bioconductor: ArrayExpress | Projects

10.1074/jbc.RA119.010302

Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription
Cited by: 51
Author(s): Leonie Kollenstart, Anton J.L. de Groot, George M.C. Janssen, Xue Cheng, Kees Vreeken, Fabrizio Martino, Jacques Côté, Peter A. van Veelen, Haico van Attikum
Software Mentions: 3
Published: over 6 years ago

10.1186/s13326-016-0079-8

NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease
Cited by: 16
Author(s): Anandhi Iyappan, Shweta Bagewadi Kawalia, Tamara Raschka, Martin Hofmann‐Apitius, Philipp Senger
Software Mentions: 3
Published: about 10 years ago

10.1074/jbc.M114.634816

Early Growth Response Genes 2 and 3 Regulate the Expression of Bcl6 and Differentiation of T Follicular Helper Cells
Cited by: 26
Author(s): Ane Ogbe, Tizong Miao, Alistair L. J. Symonds, Becky Omodho, Randeep Singh, Punamdip Bhullar, Suling Li, Ping Wang
Software Mentions: 3
Published: about 11 years ago

10.1186/jbiol53

Dosage compensation is less effective in birds than in mammals
Cited by: 300
Author(s): Yuichiro Itoh, Esther Melamed, Xia Yang, Kathy Kampf, Susanna Wang, Nadir Yehya, Atila van Nas, Kirstin Replogle, Mark Band, David F. Clayton, Eric E. Schadt, Aldons J. Lusis, Arthur P. Arnold
Software Mentions: 3
Published: over 19 years ago

10.1074/jbc.M117.784629

The transcription factor Pax6 is required for pancreatic β cell identity, glucose-regulated ATP synthesis, and Ca2+ dynamics in adult mice
Cited by: 48
Author(s): Ryan K. Mitchell, Marie‐Sophie Nguyen‐Tu, Pauline Chabosseau, Rebecca Callingham, Timothy J. Pullen, Rebecca Cheung, Isabelle Leclerc, David J. Hodson, Guy A. Rutter
Software Mentions: 3
Published: over 9 years ago

10.7150/jca.38741

Construction and validation of an eight-gene signature with great prognostic value in bladder cancer
Cited by: 13
Author(s): Xin Yan, Xun Fu, Zixin Guo, Xiaoping Li, Tong-Zu Liu, Sheng Li
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-11-27

Genomics Portals: integrative web-platform for mining genomics data
Cited by: 13
Author(s): Kaustubh Shinde, Mukta Phatak, Johannes M. Freudenberg, Jing Chen, Qian Li, Joshi K Vineet, Zhen Hu, Krishnendu Ghosh, Jarosław Meller, Mario Medvedovic
Software Mentions: 3
Published: over 16 years ago

10.1093/bib/bby051

Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application
Cited by: 103
Author(s): Gaye Lightbody, Valeriia Haberland, Fiona Browne, Laura E. Taggart, Huiru Zheng, Eileen E. Parkes, Jaine K. Blayney
Software Mentions: 3
Published: about 7 years ago

10.1172/jci.insight.148652

CD40L modulates transcriptional signatures of neutrophils in the bone marrow associated with development and trafficking
Cited by: 1
Author(s): Tábata Takahashi França, Ashraf Al-Sbiei, Ghada Bashir, Yassir A. Mohamed, Ranieri Coelho Salgado, Lucila Akune Barreiros, Sarah Maria da Silva Napoleão, Cristiane Seganfredo Weber, Janáira Fernandes Severo Ferreira, Carolina Sánchez Aranda, Carolina Prando, Mayra B. de Barros Dorna, Igor Jurišica, Maria J. Fernández-Cabezudo, Hans D. Ochs, Antônio Condino‐Neto, Basel K. al-Ramadi, Otávio Cabral-Marques
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-019-5748-4

Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets
Cited by: 1
Author(s): Dirkjan Schokker, Ina Hulsegge, H. Woelders, Johanna M.J. Rebel
Software Mentions: 3
Published: about 7 years ago

10.1186/bcr3020

Genomic and phenotypic analysis of BRCA2mutated breast cancers reveals co-occurring changes linked to progression
Cited by: 22
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Katrín Ólafsdóttir, Hörður Bjarnason, Óskar T. Jóhannsson, Sigrídur K. Bödvarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 3
Published: almost 15 years ago

10.1186/bcr2926

Identification of germline alterations of the mad homology 2 domain of SMAD3 and SMAD4 from the Ontario site of the breast cancer family registry (CFR)
Cited by: 17
Author(s): Eric Tram, Irada Ibrahim‐Zada, Laurent Briollais, Julia A. Knight, Irene L. Andrulis, Hilmi Özçelik
Software Mentions: 3
Published: about 15 years ago

