bioconductor: preprocessCore | Projects

10.1186/1471-2156-15-81

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations
Cited by: 16
Author(s): Robert B. Scharpf, Lynn Mireles, Qiong Yang, Anna Köttgen, Ingo Ruczinski, Katalin Suszták, Eitan Halper-Stromberg, Adrienne Tin, Stephen Cristiano, Aravinda Chakravarti, Eric Boerwinkle, Caroline S. Fox, Josef Coresh, W. H. Linda Kao
Software Mentions: 56
Published: almost 11 years ago

10.1371/journal.pcbi.1000227

Analyzing ChIP-chip Data Using Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: almost 16 years ago

10.1186/s12864-016-3387-6

HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking
Cited by: 64
Author(s): Charalampos Lazaris, Stephen M. Kelly, Panagiotis Ntziachristos, Iannis Aifantis, Aristotelis Tsirigos
Software Mentions: 28
Published: almost 8 years ago

10.1186/s12859-017-1905-4

ADAGE signature analysis: differential expression analysis with data-defined gene sets
Cited by: 15
Author(s): Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
Software Mentions: 25
Published: almost 7 years ago

10.3389/fmolb.2020.570702

Prognostic Prediction Using a Stemness Index-Related Signature in a Cohort of Gastric Cancer
Cited by: 27
Author(s): Xiaowei Chen, Dawei Zhang, Fei Jiang, Yan Shen, Xin Li, Xin Hu, Pingmin Wei, Xiaobing Shen
Software Mentions: 24
Published: about 4 years ago

10.3389/fonc.2021.658165

Using Tumor-Infiltrating Immune Cells and a ceRNA Network Model to Construct a Prognostic Analysis Model of Thyroid Carcinoma
Cited by: 11
Author(s): Fan Zhang, Xiao‐Juan Yu, Zheyu Lin, Xichang Wang, Tengteng Gao, Di Teng, Weiping Teng
Software Mentions: 17
Published: over 3 years ago

10.7150/ijms.53531

Identification novel prognostic signatures for Head and Neck Squamous Cell Carcinoma based on ceRNA network construction and immune infiltration analysis
Cited by: 18
Author(s): Haiting Zhou, Yi He, Lingling Li, Cheng Wu, Guoqing Hu
Software Mentions: 16
Published: almost 4 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: about 4 years ago

10.1038/s41598-021-88209-4

Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data
Cited by: 6
Author(s): François Fauteux, Anuradha Surendra, Scott McComb, Youlian Pan, Jonathan D. Hill
Software Mentions: 15
Published: over 3 years ago

10.3389/fcell.2020.00790

The Construction of Bone Metastasis-Specific Prognostic Model and Co-expressed Network of Alternative Splicing in Breast Cancer
Cited by: 4
Author(s): Runzhi Huang, Jian Guo, Penghui Yan, Suna Zhai, Peng Hu, Xiaolong Zhu, Jiayao Zhang, Yannan Qiao, Yu Zhang, Hui Liu, Ling Huang, Jie Zhang, Daoke Yang, Zongqiang Huang
Software Mentions: 15
Published: about 4 years ago

10.3389/fcell.2021.671736

Identification of a Novel Immune Landscape Signature for Predicting Prognosis and Response of Endometrial Carcinoma to Immunotherapy and Chemotherapy
Cited by: 6
Author(s): Jinhui Liu, Yichun Wang, Jie Mei, Song Nie, Yan Zhang
Software Mentions: 15
Published: over 3 years ago

10.1186/s12859-021-04261-x

Machine learning-based prediction of survival prognosis in cervical cancer
Cited by: 16
Author(s): Dongyan Ding, Tingyuan Lang, Dongling Zou, Jianrong Tan, Jia Chen, Lei Zhou, Dong Wang, Rong Li, Yunzhe Li, Jingshu Liu, Cui Ma, Qi Zhou
Software Mentions: 14
Published: over 3 years ago

10.1186/s12864-021-07542-0

Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn
Cited by: 8
Author(s): Songlin Guo, Shouxiong Huang, Xi Jiang, Haiyang Hu, Dingding Han, Carlos S. Moreno, Genevieve Fairbrother, David A. Hughes, Mark Stoneking, Philipp Khaitovich
Software Mentions: 13
Published: over 3 years ago

10.1016/j.cell.2018.08.067

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease
Cited by: 396
Author(s): James Kinchen, Hannah H. Chen, Kaushal Parikh, Agne Antanaviciute, Marta Jagielowicz, David Fawkner-Corbett, Neil Ashley, Laura Cubitt, Esther Mellado-Gomez, Moustafa Attar, Eshita Sharma, Quin F. Wills, Rory Bowden, Felix Clemens Richter, David Ahern, Kamal D. Puri, Jill Hénault, François G. Gervais, Hashem Koohy, Alison Simmons
Software Mentions: 11
Published: about 6 years ago

