bioconductor: limma | Projects | Ecosyste.ms: Papers

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

Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex
Cited by: 50
Author(s): Brian D. Eads, John K. Colbourne, Elizabeth A. Bohuski, Justen Andrews
Software Mentions: 3
Published: over 19 years ago

10.1186/1471-2164-10-419

Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation
Cited by: 32
Author(s): Sergei A. Manakov, Seth G. N. Grant, Anton J. Enright
Software Mentions: 3
Published: about 17 years ago

10.7554/eLife.57068

MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly
Cited by: 7
Author(s): Meltem Weger, Benjamin D. Weger, Andrea Schink, Masanari Takamiya, Johannes Stegmaier, Cédric Gobet, Alice Parisi, Andrei Yu Kobitski, Jonas Mertes, Nils Krone, Uwe Strähle, G. Ulrich Nienhaus, Ralf Mikut, Frédéric Gachon, Philipp Gut, Thomas Dickmeis
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-017-3488-x

Conserved gene expression in sperm reservoirs between birds and mammals in response to mating
Cited by: 23
Author(s): Mohammad Atikuzzaman, Manuel Álvarez‐Rodríguez, Alejandro Vicente-Carrillo, Martin Johnsson, Dominic Wright, Heriberto Rodríguez-Martinez
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-020-69884-1

Selective dysregulation of ROCK2 activity promotes aberrant transcriptional networks in ABC diffuse large B-cell lymphoma
Cited by: 4
Author(s): Edd Ricker, Akanksha Verma, Rossella Marullo, Sanjay Gupta, Chao Ye, Tania Pannellini, Michela Manni, Wayne Tam, Giorgio Inghirami, Olivier Elemento, Leandro Cerchietti, Alessandra B. Pernis
Software Mentions: 3
Published: about 6 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

10.1038/s41598-019-44661-x

The ion channels and transporters gene expression profile indicates a shift in excitability and metabolisms during malignant progression of Follicular Lymphoma
Cited by: 18
Author(s): Alberto Magi, Marika Masselli, Cesare Sala, Angela Guerriero, Pasquale Laise, Benedetta Puccini, Luigi Rigacci, C Breschi, Olivia Crociani, Serena Pillozzi, Annarosa Arcangeli
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-44882-0

Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development
Cited by: 15
Author(s): Elo Madissoon, Anastasios Damdimopoulos, Shintaro Katayama, Kaarel Krjutškov, Elisabet Einarsdottir, Katariina Mamia, Bert De Groef, Outi Hovatta, Juha Kere, Pauliina Damdimopoulou
Software Mentions: 3
Published: over 7 years ago

10.1186/s13040-016-0122-4

Elevated transcriptional levels of aldolase A (ALDOA) associates with cell cycle-related genes in patients with NSCLC and several solid tumors
Cited by: 25
Author(s): Fan Zhang, Jiediao Lin, Xiaoyu Zuo, Yingping Zhuang, Chao‐Qun Hong, Guojun Zhang, Xiaojiang Cui, Yukun Cui
Software Mentions: 3
Published: over 9 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

10.18632/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

10.7554/eLife.65331

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast
Cited by: 2
Author(s): Rachael Emily Turner, Paul F. Harrison, Angavai Swaminathan, Calvin A. Kraupner-Taylor, Belinda J. Goldie, Michael See, Amanda L. Peterson, Ralf B. Schittenhelm, David Powell, Darren J. Creek, Bernhard Dichtl, Traude H. Beilharz
Software Mentions: 3
Published: about 5 years ago

10.1016/j.bbrep.2015.08.012

Xanthophylls lutein and zeaxanthin modify gene expression and induce synthesis of hyaluronan in keratinocyte model of human skin
Cited by: 9
Author(s): Rasia Li, Stephen D. Turner, David L. Brautigan
Software Mentions: 3
Published: almost 11 years ago

10.1155/2019/6469420

Integrated Analysis of Oncogenic Networks in Colorectal Cancer Identifies GUCA2A as a Molecular Marker
Cited by: 24
Author(s): Hui Zhang, Yuanyuan Du, Zhuo Wang, Rui Lou, Jianzhong Wu, Jifeng Feng
Software Mentions: 3
Published: about 7 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

