression during Infection-Related Morphogenesis
Cited by: 66
Author(s): Kieu T.M. Pham, Yushi Inoue, Vu Van Ba, Hanh Hieu Nguyen, Toru Nakayashiki, Kenichi Ikeda, Hitoshi Nakayashiki
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pgen.1005819

Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age
Cited by: 21
Author(s): Н. А. Иванов, Ran Tao, Joshua G. Chenoweth, Anna C. Brandtjen, Michelle I. Mighdoll, John D. Genova, Ronald D.G. McKay, Yankai Jia, Daniel R. Weinberger, Joel E. Kleinman, Thomas M. Hyde, Andrew E. Jaffe
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0053033

Differences in Transcription Patterns between Induced Pluripotent Stem Cells Produced from the Same Germ Layer Are Erased upon Differentiation
Cited by: 2
Author(s): Iryna Pirozhkova, Ana Barat, Petr Dmitriev, Elena Kim, Robert Thomas, Justine Guégan, Chrystèle Bilhou‐Nabera, Florence Busato, Jörg Tost, Gilles Carnac, Dalila Laoudj-Chenivesse, Marc Lipinski, Yegor S. Vassetzky
Software Mentions: 5
Published: almost 12 years ago

10.1186/s12943-017-0653-4

Human germ/stem cell-specific gene TEX19 influences cancer cell proliferation and cancer prognosis
Cited by: 18
Author(s): Vicente Planells-Palop, Ali Hazazi, Julia Feichtinger, Jana Jezkova, Gerhard G. Thallinger, Naif Alsiwiehri, Mikhlid H. Almutairi, Lee Parry, Jane A. Wakeman, Ramsay J. McFarlane
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pbio.1000335

The Sexually Antagonistic Genes of Drosophila melanogaster
Cited by: 294
Author(s): Paolo Innocenti, Edward H. Morrow
Software Mentions: 5
Published: over 14 years ago

10.1186/s13059-020-02032-0

Sampling time-dependent artifacts in single-cell genomics studies
Cited by: 50
Author(s): Ramón Massoni-Badosa, Giovanni Iacono, Cátia Moutinho, Marta Kulis, Núria Palau, Domenica Marchese, Javier Rodríguez-Ubreva, Esteban Ballestar, Gustavo Rodríguez-Esteban, Sara Marsal, Marta Aymerich, Dolors Colomer, Elı́as Campo, Antonio Julià, José I. Martín‐Subero, Holger Heyn
Software Mentions: 5
Published: over 4 years ago

10.3390/nu13010179

Iron Deficiency Reprograms Phosphorylation Signaling and Reduces O-GlcNAc Pathways in Neuronal Cells
Cited by: 8
Author(s): Luke Erber, Ang Luo, Yao Gong, Montana M. Beeson, Maolin Tu, Phu V. Tran, Yue Chen
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-018-2139-9

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
Cited by: 141
Author(s): MacIntosh Cornwell, Mahesh Vangala, Len Taing, Zachary T. Herbert, Johannes Köster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X. Shirley Liu, Henry W. Long
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2105-10-242

R/BHC: fast Bayesian hierarchical clustering for microarray data
Cited by: 54
Author(s): Richard S. Savage, Katherine Heller, Yang Xu, Zoubin Ghahramani, William Truman, Murray Grant, Katherine J. Denby, David L. Wild
Software Mentions: 4
Published: over 15 years ago

10.1186/1471-2407-12-223

Estimation of groin recurrence risk in patients with squamous cell vulvar carcinoma by the assessment of marker gene expression in the lymph nodes
Cited by: 11
Author(s): Magdalena Kowalewska, Jakub Radziszewski, Krzysztof Goryca, Mateusz Bujko, Małgorzata Oczko‐Wojciechowska, Michał Jarząb, Janusz A. Siedlecki, Mariusz Bidziński
Software Mentions: 4
Published: over 12 years ago

10.1186/1471-2407-9-413

Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KITmutations and expression
Cited by: 21
Author(s): Jerzy Ostrowski, Marcin Polkowski, Agnieszka Paziewska, Magdalena Skrzypczak, Krzysztof Goryca, Tymon Rubel, Katarzyna Kokoszyńska, Piotr Rutkowski, Zbigniew Nowecki, Anna Jerzak vel Dobosz, Dorota Jarosz, W. Ruka, Lucjan Wyrwicz
Software Mentions: 4
Published: almost 15 years ago