10.1186/s12575-021-00152-w

N6-Methyladenosine Related Long Non-Coding RNAs and Immune Cell Infiltration in the Tumor Microenvironment of Gastric Cancer
Cited by: 9
Author(s): Zhong Lin Yu, Zheng Zhu
Software Mentions: 11
Published: over 3 years ago

10.3389/fgene.2019.01380

Germ Cell-Specific Gene 1-Like Protein Regulated by Splicing Factor CUGBP Elav-Like Family Member 5 and Primary Bile Acid Biosynthesis are Prognostic in Glioblastoma Multiforme
Cited by: 6
Author(s): Runzhi Huang, Zhenyu Li, Chen Li, Guanghua Wang, Penghui Yan, Li P, Jiaqi Wang, Xiaolong Zhu, Peng Hu, Junfang Zhang, Zhengyan Chang, Zongqiang Huang, Liming Cheng, Jie Zhang
Software Mentions: 11
Published: almost 5 years ago

10.3389/fbioe.2019.00270

Identification of Prognostic and Metastatic Alternative Splicing Signatures in Kidney Renal Clear Cell Carcinoma
Cited by: 46
Author(s): Tong Meng, Runzhi Huang, Zhiwei Zeng, Zongqiang Huang, Huabin Yin, Chenchen Jiao, Penghui Yan, Peng Hu, Xiaolong Zhu, Zhenyu Li, Dianwen Song, Jie Zhang, Liming Cheng
Software Mentions: 10
Published: about 5 years ago

10.1242/dev.169474

An integrated transcriptional analysis of the developing human retina
Cited by: 67
Author(s): Carla Mellough, R. Bauer, Joseph Collin, Birthe Dorgau, Darin Zerti, David Dolan, Carl M. Jones, Osagie Izuogu, Min Yu, Dean Hallam, Jannetta S. Steyn, Kathryn White, David Steel, Mauro Santibanez‐Koref, David Elliott, Michael S. Jackson, Susan Lindsay, Sushma Nagaraja Grellscheid, Majlinda Lako
Software Mentions: 10
Published: almost 6 years ago

10.1038/s41598-020-72569-4

Abiotic and past climatic conditions drive protein abundance variation among natural populations of the caddisfly Crunoecia irrorata
Cited by: 2
Author(s): Joshua Niklas Ebner, Danilo Ritz, Stefanie von Fumetti
Software Mentions: 9
Published: about 4 years ago

10.18632/aging.102424

The construction and analysis of tumor-infiltrating immune cell and ceRNA networks in recurrent soft tissue sarcoma
Cited by: 29
Author(s): Runzhi Huang, Tong Meng, Rui Chen, Penghui Yan, Jie Zhang, Peng Hu, Xiaolong Zhu, Huabin Yin, Dianwen Song, Zongqiang Huang
Software Mentions: 9
Published: almost 5 years ago

10.3389/fgene.2019.00828

The Construction and Comprehensive Analysis of ceRNA Networks and Tumor-Infiltrating Immune Cells in Bone Metastatic Melanoma
Cited by: 19
Author(s): Runzhi Huang, Zhiwei Zeng, Guangyu Li, Dianwen Song, Penghui Yan, Huabin Yin, Peng Hu, Xiaolong Zhu, Ruizhi Chang, Xu Zhang, Jie Zhang, Tong Meng, Zongqiang Huang
Software Mentions: 9
Published: about 5 years ago

10.3389/fonc.2021.582040

The Effects of Autophagy-Related Genes and lncRNAs in Therapy and Prognosis of Colorectal Cancer
Cited by: 5
Author(s): Yang Yang, Mingyang Feng, Liangliang Bai, Mengxi Zhang, Kaiyu Zhou, Wei‐Ting Liao, Wenhua Lei, Nan Zhang, Jiaxing Huang, Li Qiu
Software Mentions: 9
Published: over 3 years ago

10.3389/fbioe.2019.00257

The Construction and Analysis of ceRNA Network and Patterns of Immune Infiltration in Mesothelioma With Bone Metastasis
Cited by: 23
Author(s): Runzhi Huang, Jiawen Wu, Zixuan Zheng, Guanghua Wang, Dianwen Song, Penghui Yan, Huabin Yin, Peng Hu, Xiaolong Zhu, Haiyun Wang, Qi Lv, Tong Meng, Zongqiang Huang, Jie Zhang
Software Mentions: 9
Published: about 5 years ago

10.1038/s41598-020-60998-0

Temporal changes in the gene expression heterogeneity during brain development and aging
Cited by: 28
Author(s): Ulas Işıldak, Mehmet Somel, Janet M. Thornton, Handan Melike Dönertaş
Software Mentions: 8
Published: over 4 years ago

