bioconductor: limma | Projects | Ecosyste.ms: Papers

10.7150/ijms.63402

Bioinformatics analysis identified shared differentially expressed genes as potential biomarkers for Hashimoto's thyroiditis-related papillary thyroid cancer
Cited by: 8
Author(s): Chang Liu, Yu Pan, Qinyu Li, Yifan Zhang
Software Mentions: 3
Published: over 5 years ago

10.7150/ijms.54747

Granzyme family acts as a predict biomarker in cutaneous melanoma and indicates more benefit from anti-PD-1 immunotherapy
Cited by: 10
Author(s): Xia Wu, Xiaojie Wang, Yan Zhao, Kun Li, Bo Yu, Jianzhong Zhang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12885-021-08456-6

Elevated TYROBP expression predicts poor prognosis and high tumor immune infiltration in patients with low-grade glioma
Cited by: 20
Author(s): Jiajie Lu, Yün Peng, Rihong Huang, Zejia Feng, Yongyang Fan, Haojian Wang, Zhiyong Zeng, Yunxiang Ji, Yezhong Wang, Zhaotao Wang
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-016-1131-9

Controlling bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution
Cited by: 237
Author(s): Maarten van Iterson, Erik W. van Zwet, Bastiaan T. Heijmans, Peter A.C. ’t Hoen, Joyce B. J. van Meurs, Ritsert C. Jansen, Lude Franke, Dorret I. Boomsma, René Pool, Jenny van Dongen, Jouke Jan Hottenga, Marleen J. van Greevenbroek, Coen D.A. Stehouwer, Carla J.H. van der Kallen, Casper G. Schalkwijk, Cisca Wijmenga, Sasha Zhernakova, Ettje F. Tigchelaar, P. Eline Slagboom, Marian Beekman, Joris Deelen, Diana van Heemst, Jan H. Veldink, Leonard H van den Berg, Cornelia M. van Duijn, Bert A. Hofman, Aaron Isaacs, André G. Uitterlinden, P. Mila Jhamai, Michaël Verbiest, H. Eka D. Suchiman, Marijn Verkerk, Ruud van der Breggen, Jeroen van Rooij, Nico Lakenberg, Hailiang Mei, M.A. van Galen, Jan Bot, Dasha V. Zhernakova, Peter van ’t Hof, Patrick Deelen, Irene Nooren, Matthijs Moed, Martijn Vermaat, René Luijk, Marc Jan Bonder, Freerk van Dijk, Wibowo Arindrarto, Szymon M. Kiełbasa, Morris A. Swertz
Software Mentions: 3
Published: over 9 years ago

10.3389/fonc.2021.712746

Exploration of Lipid Metabolism in Gastric Cancer: A Novel Prognostic Genes Expression Profile
Cited by: 9
Author(s): Ze Xiong, Yu Lin, Yan Yu, Xianghui Zhou, Jun Fan, Colin J. Rog, Kailin Cai, Zheng Wang, Zhijie Chen, Guobin Wang, Kaixiong Tao, Ming Cai
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-017-1156-8

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types
Cited by: 88
Author(s): Simone Ecker, Lu Chen, Véra Pancaldi, Frederik Otzen Bagger, José Marı́a Fernández, Enrique Carrillo de Santa Pau, David Juan, Alice Mann, Stephen Watt, Francesco Paolo Casale, Nikolaos Sidiropoulos, Nicolas Rapin, Angelika Merkel, Hendrik G. Stunnenberg, Oliver Stegle, Mattia Frontini, Kate Downes, Tomi Pastinen, Taco W. Kuijpers, Daniel Rico, Alfonso Valencia, Stephan Beck, Nicole Soranzo, Dirk S. Paul
Software Mentions: 3
Published: over 9 years ago

10.1186/s12859-017-1467-5

Identifying miRNA sponge modules using biclustering and regulatory scores
Cited by: 21
Author(s): Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li
Software Mentions: 3
Published: over 9 years ago

10.1186/1476-4598-11-41

Gene expression changes as markers of early lapatinib response in a panel of breast cancer cell lines
Cited by: 23
Author(s): Fiona O’Neill, Stephen F. Madden, Sinéad Aherne, Martin Clynes, John Crown, Padraig Doolan, Robert O’Connor
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2105-16-S18-S16

Identification of aberrant gene expression associated with aberrant promoter methylation in primordial germ cells between E13 and E16 rat F3 generation vinclozolin lineage
Cited by: 23
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13059-016-1143-5

Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies
Cited by: 98
Author(s): Xiaoqi Zheng, Zhang Nai-qian, Hua‐Jun Wu, Hao Wu
Software Mentions: 3
Published: over 9 years ago

10.1186/s40303-015-0013-5

Insights into the origin of DNA methylation differences between monozygotic twins discordant for schizophrenia
Cited by: 9
Author(s): Melkaye G Melka, Christina A Castellani, Richard O’Reilly, Shiva M. Singh
Software Mentions: 3
Published: about 11 years ago

10.18632/aging.102300

COL6A6 interacted with P4HA3 to suppress the growth and metastasis of pituitary adenoma via blocking PI3K-Akt pathway
Cited by: 26
Author(s): Ruiqing Long, Zhuohui Liu, Jinghui Li, Hualin Yu
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12943-016-0548-9

Prediction of chemo-response in serous ovarian cancer
Cited by: 27
Author(s): Jesús González Bosquet, A.M. Newtson, Raphael S. Chung, Kristina W. Thiel, Timothy Ginader, Michael J. Goodheart, Kimberly K. Leslie, Brian J. Smith
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12885-020-07628-0

Analyses of metastasis-associated genes in IDH wild-type glioma
Cited by: 4
Author(s): Xiaozhi Li, Yutong Meng
Software Mentions: 3
Published: almost 6 years ago

10.3389/fonc.2021.716854

Comprehensive Analysis of the Immune Infiltrates of Pyroptosis in Kidney Renal Clear Cell Carcinoma
Cited by: 17
Author(s): Zhuolun Sun, Changying Jing, Xudong Guo, Mingxiao Zhang, Feng Kong, Zhenqing Wang, Shaobo Jiang, Hanbo Wang
Software Mentions: 3
Published: about 5 years ago

10.1186/s12859-020-03559-6

Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies
Cited by: 38
Author(s): Tristan Zindler, Helge Frieling, Alexandra Neyazi, Stefan Bleich, Eva Friedel
Software Mentions: 3
Published: about 6 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 10 years ago

10.1186/1471-2105-14-236

svapls: an R package to correct for hidden factors of variability in gene expression studies
Cited by: 3
Author(s): Sutirtha Chakraborty, Somnath Datta, Susmita Datta
Software Mentions: 3
Published: about 13 years ago

10.1186/1476-4598-9-189

The dietary isothiocyanate sulforaphane modulates gene expression and alternative gene splicing in a PTEN null preclinical murine model of prostate cancer
Cited by: 50
Author(s): Μαρία Τράκα, Caroline A Spinks, Joanne F. Doleman, Antonietta Melchini, Richard Y. Ball, Robert Mills, Richard Mithen
Software Mentions: 3
Published: about 16 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 16 years ago

10.1186/s12885-020-07216-2

Comprehensive analysis of prognostic tumor microenvironment-related genes in osteosarcoma patients
Cited by: 19
Author(s): Chuan Hu, Chuan Liu, Shaoqi Tian, Yuanhe Wang, Rui Shen, Huili Rao, Jianyi Li, Yu Xu, Bo Chen, Ye Lin
Software Mentions: 3
Published: about 6 years ago

10.18632/aging.202754

Identification of vital prognostic genes related to tumor microenvironment in pheochromocytoma and paraganglioma based on weighted gene co-expression network analysis
Cited by: 6
Author(s): Chun-Xian Chen, Dong‐Ning Chen, Xiong‐Lin Sun, Zhi‐Bin Ke, Fei Lin, Hang Chen, Xuan Tao, Fei Huang, Yong Wei, Ning Xu
Software Mentions: 3
Published: over 5 years ago

10.1186/s12885-019-6470-y

Gene signature characteristic of elevated stromal infiltration and activation is associated with increased risk of hematogenous and lymphatic metastasis in serous ovarian cancer
Cited by: 36
Author(s): Huiran Yue, Jieyu Wang, Ruifang Chen, Xiaoman Hou, Jun Li, Xin Lu
Software Mentions: 3
Published: almost 7 years ago

10.1186/1476-4598-13-27

RNAi-mediated silencing of MLL-AF9 reveals leukemia-associated downstream targets and processes
Cited by: 29
Author(s): Katrin K. Fleischmann, Philipp Pagel, Irene Schmid, Adelbert A. Roscher
Software Mentions: 3
Published: over 12 years ago

10.1186/s12885-021-08319-0

Identification of 4-genes model in papillary renal cell tumor microenvironment based on comprehensive analysis
Cited by: 4
Author(s): Lun Luo, Haiyi Zhou, Hao Su
Software Mentions: 3
Published: over 5 years ago