10.1186/1471-2164-11-23

Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development
Cited by: 37
Author(s): Wen Huang, Brian S. Yandell, Hasan Khatib
Software Mentions: 4
Published: almost 15 years ago

10.1186/1471-2164-10-373

Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers
Cited by: 170
Author(s): Xinxia Peng, Li Yu, Kathie–Anne Walters, Elizabeth Rosenzweig, Sharon Lederer, Lauri Aicher, Sean Proll, Michael G. Katze
Software Mentions: 4
Published: over 15 years ago

10.1186/s12864-019-6294-9

Refining modules to determine functionally significant clusters in molecular networks
Cited by: 2
Author(s): Rama Kaalia, Jagath C. Rajapakse
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-020-6694-x

Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing
Cited by: 22
Author(s): Diego Robledo, Alastair Hamilton, Alejandro P. Gutiérrez, James E. Bron, Ross D. Houston
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2164-15-763

Transcriptome of Saccharomyces cerevisiae during production of D-xylonate
Cited by: 5
Author(s): Dominik Mojžita, Merja Oja, Eija Rintala, Marilyn G. Wiebe, Merja Penttilä, Laura Ruohonen
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12864-018-4499-y

Transcripts within rod photoreceptors of the Zebrafish retina
Cited by: 28
Author(s): Chi Sun, Carlos Galicia, Deborah L. Stenkamp
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12920-015-0139-4

Genome-wide DNA methylome reveals the dysfunction of intronic microRNAs in major psychosis
Cited by: 27
Author(s): Hongying Zhao, Jiu Hua Xu, Lin Pang, Yunpeng Zhang, Huihui Fan, Ling Liu, Tingting Liu, Fulong Yu, Guanxiong Zhang, Yujia Lan, Jing Bai, Xia Li, Yun Xiao
Software Mentions: 4
Published: about 9 years ago

10.1186/s12920-018-0403-5

Progression-specific genes identified in microdissected formalin-fixed and paraffin-embedded tissue containing matched ductal carcinoma in situ and invasive ductal breast cancers
Cited by: 12
Author(s): S Schultz, Harald Bartsch, Karl Sotlar, Karina Petat-Dutter, Michael Bonin, Steffen Kahlert, Nadia Harbeck, Ulrich Vogel, Harald Seeger, Tanja Fehm, Hans Neubauer
Software Mentions: 4
Published: about 6 years ago

10.1186/1753-6561-3-S4-S9

Microarray data mining using Bioconductor packages
Cited by: 8
Author(s): Haisheng Nie, Pieter Neerincx, Jan van der Poel, Francesco Ferrari, Silvio Bicciato, Jack A. M. Leunissen, Martien A. M. Groenen
Software Mentions: 4
Published: over 15 years ago

10.1186/1752-0509-6-147

The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes
Cited by: 16
Author(s): Sebastian Vlaic, Wolfgang Schmidt‐Heck, Madlen Matz‐Soja, E Marbach, Jörg Linde, Anke Meyer‐Baese, Sebastian Zellmer, Reinhard Guthke, Rolf Gebhardt
Software Mentions: 4
Published: almost 13 years ago

10.1186/s40168-015-0133-2

The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles
Cited by: 64
Author(s): Yasir Tarabichi, K. Li, Shishan Hu, Cam Nguyen, X. Wang, David Elashoff, Kazima Saira, Bryan Frank, Monika Bihan, Elodie Ghedin, Barbara A. Methé, Jane C. Deng
Software Mentions: 4
Published: almost 9 years ago

10.3390/microorganisms8060940

Asexual Evolution and Forest Conditions Drive Genetic Parallelism in Phytophthora ramorum
Cited by: 3
Author(s): Jennifer Yuzon, Renaud Travadon, Mathu Malar C, Sucheta Tripathy, Nathan E. Rank, Heather K. Mehl, David M. Rizzo, Richard C. Cobb, Corinn Small, Tiffany Tang, Haley E. McCown, Matteo Garbelotto, Takao Kasuga
Software Mentions: 4
Published: over 4 years ago

10.3390/pathogens9050380

Inhibition of Asaia in Adult Mosquitoes Causes Male-Specific Mortality and Diverse Transcriptome Changes
Cited by: 12
Author(s): Maria Vittoria Mancini, Claudia Damiani, Sarah M. Short, Alessia Cappelli, Ulisse Ulissi, Aida Capone, Aurelio Serrao, Paolo Rossi, Augusto Amici, Cristina Kalogris, George Dimopoulos, Irene Ricci, Guido Favia
Software Mentions: 4
Published: over 4 years ago