10.1186/s12859-018-2069-6

A gene profiling deconvolution approach to estimating immune cell composition from complex tissues
Cited by: 12
Author(s): Shu Hwa Chen, Wen Yu Kuo, Sheng Su, Wei Chun Chung, Jen Ming Ho, Henry Horng Shing Lu, Chung Yen Lin
Software Mentions: 8
Published: over 6 years ago

10.1186/1471-2105-12-467

Empirical comparison of cross-platform normalization methods for gene expression data
Cited by: 88
Author(s): Jason R. Rudy, Faramarz Valafar
Software Mentions: 8
Published: almost 13 years ago

10.1172/jci.insight.138751

In utero human intestine harbors unique metabolome, including bacterial metabolites
Cited by: 27
Author(s): Yujia Li, Jessica Toothaker, Shira Ben-Simon, Lital Ozeri, Ron Schweitzer, Blake McCourt, Collin C. McCourt, Lael Werner, Scott B. Snapper, Dror S. Shouval, Soliman Khatib, Omry Koren, Sameer Agnihorti, George C. Tseng, Liza Konnikova
Software Mentions: 8
Published: about 4 years ago

10.1186/s12864-015-2319-1

Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes
Cited by: 3
Author(s): Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masahiro Fujita, Hajime Ohyanagi, Nori Kurata
Software Mentions: 8
Published: almost 9 years ago

10.3389/fcell.2021.665869

Enhancing Fatty Acid Catabolism of Macrophages Within Aberrant Breast Cancer Tumor Microenvironment Can Re-establish Antitumor Function
Cited by: 4
Author(s): Yucui Gu, Xingjian Niu, Lei Yin, Yiran Wang, Yue Yang, Xudong Yang, Qingyuan Zhang, Hongfei Ji
Software Mentions: 8
Published: over 3 years ago

10.18632/aging.101912

The widespread increase in inter-individual variability of gene expression in the human brain with age
Cited by: 19
Author(s): Veronika R. Kedlian, Handan Melike Dönertaş, Janet M. Thornton
Software Mentions: 7
Published: over 5 years ago

10.1111/acel.12819

Gene expression-based drug repurposing to target aging
Cited by: 53
Author(s): Handan Melike Dönertaş, Matías Fuentealba, Linda Partridge, Janet M. Thornton
Software Mentions: 7
Published: over 6 years ago

10.1186/s12920-020-0695-0

Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain
Cited by: 20
Author(s): Wesley L. Cai, Celeste B. Greer, Jocelyn F. Chen, Anna Arnal-Estapé, Jian Cao, Qin Yan, Don X. Nguyen
Software Mentions: 7
Published: over 4 years ago

10.1186/1752-0509-6-63

Network methods for describing sample relationships in genomic datasets: application to Huntington’s disease
Cited by: 121
Author(s): Michael C. Oldham, Peter Langfelder, Steve Horvath
Software Mentions: 7
Published: almost 13 years ago

10.1186/s13040-018-0166-8

Gene set analysis methods: a systematic comparison
Cited by: 57
Author(s): Ravi Mathur, Daniel M. Rotroff, Ma Jun, Ali Shojaie, Alison A. Motsinger‐Reif
Software Mentions: 7
Published: over 6 years ago

10.1002/1878-0261.12389

Using microarray‐based subtyping methods for breast cancer in the era of high‐throughput RNA sequencing
Cited by: 6
Author(s): Christina Bligaard Pedersen, Finn C. Nielsen, Maria Rossing, Lars Rønn Olsen
Software Mentions: 7
Published: about 6 years ago

10.7717/peerj.1621

Cross-platform normalization of microarray and RNA-seq data for machine learning applications
Cited by: 71
Author(s): Jeffrey Thompson, Jie Tan, Casey S. Greene
Software Mentions: 7
Published: almost 9 years ago

10.1371/journal.pone.0159138

Technical Advances of the Recombinant Antibody Microarray Technology Platform for Clinical Immunoproteomics
Cited by: 26
Author(s): Payam Delfani, Linda Dexlin Mellby, Malin Nordström, Andreas Holmér, Mattias Ohlsson, Carl Borrebaeck, Christer Wingren
Software Mentions: 7
Published: over 8 years ago