10.3892/ijo.2014.2648

Microarray phosphatome profiling of breast cancer patients unveils a complex phosphatase regulatory role of the MAPK and PI3K pathways in estrogen receptor-negative breast cancers
Cited by: 13
Author(s): Ramón González Manzano, E. Martinez-Navarro, Jerónimo Forteza, Antonio Brugarolas
Software Mentions: 3
Published: about 12 years ago

10.18632/aging.102693

Immunological analyses reveal an immune subtype of uveal melanoma with a poor prognosis
Cited by: 15
Author(s): Hui Pan, Lu Liu, Junqi Cui, Yuan Yang, Zhaoyang Wang, Xianqun Fan
Software Mentions: 3
Published: over 6 years ago

10.1186/s12885-021-08356-9

Genome instability-related long non-coding RNA in clear renal cell carcinoma determined using computational biology
Cited by: 9
Author(s): Yutao Wang, Kexin Yan, Linhui Wang, Jianbin Bi
Software Mentions: 3
Published: about 5 years ago

10.1016/j.molcel.2019.02.031

MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation
Cited by: 79
Author(s): Apoorva Baluapuri, Julia Hofstetter, Nevenka Dudvarski Stanković, Theresa Endres, Pranjali Bhandare, Seychelle M. Vos, Bikash Adhikari, Jessica Denise Schwarz, Ashwin Narain, Markus Vogt, Shuangyan Wang, Robert Düster, Lisa Anna Jung, Jens T. Vanselow, Armin Wiegering, Matthias Geyer, Hans Michael Maric, Peter Gallant, Susanne Walz, Andreas Schlösser, Patrick Cramer, Martin Eilers, Elmar Wolf
Software Mentions: 3
Published: over 7 years ago

10.1186/s12885-021-08358-7

Identification of novel hub genes associated with gastric cancer using integrated bioinformatics analysis
Cited by: 17
Author(s): Xin Lu, Jiaqian Zhang, Sheng‐Xiao Zhang, Jun Qiao, Mengting Qiu, Xiangrong Liu, Xiaoxia Chen, Chong Gao, Huan-Hu Zhang
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-015-0600-x

A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies
Cited by: 260
Author(s): Benjamin Lehne, Alexander W. Drong, Marie Loh, Weihua Zhang, William R. Scott, Sian-Tsung Tan, Uzma Afzal, James A. Scott, Marjo‐Riitta Järvelin, Paul Elliott, Mark I. McCarthy, Jaspal S. Kooner, John C. Chambers
Software Mentions: 3
Published: over 11 years ago

10.1186/s12885-021-08541-w

Molecular identification of an immunity- and Ferroptosis-related gene signature in non-small cell lung Cancer
Cited by: 10
Author(s): Taisheng Liu, Honglian Luo, Jinye Zhang, Xiaoshan Hu, Jian Zhang
Software Mentions: 3
Published: about 5 years ago

10.18632/aging.102161

Identification of 9 key genes and small molecule drugs in clear cell renal cell carcinoma
Cited by: 47
Author(s): Yongwen Luo, Dexin Shen, Liang Chen, Gang Wang, Xuefeng Li, Kaiyu Qian, Yu Xiao, Xinghuan Wang, Lingao Ju
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0009983

Identification of Candidate Growth Promoting Genes in Ovarian Cancer through Integrated Copy Number and Expression Analysis
Cited by: 100
Author(s): Manasa Ramakrishna, Lauren Williams, Samantha E. Boyle, Jennifer L. Bearfoot, Anita Sridhar, Terence P. Speed, Kylie L. Gorringe, Ian Campbell
Software Mentions: 3
Published: over 16 years ago

10.18632/aging.203432

A comprehensive transcriptomic analysis of alternate interferon signaling pathways in peripheral blood mononuclear cells in rheumatoid arthritis
Cited by: 4
Author(s): Han Liang, Shenghao Tu, Pan Shen, Jiahui Yan, Yao Huang, Xin Ba, Tingting Li, Wei Chen Lin, Huihui Li, Kun Yu, Jing Guo, Ying Huang, Kai Qin, Yu Wang, Zhe Chen
Software Mentions: 3
Published: about 5 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

10.18632/aging.103868

Construction of a new tumor immunity-related signature to assess and classify the prognostic risk of ovarian cancer
Cited by: 6
Author(s): Jiashan Ding, Qiaoling Zhang, Shichao Chen, Huikai Huang, Linsheng He
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12859-020-03768-z