10.7717/peerj.3509

GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis
Cited by: 9
Author(s): Raquel L. Costa, Luiz M. R. Gadelha, Marcelo Ribeiro-Alves, Fábio Porto
Software Mentions: 4
Published: over 7 years ago

10.1007/s11105-017-1032-4

Drought-Tolerant Brassica rapa Shows Rapid Expression of Gene Networks for General Stress Responses and Programmed Cell Death Under Simulated Drought Stress
Cited by: 25
Author(s): Yi Guo, Birgit Samans, Sheng Chen, Kidist B. Kibret, Sarah Hatzig, Neil C. Turner, Matthew N. Nelson, Wallace Cowling, Rod J. Snowdon
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pbio.1002307

Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets
Cited by: 51
Author(s): Gregory J. Hogan, Patrick O. Brown, Daniel Herschlag
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pcbi.1009373

Genetic dissection of complex traits using hierarchical biological knowledge
Cited by: 1
Author(s): Hidenori Tanaka, Jason F. Kreisberg, Trey Ideker
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pgen.1008501

The MITF-SOX10 regulated long non-coding RNA DIRC3 is a melanoma tumour suppressor
Cited by: 51
Author(s): Elizabeth A. Coe, Jennifer Y. Tan, Michael Shapiro, Pakavarin Louphrasitthiphol, Andrew Bassett, Ana C. Marques, Colin R. Goding, Keith W. Vance
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1008617

Inhibition of the oligosaccharyl transferase in Caenorhabditis elegans that compromises ER proteostasis suppresses p38-dependent protection against pathogenic bacteria
Cited by: 8
Author(s): Dae‐Eun Jeong, Yujin Lee, Seokjin Ham, Dong-Yeop Lee, Sujeong Kwon, Hae‐Eun H. Park, Sunyoung Hwang, Joo‐Yeon Yoo, Tae-Young Roh, Seung-Jae Lee
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pntd.0001274

Gene Expression Patterns in Larval Schistosoma mansoni Associated with Infection of the Mammalian Host
Cited by: 88
Author(s): Sophia J. Parker-Manuel, Alasdair Ivens, G. Dillon, R. A. Wilson
Software Mentions: 4
Published: about 13 years ago

10.1371/journal.pone.0095875

The DNA Methylome and Transcriptome of Different Brain Regions in Schizophrenia and Bipolar Disorder
Cited by: 70
Author(s): Yun Xiao, Cynthia Camarillo, Yanyan Ping, Tania Bedard Arana, Hongying Zhao, Peter M. Thompson, Chaohan Xu, Bai-Horng Su, Huihui Fan, Javier Ordoñez, Li Wang, Chunxiang Mao, Yunpeng Zhang, Dianne A. Cruz, Michael Escamilla, Xia Li, Xu Chun
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0029021

Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in T47D Breast Cancer Cells and Primary Leiomyoma Cells
Cited by: 72
Author(s): Ping Yin, Damian Roqueiro, Lei Huang, Jonas K. Owen, Anna Xie, Antònia Navarro, Diana Monsivais, John S. Coon, Julie Kim, Yang Dai, Serdar E. Bulun
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0158247

Nonlinear Network Reconstruction from Gene Expression Data Using Marginal Dependencies Measured by DCOL
Cited by: 10
Author(s): Haodong Liu, Peng Li, Mengyao Zhu, Xiaofei Wang, Jianwei Lu, Tianwei Yu
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0032394

pcaGoPromoter - An R Package for Biological and Regulatory Interpretation of Principal Components in Genome-Wide Gene Expression Data
Cited by: 24
Author(s): Morten Hansen, Thomas Alexander Gerds, Ole Haagen Nielsen, Jakob Benedict Seidelin, Jesper T. Troelsen, Jørgen Olsen
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0014782

Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA
Cited by: 122
Author(s): Andreia J. Amaral, Luca Ferretti, Hendrik‐Jan Megens, R.P.M.A. Crooijmans, Haisheng Nie, Sebastián E. Ramos-Onsins, Miguel Pérez‐Enciso, Lawrence B. Schook, Martien A. M. Groenen
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0180751

Increased dermal collagen bundle alignment in systemic sclerosis is associated with a cell migration signature and role of Arhgdib in directed fibroblast migration on aligned ECMs
Cited by: 14
Author(s): Lizhi Cao, Robert Lafyatis, Linda C. Burkly
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0127103