10.3390/cancers12113079

Comprehensive Analysis of DNA Methylation and Prediction of Response to NeoadjuvantTherapy in Locally Advanced Rectal Cancer
Cited by: 12
Author(s): Luísa Matos do Canto, Mateus Camargo Barros-Filho, Cláudia Aparecida Rainho, Diogo Marinho, Bruna Elisa Catin Kupper, Maria D. Begnami, Cristovam Scapulatempo‐Neto, Birgitte Mayland Havelund, Jan Lindebjerg, Fábio Albuquerque Marchi, Jan Baumbach, Samuel Aguiar, Sílvia Regina Rogatto
Software Mentions: 3
Published: almost 6 years ago

10.1007/s10522-016-9638-8

The functional consequences of age-related changes in microRNA expression in skeletal muscle
Cited by: 49
Author(s): Ana Soriano‐Arroquia, Louise House, Luke Tregilgas, Elizabeth G. Canty‐Laird, Katarzyna Goljanek‐Whysall
Software Mentions: 3
Published: over 10 years ago

10.1093/bioinformatics/btv425

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment
Cited by: 72
Author(s): Marek Gierliński, Christian Callebaut, Pietà Schofield, Nicholas J. Schurch, Alexander Sherstnev, Vijender Singh, Nicola Wrobel, Karim Gharbi, Gordon G. Simpson, Tom Owen-Hughes, Mark Blaxter, Geoffrey J. Barton
Software Mentions: 3
Published: about 11 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

10.3390/cancers11040479

Combined Targeting of Estrogen Receptor Alpha and XPO1 Prevent Akt Activation, Remodel Metabolic Pathways and Induce Autophagy to Overcome Tamoxifen Resistance
Cited by: 13
Author(s): Eylem Kulkoyluoglu-Cotul, Brandi Patrice Smith, Kinga Wrobel, Yijia Zhao, Karen Lee Ann Chen, Kadriye Hieronymi, Ozan Berk Imir, Kevin Duong, Caitlin O’Callaghan, Aditi Mehta, Sunati Sahoo, Barbara Haley, Hua Chang, Yosef Landesman, Zeynep Madak-Erdoğan
Software Mentions: 3
Published: over 7 years ago

10.1093/bioinformatics/bts680

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
Cited by: 1,196
Author(s): Andrew E. Teschendorff, Francesco Marabita, Matthias Lechner, Thomas E. Bartlett, Jesper Tegnér, David Gomez-Cabrero, Stephan Beck
Software Mentions: 3
Published: almost 14 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

10.1093/bioinformatics/btx513

ChAMP: updated methylation analysis pipeline for Illumina BeadChips
Cited by: 496
Author(s): Yuan Tian, Tiffany Morris, Amy P Webster, Zhen Yang, Stephan Beck, Andrew Feber, Andrew E. Teschendorff
Software Mentions: 3
Published: about 9 years ago

10.1186/s13018-021-02402-9

Identification of key regulators responsible for dysregulated networks in osteoarthritis by large-scale expression analysis
Cited by: 7
Author(s): Shuangshuang Song, Fuyin Wan, Zhenyu Zhou, Ran Tao, Yue Lü, Ming Zhou, Fan Liu, Yake Liu
Software Mentions: 3
Published: over 5 years ago

10.1093/bioinformatics/bts656

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
Cited by: 62
Author(s): Clare Pacini, Francesco Iorio, Emanuel Gonçalvès, Murat Iskar, Thomas Klabunde, Peer Bork, Julio Sáez-Rodríguez
Software Mentions: 3
Published: almost 14 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

10.1093/bioinformatics/btx355

Hierarchical probabilistic models for multiple gene/variant associations based on next-generation sequencing data
Cited by: 5
Author(s): Dimitrios V Vavoulis, Jenny C. Taylor, Anna Schuh
Software Mentions: 3
Published: over 9 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

10.1186/s12967-021-03014-x

Identification of tumor antigens and immune subtypes in lower grade gliomas for mRNA vaccine development
Cited by: 14
Author(s): Liguo Ye, Long Wang, Jian Yang, Ping Hu, Chunyu Zhang, Shiao Tong, Zhennan Liu, Daofeng Tian
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-43512-z