MADloy: robust detection of mosaic loss of chromosome Y from genotype-array-intensity data
Cited by: 6
Author(s): Juan R. González, Marcos López-Sánchez, Alejandro Cáceres, Pere Puig, Tõnu Esko, Luis A. Pérez‐Jurado
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-014-0526-8

Combined image and genomic analysis of high-grade serous ovarian cancer reveals PTEN loss as a common driver event and prognostic classifier
Cited by: 92
Author(s): Filipe Correia Martins, Inês de Santiago, Anne Trinh, Xian Jian, Anne Guo, Karen Sayal, Mercedes Jimenez-Liñan, Suha Deen, Kristy Driver, Marie Mack, Jennifer Aslop, Paul D.P. Pharoah, Florian Markowetz, James D. Brenton
Software Mentions: 3
Published: almost 12 years ago

10.3389/fonc.2020.606765

KIF21B Expression in Osteosarcoma and Its Regulatory Effect on Osteosarcoma Cell Proliferation and Apoptosis Through the PI3K/AKT Pathway
Cited by: 7
Author(s): Songjia Ni, Jianjun Li, Sujun Qiu, Yingming Xie, Kaiqin Gong, Yang Duan
Software Mentions: 3
Published: over 5 years ago

10.1016/j.mcpro.2021.100096

Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury
Cited by: 14
Author(s): Michael A. Skinnider, Jason C. Rogalski, Seth Tigchelaar, Neda Manouchehri, Anna Prudova, Angela Jackson, Karina Nielsen, Jaihyun Jeong, Shalini Chaudhary, Katelyn Shortt, Ylonna Gallagher-Kurtzke, Kitty So, Allan Fong, Rishab Gupta, Elena B. Okon, Michael A. Rizzuto, Kevin Dong, Femke Streijger, Lise Bélanger, Leanna Ritchie, Angela Tsang, Sean Christie, Jean-Marc Mac-Thiong, Chris Bailey, Tamir Ailon, Raphaële Charest-Morin, Nicolas Dea, Jefferson R. Wilson, Sanjay S. Dhall, Scott Paquette, John Street, Charles G. Fisher, Marcel F. Dvorak, Casey P. Shannon, Christoph H. Borchers, Robert Balshaw, Leonard J. Foster, Brian K. Kwon
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.6678

Genetic deletion of osteopontin in TRAMP mice skews prostate carcinogenesis from adenocarcinoma to aggressive human-like neuroendocrine cancers
Cited by: 8
Author(s): Giorgio Mauri, Elena Jachetti, Barbara Comuzzi, Matteo Dugo, Ivano Arioli, Silvia Miotti, Sabina Sangaletti, Emma Di Carlo, Claudio Tripodo, Mario P. Colombo
Software Mentions: 3
Published: over 10 years ago

10.1093/infdis/jix519

Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus Infection
Cited by: 28
Author(s): Lien Anh Ha, Johann Pellet, H. Rogier van Doorn, Anh Tuấn Trần, Bach Hue Nguyen, Thi Thu Loan Tran, Quynh Huong Tran, Quoc Bao Vo, Nguyen Anh Tran Dac, Hong Nhien Trinh, Thi Thanh Hai Nguyen, Bao Tinh Le Binh, Huu Mai Khanh Nguyen, Minh Tien Nguyen, Quang Tung Thai, Thanh Vu Vo, Ngoc Quang Minh Ngo, Thi Kim Huyen Dang, Ngoc Huong Cao, Thu Van Tran, Lu Viet Ho, Bertrand De Meulder, Charles Auffray, Jorrit–Jan H. Hofstra, Jeremy Farrar, Juliet E. Bryant, Menno D. de Jong, Martin L. Hibberd
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2105-12-480

GC-Content Normalization for RNA-Seq Data
Cited by: 656
Author(s): Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit
Software Mentions: 3
Published: almost 15 years ago

10.4049/jimmunol.1901072

CXCR3 Identifies Human Naive CD8+ T Cells with Enhanced Effector Differentiation Potential
Cited by: 30
Author(s): Gabriele De Simone, Emilia Maria Cristina Mazza, Antonino Cassotta, Alexey N. Davydov, Mirela Kuka, Veronica Zanon, Fédérica De Paoli, Eloise Scamardella, Maria Metsger, Alessandra Roberto, Karolina Pilipow, Federico Colombo, Elena Tenedini, Enrico Tagliafico, Luca Gattinoni, Domenico Mavilio, Clelia Peano, David A. Price, Satya P. Singh, Joshua M. Farber, Valentina Serra, Francesco Cucca, Francesco Ferrari, Valeria Orrù, Edoardo Fiorillo, Matteo Iannacone, Dmitriy M. Chudakov, Federica Sallusto, Enrico Lugli
Software Mentions: 3
Published: almost 7 years ago