10.1093/dnares/dsaa011

Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus
Cited by: 28
Author(s): Shingo Miyauchi, Hayat Hage, Élodie Drula, Laurence Lesage‐Meessen, Jean‐Guy Berrin, David Navarro, Anne Favel, Delphine Chaduli, Sacha Grisel, Mireille Haon, François Piumi, Anthony Levasseur, Anne Lomascolo, Steven Ahrendt, Kerrie Barry, Kurt LaButti, Didier Chevret, Chris Daum, Jérôme Mariette, Christophe Klopp, Daniel Cullen, Ronald P. de Vries, Allen C. Gathman, Matthieu Hainaut, Bernard Henrissat, Kristiina Hildén, Ursula Kües, Walt W. Lilly, Anna Lipzen, Miia Mäkelä, Ángel T. Martı́nez, Mélanie Morel‐Rouhier, Emmanuelle Morin, Jasmyn Pangilinan, Arthur F. J. Ram, Han A. B. Wösten, Francisco J. Ruíz-Dueñas, Robert Riley, Éric Record, Igor V. Grigoriev, Marie‐Noëlle Rosso
Software Mentions: 7
Published: over 4 years ago

10.3389/fonc.2021.657094

LINC01977 Promotes Breast Cancer Progression and Chemoresistance to Doxorubicin by Targeting miR-212-3p/GOLM1 Axis
Cited by: 12
Author(s): Zheng Li, Yaming Li, Xiaolong Wang, Yiran Liang, Dan Luo, Dianwen Han, Chen Li, Tong Chen, Hanwen Zhang, Ying Liu, Zekun Wang, Bing Chen, Limin Wang, Wenjing Zhao, Qifeng Yang
Software Mentions: 7
Published: over 3 years ago

10.1534/g3.115.023739

argyle: An R Package for Analysis of Illumina Genotyping Arrays
Cited by: 34
Author(s): Andrew P. Morgan
Software Mentions: 7
Published: almost 9 years ago

10.1093/gigascience/giaa162

Lilikoi V2.0: a deep learning–enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data
Cited by: 10
Author(s): Xinying Fang, Yu Liu, Zhijie Ren, Yuheng Du, Qizhao Huang, Lana X. Garmire
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-019-42784-9

Transcriptomic profiles conducive to immune-mediated tumor rejection in human breast cancer skin metastases treated with Imiquimod
Cited by: 23
Author(s): Mariya Rozenblit, Wouter Hendrickx, Adriana Heguy, Luis Chiriboga, Cynthia A. Loomis, Karina Ray, Farbod Darvishian, Mikala Egeblad, Sandra Demaria, Francesco M. Marincola, Davide Bedognetti, Sylvia Adams
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-021-92036-y

Capitalizing on transcriptome profiling to optimize and identify targets for promoting early murine folliculogenesis in vitro
Cited by: 6
Author(s): Andrea Jones, Beatriz Peñalver Bernabé, Vasantha Padmanabhan, Jun Li, Ariella Shikanov
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0037714

Dynamic Gene Expression in the Human Cerebral Cortex Distinguishes Children from Adults
Cited by: 32
Author(s): Kirstin N. Sterner, Amy Weckle, Harry T. Chugani, Adi L. Tarca, Chet C. Sherwood, Patrick R. Hof, Christopher W. Kuzawa, Amy M. Boddy, Asad Abbas, Ryan L. Raaum, Lucie Grégoire, Leonard Lipovich, Lawrence I. Grossman, Monica Uddin, Morris Goodman, Derek E. Wildman
Software Mentions: 6
Published: over 12 years ago

10.1038/s41598-017-09094-4

Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study
Cited by: 33
Author(s): Stephen P. Ficklin, Leland J. Dunwoodie, William L. Poehlman, Christopher Watson, Kimberly Roche, F. Alex Feltus
Software Mentions: 6
Published: about 7 years ago

10.1186/gm496

A robust prognostic signature for hormone-positive node-negative breast cancer
Cited by: 18
Author(s): Obi L. Griffith, François Pépin, Oana Enache, Laura M. Heiser, Eric A. Collisson, Paul T. Spellman, Joe W. Gray
Software Mentions: 6
Published: almost 12 years ago

10.1534/g3.117.300489

DrosophilaLarval Brain Neoplasms Present Tumour-Type Dependent Genome Instability
Cited by: 4
Author(s): Fabrizio Rossi, Camille Stephan‐Otto Attolini, José Luis Mosquera, Cayetano González
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2018.00052

Gene Expression Meta-Analysis of Seven Candidate Gene Sets for Diabetes Traits Following a GWAS Pathway Study
Cited by: 2
Author(s): Hao Mei, Lianna Li, Michael Griswold, Thomas H. Mosley
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0052299

Cell-Type Specific DNA Methylation Patterns Define Human Breast Cellular Identity
Cited by: 22
Author(s): Petr Novák, Martha R. Stampfer, José L. Muñoz-Rodríguez, James C. Garbe, Mathias Ehrich, Bernard W. Futscher, Taylor J. Jensen
Software Mentions: 6
Published: almost 12 years ago