Melanoma proteomics suggests functional differences related to mutational status
Cited by: 9
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Claudia Fortes, María Ferrer-Gómez, Rocío López-Vacas, Verónica Parra Blanco, Iván Márquez-Rodas, Ainara Soria, Juan Ángel Fresno Vara, Enrique Espinosa
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.27746

Distinct SoxB1 networks are required for naïve and primed pluripotency
Cited by: 16
Author(s): Andrea Corsinotti, Frederick C K Wong, Tülin Tatar, Iwona Szczerbinska, Florian Halbritter, Douglas Colby, Sabine Gogolok, Raphaël Pantier, Kirsten Liggat, Elham Sadat Mirfazeli, Elisa Hall-Ponselé, Nicholas P. Mullin, Valerie Wilson, Ian Chambers
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.15635

Sox9 and Sox8 protect the adult testis from male-to-female genetic reprogramming and complete degeneration
Cited by: 65
Author(s): Francisco Barrionuevo, Alicia Hurtado, Gwang-Jin Kim, Francisca M. Real, Mohammed Bakkali, Janel L. Kopp, Maike Sander, Gerd Scherer, Miguel Burgos, Rafael Jiménez
Software Mentions: 3
Published: about 10 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

10.1186/s13062-018-0223-8

Predicting clinical outcomes in neuroblastoma with genomic data integration
Cited by: 9
Author(s): Ilyes Baali, Durmus Alp Emre Acar, Tunde Aderinwale, Saber Hafezqorani, Hilal Kazan
Software Mentions: 3
Published: almost 8 years ago

10.1242/bio.054189

A stem cell based in vitro model of NAFLD enables the analysis of patient specific individual metabolic adaptations in response to a high fat diet and AdipoRon interference
Cited by: 6
Author(s): Nina Graffmann, Audrey Ncube, Soraia Martins, Aurelian Robert Fiszl, Philipp Reuther, Martina Bohndorf, Wasco Wruck, Mathias Beller, Constantin Czekelius, James Adjaye
Software Mentions: 3
Published: over 6 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

10.18632/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

10.1038/s41598-019-42680-2

Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts
Cited by: 31
Author(s): Yuanhang Liu, Pritha Chanana, Jaime Davila, Xiaonan Hou, Valentina Zanfagnin, Cordelia D. McGehee, Ellen L. Goode, Eric C. Polley, Paul Haluska, S. John Weroha, Chen Wang
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.65715

Epigenetic analysis of Paget’s disease of bone identifies differentially methylated loci that predict disease status
Cited by: 8
Author(s): Ilhame Diboun, Sachin Wani, Stuart H. Ralston, Omar Albagha
Software Mentions: 3
Published: over 5 years ago

10.1186/s13018-021-02201-2

Bioinformatics analysis of miRNA and mRNA expression profiles to reveal the key miRNAs and genes in osteoarthritis
Cited by: 13
Author(s): Peiyan Huang, Junguo Wu, Jun Gu, Tie-qi Zhang, Lingfeng Li, Siqun Wang, Ming-Hai Wang
Software Mentions: 3
Published: over 5 years ago

10.1186/s40659-016-0085-4

Candidate genes and pathogenesis investigation for sepsis-related acute respiratory distress syndrome based on gene expression profile
Cited by: 16
Author(s): Min Wang, Jingjun Yan, Xingxing He, Qiang Zhong, Zhan Chen, Shusheng Li
Software Mentions: 3
Published: over 10 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

10.1038/s41598-019-40857-3

Profiling of gallbladder carcinoma reveals distinct miRNA profiles and activation of STAT1 by the tumor suppressive miRNA-145-5p
Cited by: 23
Author(s): Benjamin Goeppert, Felicia Truckenmueller, Alessandro Ori, Valerie Fritz, Thomas Albrecht, Angelika Fraas, Dominique Scherer, Rosa González Silos, Carsten Sticht, Norbert Gretz, Arianeb Mehrabi, Melanie Bewerunge-Hudler, Stefan Pusch, Justo Lorenzo Bermejo, Péter Dietrich, Peter Schirmacher, Marcus Renner, Stephanie Roessler
Software Mentions: 3
Published: over 7 years ago

