bioconductor: annotate | Projects

10.1371/journal.pcbi.1000227

Analyzing ChIP-chip Data Using Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: over 15 years ago

Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma
Cited by: 12
Author(s): Vinay Randhawa, Vishal Acharya
Software Mentions: 17
Published: almost 9 years ago

10.1371/journal.pgen.1008927

On the cross-population generalizability of gene expression prediction models
Cited by: 34
Author(s): Kevin L. Keys, Angel C. Y. Mak, Marquitta J. White, Walter L. Eckalbar, Andrew Dahl, Joel Mefford, Anna V. Mikhaylova, María G. Contreras, Jennifer R. Elhawary, Celeste Eng, Donglei Hu, Scott Huntsman, Sam S. Oh, Sandra Salazar, Michael A. LeNoir, Jimmie C. Ye, Timothy A. Thornton, Noah Zaitlen, Esteban G. Burchard, Christopher R. Gignoux
Software Mentions: 16
Published: almost 4 years ago

10.12688/f1000research.10742.2

haploR: an R package for querying web-based annotation tools
Cited by: 20
Author(s): Ilya Y. Zhbannikov, Konstantin G. Arbeev, Svetlana V. Ukraintseva, Anatoliy I. Yashin
Software Mentions: 13
Published: about 7 years ago

10.3390/ijms22062790

Differential Methylation in the GSTT1 Regulatory Region in Sudden Unexplained Death and Sudden Unexpected Death in Epilepsy
Cited by: 4
Author(s): Steffan Noe Christiansen, Stine Jacobsen, Jeppe Dyrberg Andersen, Marie-Louise Kampmann, Linea C Trudsø, Karsten Olsen, Jacob Tfelt-Hansen, Jytte Banner, Niels Morling
Software Mentions: 13
Published: about 3 years ago

10.1002/cam4.2786

FOLFOX treatment response prediction in metastatic or recurrent colorectal cancer patients via machine learning algorithms
Cited by: 24
Author(s): Wei Lu, Dongliang Fu, Xianglong Kong, Zhiheng Huang, Maxwell Hwang, Yaowu Zhu, Liubo Chen, Kai Jiang, Xinlin Li, Yihua Wu, Jun Li, Ying Yuan, Kefeng Ding
Software Mentions: 12
Published: over 4 years ago

10.3389/fgene.2021.640242

A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects
Cited by: 7
Author(s): Dustin Miller, Stephen R. Piccolo
Software Mentions: 11
Published: about 3 years ago

10.1371/journal.pone.0041169

Global Transcriptome Analysis in Influenza-Infected Mouse Lungs Reveals the Kinetics of Innate and Adaptive Host Immune Responses
Cited by: 93
Author(s): Claudia Pommerenke, Esther Wilk, Barkha Srivastava, Annika Schulze, Natalia Novoselova, Robert Geffers, Klaus Schughart
Software Mentions: 11
Published: almost 12 years ago

10.3390/cancers11081104

Differential Expression of DNA Repair Genes in Prognostically-Favorable versus Unfavorable Uveal Melanoma
Cited by: 10
Author(s): Mehmet Doğrusöz, Andrea Ruschel Träsel, Jinfeng Cao, Selҫuk Ҫolak, Sake I. van Pelt, Wilma G. M. Kroes, Amina F.A.S. Teunisse, Samar Alsafadi, Sjoerd G. van Duinen, Gregorius P M Luyten, Pieter A. van der Velden, Adriana Amaro, Ulrich Pfeffer, Aart G. Jochemsen, Martine J. Jager
Software Mentions: 11
Published: almost 5 years ago

10.1186/1471-2164-9-419

Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: Comparison of rat and mouse
Cited by: 74
Author(s): Paul C. Boutros, Rui Yan, Ivy D. Moffat, Raimo Pohjanvirta, Allan B. Okey
Software Mentions: 11
Published: over 16 years ago

10.1155/2008/147563

Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data: Tools for the First Steps
Cited by: 6
Author(s): Grier P. Page, Issa Coulibaly
Software Mentions: 10
Published: almost 16 years ago

10.1371/journal.pone.0018337

mRNA Levels in Control Rat Liver Display Strain-Specific, Hereditary, and AHR-Dependent Components
Cited by: 7
Author(s): Paul C. Boutros, Ivy D. Moffat, Allan B. Okey, Raimo Pohjanvirta
Software Mentions: 9
Published: almost 13 years ago