10.1016/j.celrep.2021.109101

Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation
Cited by: 18
Author(s): Nicholas T. Crump, Andreas V. Hadjinicolaou, Meng Xia, John Walsby-Tickle, Uzi Gileadi, Ji‐Li Chen, Mashiko Setshedi, Lars Rønn Olsen, I-Jun Lau, Laura Godfrey, Lynn Quek, Zhanru Yu, Erica Ballabio, Mike Bogetofte Barnkob, Giorgio Napolitani, Mariolina Salio, Hashem Koohy, Benedikt M. Kessler, Stephen Taylor, Paresh Vyas, James McCullagh, Thomas A. Milne, Vincenzo Cerundolo
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-018-4929-x

Gene expression analysis indicates reduced memory and cognitive functions in the hippocampus and increase in synaptic reorganization in the frontal cortex 3 weeks after MDMA administration in Dark Agouti rats
Cited by: 12
Author(s): Péter Petschner, Viola Tamási, Csaba Ádori, Eszter Kirilly, Rómeó D. Andó, László Tóthfalusi, György Bagdy
Software Mentions: 5
Published: over 6 years ago

10.7717/peerj.4584

Empirical evaluation of data normalization methods for molecular classification
Cited by: 12
Author(s): Hsin‐Chieh Huang, Li‐Xuan Qin
Software Mentions: 5
Published: over 6 years ago

10.18632/oncotarget.19662

Gene expression and molecular pathway activation signatures ofMYCN-amplified neuroblastomas
Cited by: 27
Author(s): Ivan Petrov, Maria Suntsova, Elena Tarasovna Ilnitskaya, S. A. Roumiantsev, Maxim Sorokin, Andrew Garazha, Pavel Spirin, Timofey Lebedev, Нуршат Гайфуллин, Sergey Larin, Olga Kovalchuk, Д. М. Коновалов, Vladimir Prassolov, Alexander Roumiantsev, Anton Buzdin
Software Mentions: 5
Published: over 7 years ago

10.1155/2020/3909416

Recognition of Immune Microenvironment Landscape and Immune-Related Prognostic Genes in Breast Cancer
Cited by: 7
Author(s): Huiling Wang, Sylvaine You, Meng Fang, Qian Fang
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12859-019-2969-0

Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models
Cited by: 24
Author(s): Marina Esteban-Medina, María Peña‐Chilet, Carlos Loucera, Joaquı́n Dopazo
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-14-930

RETRACTED ARTICLE: Gene expression analysis indicates CB1 receptor upregulation in the hippocampus and neurotoxic effects in the frontal cortex 3 weeks after single-dose MDMA administration in Dark Agouti rats
Cited by: 9
Author(s): Péter Petschner, Viola Tamási, Csaba Ádori, Eszter Kirilly, Rómeó D. Andó, László Tóthfalusi, György Bagdy
Software Mentions: 5
Published: almost 11 years ago

10.1186/s12859-019-3017-9

Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods
Cited by: 8
Author(s): Shintaro Katayama, Tiina Skoog, Cilla Söderhäll, Elisabet Einarsdottir, Kaarel Krjutškov, Juha Kere
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-83886-7

Using protein turnover to expand the applications of transcriptomics
Cited by: 2
Author(s): Marissa A. Smail, James Reigle, Robert E. McCullumsmith
Software Mentions: 4
Published: over 3 years ago

10.1074/mcp.RA117.000189

Spatial Tissue Proteomics Quantifies Inter- and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC)
Cited by: 63
Author(s): Katarzyna Buczak, Alessandro Ori, Joanna Kirkpatrick, Kerstin Hölzer, Daniel Dauch, Stephanie Roessler, Volker Endris, Felix Lasitschka, Luca Parca, Alexander Schmidt, Lars Zender, Peter Schirmacher, Jeroen Krijgsveld, Stephan Singer, Martin Beck
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0038946

Profound Effect of Profiling Platform and Normalization Strategy on Detection of Differentially Expressed MicroRNAs – A Comparative Study
Cited by: 51
Author(s): Swanhild U. Meyer, Sebastian Kaiser, Carola Wagner, Christian Thirion, Michael W. Pfaffl
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0025023

Determining Signalling Nodes for Apoptosis by a Genetic High-Throughput Screen
Cited by: 5
Author(s): Bevan Lin, Derek Huntley, Ghada AbuAli, Sarah R. Langley, George Sindelar, Enrico Petretto, Sarah Butcher, Stefan Grimm
Software Mentions: 4
Published: about 13 years ago

10.1371/journal.pone.0113662

Transcriptional Evidence for the Role of Chronic Venlafaxine Treatment in Neurotrophic Signaling and Neuroplasticity Including also Glutatmatergic- and Insulin-Mediated Neuronal Processes
Cited by: 52
Author(s): Viola Tamási, Péter Petschner, Csaba Ádori, Eszter Kirilly, Rómeó D. Andó, László Tóthfalusi, Gabriella Juhász, György Bagdy
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0253037