10.1186/s12859-019-2912-4

TACITuS: transcriptomic data collector, integrator, and selector on big data platform
Cited by: 2
Author(s): Salvatore Alaimo, Annalisa Di Maria, Dennis Shasha, Alfredo Ferro, Alfredo Pulvirenti
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.1005250

Genetic Regulation of Bone Metabolism in the Chicken: Similarities and Differences to Mammalian Systems
Cited by: 41
Author(s): Martin Johnsson, Kenneth B. Jonsson, Leif C. Andersson, Per Jensen, I. A. Wright
Software Mentions: 3
Published: about 11 years ago

10.1093/gbe/evw059

Genetic Evidence of Human Adaptation to a Cooked Diet
Cited by: 26
Author(s): Rachel N. Carmody, Michael Dannemann, Adrian W. Briggs, Birgit Nickel, Emily Groopman, Richard W. Wrangham, Janet Kelso
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0222432

The intermediate proteasome is constitutively expressed in pancreatic beta cells and upregulated by stimulatory, low concentrations of interleukin 1 β
Cited by: 13
Author(s): Muhammad Saad Khilji, Danielle Verstappen, Tina Dahlby, Michala Prause, Celina Pihl, Sophie Emilie Bresson, Tenna Holgersen Bryde, Phillip Alexander Keller Andersen, Kristian Klindt, Dušan Živković, Marie‐Pierre Bousquet, Björn Tyrberg, Thomas Mandrup‐Poulsen, Michał Marzec
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0239450

Integrative analysis of long non-coding RNA and mRNA in broilers with valgus-varus deformity
Cited by: 10
Author(s): Hehe Tang, Yaping Guo, Zhenzhen Zhang, Zhuanjian Li, Yanhua Zhang, Yuanfang Li, Xiangtao Kang, Ruili Han
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0006646

Genome-Wide mRNA Expression Analysis of Hepatic Adaptation to High-Fat Diets Reveals Switch from an Inflammatory to Steatotic Transcriptional Program
Cited by: 55
Author(s): Marijana Radonjić, Jorn R. de Haan, Marjan J. van Erk, Ko Willems van Dijk, Sjoerd A.A. van den Berg, Philip J. de Groot, Michael Müller, Ben van Ommen
Software Mentions: 3
Published: about 17 years ago

10.1371/journal.pone.0251565

The protein and volatile components of trail mucus in the Common Garden Snail, Cornu aspersum
Cited by: 7
Author(s): Kaylene R. Ballard, Anne Klein, R. Andrew Hayes, Tianfang Wang, Scott F. Cummins
Software Mentions: 3
Published: about 5 years ago

10.3389/fnmol.2017.00250

Expression and Regulatory Network Analysis of miR-140-3p, a New Potential Serum Biomarker for Autism Spectrum Disorder
Cited by: 25
Author(s): Matilde Cirnigliaro, Cristina Barbagallo, Mariangela Gulisano, Carla Noemi Domini, Rita Barone, Davide Barbagallo, Marco Ragusa, Cinzia Di Pietro, Renata Rizzo, Michele Purrello
Software Mentions: 3
Published: about 9 years ago

10.3389/fnins.2012.00156

A Neuronal Transcriptome Response Involving Stress Pathways is Buffered by Neuronal microRNAs
Cited by: 13
Author(s): Sergei A. Manakov, Andrew Morton, Anton J. Enright, Seth G. N. Grant
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0179065

Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesis
Cited by: 64
Author(s): Thomas Mohr, Verena Haudek-Prinz, Astrid Slany, Johannes Grillari, M. Micksche, Christopher Gerner
Software Mentions: 3
Published: about 9 years ago

10.3389/fonc.2019.00190

OSlms: A Web Server to Evaluate the Prognostic Value of Genes in Leiomyosarcoma
Cited by: 24
Author(s): Qiang Wang, Longxiang Xie, Yifang Dang, Xiaoxiao Sun, Tiantian Xie, JJ Guo, Yali Han, Zhongyi Yan, Wan Zhu, Yunlong Wang, Wei Li, Xiangqian Guo
Software Mentions: 3
Published: over 7 years ago

10.3389/fonc.2020.570281

A Three-Metabolic-Genes Risk Score Model Predicts Overall Survival in Clear Cell Renal Cell Carcinoma Patients
Cited by: 8
Author(s): Yiqiao Zhao, Zijia Tao, Xiaonan Chen
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0004001

TranscriptomeBrowser: A Powerful and Flexible Toolbox to Explore Productively the Transcriptional Landscape of the Gene Expression Omnibus Database
Cited by: 29
Author(s): Fabrice Lopez, Julien Textoris, Aurélie Bergon, Gilles Didier, Élisabeth Rémy, Samuel Granjeaud, Jean Imbert, Catherine Nguyen, Denis Puthier
Software Mentions: 3
Published: over 17 years ago