10.3389/fonc.2021.645912

Identification of Tumor Microenvironment-Related Alternative Splicing Events to Predict the Prognosis of Endometrial Cancer
Cited by: 4
Author(s): Xuan Li, Chuan Liu, Jie Liu, Ying Song, Shanshan Wang, Miaoqing Wu, Shanshan Yu, Luya Cai
Software Mentions: 3
Published: over 5 years ago

10.1074/mcp.RA119.001737

The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease
Cited by: 19
Author(s): Hazal Haytural, Georgios Mermelekas, Ceren Emre, Saket Milind Nigam, Steven L. Carroll, Bengt Winblad, Nenad Bogdanović, Gaël Barthet, Ann‐Charlotte Granholm, Lukas M. Orre, Lars O. Tjernberg, Susanne Frykman
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.583316

Key Modules and Hub Genes Identified by Coexpression Network Analysis for Revealing Novel Biomarkers for Spina Bifida
Cited by: 6
Author(s): Zijian Li, Juan Feng, Zhengwei Yuan
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2020.00778

Identification of Potential Biomarkers for CAD Using Integrated Expression and Methylation Data
Cited by: 5
Author(s): Xiaokang Zhang, Yu‐Tao Xiang, Dingdong He, Bin Liang, Chen Wang, Jing Luo, Fang Zheng
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0019322

Generation of a Predictive Melphalan Resistance Index by Drug Screen of B-Cell Cancer Cell Lines
Cited by: 19
Author(s): Martin Boegsted, Johanne Marie Holst, Kirsten Fogd, Steffen Falgreen, Susanne Sørensen, Alexander Schmitz, Anne Bukh, Hans Erik Johnsen, Mette Nyegaard, Karen Dybkær
Software Mentions: 3
Published: over 15 years ago

10.18632/aging.102804

The IL1β-HER2-CLDN18/CLDN4 axis mediates lung barrier damage in ARDS
Cited by: 9
Author(s): Xiaochun Ma, Xin Yu, Qi Zhou
Software Mentions: 3
Published: over 6 years ago

10.1111/mec.14134

Copy number increases of transposable elements and protein‐coding genes in an invasive fish of hybrid origin
Cited by: 24
Author(s): Stefan Dennenmoser, Fritz J. Sedlazeck, Elzbieta Iwaszkiewicz, Xiangyi Li, Janine Altmüller, Arne W. Nolte
Software Mentions: 3
Published: over 9 years ago

10.1186/s13059-014-0522-z

Sex differences in the genome-wide DNA methylation pattern and impact on gene expression, microRNA levels and insulin secretion in human pancreatic islets
Cited by: 186
Author(s): Elin Hall, Petr Volkov, Tasnim Dayeh, Jonathan L.S. Esguerra, Sofia Salö, Lena Eliasson, Tina Rönn, Karl Bacos, Charlotte Ling
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12859-018-2318-8

Identification of differentially expressed genes by means of outlier detection
Cited by: 5
Author(s): Itziar Irigoien, C. Arenas
Software Mentions: 3
Published: about 8 years ago

10.3390/molecules25092155

Repurposing Zileuton as a Depression Drug Using an AI and In Vitro Approach
Cited by: 9
Author(s): Norwin Kubick, Marta Pajares, Ioana Enache, Gina Manda, Michel‐Edwar Mickael
Software Mentions: 3
Published: over 6 years ago

10.1210/me.2013-1254

RIP140 Represses the “Brown-in-White” Adipocyte Program Including a Futile Cycle of Triacyclglycerol Breakdown and Synthesis
Cited by: 41
Author(s): Evangelos Kiskinis, Lemonia Chatzeli, Ed Curry, Myrsini Kaforou, Andrea Frontini, Saverio Cinti, Giovanni Montana, Malcolm G. Parker, Mark Christian
Software Mentions: 3
Published: over 12 years ago

10.3389/fgene.2020.00195

Genomic and Transcriptomic Landscape of Tumor Clonal Evolution in Cholangiocarcinoma
Cited by: 3
Author(s): Geng Chen, Zhixiong Cai, Xiaoli Dong, Jing Hua Zhao, Lin Song, Xiaobing Hu, Fange Liu, Xiaolong Liu, Huqing Zhang
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0049918