A meta-analysis of transcriptomic profiles of Huntington’s disease patients
Cited by: 14
Author(s): Manuel Seefelder, Stefan Kochanek
Software Mentions: 4
Published: over 3 years ago

10.1016/j.celrep.2020.108337

Human and Mouse Transcriptome Profiling Identifies Cross-Species Homology in Pulmonary and Lymph Node Mononuclear Phagocytes
Cited by: 37
Author(s): Sonia M. Leach, Sophie L. Gibbings, Anita Tewari, Shaikh M. Atif, Brian Vestal, Thomas Danhorn, William J. Janssen, Tor D. Wager, Claudia Jakubzick
Software Mentions: 4
Published: about 4 years ago

10.1002/ctm2.434

Integrated transcriptional‐phenotypic analysis captures systemic immunomodulation following antiangiogenic therapy in renal cell carcinoma patients
Cited by: 3
Author(s): Darawan Rinchai, Elena Verzoni, Veronica Huber, Agata Cova, Paola Squarcina, Loris De Cecco, Filippo de Braud, Raffaele Ratta, Matteo Dugo, Luca Lalli, Viviana Vallacchi, Monica Rodolfo, Jessica Roelands, Chiara Castelli, Damien Chaussabel, Giuseppe Procopio, Davide Bedognetti, Licia Rivoltini
Software Mentions: 4
Published: over 3 years ago

10.1186/s12916-021-01925-6

Glycolysis-associated lncRNAs identify a subgroup of cancer patients with poor prognoses and a high-infiltration immune microenvironment
Cited by: 17
Author(s): Kuo Hao Ho, Tzu Wen Huang, Chwen Ming Shih, Yi Ting Lee, Ann Jeng Liu, Peng Hsu Chen, Ku Chung Chen
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2164-15-474

The human miRNA repertoire of different blood compounds
Cited by: 56
Author(s): Petra Leidinger, Christina Backes, Benjamin Meder, Eckart Meese, Andreas Keller
Software Mentions: 4
Published: over 10 years ago

10.1186/s13018-021-02658-1

Potential genes and pathways associated with heterotopic ossification derived from analyses of gene expression profiles
Cited by: 5
Author(s): Zhanyu Yang, Delong Liu, Rui Guan, Li X, Yiwei Wang, Bin Sheng
Software Mentions: 4
Published: about 3 years ago

10.1186/s12859-017-1501-7

Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data
Cited by: 31
Author(s): Anna C. Reisetter, Michael J. Muehlbauer, James R. Bain, Michael Nodzenski, Robert Stevens, Olga Ilkayeva, Boyd E. Metzger, Christopher B. Newgard, William L. Lowe
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-021-87137-7

Distinct SARS-CoV-2 antibody reactivity patterns in coronavirus convalescent plasma revealed by a coronavirus antigen microarray
Cited by: 10
Author(s): Rafael de Assis, Aarti Jain, Rie Nakajima, Algis Jasinskas, Saahir Khan, Huw Davies, Laurence Corash, Larry J. Dumont, Kathleen Kelly, Graham Simmons, Mars Stone, Clara Di Germanio, Michael P. Busch, Philip L. Felgner
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.15477

Increasing Notch signaling antagonizes PRC2-mediated silencing to promote reprograming of germ cells into neurons
Cited by: 31
Author(s): Stefanie Seelk, Irene Adrian‐Kalchhauser, Balázs Hargitai, Martina Hajdůšková, Silvia Gutnik, Baris Tursun, Rafal Ciosk
Software Mentions: 4
Published: about 8 years ago

10.1155/2017/6896390

Gene Expression Profiling of the Optic Nerve Head of Patients with Primary Open-Angle Glaucoma
Cited by: 4
Author(s): Xinrong Wang, KeWei Gong, Haiyan Li, Cong Yi Wang, Chaoyi Qu, Hui Li
Software Mentions: 4
Published: almost 8 years ago

10.1093/bib/bbw008

A benchmark of gene expression tissue-specificity metrics
Cited by: 231
Author(s): Nadezda Kryuchkova-Mostacci, Marc Robinson‐Rechavi
Software Mentions: 4
Published: over 8 years ago

10.1038/s41375-020-0965-z

A transcriptomic continuum of differentiation arrest identifies myeloid interface acute leukemias with poor prognosis
Cited by: 6
Author(s): Jonathan Bond, Aleksandra Krzywon, Ludovic Lhermitte, Christophe Roumier, Anne Roggy, Mohamed Belhocine, Alexander Abdulkader Kheirallah, Patrick Villarèse, Guillaume Hypolite, Francine Garnache‐Ottou, Sylvie Castaigné, Nicolas Boissel, Vahid Asnafi, Claude Preudhomme, Hervé Dombret, Elisa Laurenti, Elizabeth Macintyre
Software Mentions: 4
Published: over 4 years ago