10.3389/fphar.2019.00198

A Meta-Analysis of the Performance of a Blood-Based Exposure Response Gene Signature Across Clinical Studies on the Tobacco Heating System 2.2 (THS 2.2)
Cited by: 2
Author(s): Florian Martin, Marja Talikka, Nikolai V. Ivanov, Christelle Haziza, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0226905

Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells
Cited by: 9
Author(s): Xiangqin Ji, Penglei Jiang, Juntao Luo, Mengjia Li, Yajing Bai, Junfang Zhang, Bingshe Han
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0253859

Position effects of 22q13 rearrangements on candidate genes in Phelan-McDermid syndrome
Cited by: 8
Author(s): Sujata Srikanth, Lavanya Jain, Cinthya J. Zepeda-Mendoza, Lauren Cascio, Kelly A. Jones, Rini Pauly, Barb DuPont, Curtis Rogers, Sara M. Sarasua, Katy Phelan, Cynthia C. Morton, Luigi Boccuto
Software Mentions: 3
Published: about 5 years ago

10.3389/fphys.2019.00433

Increasing Upstream Chromatin Long–Range Interactions May Favor Induction of Circular RNAs in LysoPC-Activated Human Aortic Endothelial Cells
Cited by: 16
Author(s): Angus Li, Yu Sun, Charles Drummer, Yifan Lu, Daohai Yu, Yan Zhou, Xinyuan Li, Simone J. Pearson, Candice Johnson, Catherine C. Yu, William Y. Yang, Kevin Mastascusa, Xiaohua Jiang, Jianxin Sun, Thomas J. Rogers, Wenhui Hu, Hong Wang, Xiaofeng Yang
Software Mentions: 3
Published: over 7 years ago

10.3389/fphys.2018.00618

Coactivation of TLR2 and TLR8 in Primary Human Monocytes Triggers a Distinct Inflammatory Signaling Response
Cited by: 14
Author(s): Korbinian Bösl, Miriam S. Giambelluca, Markus Haug, Marit Bugge, Terje Espevik, Richard K. Kandasamy, Bjarte Bergstrøm
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0031623

Genome Wide Adaptations of Plasmodium falciparum in Response to Lumefantrine Selective Drug Pressure
Cited by: 26
Author(s): Leah Mwai, Abdi Diriye, Victor Masseno, Steven Muriithi, Theresa Feltwell, Jennifer Musyoki, Jacob E. Lemieux, Avi Feller, Gunnar R. Mair, Kevin Marsh, Chris Newbold, Alexis Nzila, Céline Carret
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0242880

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows
Cited by: 7
Author(s): Lisa Ekman, Elisabeth Bagge, Ann-Kristin Nyman, Karin Persson Waller, Märit Pringle, Bo Segerman
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0243684

Effects of ploidy and salmonid alphavirus infection on the skin and gill microbiome of Atlantic salmon (Salmo salar)
Cited by: 19
Author(s): Roger Brown, Lindsey Moore, Amir Mani, Sonal Patel, Irene Salinas
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0222921

Computational identification of key genes that may regulate gene expression reprogramming in Alzheimer’s patients
Cited by: 20
Author(s): Judith A. Potashkin, Virginie Bottero, José A. Santiago, James P. Quinn
Software Mentions: 3
Published: almost 7 years ago

10.1534/g3.119.401031

Loss of N-Glycanase 1 Alters Transcriptional and Translational Regulation in K562 Cell Lines
Cited by: 13
Author(s): William F. Mueller, Petra Jakob, Han Sun, Sandra Clauder‐Münster, Sonja Ghidelli-Disse, Diana Paola Serralde Ordóñez, Markus Böesche, Marcus Bantscheff, Paul Collier, Bettina Haase, Vladimı́r Beneš, Malte Paulsen, Peter Sehr, Joe Lewis, Gerard Drewes, Lars M. Steinmetz
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0029917

Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe
Cited by: 29
Author(s): Huei-Mei Chen, Adam P. Rosebrock, Sohail Khan, Bruce Futcher, Janet Leatherwood
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0154556

The Ontology for Biomedical Investigations
Cited by: 228
Author(s): Anita Bandrowski, Ryan R. Brinkman, Mathias Brochhausen, Matthew Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, F. Gibson, Alejandra González-Beltrán, Melissa Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez‐Boussard, Mark A. Jensen, Yuling Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa Soldatova, Christian J. Stoeckert, Chris Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel, Jie Zheng
Software Mentions: 3
Published: over 10 years ago

10.1186/s13395-015-0059-1

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging
Cited by: 72
Author(s): Jing Su, Carl Johan Ekman, Nikolay Oskolkov, Leo Lahti, Kristoffer Ström, Alvis Brāzma, Leif Groop, Johan Rung, Ola Hansson
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0228964