Expression of MicroRNAs in the NCI-60 Cancer Cell-Lines
Cited by: 17
Author(s): Santosh K. Patnaik, Jesper Dahlgaard, Wiktor Mazin, Eric Kannisto, Thomas E. Jensen, Steen Knudsen, Sai Yendamuri
Software Mentions: 3
Published: almost 14 years ago

10.3389/fgene.2019.01039

Genetic Study of Severe Prolonged Lymphopenia in Multiple Sclerosis Patients Treated With Dimethyl Fumarate
Cited by: 3
Author(s): Dipen Sangurdekar, Chao Sun, Helen McLaughlin, Katherine Ayling-Rouse, Norm Allaire, M. A. Penny, Paola G. Bronson
Software Mentions: 3
Published: almost 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 16 years ago

10.3389/fonc.2021.659201

Prognostic Prediction of Cytogenetically Normal Acute Myeloid Leukemia Based on a Gene Expression Model
Cited by: 4
Author(s): Yang Liu, Houyu Zhang, Xue Yang, Ting Lu, Shihui Ma, Hui Cheng, Kuangyu Yen, Tao Cheng
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-10-288

Exploratory and inferential analysis of gene cluster neighborhood graphs
Cited by: 4
Author(s): Theresa Scharl, Ingo Voglhuber, Friedrich Leisch
Software Mentions: 3
Published: about 17 years ago

10.1186/s10020-019-0113-2

Integrated transcriptomic analysis reveals hub genes involved in diagnosis and prognosis of pancreatic cancer
Cited by: 30
Author(s): Yangyang Zhou, Liping Chen, Yi Zhang, Sunkuan Hu, Zhaojun Dong, Ming Wu, Qiuxiang Chen, Zhizhi Zhuang, Xiaojing Du
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0131627

Ensemble Methods for MiRNA Target Prediction from Expression Data
Cited by: 29
Author(s): Thuc Duy Le, Junpeng Zhang, Lin Liu, Jiuyong Li
Software Mentions: 3
Published: about 11 years ago

10.1186/s10020-020-00203-0

Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Cited by: 14
Author(s): Lara Kim Brackmann, Alicia Schulze, Caine Lucas Grandt, Heike Schwarz, Thomas Hankeln, Steffen Rapp, Sebastian Zahnreich, Danuta Galetzka, Iris Schmitt, Christian Grad, Lukas Eckhard, Johanna Mirsch, Maria Blettner, Peter Scholz-Kreisel, Moritz Hess, Harald Binder, Heinz Schmidberger, Manuela Marron
Software Mentions: 3
Published: about 6 years ago

10.18632/aging.103698

A two-gene-based prognostic signature for pancreatic cancer
Cited by: 8
Author(s): Shengqian Zhou, Yuanliang Yan, Xi Chen, Shuangshuang Zeng, Jie Wei, Xiang Wang, Zhicheng Gong, Zhijie Xu
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2019.00419

Expression Profile Analysis Identifies a Novel Five-Gene Signature to Improve Prognosis Prediction of Glioblastoma
Cited by: 42
Author(s): Yin Wu, Guihua Tang, Quanwei Zhou, Yudong Cao, Haixia Li, Xianyong Fu, Zhaoping Wu, Xingjun Jiang
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-15-238

Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models
Cited by: 92
Author(s): Florian Martin, Alain Sewer, Marja Talikka, Yu‐Tao Xiang, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0113496

Synergy: A Web Resource for Exploring Gene Regulation in Synechocystis sp. PCC6803
Cited by: 4
Author(s): Niklas Mähler, Otilia Cheregi, Christiane Funk, Sergiu Netotea, Torgeir R. Hvidsten
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0056274

Headbobber: A Combined Morphogenetic and Cochleosaccular Mouse Model to Study 10qter Deletions in Human Deafness
Cited by: 7
Author(s): Annalisa Buniello, Rachel E. Hardisty-Hughes, Johanna Pass, Eva Bober, Richard J.H. Smith, Karen P. Steel
Software Mentions: 3
Published: over 13 years ago

10.3389/fgene.2020.622659

Identification of a Five-Gene Prognostic Model and Its Potential Drug Repurposing in Colorectal Cancer Based on TCGA, GTEx and GEO Databases
Cited by: 9
Author(s): Feng Yang, Shaoyi Cai, Ling Li, Haiji Zhang, Liang Tao, Qin Wang
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-9-502

Microarray-based gene set analysis: a comparison of current methods
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Author(s): Sarah Song, Michael A. Black
Software Mentions: 3
Published: almost 18 years ago