10.18632/oncotarget.26668

mTOR inhibition affects Yap1-β-catenin-induced hepatoblastoma growth and development
Cited by: 11
Author(s): Laura Molina, Hong Yang, Adeola O. Adebayo Michael, Michael Oertel, Aaron Bell, Sucha Singh, Xin Chen, Junyan Tao, Satdarshan P. Monga
Software Mentions: 8
Published: about 5 years ago

10.1186/s12859-019-3145-2

MoMI-G: modular multi-scale integrated genome graph browser
Cited by: 20
Author(s): Toshiyuki Yokoyama, Yoshitaka Sakamoto, Masahide Seki, Yutaka Suzuki, Masahiro Kasahara
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0164292

Upregulation of HLA Expression in Primary Uveal Melanoma by Infiltrating Leukocytes
Cited by: 55
Author(s): T. Huibertus van Essen, Sake I. van Pelt, Inge H. G. Bronkhorst, Mieke Versluis, Fariba Némati, Cécile Laurent, Gregorius P M Luyten, Thorbald van Hall, Peter J. van den Elsen, Pieter A. van der Velden, Didier Decaudin, Martine J. Jager
Software Mentions: 8
Published: over 7 years ago

10.3390/microorganisms8101505

Reanalysis of Gene Expression Profiles of CD4+ T Cells Treated with HIV-1 Latency Reversal Agents
Cited by: 3
Author(s): Antônio Victor Campos Coelho, Romero Marinho de Moura, Sérgio Crovella
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2105-14-164

Learning smoothing models of copy number profiles using breakpoint annotations
Cited by: 44
Author(s): Toby Dylan Hocking, Gudrun Schleiermacher, Isabelle Janoueix‐Lerosey, Valentina Boeva, Julie Cappo, Olivier Delattre, Francis Bach, Jean-Philippe Vert
Software Mentions: 6
Published: almost 11 years ago

10.3390/v13020244

HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles
Cited by: 5
Author(s): Antônio Victor Campos Coelho, Rossella Gratton, João Paulo Britto de Melo, José Leandro Andrade‐Santos, Rafael Lima Guimarães, Sérgio Crovella, Paola Maura Tricarico, Lucas André Cavalcanti Brandão
Software Mentions: 6
Published: over 3 years ago

10.1002/bit.25990

Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time
Cited by: 109
Author(s): Julia Feichtinger, Inmaculada Hernández, Christoph Fischer, Michael Hanscho, Norbert Auer, Matthias Hackl, Vaibhav Jadhav, Martina Baumann, Peter M. Krempl, Christian Schmidl, Matthias Farlik, Michael Schuster, Angelika Merkel, Andreas Sommer, Simon Heath, Daniel Rico, Christoph Bock, Gerhard Thallinger, Nicole Borth
Software Mentions: 5
Published: about 8 years ago

10.3390/ijms21218016

Enhancer of Zeste Homolog 2 (EZH2) Mediates Glucolipotoxicity-Induced Apoptosis in β-Cells
Cited by: 3
Author(s): Tina Dahlby, Christian Simon, Marie Balslev Backe, Mattias Salling Dahllöf, Edward B. Holson, Bridget K. Wagner, Marianne Böni-Schnetzler, Michał Marzec, Morten Lundh, Thomas Mandrup‐Poulsen
Software Mentions: 5
Published: over 3 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: over 11 years ago

10.1371/journal.pone.0112909

Gene Expression Analyses of the Spatio-Temporal Relationships of Human Medulloblastoma Subgroups during Early Human Neurogenesis
Cited by: 24
Author(s): Cornelia M. Hooper, Susan Melanie Hawes, Ursula R. Kees, Nicholas G. Gottardo, Peter B. Dallas
Software Mentions: 5
Published: over 9 years ago

10.1515/med-2020-0114

CCTs as new biomarkers for the prognosis of head and neck squamous cancer
Cited by: 11
Author(s): Yanbo Dong, Siyu Lu, Zhenxiao Wang, Liangfa Liu
Software Mentions: 5
Published: over 4 years ago