Genetic characteristics of Jiaji Duck by whole genome re-sequencing
Cited by: 7
Author(s): Lihong Gu, Wang Feng, Zhemin Lin, Tieshan Xu, Dajie Lin, Manping Xing, Shuo Yang, Zhe Chao, Baoguo Ye, Licong Peng, Chunhui Hui, Lizhi Liu, Shuisheng Hou
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0032080

Knockdown of SF-1 and RNF31 Affects Components of Steroidogenesis, TGFβ, and Wnt/β-catenin Signaling in Adrenocortical Carcinoma Cells
Cited by: 20
Author(s): Anna Ehrlund, Philip Jonsson, Lise Lotte Vedin, Cecilia Williams, Jan Åke Gustafsson, Eckardt Treuter
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0253340

Placental DNA methylation changes and the early prediction of autism in full-term newborns
Cited by: 11
Author(s): Ray O. Bahado‐Singh, Sangeetha Vishweswaraiah, Buket Aydas, Uppala Radhakrishna
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0240178

Occurrence of Brucella ceti in striped dolphins from Italian Seas
Cited by: 14
Author(s): Giuliano Garofolo, A. Petrella, Giuseppe Lucifora, Gabriella Di Francesco, Giovanni Di Guardo, Alessandra Pautasso, Barbara Iulini, Katia Varello, Federica Giorda, Maria Goria, Alessandro Dondo, Simona Zoppi, Cristina Esmeralda Di Francesco, Stefania Giglio, Furio Ferringo, Luigina Serrecchia, Mattia Anna Rita Ferrantino, Katiuscia Zilli, Anna Janowicz, Manuela Tittarelli, Walter Mignone, Cristina Casalone, Carla Grattarola
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0239938

Severity of bovine tuberculosis is associated with innate immune-biased transcriptional signatures of whole blood in early weeks after experimental Mycobacterium bovis infection
Cited by: 6
Author(s): Jayne E Wiarda, Paola M. Boggiatto, Darrell O. Bayles, W. Ray Waters, Tyler C. Thacker, Mitchell V. Palmer
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0224900

UM171 induces a homeostatic inflammatory-detoxification response supporting human HSC self-renewal
Cited by: 28
Author(s): Jalila Chagraoui, Bernhard Lehnertz, Simon Girard, Jean François Spinella, Iman Fares, Elisa Tomellini, Nadine Mayotte, Sophie Corneau, Tara MacRae, Laura Simon, Guy Sauvageau
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0128845

Comparison of High-Level Microarray Analysis Methods in the Context of Result Consistency
Cited by: 37
Author(s): Kornel Chromiński, Magdalena Tkacz
Software Mentions: 3
Published: about 11 years ago

10.1128/mBio.01871-18

Structural and Nonstructural Genes Contribute to the Genetic Diversity of RNA Viruses
Cited by: 27
Author(s): Natalie D. Collins, Andrew S. Beck, Steven G. Widen, Thomas G. Wood, Stephen Higgs, Alan D.T. Barrett
Software Mentions: 3
Published: almost 8 years ago

10.1128/mBio.02684-19

Contextual Flexibility in Pseudomonas aeruginosa Central Carbon Metabolism during Growth in Single Carbon Sources
Cited by: 49
Author(s): Stephen K. Dolan, Michael Kohlstedt, Stephen Trigg, Pedro P. Vallejo Ramirez, Clemens F. Kaminski, Christoph Wittmann, Martin Welch
Software Mentions: 3
Published: over 6 years ago

10.1128/mSphere.00305-16

Coordinate Regulation of Antimycin and Candicidin Biosynthesis
Cited by: 34
Author(s): Thomas C McLean, Paul A. Hoskisson, Ryan F. Seipke
Software Mentions: 3
Published: over 9 years ago

10.1128/mSystems.00025-15

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions
Cited by: 111
Author(s): Jie Tan, John H. Hammond, Deborah A. Hogan, Casey S. Greene
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0238809

MicroRNA expression profiles in molecular subtypes of clear-cell renal cell carcinoma are associated with clinical outcome and repression of specific mRNA targets
Cited by: 3
Author(s): Annelies Verbiest, Vincent van Hoef, Cristina Rodríguez‐Antona, Jesús García-Donás, Osvaldo Graña‐Castro, Maarten Albersen, Marcella Baldewijns, Annouschka Laenen, Eduard Roussel, Patrick Schöffski, Agnieszka Woźniak, Stefano Caruso, Gabrielle Couchy, Jessica Zucman–Rossi, Benoît Beuselinck
Software Mentions: 3
Published: almost 6 years ago