10.1186/s40659-018-0192-5

Dysregulation of NCAPG, KNL1, miR-148a-3p, miR-193b-3p, and miR-1179 may contribute to the progression of gastric cancer
Cited by: 52
Author(s): Bin Song, Juan Du, Defeng Song, Jian Ren, Yan Feng
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-019-40963-2

DNA methylation signature of smoking in lung cancer is enriched for exposure signatures in newborn and adult blood
Cited by: 27
Author(s): Kelly M. Bakulski, John Dou, Nan Lin, Stephanie J. London, Justin A. Colacino
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.51406

Proteome profile of peripheral myelin in healthy mice and in a neuropathy model
Cited by: 52
Author(s): Sophie B Siems, Olaf Jahn, Maria A Eichel, Nirmal Kannaiyan, Lai Man Natalie Wu, Diane L. Sherman, Kathrin Kusch, Dörte Hesse, Ramona B. Jung, Robert Fledrich, Michael W. Sereda, Moritz J. Rossner, Peter Brophy, Hauke Werner
Software Mentions: 3
Published: over 6 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

10.1186/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

10.1186/1471-2105-9-502

Microarray-based gene set analysis: a comparison of current methods
Cited by: 68
Author(s): Sarah Song, Michael A. Black
Software Mentions: 3
Published: almost 18 years ago

10.3390/biology10050432

Identifying an lncRNA-Related ceRNA Network to Reveal Novel Targets for a Cutaneous Squamous Cell Carcinoma
Cited by: 7
Author(s): Yaqin Xu, Yingying Dong, Yansha Deng, Qian-Rong Qi, Mi Wu, Hongmei Liang, Qiuyun She, Qing Guo
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0063419

HMGA1: A Master Regulator of Tumor Progression in Triple-Negative Breast Cancer Cells
Cited by: 102
Author(s): Sandeep N. Shah, Leslie Cope, Weijie Poh, Amy Belton, Suheeta Roy, C. Conover Talbot, Saraswati Sukumar, David L. Huso, Linda M.S. Resar
Software Mentions: 3
Published: over 13 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

10.1038/s41598-018-38441-2

Elastic net-based prediction of IFN-β treatment response of patients with multiple sclerosis using time series microarray gene expression profiles
Cited by: 11
Author(s): Arika Fukushima, Masahiro Sugimoto, Satoru Hiwa, Tomoyuki Hiroyasu
Software Mentions: 3
Published: over 7 years ago

10.1155/2020/8571932

AHNAK2 Is Associated with Poor Prognosis and Cell Migration in Lung Adenocarcinoma
Cited by: 9
Author(s): Shusen Zhang, Yuanyuan Lu, Ling Qi, Hongyan Wang, Zhihua Wang, Zhigang Cai
Software Mentions: 3
Published: about 6 years ago

10.1186/s12967-019-1790-x

Bioinformatic gene analysis for potential biomarkers and therapeutic targets of atrial fibrillation-related stroke
Cited by: 60
Author(s): Rongjun Zou, Dingwen Zhang, Lei Lv, Wu Shi, Zilin Song, Bin Yi, Bingjia Lai, Qian Chen, Shiming Yang, Peng Hua
Software Mentions: 3
Published: over 7 years ago

10.1155/2020/4037639

A Five-Gene Signature for Recurrence Prediction of Hepatocellular Carcinoma Patients
Cited by: 6
Author(s): Zeyu Wang, Ningning Zhang, Jiayu Lv, Cuihua Ma, Jun Gu, Yawei Du, Yulan Qiu, Zhiguang Zhang, Man Li, Yong Jiang, Jianqiu Zhao, Hui-Qin Du, Zhiwei Zhang, Yan Zhang
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0159197

Comparative Transcriptome Profiling of Human Foreskin Fibroblasts Infected with the Sylvio and Y Strains of Trypanosoma cruzi
Cited by: 22
Author(s): Genevieve A. Houston-Ludlam, Ashton T. Belew, Najib M. El-Sayed
Software Mentions: 3
Published: about 10 years ago

10.18632/aging.102943

Genetic networks in Parkinson’s and Alzheimer’s disease
Cited by: 23
Author(s): Jack Kelly, Rana Moyeed, Camille Carroll, Shouqing Luo, Xinzhong Li
Software Mentions: 3
Published: over 6 years ago