From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response
Cited by: 31
Author(s): Barbara Blasi, Hakim Tafer, Donatella Tesei, Katja Sterflinger
Software Mentions: 4
Published: over 9 years ago

10.1038/cr.2017.82

Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells
Cited by: 262
Author(s): Fan Guo, Lin Li, Jingyun Li, Xinglong Wu, Boqiang Hu, Ping Zhu, Lu Wen, Fuchou Tang
Software Mentions: 4
Published: over 7 years ago

10.1016/j.devcel.2016.08.013

Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis
Cited by: 61
Author(s): Stefano Bencivenga, Antonio Serrano-Mislata, Maxwell S. Bush, Samantha Fox, Robert Sablowski
Software Mentions: 4
Published: about 8 years ago

10.1016/j.devcel.2020.09.025

Functional Diversification of SRSF Protein Kinase to Control Ubiquitin-Dependent Neurodevelopmental Signaling
Cited by: 27
Author(s): Francisco Bustos, Anna Segarra-Fas, Gino Nardocci, Andrew Cassidy, Odetta Antico, L. S. P. Davidson, Lennart Brandenburg, Thomas Macartney, Rachel Toth, Claire Hastie, Jennifer L. Moran, Robert Gourlay, Joby Varghese, Renata Soares, Martín Montecino, Greg M. Findlay
Software Mentions: 4
Published: almost 4 years ago

10.1007/s00125-018-4612-4

Patterns of differential gene expression in a cellular model of human islet development, and relationship to type 2 diabetes predisposition
Cited by: 12
Author(s): Marta Perez-Alcantara, Christian Honoré, Agata Wesolowska-Andersen, Anna L. Gloyn, Mark I. McCarthy, Mattias Hansson, Nicola L. Beer, Martijn van de Bunt
Software Mentions: 4
Published: over 6 years ago

10.3389/fcell.2021.717772

Human Induced Pluripotent Stem Cell-Derived Mesenchymal Stem Cells Acquire Rejuvenation and Reduced Heterogeneity
Cited by: 21
Author(s): Wasco Wruck, Nina Graffmann, Lucas‐Sebastian Spitzhorn, James Adjaye
Software Mentions: 4
Published: about 3 years ago

10.3389/fgene.2020.581789

Integrated Analysis of Key Genes and Pathways Involved in Fetal Growth Restriction and Their Associations With the Dysregulation of the Maternal Immune System
Cited by: 2
Author(s): Xue Wang, Hong Zhu, Lei Lei, Yang Zhang, Chao Tang, Jingyi Wu, Jing Zhou, Xirong Xiao
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2016.01084

Genome and Transcriptome Sequences Reveal the Specific Parasitism of the Nematophagous Purpureocillium lilacinum 36-1
Cited by: 27
Author(s): Jialian Xie, Shaojun Li, Chenmi Mo, Xiangyu Xiao, Deliang Peng, Gaofeng Wang, Yanan Xiao
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2019.02195

Different Pathways Mediate Amphotericin-Lactoferrin Drug Synergy in Cryptococcus and Saccharomyces
Cited by: 5
Author(s): Yu-Wen Lai, Chi Nam Ignatius Pang, Leona T. Campbell, Wen Chen, Marc R. Wilkins, Dee Carter
Software Mentions: 4
Published: about 5 years ago

10.3389/fnins.2017.00112

Antidyskinetic Effects of MEK Inhibitor Are Associated with Multiple Neurochemical Alterations in the Striatum of Hemiparkinsonian Rats
Cited by: 21
Author(s): Guiqin Chen, Shuke Nie, Chao Han, Kai Ma, Xu Yan, Zhentao Zhang, Stella M. Papa, Xin Cao
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2018.01864

Revisiting the Soybean GmNAC Superfamily
Cited by: 37
Author(s): Bruno Paes de Melo, Otto Teixeira Fraga, José Cleydson Ferreira da Silva, Dalton O Ferreira, Otávio J. B. Brustolini, Paola A. Carpinetti, João Paulo Machado, Pedro A. B. Reis, Elizabeth P. B. Fontes
Software Mentions: 4
Published: almost 6 years ago