10.1155/2014/345106

Comparison of Merging and Meta-Analysis as Alternative Approaches for Integrative Gene Expression Analysis
Cited by: 45
Author(s): Jonatan Taminau, Cosmin Lazar, Stijn Meganck, Ann Nowé
Software Mentions: 3
Published: over 12 years ago

10.3390/jof4030081

Identification of Antifungal Targets Based on Computer Modeling
Cited by: 10
Author(s): Elena Bencúrová, Shishir Gupta, Edita Sarukhanyan, Thomas Dandekar
Software Mentions: 3
Published: about 8 years ago

10.1155/2017/2568706

Genomewide Expression and Functional Interactions of Genes under Drought Stress in Maize
Cited by: 34
Author(s): Nepolean Thirunavukkarasu, R.C. Sharma, Nidhi Singh, Kaliyugam Shiriga, Sweta Mohan, Swati Mittal, Mittal Shikha, Mallana Gowdra Mallikarjuna, Atmakuri Ramakrishna Rao, Prasanta K. Dash, Firoz Hossain, H. S. Gupta
Software Mentions: 3
Published: over 9 years ago

10.1016/j.jhepr.2021.100237

Aramchol downregulates stearoyl CoA-desaturase 1 in hepatic stellate cells to attenuate cellular fibrogenesis
Cited by: 26
Author(s): Dipankar Bhattacharya, Brittany Basta, José M. Mato, Amanda Craig, David Fernández–Ramos, Fernando Lopitz‐Otsoa, Darya Tsvirkun, Liat Hayardeny, Vasuretha Chandar, Robert E. Schwartz, Augusto Villanueva, Scott L. Friedman
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0142443

Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma
Cited by: 9
Author(s): Abhinav Kaushik, Yashuma Bhatia, Shakir Ali, Dinesh Gupta
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0229490

NAA and 6-BA promote accumulation of oleanolic acid by JA regulation in Achyranthes bidentata Bl
Cited by: 1
Author(s): Yanqing Liu, Li Tang, Can Wang, Jinting Li
Software Mentions: 3
Published: over 6 years ago

10.1155/2015/140819

MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation
Cited by: 13
Author(s): Luman Wang, Qiaochu Mo, Jianxin Wang
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0231718

Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish
Cited by: 20
Author(s): Sayaka Takahashi, Masato Sakata, Toshifumi Minamoto, Reiji Masuda
Software Mentions: 3
Published: over 6 years ago

10.1038/onc.2015.399

The NF-κB subunit c-Rel regulates Bach2 tumour suppressor expression in B-cell lymphoma
Cited by: 32
Author(s): Jill E. Hunter, Jacqueline Butterworth, Bo Zhao, Hélène Sellier, Kirsteen J. Campbell, Huw D. Thomas, Chris M. Bacon, Simon Cockell, Benjamin E. Gewurz, Neil D. Perkins
Software Mentions: 3
Published: almost 11 years ago

10.1515/jib-2018-0080

Gene Expression Studies to Identify Significant Genes in AR, MTOR, MAPK Pathways and their Overlapping Regulatory Role in Prostate Cancer
Cited by: 0
Author(s): Nimisha Asati, Abhinav Mishra, Ayush Shukla, Tiratha Raj Singh
Software Mentions: 3
Published: about 7 years ago

10.1111/jipb.13026

Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores
Cited by: 14
Author(s): M. Estrella Santamaría, Alejandro Dorado García, Ana Arnáiz, Irene Rosa‐Diaz, Gara Romero‐Hernandez, Isabel Dı́az, Manuel Martínez
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0251233

Mapping Rora expression in resting and activated CD4+ T cells
Cited by: 23
Author(s): Liora Haim-Vilmovsky, Johan Henriksson, Jennifer Walker, Zhichao Miao, Eviatar Natan, Gozde Kar, Simon Clare, Jillian L. Barlow, Evelina Charidemou, Lira Mamanova, Xi Chen, Valentina Proserpio, Jhuma Pramanik, Steven Woodhouse, Anna V. Protasio, Mirjana Efremova, Julian L. Griffin, Matt Berriman, Gordon Dougan, Jasmin Fisher, John C. Marioni, Andrew N. J. McKenzie, Sarah A. Teichmann
Software Mentions: 3
Published: about 5 years ago

10.1007/s00109-012-0925-9

Early steps of microglial activation are directly affected by neuroprotectant FK506 in both in vitro inflammation and in rat model of stroke
Cited by: 33
Author(s): Małgorzata Zawadzka, Michal Dabrowski, Agata Gozdz, Barbara Szadujkis, Marcin Sliwa, Maciej Lipko, Bożena Kamińska
Software Mentions: 3
Published: about 14 years ago