10.1155/2021/5584681

Biodata Mining of Differentially Expressed Genes between Acute Myocardial Infarction and Unstable Angina Based on Integrated Bioinformatics
Cited by: 4
Author(s): Siyu Guo, Zhihong Huang, Xinkui Liu, Jingyuan Zhang, Peizhi Ye, Chao Wu, Shan Lu, Shanshan Jia, Xiaomeng Zhang, Xiuping Chen, Miaomiao Wang, Jiarui Wu
Software Mentions: 3
Published: about 5 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

10.7554/eLife.56095

Inflammatory osteolysis is regulated by site-specific ISGylation of the scaffold protein NEMO
Cited by: 16
Author(s): Naga Suresh Adapala, Gaurav Swarnkar, Manoj Arra, Jie Shen, Gabriel Mbalaviele, Ke Ke, Yousef Abu‐Amer
Software Mentions: 3
Published: over 6 years ago

10.1155/2021/3947350

Identification of MEDAG as a Hub Candidate Gene in the Onset and Progression of Type 2 Diabetes Mellitus by Comprehensive Bioinformatics Analysis
Cited by: 3
Author(s): Jing Yang, Ping Yü
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-019-2705-9

Network meta-analysis correlates with analysis of merged independent transcriptome expression data
Cited by: 11
Author(s): Christine Winter, Robin Kosch, Martin Ludlow, Albert D. M. E. Osterhaus, Klaus Jung
Software Mentions: 3
Published: over 7 years ago

10.3390/cancers11101410

An IKK/NF-κB Activation/p53 Deletion Sequence Drives Liver Carcinogenesis and Tumor Differentiation
Cited by: 3
Author(s): Michael Svinarenko, Sarah‐Fee Katz, Umesh Tharehalli, Medhanie Mulaw, Harald J. Maier, Yoshiaki Sunami, Sarah Fischer, Yuexin Chen, Sabine Heurich, Lena Erkert, Andrea Tannapfel, Thomas Wirth, Reinhold Schirmbeck, Thomas Seufferlein, André Lechel
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-37411-y

INSIdE NANO: a systems biology framework to contextualize the mechanism-of-action of engineered nanomaterials
Cited by: 25
Author(s): Angela Serra, Ivica Letunić, Vittorio Fortino, Richard D. Handy, Bengt Fadeel, Roberto Tagliaferri, Dario Greco
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-018-2107-4

Watchdog – a workflow management system for the distributed analysis of large-scale experimental data
Cited by: 20
Author(s): Michael Kluge, Caroline C. Friedel
Software Mentions: 3
Published: over 8 years ago

10.1186/s40478-019-0665-y

Comprehensive gene expression meta-analysis identifies signature genes that distinguish microglia from peripheral monocytes/macrophages in health and glioma
Cited by: 109
Author(s): Verena Haage, Marcus Semtner, Ramón Vidal, Daniel Hernández, Winnie W. Pong, Zhihong Chen, Dolores Hambardzumyan, Vincent Magrini, Amy Ly, Jason Walker, Elaine R. Mardis, Philipp Mertins, Sascha Sauer, Helmut Kettenmann, David H. Gutmann
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-13-329

Generalization of the normal-exponential model: exploration of a more accurate parametrisation for the signal distribution on Illumina BeadArrays
Cited by: 12
Author(s): Sandra Plancade, Yves Rozenholc, Eiliv Lund
Software Mentions: 3
Published: almost 14 years ago

10.1038/s41598-018-35868-5

In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors
Cited by: 11
Author(s): Suzanne Vanhauwaert, Bieke Decaesteker, Sara De Brouwer, Carina Leonelli, Kaat Durinck, Pieter Mestdagh, Jo Vandesompele, Karen Sermon, Geertrui Denecker, Christophe Van Neste, Franki Speleman, Katleen De Preter
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13018-020-01839-8

Bioinformatics analysis of differentially expressed genes in subchondral bone in early experimental osteoarthritis using microarray data
Cited by: 2
Author(s): Wang Zhao, Yong Ji, Hongwei Bao
Software Mentions: 3
Published: about 6 years ago