10.3390/genes6010001

Down-Regulation of miR-129-5p and the let-7 Family in Neuroendocrine Tumors and Metastases Leads to Up-Regulation of Their Targets Egr1, G3bp1, Hmga2 and Bach1
Cited by: 53
Author(s): Kristina B. V. Døssing, Tina Binderup, Bogumił Kaczkowski, Anders Jacobsen, Maria Rossing, Ole Winther, Birgitte Federspiel, Ulrich Knigge, Andreas Kjær, Lennart Friis‐Hansen
Software Mentions: 4
Published: almost 10 years ago

10.1093/gbe/evv115

Complete Dosage Compensation in<i>Anopheles stephensi</i>and the Evolution of Sex-Biased Genes in Mosquitoes
Cited by: 40
Author(s): Xiaofang Jiang, James K. Biedler, Yumin Qi, Andrew Brantley Hall, Zhijian Tu
Software Mentions: 4
Published: over 9 years ago

10.1002/reg2.48

Genome‐wide analysis reveals conserved transcriptional responses downstream of resting potential change in<i>Xenopus</i>embryos, axolotl regeneration, and human mesenchymal cell differentiation
Cited by: 51
Author(s): Vaibhav P. Pai, Christopher J. Martyniuk, Karen Echeverri, Sarah Sundelacruz, David L. Kaplan, Michael Levin
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-019-41298-8

Regeneration associated transcriptional signature of retinal microglia and macrophages
Cited by: 54
Author(s): Diana Mitchell, Chi Sun, Samuel S. Hunter, Daniel D. New, Deborah L. Stenkamp
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-40883-1

Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315
Cited by: 13
Author(s): Jonna Teikari, Rafael Vicentini Popin, Songjun Hou, Matti Wahlsten, Wolfgang R. Hess, Kaarina Sivonen
Software Mentions: 4
Published: over 5 years ago

10.1038/s41396-020-00859-w

Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments
Cited by: 18
Author(s): Anik Dutta, Fanny E. Hartmann, C. L. Francisco, Bruce A. McDonald, Daniel Croll
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41396-020-0729-9

Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens
Cited by: 35
Author(s): Pilar Vesga, Pascale Flury, Jordan Vacheron, Christoph Keel, Daniel Croll, M. Maurhofer
Software Mentions: 4
Published: about 4 years ago

10.1016/j.ijpara.2007.02.006

Altered phenotype and gene transcription in endothelial cells, induced by Plasmodium falciparum-infected red blood cells: Pathogenic or protective?
Cited by: 40
Author(s): Srabasti J. Chakravorty, Céline Carret, Gerard B. Nash, Alasdair Ivens, Tadge Szestak, Alister G. Craig
Software Mentions: 4
Published: over 17 years ago

10.7554/eLife.08411

Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions
Cited by: 39
Author(s): Anne Plessis, Christoph Hafemeister, Olivia Wilkins, Zennia Jean Gonzaga, Rachel S. Meyer, Inês S. Pires, Christian Müller, Endang M. Septiningsih, Richard Bonneau, Michael D. Purugganan
Software Mentions: 4
Published: almost 9 years ago

10.18632/oncotarget.23065

Transcriptome evolution from breast epithelial cells to basal-like tumors
Cited by: 11
Author(s): Gabriel Santpere, Ana Alcaráz-Sanabria, Verónica Corrales-Sánchez, Atanasio Pandiella, Balázs Győrffy, Alberto Ocaña
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0013984

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
Cited by: 1,757
Author(s): Daniele Merico, Ruth Isserlin, Oliver Stueker, Andrew Emili, Gary D. Bader
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0121507

Alternative Polyadenylation Allows Differential Negative Feedback of Human miRNA miR-579 on Its Host Gene ZFR
Cited by: 22
Author(s): Christian Hinske, Pedro A. F. Galante, Elisabeth Limbeck, Patrick Möhnle, Raphael B. Parmigiani, Lucila Ohno-Machado, Anamaria A. Camargo, Simone Kreth
Software Mentions: 3
Published: over 9 years ago

10.1038/s41389-018-0083-1

The FAK inhibitor BI 853520 exerts anti-tumor effects in breast cancer
Cited by: 49
Author(s): Stefanie Tiede, Nathalie Meyer-Schaller, Ravi Kiran Reddy Kalathur, Robert Ivánek, Ernesta Fagiani, Philip Schmassmann, Patrick Stillhard, Simon Häfliger, Norbert Kraut, Norbert Schweifer, Irene C. Waizenegger, Ruben Bill, Gerhard Christofori
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2229-10-59