10.7554/eLife.38309

High N-glycan multiplicity is critical for neuronal adhesion and sensitizes the developing cerebellum to N-glycosylation defect
Cited by: 41
Author(s): Daniel Medina-Cano, Ekin Ucuncu, Lam Son Nguyen, Michaël Nicouleau, Joanna Lipecka, Jean-Charles Bizot, Christian Thiel, François Foulquier, Nathalie Lefort, Catherine Faivre‐Sarrailh, Laurence Colleaux, Ida Chiara Guerrera, Vincent Cantagrel
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0241754

Emergence of a novel chikungunya virus strain bearing the E1:V80A substitution, out of the Mombasa, Kenya 2017-2018 outbreak
Cited by: 9
Author(s): Fredrick Eyase, Solomon Langat, Irina Maljkovic Berry, Francis Mulwa, Albert Nyunja, James Mu, Samuel Owaka, Samson Limbaso, Victor Ofula, Hellen Koka, Edith Koskei, Joel Lutomiah, Richard G. Jarman, Rosemary Sang
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.31362

A tissue-specific, Gata6-driven transcriptional program instructs remodeling of the mature arterial tree
Cited by: 11
Author(s): Marta Losa, Víctor Latorre, Munazah Andrabi, Franck Ladam, Charles G. Sagerström, Ana Nóvoa, Peyman Zarrineh, Laure Bridoux, Neil A. Hanley, Bernard Malissen, Nicoletta Bobola
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.53944

Loss of centromere function drives karyotype evolution in closely related Malassezia species
Cited by: 37
Author(s): Sundar Ram Sankaranarayanan, Giuseppe Ianiri, Marco A. Coelho, Hashim Reza, Bhagya C. Thimmappa, Promit Ganguly, Rakesh Netha Vadnala, Sheng Sun, Rahul Siddharthan, Christian Tellgren-Roth, Thomas L. Dawson, Joseph Heitman, Kaustuv Sanyal
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0251732

Phlpp1 is induced by estrogen in osteoclasts and its loss in Ctsk-expressing cells does not protect against ovariectomy-induced bone loss
Cited by: 2
Author(s): Marcelline K. Hanson, Ismael Y. Karkache, David H. H. Molstad, Andrew Norton, Kim C. Mansky, Elizabeth W. Bradley
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms18091900

Sample Size Estimation for Detection of Splicing Events in Transcriptome Sequencing Data
Cited by: 3
Author(s): Wolfgang Kaisers, Holger Schwender, Heiner Schaal
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0157426

An Integrative Transcriptomic Analysis for Identifying Novel Target Genes Corresponding to Severity Spectrum in Spinal Muscular Atrophy
Cited by: 6
Author(s): Chunrong Yang, Chien‐Lin Chen, Wei-Chun Chou, Ho-Chen Lin, Yuh Jyh Jong, Li-Kai Tsai, Chun‐Yu Chuang
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0246983

Who infects whom?—Reconstructing infection chains of Mycobacterium avium ssp. paratuberculosis in an endemically infected dairy herd by use of genomic data
Cited by: 9
Author(s): Annette Nigsch, Suelee Robbe‐Austerman, Tod Stuber, Paulina D. Pavinski Bitar, Yrjö T. Gröhn, Y.H. Schukken
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0130262

How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq
Cited by: 31
Author(s): Luis Fernando García-Ortega, Octavio Martínez
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0227154

Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers
Cited by: 8
Author(s): A. K. Lindholm‐Perry, H. C. Freetly, W. T. Oliver, Lea A. Rempel, Brittney N Keel
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0240062

Phylogenomics from transcriptomic “bycatch” clarify the origins and diversity of avian trypanosomes in North America
Cited by: 7
Author(s): Spencer C. Galen, Janus Borner, Susan L. Perkins, Jason D. Weckstein
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0037287

Chemical PARP Inhibition Enhances Growth of Arabidopsis and Reduces Anthocyanin Accumulation and the Activation of Stress Protective Mechanisms
Cited by: 45
Author(s): Philipp Schulz, Jenny Neukermans, Katrien Van Der Kelen, Per Mühlenbock, Frank Van Breusegem, Graham Noctor, Markus Teige, Michael Metzlaff, Matthew A. Hannah
Software Mentions: 3
Published: about 14 years ago

10.1038/s41419-019-1397-4

EMT is associated with an epigenetic signature of ECM remodeling genes
Cited by: 83
Author(s): Paul Peixoto, Amandine Etcheverry, Marc Aubry, Anaïs Missey, Camille Lachat, Jérôme Perrard, Elodie Hendrick, Régis Delage-Mourroux, Jean Mosser, Christophe Borg, Jean-Paul Feugeas, Michaël Herfs, Michaël Boyer-Guittaut, Éric Hervouet
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0096063

Evaluation of Gene Expression Classification Studies: Factors Associated with Classification Performance
Cited by: 13
Author(s): Putri W. Novianti, Kit C. B. Roes, Marinus J.C. Eijkemans
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0240269