10.1155/2017/2421459

Prediction and Validation of Hub Genes Associated with Colorectal Cancer by Integrating PPI Network and Gene Expression Data
Cited by: 19
Author(s): Yong Xiong, Wenxian You, Rong Wang, Linglong Peng, Zhongxue Fu
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2105-9-85

Statistical issues in the analysis of Illumina data
Cited by: 91
Author(s): Mark J. Dunning, Nuno L. Barbosa‐Morais, Andy G. Lynch, Simon Tavaré, Matthew E. Ritchie
Software Mentions: 3
Published: over 18 years ago

10.1155/2021/6653802

Multiomics Analysis of Transcriptome, Epigenome, and Genome Uncovers Putative Mechanisms for Dilated Cardiomyopathy
Cited by: 5
Author(s): Li Liu, Jianjun Huang, Yan Liu, Xingshou Pan, Zhile Li, Liufang Zhou, Tengfang Lai, Chengcai Chen, Baomin Wei, Jianjiao Mo, Qinjiang Wei, Yan Wang, Xian-Nan Huang, Zhen Zhang, Zhuohua Zhang, Meidan Huang, Fengzhen He, Zhaohe Huang
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-34292-z

Comprehensive Analysis of Gene Expression Profiles and DNA Methylome reveals Oas1, Ppie, Polr2g as Pathogenic Target Genes of Gestational Diabetes Mellitus
Cited by: 9
Author(s): Yan Zhang, Tiancheng Zhang, Yunyan Chen
Software Mentions: 3
Published: almost 8 years ago

10.18632/aging.202882

Transcriptome integration analysis and specific diagnosis model construction for Hodgkin's lymphoma, diffuse large B-cell lymphoma, and mantle cell lymphoma
Cited by: 2
Author(s): Wen‐Xing Li, Shao‐Xing Dai, Sanqi An, Tingting Sun, Justin Liu, Jun Wang, Leyna G. Liu, Yang Xiao, Hua Yang, Lixia Fan, Xiaoli Zhang, Wanqin Liao, Hua You, Luca Tamagnone, Fang Liu, Jing‐Fei Huang, Dahai Liu
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-019-3028-6

Influence of batch effect correction methods on drug induced differential gene expression profiles
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Author(s): Wei Zhou, Karel K.M. Koudijs, Stefan Böhringer
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-018-33897-8

Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation
Cited by: 13
Author(s): Mercedes Rivas, María Saura, Andrés Pérez‐Figueroa, Marina Panova, Tomas Johansson, Carl André, Armando Caballero, Emilio Rolán‐Alvarez, Kerstin Johannesson, Humberto Quesada
Software Mentions: 3
Published: almost 8 years ago

10.18632/aging.102169

Analysis of transcription factor- and ncRNA-mediated potential pathogenic gene modules in Alzheimer’s disease
Cited by: 13
Author(s): Cuihua Zou, Jie Wang, Xiaohua Huang, Chongdong Jian, Donghua Zou, Xuebin Li
Software Mentions: 3
Published: about 7 years ago

10.18632/oncotarget.24512

Aberrant expression of NKL homeobox gene HLX in Hodgkin lymphoma
Cited by: 12
Author(s): Stefan Nagel, Claudia Pommerenke, Corinna Meyer, Maren Kaufmann, Roderick A.F. MacLeod, Hans Drexler
Software Mentions: 3
Published: over 8 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

10.18632/oncotarget.24035

Reversible LSD1 inhibition with HCI-2509 induces the p53 gene expression signature and disrupts the MYCN signature in high-risk neuroblastoma cells
Cited by: 21
Author(s): Sumati Gupta, Kelly Doyle, Timothy Mosbruger, Andrew Butterfield, Alexis Weston, Allison Ast, Mohan R. Kaadige, Anupam Verma, Sunil Sharma
Software Mentions: 3
Published: over 8 years ago

10.1155/2021/8357585

Comprehensive Analysis of CD163 as a Prognostic Biomarker and Associated with Immune Infiltration in Glioblastoma Multiforme
Cited by: 3
Author(s): Hao Li, Di Wang, Bolong Yi, Heng Cai, Zhuo Xi, Xin Lou, Zhen Li
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-34191-3