10.3390/md19080442

Ubiquitousness of Haloferax and Carotenoid Producing Genes in Arabian Sea Coastal Biosystems of India
Cited by: 4
Author(s): Jamseel Moopantakath, Madangchanok Imchen, Ranjith Kumavath, Rosa María Martínez‐Espinosa
Software Mentions: 4
Published: over 3 years ago

10.1093/molbev/msx190

Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome
Cited by: 37
Author(s): Ann Kathrin Huylmans, Ariana Macon, Beatriz Vicoso
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2105-11-553

Algorithm-driven Artifacts in median polish summarization of Microarray data
Cited by: 50
Author(s): Federico M. Giorgi, Anthony Bolger, Marc Lohse, Björn Usadel
Software Mentions: 3
Published: almost 14 years ago

10.15252/msb.20177532

Quantitative analysis of protein interaction network dynamics in yeast
Cited by: 38
Author(s): Albi Celaj, Ulrich Schlecht, Justin D. Smith, Weihong Xu, Sundari Suresh, Molly Miranda, Ana Aparicio, Michael Proctor, Ronald W. Davis, Frederick P. Roth, Robert P. St.Onge
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2021.626418

Regulation of B Lymphocyte Development by Histone H2A Deubiquitinase BAP1
Cited by: 4
Author(s): Yun Lin, Yue Liang, HanChen Wang, Lin Tze Tung, Michael Förster, Poorani Ganesh Subramani, Javier M. Di Noia, Simon Clare, David Langlais, Anastasia Nijnik
Software Mentions: 3
Published: over 3 years ago

10.1038/s41597-019-0116-4

Single-cell RNA sequencing of a European and an African lymphoblastoid cell line
Cited by: 24
Author(s): Daniel Osorio, Xue Yu, Peng Yu, Erchin Serpedin, James J. Cai
Software Mentions: 3
Published: over 5 years ago

10.1186/s12885-020-07494-w

Identification of common signatures in idiopathic pulmonary fibrosis and lung cancer using gene expression modeling
Cited by: 7
Author(s): Liubing Dong, Jiawen Yi, Maodong Xiang, Hongying Zhao, Yuhui Zhang
Software Mentions: 3
Published: about 4 years ago

10.1016/j.ymthe.2019.09.023

Rescue from Stx2-Producing E. coli-Associated Encephalopathy by Intravenous Injection of Muse Cells in NOD-SCID Mice
Cited by: 13
Author(s): Ryo Ozuru, Shohei Wakao, Takahiro Tsuji, Naoya Ohara, Takashi Matsuba, Muhammad Y. Amuran, Junko Isobe, Morio Iino, Naoki Nishida, Sari Matsumoto, Kimiharu Iwadate, Noriko Konishi, Kaori Yasuda, Kosuke Tashiro, Misato Hida, Arisato Yadoiwa, Shinsuke Kato, Eijiro Yamashita, Sohkichi Matsumoto, Yoichi Kurozawa, Mari Dezawa, Jun Fujii
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13068-019-1612-7

Common metabolic networks contribute to carbon sink strength of sorghum internodes: implications for bioenergy improvement
Cited by: 7
Author(s): Yin Li, Min Tu, Yaping Feng, Wenqing Wang, Joachim Messing
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1005101

The Fun30 Chromatin Remodeler Fft3 Controls Nuclear Organization and Chromatin Structure of Insulators and Subtelomeres in Fission Yeast
Cited by: 52
Author(s): Babett Steglich, Annelie Strålfors, Olga Khorosjutina, Jenna Persson, Agata Smialowska, J.P. Javerzat, Karl Ekwall
Software Mentions: 3
Published: over 9 years ago

10.1186/s13059-016-0946-8

Epigenetic assimilation in the aging human brain
Cited by: 43
Author(s): Gabriel Oh, Sasha Ebrahimi, Sun Chong Wang, Rene Cortese, Zachary Kaminsky, Irving I. Gottesman, James R. Burke, Brenda L. Plassman, Art Petronis
Software Mentions: 3
Published: over 8 years ago

10.1186/gb-2008-9-7-r112

At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana
Cited by: 98
Author(s): Sascha Laubinger, Georg Zeller, Stefan R. Henz, Timo Sachsenberg, Christian Widmer, Naïra Naouar, Marnik Vuylsteke, Bernhard Schölkopf, Gunnar Rätsch, Detlef Weigel
Software Mentions: 3
Published: almost 17 years ago

10.18632/aging.101102

Molecular pathway activation features of pediatric acute myeloid leukemia (AML) and acute lymphoblast leukemia (ALL) cells
Cited by: 15
Author(s): Ivan Petrov, Maria Suntsova, Olga Mutorova, Maxim Sorokin, Andrew Garazha, Elena Tarasovna Ilnitskaya, Pavel Spirin, Sergey Larin, Olga Kovalchuk, Vladimir Prassolov, Alex Zhavoronkov, Alexander Roumiantsev, Anton Buzdin
Software Mentions: 3
Published: almost 8 years ago