Using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseases
Cited by: 6
Author(s): Rosana Veroneze, Sâmia Cruz Tfaile Corbi, Bárbara Roque da Silva, Cristiane S. Rocha, Cláudia Vianna Maurer-Morelli, Silvana Regina Perez Orrico, Joni Augusto Cirelli, Fernando J. Von Zuben, Raquel Mantuaneli Scarel‐Caminaga
Software Mentions: 3
Published: almost 6 years ago

10.3389/fcell.2021.642697

Tlx3 Exerts Direct Control in Specifying Excitatory Over Inhibitory Neurons in the Dorsal Spinal Cord
Cited by: 3
Author(s): Filipe Almeida Monteiro, Rafael Mendes Miranda, Marta C Samina, Ana Cristina Dias, Alexandre A.S.F. Raposo, Patrícia Oliveira, Carlos Reguenga, Diogo S. Castro, Deolinda Lima
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2021.703489

Reconstruction of the Cytokine Signaling in Lysosomal Storage Diseases by Literature Mining and Network Analysis
Cited by: 3
Author(s): Silvia Parolo, Danilo Tomasoni, Pranami Bora, Alan Ramponi, Chanchala Kaddi, Karim Azer, Enrico Domenici, Susana Neves-Zaph, Rosario Lombardo
Software Mentions: 3
Published: almost 5 years ago

10.3389/fncel.2020.599152

Intrinsically Self-renewing Neuroprogenitors From the A/J Mouse Spiral Ganglion as Virtually Unlimited Source of Mature Auditory Neurons
Cited by: 7
Author(s): Francis Rousset, Vivianne Beatrix Christina Kokje, Rebecca Sipione, Dominik Schmidbauer, German Nacher-Soler, Sten Ilmjärv, Marta Coelho, Stefan Fink, François Voruz, Antoun El Chemaly, Antoine Marteyn, Hubert Löwenheim, Karl‐Heinz Krause, Marcus Müller, Rudolf Glückert, Pascal Senn
Software Mentions: 3
Published: over 5 years ago

10.3389/fendo.2021.628907

Identification of Key Pathways and Genes in Obesity Using Bioinformatics Analysis and Molecular Docking Studies
Cited by: 7
Author(s): Harish Joshi, Basavaraj Vastrad, Nidhi Joshi, Chanabasayya Vastrad, Anandkumar Tengli, Iranna Kotturshetti
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2018.00083

Adjusting for Batch Effects in DNA Methylation Microarray Data, a Lesson Learned
Cited by: 57
Author(s): Emily Price, Wendy P. Robinson
Software Mentions: 3
Published: over 8 years ago

10.3389/fimmu.2019.02136

Identification and Characterization of Post-activated B Cells in Systemic Autoimmune Diseases
Cited by: 37
Author(s): Sarah Y. Weißenberg, Franziska Szelinski, Eva Schrezenmeier, Ana‐Luisa Stefanski, Annika Wiedemann, Héctor Rincón‐Arévalo, Anna Welle, Annemarie Jungmann, Karl Nordström, Jörn Walter, Juliana Imgenberg‐Kreuz, Gunnel Nordmark, Lars Rönnblom, Prathyusha Bachali, Michelle D. Catalina, Amrie C. Grammer, Peter E. Lipsky, Andreia C. Lino, Thomas Dörner
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0039205

Effect of Chemical Mutagens and Carcinogens on Gene Expression Profiles in Human TK6 Cells
Cited by: 15
Author(s): Lode Godderis, Reuben Thomas, Alan Hubbard, Ali Mustafa Tabish, Peter Hoet, Luoping Zhang, Martyn T. Smith, Hendrik Veulemans, Cliona M. McHale
Software Mentions: 3
Published: about 14 years ago

10.7554/eLife.12717

Zeb1 controls neuron differentiation and germinal zone exit by a mesenchymal-epithelial-like transition
Cited by: 58
Author(s): Shalini Singh, Danielle Howell, Niraj Trivedi, Ketty Kessler, Taren Ong, Pedro Rosmaninho, Alexandre A.S.F. Raposo, Giles Robinson, Martine F. Roussel, Diogo S. Castro, David J. Solecki
Software Mentions: 2
Published: over 10 years ago

10.1128/mBio.00465-20

Chlorpromazine and Amitriptyline Are Substrates and Inhibitors of the AcrB Multidrug Efflux Pump
Cited by: 48
Author(s): Elizabeth Grimsey, Chiara Fais, Robert L. Marshall, Vito Ricci, Maria Laura Ciusa, Jack Stone, Alasdair Ivens, Giuliano Malloci, Paolo Ruggerone, Attilio Vittorio Vargiu, Laura J. V. Piddock
Software Mentions: 2
Published: about 6 years ago