Transcriptome analysis of extended-spectrum β-lactamase-producing Escherichia coli and methicillin-resistant Staphylococcus aureus exposed to cefotaxime
Cited by: 12
Author(s): P. R. Brochmann, Andrew Hesketh, Bimal Jana, G. H. Brodersen, Luca Guardabassi
Software Mentions: 3
Published: almost 8 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

10.1038/s41598-018-33807-y

Characterization of the miRNA regulators of the human ovulatory cascade
Cited by: 23
Author(s): Gil M. Yerushalmi, Mali Salmon‐Divon, Libby Ophir, Yuval Yung, Micha Baum, Giovanni Coticchio, Rubens Fadini, Mario Mignini-Renzini, Mariabeatrice Dal Canto, Ronit Machtinger, Ettie Maman, Ariel Hourvitz
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-33478-9

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues
Cited by: 54
Author(s): Bryan J. Pavlovic, Lauren E. Blake, Julien Roux, Claudia Chavarria, Yoav Gilad
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2105-8-346

A framework for significance analysis of gene expression data using dimension reduction methods
Cited by: 41
Author(s): Lars Gidskehaug, Endre Anderssen, Arnar Flatberg, Bjørn K. Alsberg
Software Mentions: 3
Published: about 19 years ago

10.1186/1471-2105-8-108

Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays
Cited by: 52
Author(s): Jun Lü, Joseph C. Lee, Marc Salit, Margaret C. Cam
Software Mentions: 3
Published: over 19 years ago

10.1186/1471-2105-14-S14-S17

mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis
Cited by: 17
Author(s): Cory B. Giles, G. Reshmi, Mikhail G. Dozmorov, Jonathan D. Wren
Software Mentions: 3
Published: almost 13 years ago

10.18632/aging.203140

A novel ferroptosis-related gene signature for prognostic prediction of patients with lung adenocarcinoma
Cited by: 13
Author(s): Jingjing Jin, Chuan Liu, Shanshan Yu, Lingyi Cai, Andriamifahimanjaka Sitrakiniaina, Ruihong Gu, Wenfeng Li, Fangfang Wu, Xiangyang Xue
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-33272-7

Increased levels of circulating MMP3 correlate with severe rejection in face transplantation
Cited by: 18
Author(s): Branislav Kollar, Andrey V. Shubin, Thiago J. Borges, Sotirios Tasigiorgos, Thet Su Win, Christine G. Lian, Simon T. Dillon, Xuesong Gu, Iris Wyrobnik, Gëorge F. Murphy, Bohdan Pomahac, Towia A. Libermann, Leonardo V. Riella
Software Mentions: 3
Published: almost 8 years ago

10.18632/aging.202922

A novel gene signature for prognosis prediction and chemotherapy response in patients with pancreatic cancer
Cited by: 4
Author(s): Hongcao Lin, Chonghui Hu, Shusen Zheng, Xiang Zhang, Rufu Chen, Quanbo Zhou
Software Mentions: 3
Published: over 5 years ago

10.1111/cns.13688

TROAP regulates cell cycle and promotes tumor progression through Wnt/β‐Catenin signaling pathway in glioma cells
Cited by: 17
Author(s): Zongqing Zhao, Xiujie Wu, Yalin Cheng, Yunfei Zhou, Xi-Meng Ma, Jian Zhang, Xueyuan Heng, Fang Fěng
Software Mentions: 3
Published: over 5 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.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

10.1038/s41598-018-32579-9

ADIPOR1 is essential for vision and its RPE expression is lost in the Mfrprd6 mouse
Cited by: 32
Author(s): Valentin M. Sluch, Angela Banks, Hui Li, Maura Crowley, Vanessa Davis, Chuanxi Xiang, Junzheng Yang, John Demirs, Joanna Vrouvlianis, Barrett Leehy, Shawn Hanks, Alexandra M. Hyman, Jorge Aranda, Bo Chang, Chad E. Bigelow, Dennis S. Rice
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.65306

A fungal member of the Arabidopsis thaliana phyllosphere antagonizes Albugo laibachii via a GH25 lysozyme
Cited by: 26
Author(s): Katharina Eitzen, Priyamedha Sengupta, Samuel Kroll, Eric Kemen, Gunther Doehlemann
Software Mentions: 3
Published: over 5 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776