Transcriptional responses to polycyclic aromatic hydrocarbon-induced stress in Arabidopsis thalianareveal the involvement of hormone and defense signaling pathways
Cited by: 89
Author(s): David Weisman, Merianne Alkio, Adán Colón‐Carmona
Software Mentions: 3
Published: over 14 years ago

10.1186/1741-7007-8-146

2R and remodeling of vertebrate signal transduction engine
Cited by: 77
Author(s): Łukasz Huminiecki, Carl Henrik Heldin
Software Mentions: 3
Published: almost 14 years ago

10.3389/fgene.2019.00903

SCDevDB: A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes
Cited by: 12
Author(s): Zishuai Wang, Xikang Feng, Shuai Cheng Li
Software Mentions: 3
Published: about 5 years ago

10.1128/mBio.02818-18

Cdk8 and Ssn801 Regulate Oxidative Stress Resistance and Virulence in Cryptococcus neoformans
Cited by: 9
Author(s): Andrew L. Chang, Yiming Kang, Tamara L. Doering
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pbio.3000540

Loss of adenomatous polyposis coli function renders intestinal epithelial cells resistant to the cytokine IL-22
Cited by: 7
Author(s): Yu Chen, Maud Vandereyken, Ian P. Newton, Ignacio Moraga, Inke Näthke, Mahima Swamy
Software Mentions: 3
Published: almost 5 years ago

10.1186/1741-7007-10-55

Low level genome mistranslations deregulate the transcriptome and translatome and generate proteotoxic stress in yeast
Cited by: 31
Author(s): João A. Paredes, Laura Carreto, João Simões, Ana R. Bezerra, Ana Catarina Gomes, Rodrigo Santamaría, Misha Kapushesky, Gabriela Moura, Manuel A. S. Santos
Software Mentions: 3
Published: over 12 years ago

10.1038/s41598-018-28948-z

GOATOOLS: A Python library for Gene Ontology analyses
Cited by: 606
Author(s): D. V. Klopfenstein, Liangsheng Zhang, Brent S. Pedersen, Fidel Ramírez, Alex Warwick Vesztrocy, Aurélien Naldi, Christopher J. Mungall, Jeffrey M. Yunes, Olga Botvinnik, Mark Weigel, Will Dampier, Christophe Dessimoz, Patrick Flick, Haibao Tang
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2019.02728

The Glycerol Phosphatase Gpp2: A Link to Osmotic Stress, Sulfur Assimilation and Virulence in Cryptococcus neoformans
Cited by: 4
Author(s): Kevin Felipe Cruz Martho, Otávio J. B. Brustolini, Ana Tereza Ribeiro de Vasconcelos, Marcelo A. Vallim, Renata C. Pascon
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41389-021-00338-7

USP29-mediated HIF1α stabilization is associated with Sorafenib resistance of hepatocellular carcinoma cells by upregulating glycolysis
Cited by: 29
Author(s): Ruize Gao, David Buechel, Ravi Kiran Reddy Kalathur, Marco Morini, Mairene Coto‐Llerena, Caner Ercan, Salvatore Piscuoglio, Qian Chen, Tanja Blumer, Xueya Wang, Eva Dazert, Markus H. Heim, Michael N. Hall, Fengyuan Tang, Gerhard Christofori
Software Mentions: 3
Published: over 3 years ago

10.1186/2044-5040-2-7

miR-206 integrates multiple components of differentiation pathways to control the transition from growth to differentiation in rhabdomyosarcoma cells
Cited by: 36
Author(s): Kyle L. MacQuarrie, Zizhen Yao, Janet M. Young, Yi Cao, Stephen J. Tapscott
Software Mentions: 3
Published: over 12 years ago

10.1186/s13148-017-0376-9

Long-term prenatal exposure to paracetamol is associated with DNA methylation differences in children diagnosed with ADHD
Cited by: 50
Author(s): Kristina Gervin, Hedvig Nordeng, Eivind Ystrøm, Ted Reichborn‐Kjennerud, Robert Lyle
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-30640-1

PyMT-1099, a versatile murine cell model for EMT in breast cancer
Cited by: 14
Author(s): Mohit Saxena, Ravi Kiran Reddy Kalathur, Melanie Neutzner, Gerhard Christofori
Software Mentions: 3
Published: over 6 years ago

10.18632/oncotarget.7579

A nuclear-directed human pancreatic ribonuclease (PE5) targets the metabolic phenotype of cancer cells
Cited by: 15
Author(s): Anna Vert, Jessica Castro, Marc Ribó, Antoni Benito, María Vilanova
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-019-5661-x

Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis
Cited by: 27
Author(s): Yajuan Li, Lingling Zhang, Ruojiao Li, Meiwei Zhang, Yangping Li, Hao Wang, Shi Wang, Zhenmin Bao
Software Mentions: 3
Published: over 5 years ago

10.1186/s12918-016-0336-6

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus
Cited by: 51
Author(s): Jason McDermott, Hugh D. Mitchell, Lisa E. Gralinski, Amie J. Eisfeld, Laurence Josset, Armand Bankhead, Gabriele Neumann, Susan C. Tilton, Alexandra Schäfer, Chengjun Liu, Shufang Fan, Shannon K. McWeeney, Ralph S. Baric, Michael G. Katze, Katrina M. Waters
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0097780

Initiation of an Inflammatory Response in Resident Intestinal Lamina Propria Cells -Use of a Human Organ Culture Model
Cited by: 8
Author(s): Jutta Schröder–Braunstein, Judith Gras, Benedikt Brors, Sonja Schwarz, Timea Szikszai, Felix Lasitschka, Guido H. Wabnitz, Antje Heidtmann, Young-Seon Lee, Serin Schiessling, Christine Leowardi, Mohammed Al-Saeedi, Alexis Ulrich, Antonia Engelke, Johannes Winter, Yvonne Samstag, Thomas Giese, Stefan Meuer
Software Mentions: 3
Published: over 10 years ago

10.3389/fpls.2016.01934

De novo Sequencing and Comparative Transcriptomics of Floral Development of the Distylous Species Lithospermum multiflorum
Cited by: 14
Author(s): James I. Cohen
Software Mentions: 3
Published: almost 8 years ago

10.1128/mSystems.00491-20

Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli
Cited by: 8
Author(s): Alyaa M. Abdel-Haleem, Vaishnavi Ravikumar, Boyang Ji, Katsuhiko Mineta, Xin Gao, Jens Nielsen, Takashi Gojobori, Ivan Mijaković
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2164-11-28

Regional regulation of transcription in the chicken genome
Cited by: 8
Author(s): Haisheng Nie, R.P.M.A. Crooijmans, J.W.M. Bastiaansen, Hendrik‐Jan Megens, Martien A. M. Groenen
Software Mentions: 3
Published: almost 15 years ago

10.3389/fpls.2019.00823

Transcriptional Insight Into Brassica napus Resistance Genes LepR3 and Rlm2-Mediated Defense Response Against the Leptosphaeria maculans Infection
Cited by: 13
Author(s): Tengsheng Zhou, Wen Xu, Arvind H. Hirani, Zheng Liu, Phạm Anh Tuấn, Belay T. Ayele, Fouad Daayf, P. B. E. McVetty, Robert Duncan, Genyi Li
Software Mentions: 3
Published: over 5 years ago

10.1242/bio.014308

Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells
Cited by: 40
Author(s): Catriona Manville, Kayleigh A. Smith, Zbysław Sońdka, Holly Ashlene Rance, Simon Cockell, Ian G. Cowell, Ka Cheong Lee, Nicholas J. Morris, Kay Padget, Graham Jackson, Caroline A. Austin
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2164-12-610

Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease
Cited by: 10
Author(s): Rudi Alberts, Hairong Chen, Claudia Pommerenke, August B. Smit, Sabine Spijker, Robert W. Williams, Robert Geffers, Dunja Bruder, Klaus Schughart
Software Mentions: 3
Published: almost 13 years ago

10.1186/s13068-020-01758-0

Comparative transcriptome analyses define genes and gene modules differing between two Populus genotypes with contrasting stem growth rates
Cited by: 14
Author(s): Xiao Han, Yi An, Yangyan Zhou, Chao Liu, Weilun Yin, Xinli Xia
Software Mentions: 3
Published: over 4 years ago

10.1534/g3.116.031096

MeSH-Informed Enrichment Analysis and MeSH-Guided Semantic Similarity Among Functional Terms and Gene Products in Chicken
Cited by: 10
Author(s): Gota Morota, Timothy Beissinger, Francisco Peñagaricano
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1009245

bsAS, an antisense long non-coding RNA, essential for correct wing development through regulation of blistered/DSRF isoform usage
Cited by: 5
Author(s): Sílvia Pérez-Lluch, Cecília C. Klein, Alessandra Breschi, Marina Ruiz-Romero, Amaya Abad, Emilio Palumbo, Lyazzat Bekish, Carme Arnan, Roderic Guigó
Software Mentions: 3
Published: almost 4 years ago