10.1128/mBio.00966-18

cAMP Receptor Protein Controls Vibrio cholerae Gene Expression in Response to Host Colonization
Cited by: 41
Author(s): Jainaba Manneh-Roussel, James R. J. Haycocks, Andrés Magán, Nicolás Pérez-Soto, Kerstin Voelz, Andrew Camilli, Anne Marie Krachler, David C. Grainger
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.33506

Epidermal LysM receptor ensures robust symbiotic signalling in Lotus japonicus
Cited by: 48
Author(s): Eiichi Murakami, Jeryl Cheng, Kira Gysel, Zoltán Bozsóki, Yasuyuki Kawaharada, Christian T. Hjuler, Kasper K. Sørensen, Ke Tao, Simon Kelly, Francesco Venice, Andrea Genre, Mikkel B. Thygesen, Noor de Jong, Maria Vinther, Dorthe Bødker Jensen, Knud J. Jensen, Mickaël Blaise, Lene Heegaard Madsen, Kasper R. Andersen, Jens Stougaard, Simona Radutoiu
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0232972

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet
Cited by: 17
Author(s): Lei Chen, Liangyu Zhang, Wendong Wang, Wei Qiu, Lei Liu, Anhong Ning, Jing Cao, Min Huang, Ming-Chao Zhong
Software Mentions: 2
Published: about 6 years ago

10.3389/fimmu.2017.00557

Predicting RTS,S Vaccine-Mediated Protection from Transcriptomes in a Malaria-Challenge Clinical Trial
Cited by: 49
Author(s): Robert A. van den Berg, Margherita Coccia, W. Ripley Ballou, Kent E. Kester, Christian F. Ockenhouse, Johan Vekemans, Erik Jongert, Arnaud M. Didierlaurent, Robbert G. van der Most
Software Mentions: 2
Published: about 9 years ago

10.3389/fimmu.2020.587756

A Conserved TCRβ Signature Dominates a Highly Polyclonal T-Cell Expansion During the Acute Phase of a Murine Malaria Infection
Cited by: 9
Author(s): Natasha L. Smith, Wiebke Nahrendorf, Catherine Sutherland, Jason P. Mooney, Joanne Thompson, Philip J. Spence, Gillian Cowan
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.65722

Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast
Cited by: 18
Author(s): Rong Yu, Egor Vorontsov, Carina Sihlbom, Jens Nielsen
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0006447

Mining Biological Pathways Using WikiPathways Web Services
Cited by: 107
Author(s): Thomas Kelder, Alexander R. Pico, Kristina Hanspers, Martijn P. van Iersel, Chris T. Evelo, Bruce R. Conklin
Software Mentions: 2
Published: about 17 years ago

10.7554/eLife.18715

A computational interactome and functional annotation for the human proteome
Cited by: 59
Author(s): José Ignacio Garzón, Lei Deng, Diana Murray, Sagi Shapira, Donald Petrey, Barry Honig
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0042490

Gene Profile of Chemokines on Hepatic Stellate Cells of Schistosome-Infected Mice and Antifibrotic Roles of CXCL9/10 on Liver Non-Parenchymal Cells
Cited by: 26
Author(s): Yuejin Liang, Jie Luo, Qiao Lu, Ying Zhou, Hai Wei Wu, Dan Zheng, Yong ya Ren, Ke Sun, Yong Wang, Zhao Song Zhang
Software Mentions: 2
Published: about 14 years ago

10.7554/eLife.33761

Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair
Cited by: 116
Author(s): Nataša Savić, Femke Ringnalda, Helen Lindsay, Christian Berk, Katja Bargsten, Yizhou Li, Dario Neri, Mark D. Robinson, Constance Ciaudo, Jonathan Hall, Martin Jínek, Gerald Schwank
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0036351

Transcriptome Sequencing Revealed Significant Alteration of Cortical Promoter Usage and Splicing in Schizophrenia
Cited by: 96
Author(s): Jing Qin Wu, Xi Wang, Natalie J. Beveridge, Paul A. Tooney, Rodney J. Scott, Vaughan J. Carr, Murray J. Cairns
Software Mentions: 2
Published: over 14 years ago

10.3389/fgene.2021.625797

Identification of m6A-Associated RNA Binding Proteins Using an Integrative Computational Framework
Cited by: 4
Author(s): Yiqian Zhang, Michiaki Hamada
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0230822

Characterization of the fungal community in the canopy air of the invasive plant Ageratina adenophora and its potential to cause plant diseases
Cited by: 7
Author(s): Chinho Lin, Kai Fang, Xing-Fan Dong, Ai-Ling Yang, Yuxuan Li, Hanbo Zhang
Software Mentions: 2
Published: over 6 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

Bonuses:

Penalties:

Papers Mentioning ArrayExpress 1,962