10.1186/gb-2012-13-6-r54

Regulation of alternative splicing by the circadian clock and food related cues
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Author(s): Nicholas J. McGlincy, Amandine Valomon, Johanna E. Chesham, Elizabeth S. Maywood, Michael H. Hastings, Jernej Ule
Software Mentions: 3
Published: over 14 years ago

10.1186/gb-2012-13-6-r44

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips
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Author(s): Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack
Software Mentions: 3
Published: over 14 years ago

10.3389/fgene.2021.580390

Systematic Identification of circRNA–miRNA–mRNA Regulatory Network in Esophageal Squamous Cell Carcinoma
Cited by: 6
Author(s): Yi Shen, Yi Shao, Chen Niu, Xiaoli Ruan, Zhaoping Zang, Rena Nakyeyune, Xiuhua Guo, Fen Liu
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2020.00816

Identification and Validation of Key Genes Associated With Systemic Sclerosis-Related Pulmonary Hypertension
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Author(s): Ji-Na Zheng, Yang Li, Yue-Mei Yan, Hui Shi, Tiantian Zou, Wenqi Shao, Qiang Wang
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2105-11-280

Data analysis issues for allele-specific expression using Illumina's GoldenGate assay
Cited by: 4
Author(s): Matthew E. Ritchie, Matthew S. Forrest, Antigone S. Dimas, Caroline Daelemans, Emmanouil T. Dermitzakis, Panos Deloukas, Simon Tavaré
Software Mentions: 3
Published: over 16 years ago

10.1186/gb-2010-11-10-r106

Differential expression analysis for sequence count data
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Author(s): Simon Anders, Wolfgang Huber
Software Mentions: 3
Published: almost 16 years ago

10.3389/fgene.2020.586814

Differential Expression and Bioinformatics Analysis of circRNA in Non-small Cell Lung Cancer
Cited by: 21
Author(s): Qian Sun, Xia Li, Muchen Xu, Li Zhang, Haiwei Zuo, Yong Xin, Longzhen Zhang, Ping Gong
Software Mentions: 3
Published: almost 6 years ago

10.18632/oncotarget.16252

Niclosamide is a potential therapeutic for familial adenomatosis polyposis by disrupting Axin-GSK3 interaction
Cited by: 26
Author(s): Ahn Sk, Nam Hee Kim, Kyungro Lee, Yong Hoon, Ji Hye Yang, So Young, Eunae Sandra Cho, Yoonmi Lee, Jeong Ho Seok, Hyun Soo Cho, Yongseok Jeon, Young Su Yuk, Suebean Cho, Kyoung Tai No, Hyun Sil Kim, Ho Lee, Jiwon Choi, Jong In Yook
Software Mentions: 3
Published: over 9 years ago

10.3389/fonc.2019.00957

ACAT1 and Metabolism-Related Pathways Are Essential for the Progression of Clear Cell Renal Cell Carcinoma (ccRCC), as Determined by Co-expression Network Analysis
Cited by: 32
Author(s): Liang Chen, Tianchen Peng, Yongwen Luo, Fenfang Zhou, Gang Wang, Kaiyu Qian, Yu Xiao, Xinghuan Wang
Software Mentions: 3
Published: almost 7 years ago

10.3389/fgene.2019.00059

Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome
Cited by: 10
Author(s): Ryan Miller, Friederike Ehrhart, Lars Eijssen, Denise Slenter, Leopold Curfs, Chris T. Evelo, Egon Willighagen, Martina Kutmon
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0054398

miRNA Gene Promoters Are Frequent Targets of Aberrant DNA Methylation in Human Breast Cancer
Cited by: 114
Author(s): Lukáš Vrba, J. Muñoz-Rodríguez, Martha R. Stampfer, Bernard W. Futscher
Software Mentions: 3
Published: over 13 years ago

10.3389/fgene.2021.712150

Construction of Circulating MicroRNAs-Based Non-invasive Prediction Models of Recurrent Implantation Failure by Network Analysis
Cited by: 2
Author(s): Peigen Chen, Tingting Li, Yingchun Guo, Jia Lu, Yanfang Wang, Cong Fang
Software Mentions: 3
Published: about 5 years ago

10.1186/gb-2010-11-8-r90

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
Cited by: 1,374
Author(s): Doron Betel, Anjali Koppal, Phaedra Agius, Chris Sander, Christina C. Leslie
Software Mentions: 3
Published: over 16 years ago

10.3389/fgene.2021.583568

Aberrantly DNA Methylated-Differentially Expressed Genes in Pancreatic Cancer Through an Integrated Bioinformatics Approach
Cited by: 4
Author(s): Haifeng Sun, Rui Xin, Changjun Zheng, Ge Huang
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.8611