10.3390/cancers13010027

Inflammatory Proteins HMGA2 and PRTN3 as Drivers of Vulvar Squamous Cell Carcinoma Progression
Cited by: 12
Author(s): Agnieszka Fatalska, Natalia Rusetska, Elwira Bakuła‐Zalewska, Artur Kowalik, Sebastian Zięba, Agnieszka Wroblewska, Kamil Zalewski, Krzysztof Goryca, Dominik Domański, Magdalena Kowalewska
Software Mentions: 5
Published: over 3 years ago

10.1186/s12882-018-0944-z

Gene alterations in monocytes are pathogenic factors for immunoglobulin a nephropathy by bioinformatics analysis of microarray data
Cited by: 3
Author(s): Yingbo Guo, Weijie Gao, Danyang Wang, Weijing Liu, Zhongjie Liu
Software Mentions: 5
Published: almost 6 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: almost 12 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: almost 4 years ago

10.3389/fgene.2013.00237

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots
Cited by: 238
Author(s): Sujai Kumar, Martin O. Jones, Georgios Koutsovoulos, Michael J. Clarke, Mark Blaxter
Software Mentions: 4
Published: over 11 years ago

10.3389/fpls.2017.01860

Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine (Vitis vinifera cv. Shiraz)
Cited by: 46
Author(s): Huahan Xie, Moumouni Konaté, Na Sai, Kiflu Tesfamicael, Timothy R. Cavagnaro, Matthew Gilliham, James Breen, Andrew Metcalfe, J. Stephen, Roberta De Bei, Cassandra Collins, Carlos M. Rodríguez López
Software Mentions: 4
Published: over 6 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: over 14 years ago

10.1186/1756-0500-4-160

The dynamics of E1A in regulating networks and canonical pathways in quiescent cells
Cited by: 6
Author(s): Jean-Eudes Dazard, Keman Zhang, Jingfeng Sha, Yasin Omar, Linda Cai, Chien Ngoc Nguyen, Mrinal K. Ghosh, Jennifer Bongorno, Marian L. Harter
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0024676

Gene Expression Modifications by Temperature-Toxicants Interactions in Caenorhabditis elegans
Cited by: 17
Author(s): Ana Viñuela, L. Basten Snoek, J.A.G. Riksen, J.E. Kammenga
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0028761

A “Crossomics” Study Analysing Variability of Different Components in Peripheral Blood of Healthy Caucasoid Individuals
Cited by: 20
Author(s): Kristina Gruden, Matjaž Hren, Ana Herman, Andrej Blejec, Tanja Albrecht, Joachim Selbig, Chris Bauer, Jochannes Schuchardt, Michal Or-Guil, Klemen Zupančič, Urban Švajger, Borut Štabuc, Alojz Ihan, Andreja Nataša Kopitar, Maja Ravnikar, Miomir Knežević, Primož Rožman, Matjaž Jeras
Software Mentions: 3
Published: over 12 years ago

10.3390/tropicalmed5020105

The Emergence of Chikungunya ECSA Lineage in a Mayaro Endemic Region on the Southern Border of the Amazon Forest
Cited by: 9
Author(s): Carla Júlia da Silva Pessoa Vieira, David José Ferreira da Silva, Laís Ceschini Machado, Lindomar Pena, Roberta Vieira de Morais Bronzoni, Gabriel Luz Wallau
Software Mentions: 2
Published: almost 4 years ago

10.1534/g3.117.041749

Adaptive Roles ofSSY1andSIR3During Cycles of Growth and Starvation inSaccharomyces cerevisiaePopulations Enriched for Quiescent or Nonquiescent Cells
Cited by: 12
Author(s): Dominika Wloch‐Salamon, K. Tomala, Dimitra Aggeli, Barbara Dunn
Software Mentions: 2
Published: almost 7 years ago

10.3390/molecules18044267

Metabolomic Analysis of Methyl Jasmonate-Induced Triterpenoid Production in the Medicinal Herb Centella asiatica (L.) Urban
Cited by: 49
Author(s): Jacinda T. James, Fidele Tugizimana, Paul A. Steenkamp, Ian A. Dubery
Software Mentions: 2
Published: about 11 years ago

Ecosyste.ms: Papers

Projects: bioconductor: annotate

Papers Mentioning annotate 36