10.7717/peerj.7456

lncRNA TMEM51-AS1 and RUSC1-AS1 function as ceRNAs for induction of laryngeal squamous cell carcinoma and prediction of prognosis
Cited by: 23
Author(s): Lian Hui, Jing Wang, Jialiang Zhang, Long Jin
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22094888

Death Processes in Bovine Theca and Granulosa Cells Modelled and Analysed Using a Systems Biology Approach
Cited by: 6
Author(s): Malgorzata J. McEvoy, Emilia Sinderewicz, Leo Creedon, Marion McAfee, A.W. Jończyk, K.K. Piotrowska-Tomala, Dariusz J. Skarzynski
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0045249

A Gene-Phenotype Network Based on Genetic Variability for Drought Responses Reveals Key Physiological Processes in Controlled and Natural Environments
Cited by: 53
Author(s): David Rodrı́guez-Lázaro, Sandrine Arribat, Pierre Maury, Marie‐Laure Martin‐Magniette, Thibaut Hourlier, Marion Laporte, Didier Varès, Sébastien Carrère, Philippe Grieu, Sandrine Balzergue, Jérôme Gouzy, Patrick Vincourt, Nicolas Langlade
Software Mentions: 2
Published: about 12 years ago

10.1186/s40001-020-00443-0

Screening and evaluation of key genes in contributing to pathogenesis of hepatic fibrosis based on microarray data
Cited by: 1
Author(s): Fuqiang Wu, Ning Lv, Ran Zhou, Albert Yuh-Jer Shen
Software Mentions: 2
Published: about 4 years ago

10.1186/s12903-015-0086-7

Genes related to inflammation and bone loss process in periodontitis suggested by bioinformatics methods
Cited by: 31
Author(s): Liang Song, Jueqi Yao, Zhijing He, Bin Xu
Software Mentions: 2
Published: about 9 years ago

10.1002/cam4.3574

N6‐methyladenine‐related genes affect biological behavior and the prognosis of glioma
Cited by: 19
Author(s): Shanqiang Qu, Zhuo Chen, Bin Liu, Jin Liu, Huafu Wang
Software Mentions: 2
Published: almost 4 years ago

10.1155/2014/836397

Upregulation of Relaxin after Experimental Subarachnoid Hemorrhage in Rabbits
Cited by: 6
Author(s): Yuichiro Kikkawa, Seiichiro Matsuo, Ryota Kurogi, Akira Nakamizo, Masahiro Mizoguchi, Tatsuya Sasaki
Software Mentions: 2
Published: almost 11 years ago

10.1093/pcp/pcv190

ALCOdb: Gene Coexpression Database for Microalgae
Cited by: 34
Author(s): Yosuke Aoki, Yasunobu Okamura, Hiroyuki Ohta, Kengo Kinoshita, Takeshi Obayashi
Software Mentions: 2
Published: almost 9 years ago

10.3389/fgene.2015.00163

Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways
Cited by: 12
Author(s): Adrián Mosquera Orgueira
Software Mentions: 2
Published: over 9 years ago

10.3389/fgene.2018.00242

Machine Learning on Human Muscle Transcriptomic Data for Biomarker Discovery and Tissue-Specific Drug Target Identification
Cited by: 128
Author(s): Polina Mamoshina, Marina Volosnikova, Ivan V. Ozerov, Evgeny Putin, Ekaterina Skibina, Filomeno Cortese, Alex Zhavoronkov
Software Mentions: 2
Published: over 6 years ago

10.18632/oncotarget.24228

Discovery and validation of a glioblastoma co-expressed gene module
Cited by: 8
Author(s): Leland J. Dunwoodie, William L. Poehlman, Stephen P. Ficklin, Frank Alexander Feltus
Software Mentions: 2
Published: almost 7 years ago

10.3389/fphar.2018.01373

Downregulation of the Vitamin D Receptor Regulated Gene Set in the Hippocampus After MDMA Treatment
Cited by: 1
Author(s): Péter Petschner, Noemi Balogh, Csaba Ádori, Viola Tamási, S. Kumar, Gabriella Juhász, György Bagdy
Software Mentions: 2
Published: almost 6 years ago

10.3389/fphys.2016.00208

Cancer Markers Selection Using Network-Based Cox Regression: A Methodological and Computational Practice
Cited by: 15
Author(s): Antonella Iuliano, Annalisa Occhipinti, Claudia Angelini, Italia De Feis, Píetro Lió
Software Mentions: 2
Published: over 8 years ago

Projects: bioconductor: preprocessCore

Papers Mentioning preprocessCore 146