Co-expression network analysis reveals the pivotal role of mitochondrial dysfunction and interferon signature in juvenile dermatomyositis
Cited by: 7
Author(s): Danli Zhong, Caimei Wu, Jingjing Bai, Duanfu Xu, Xiaofeng Zeng, Qian Wang
Software Mentions: 3
Published: over 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: over 18 years ago

10.3389/fonc.2021.682917

Apigenin Inhibits the Histamine-Induced Proliferation of Ovarian Cancer Cells by Downregulating ERα/ERβ Expression
Cited by: 9
Author(s): Manman Liu, Yani Zhang, Qiqi Xu, Guirong Liu, Na Sun, Huilian Che, Tong‐Chuan He
Software Mentions: 3
Published: about 5 years ago

10.7717/peerj.8930

Transcriptome analysis revealed key prognostic genes and microRNAs in hepatocellular carcinoma
Cited by: 24
Author(s): Xi Ma, Lin Zhou, Shusen Zheng
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.00615

A Long Non-coding RNA, LOC157273, Is an Effector Transcript at the Chromosome 8p23.1-PPP1R3B Metabolic Traits and Type 2 Diabetes Risk Locus
Cited by: 14
Author(s): Alisa K. Manning, Anton Scott Goustin, Erica L. Kleinbrink, Pattaraporn Thepsuwan, Juan Cai, Donghong Ju, Aaron Leong, Miriam S. Udler, James Brown, Mark O. Goodarzi, Jerome I. Rotter, Robert Sladek, James B. Meigs, Leonard Lipovich
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2020.602908

Identifying RBM47, HCK, CD53, TYROBP, and HAVCR2 as Hub Genes in Advanced Atherosclerotic Plaques by Network-Based Analysis and Validation
Cited by: 19
Author(s): Chiyu Liu, Haifeng Zhang, Yangxin Chen, Shaohua Wang, Zhiteng Chen, Zhaoyu Liu, Jingfeng Wang
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.7873

Identification of crucial genes in abdominal aortic aneurysm by WGCNA
Cited by: 61
Author(s): Siliang Chen, Dan Yang, Chuxiang Lei, Yuan Li, Xiaoning Sun, Mengyin Chen, Xiaoxian Wu, Yuehong Zheng
Software Mentions: 3
Published: almost 7 years ago

10.3389/fgene.2020.00722

Identification of Gene Modules and Hub Genes Involved in Mastitis Development Using a Systems Biology Approach
Cited by: 36
Author(s): Mohammad Reza Bakhtiarizadeh, Shabnam Mirzaei, Milad Norouzi, Negin Sheybani, Mohammad Sadegh Vafaei Sadi
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0131103

The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis
Cited by: 13
Author(s): Kim L. Johnson, Sascha Ramm, Christian Kappel, Sally Ward, Ottoline Leyser, Tomoaki Sakamoto, Takeshi Kurata, Michael W. Bevan, Michael Lenhard
Software Mentions: 3
Published: about 11 years ago

10.3389/fgene.2020.573877

Analysis of Hub Genes Involved in Distinction Between Aged and Fetal Bone Marrow Mesenchymal Stem Cells by Robust Rank Aggregation and Multiple Functional Annotation Methods
Cited by: 6
Author(s): Xiaoyao Liu, Mingjing Yin, Junlong Da, Kai Zhang, Xinjian Zhang, Lixue Liu, Jianqun Wang, Han Jin, Zhongshuang Liu, Bin Zhang, Ying Li
Software Mentions: 3
Published: almost 6 years ago

10.7717/peerj.6555

Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA
Cited by: 33
Author(s): Wangxiao Xia, Qin Yu, Gong‐Hua Li, Yaowen Liu, Fu-Hui Xiao, Libin Yang, Zia Ur Rahman, Haotian Wang, Qing‐Peng Kong
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.102943

Genetic networks in Parkinson’s and Alzheimer’s disease
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Author(s): Jack Kelly, Rana Moyeed, Camille Carroll, Shouqing Luo, Xinzhong Li
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-018-2513-7

Capturing context-specific regulation in molecular interaction networks
Cited by: 5
Author(s): Stephen Rush, Dirk Repsilber
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0089187

Miz1 Deficiency in the Mammary Gland Causes a Lactation Defect by Attenuated Stat5 Expression and Phosphorylation
Cited by: 7
Author(s): Adrián Sanz-Moreno, David Fuhrmann, Elmar Wolf, Björn von Eyß, Martin Eilers, Hans–Peter Elsässer
Software Mentions: 3
Published: over 12 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776