10.18632/oncotarget.14302

Activating transcription factor 3 is crucial for antitumor activity and to strengthen the antiviral properties of Onconase
Cited by: 20
Author(s): Anna Vert, Jessica Castro, Marc Ribó, Antoni Benito, María Vilanova
Software Mentions: 3
Published: almost 8 years ago

10.1186/1752-0509-5-56

Systems biology approach to identify transcriptome reprogramming and candidate microRNA targets during the progression of polycystic kidney disease
Cited by: 72
Author(s): Priyanka Pandey, Shan Qin, Jacqueline Ho, Jing Zhou, Jordan A. Kreidberg
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0154882

An Integrated Bioinformatics Analysis Reveals Divergent Evolutionary Pattern of Oil Biosynthesis in High- and Low-Oil Plants
Cited by: 18
Author(s): Li Zhang, Shibo Wang, Qi-Gang Li, Jian Song, Yuqi Hao, Ling Zhou, Huanquan Zheng, J. M. Dunwell, Yuanming Zhang
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2407-10-126

The RNA binding protein HuR differentially regulates unique subsets of mRNAs in estrogen receptor negative and estrogen receptor positive breast cancer
Cited by: 54
Author(s): Robert Calaluce, Matthew M. Gubin, J. Wade Davis, Joseph Magee, Jing Chen, Yuki Kuwano, Myriam Gorospe, Ulus Atasoy
Software Mentions: 3
Published: over 14 years ago

10.1038/srep37814

Environmental Intervention as a Therapy for Adverse Programming by Ancestral Stress
Cited by: 46
Author(s): J. Keiko McCreary, Zachary T. Erickson, Yongxin Hao, Yaroslav Ilnytskyy, Igor Kovalchuk, Gerlinde A. S. Metz
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13068-016-0547-5

Genome wide analysis of protein production load in Trichoderma reesei
Cited by: 22
Author(s): Tiina Pakula, Heli Nygrén, Dorothee Barth, Markus Heinonen, Sandra Castillo, Merja Penttilä, Mikko Arvas
Software Mentions: 3
Published: over 8 years ago

10.1016/j.omtn.2018.04.018

Parallel Genome-wide Profiling of Coding and Non-coding RNAs to Identify Novel Regulatory Elements in Embryonic and Maturated Heart
Cited by: 10
Author(s): Davood Sabour, Rui S. R. Machado, José Pinto, Susan Rohani, Raja Ghazanfar Ali Sahito, Jürgen Hescheler, Matthias E. Futschik, Agapios Sachinidis
Software Mentions: 3
Published: about 6 years ago

10.1186/gb-2008-9-10-r146

A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection
Cited by: 19
Author(s): Amanda Greenall, Guiyuan Lei, Daniel Swan, Katherine James, Liming Wang, Heiko Peters, Anil Wipat, Darren J. Wilkinson, David Lydall
Software Mentions: 3
Published: almost 17 years ago

10.1186/s12864-015-2336-0

Sex-specific gene expression in the mosquito Culex pipiens f. molestus in response to artificial light at night
Cited by: 25
Author(s): Ann‐Christin Honnen, Paul R. Johnston, Michael T. Monaghan
Software Mentions: 3
Published: almost 9 years ago

10.18632/aging.101446

Common and unique transcriptional responses to dietary restriction and loss of insulin receptor substrate 1 (IRS1) in mice
Cited by: 7
Author(s): Melissa M. Page, Eugene F. Schuster, Manikhandan Mudaliar, Paweł Herzyk, Dominic J. Withers, Colin Selman
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0150591

Analysis of the Phialocephala subalpina Transcriptome during Colonization of Its Host Plant Picea abies
Cited by: 11
Author(s): Vanessa Reininger, Markus Schlegel
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-11-585

Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation
Cited by: 15
Author(s): Andreas Kowarsch, Florian Blöchl, Sebastian Böhl, Maria Saile, Norbert Gretz, Ursula Klingmüller, Fabian J. Theis
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12870-019-1952-2

Genome-wide transcriptional adaptation to salt stress in Populus
Cited by: 28
Author(s): Jin-Gui Liu, Xiao Han, Tianbo Yang, Wenhui Cui, Aimin Wu, Chunxiang Fu, Baichen Wang, Lijun Liu
Software Mentions: 3
Published: over 5 years ago

Projects: bioconductor: GOstats

Papers Mentioning GOstats 368