bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3389/fgene.2018.00183

Network-Based Predictors of Progression in Head and Neck Squamous Cell Carcinoma
Cited by: 20
Author(s): Nasim Sanati, Ovidiu D. Iancu, Guanming Wu, Jan Jacobs, Shannon K. McWeeney
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-021-07729-5

The holobiont transcriptome of teneral tsetse fly species of varying vector competence
Cited by: 3
Author(s): Miguel Medina Munoz, Caitlyn Brenner, Dylan Richmond, Noah Spencer, Rita V. M. Rio
Software Mentions: 4
Published: over 5 years ago

10.1186/s13046-021-02122-2

Mutant NPM1-regulated lncRNA HOTAIRM1 promotes leukemia cell autophagy and proliferation by targeting EGR1 and ULK3
Cited by: 19
Author(s): Yipei Jing, Xueke Jiang, Lei Li, Meixi Peng, Jun Ren, Qiaoling Xiao, Tao Yao, Yonghong Tao, Junpeng Huang, Lu Wang, Yuting Tang, Zailin Yang, Yang Zhou, Ling Zhang
Software Mentions: 4
Published: almost 5 years ago

10.3390/ijms21082966

Differential Expression and Function of Bicellular Tight Junctions in Skin and Oral Wound Healing
Cited by: 20
Author(s): Trevor R. Leonardo, Junhe Shi, Dandan Chen, Harsh M. Trivedi, Lin Chen
Software Mentions: 4
Published: over 6 years ago

10.1038/srep43315

An inflammatory gene signature distinguishes neurofibroma Schwann cells and macrophages from cells in the normal peripheral nervous system
Cited by: 35
Author(s): Kwangmin Choi, Kakajan Komurov, Jonathan S. Fletcher, Edwin Jousma, José A. Cancelas, Jianqiang Wu, Nancy Ratner
Software Mentions: 4
Published: over 9 years ago

10.3389/fgene.2021.591623

Identification of Prognostic Biomarkers and Correlation With Immune Infiltrates in Hepatocellular Carcinoma Based on a Competing Endogenous RNA Network
Cited by: 3
Author(s): Zhaoxia Pu, Yuanyuan Zhu, Xiaofang Wang, Yun Zhong, Fang Peng, Yiya Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.628136

Breast Cancer Case Identification Based on Deep Learning and Bioinformatics Analysis
Cited by: 8
Author(s): Dongfang Jia, Cheng Chen, Fangfang Chen, Ningrui Zhang, Ziwei Yan
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-60025-2

Identification of putative biomarkers for Infantile Hemangiomas and Propranolol treatment via data integration
Cited by: 14
Author(s): Horacio Gómez-Acevedo, Yuemeng Dai, Graham M. Strub, Carrie J. Shawber, June K. Wu, Gresham T. Richter
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1007603

SuperFreq: Integrated mutation detection and clonal tracking in cancer
Cited by: 34
Author(s): Christoffer Flensburg, Tobias Sargeant, Alicia Oshlack, Ian J. Majewski
Software Mentions: 4
Published: over 6 years ago

10.1084/jem.20201290

Neuronal metabotropic glutamate receptor 8 protects against neurodegeneration in CNS inflammation
Cited by: 16
Author(s): Marcel S Woo, Friederike Ufer, Nicola Rothammer, Giovanni Di Liberto, Lars Binkle, Undine Haferkamp, Jana K. Sonner, Jan Broder Engler, Sönke Hornig, Simone Bauer, Ingrid Wagner, Kristóf Égervári, Jacob Raber, Robert M. Duvoisin, Ole Pleß, Doron Merkler, Manuel A. Friese
Software Mentions: 4
Published: over 5 years ago

10.1155/2021/4582082

Identification of a Two-m6A RNA Methylation Regulator Risk Signature as an Independent Prognostic Biomarker in Papillary Renal Cell Carcinoma by Bioinformatic Analysis
Cited by: 5
Author(s): Fusheng Yang, Guojiang Zhao, Liyuan Ge, Yimeng Song, Kai Hong, Hongxian Zhang, Cheng Liu, Hong Peng, Lulin Ma
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2646-x

A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species
Cited by: 25
Author(s): Montserrat Torres-Oliva, Isabel Almudí, Alistair P. McGregor, Nico Posnien
Software Mentions: 4
Published: over 10 years ago

10.1093/bioinformatics/btx094

Glimma: interactive graphics for gene expression analysis
Cited by: 120
Author(s): Shian Su, Charity W. Law, Casey Ah-Cann, Marie Liesse Asselin-Labat, Marnie E. Blewitt, Matthew E. Ritchie
Software Mentions: 4
Published: over 9 years ago

10.1186/s12935-019-0975-y

Identification of differentially expressed circRNAs and a novel hsa_circ_0000144 that promote tumor growth in gastric cancer
Cited by: 27
Author(s): Jianming Wei, Jinmiao Wang, Xibo Gao, Feng Qi
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmolb.2021.670893

Low Expression of RILPL2 Predicts Poor Prognosis and Correlates With Immune Infiltration in Endometrial Carcinoma
Cited by: 2
Author(s): Jinhui Liu, Mengting Xu, Zhipeng Wu, Yan Yang, Shuang Yuan, J. Liang, Hongjun Zhu
Software Mentions: 4
Published: over 5 years ago

10.1155/2019/1742341

Based on Integrated Bioinformatics Analysis Identification of Biomarkers in Hepatocellular Carcinoma Patients from Different Regions
Cited by: 9
Author(s): Linxin Teng, Kaiyuan Wang, Yu Liu, Yanxia Ma, Weiping Chen, Lei Bi
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-58711-2

Nucleus accumbens pathways control cell-specific gene expression in the medial prefrontal cortex
Cited by: 5
Author(s): Takatoshi Hikida, Shuhei Yao, Tom Macpherson, Ayumi Fukakusa, Maki Morita, Haruhide Kimura, Keisuke Hirai, Tatsuya Ando, Hiroyoshi Toyoshiba, Akira Sawa
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2019.00697

Cross-Species Gene Expression Analysis Reveals Gene Modules Implicated in Human Osteosarcoma
Cited by: 12
Author(s): Zheng Jin, Shanshan Liu, Pei‐Wen Zhu, Mengyan Tang, Yuanxin Wang, Yuan Tian, Li Dong, X. D. Zhu, Dongmei Yan, Zhifeng Zhu
Software Mentions: 4
Published: about 7 years ago

10.3389/fgene.2021.608936

Whole Genome Level Analysis of the Wnt and DIX Gene Families in Mice and Their Coordination Relationship in Regulating Cardiac Hypertrophy
Cited by: 6
Author(s): Zhongchao Gai, Yujiao Wang, Lü Tian, Guoli Gong, Jieqiong Zhao
Software Mentions: 4
Published: over 5 years ago

10.1155/2021/6697810

Shared Genetic and Epigenetic Mechanisms between the Osteogenic Differentiation of Dental Pulp Stem Cells and Bone Marrow Stem Cells
Cited by: 14
Author(s): Sebastian Gaus, Hanluo Li, Simin Li, Qian Wang, Tina Kottek, Sebastian Hahnel, Xiangqiong Liu, Yupei Deng, Dirk Ziebolz, Rainer Haak, Gerhard Schmalz, Lei Liu, Vuk Savković, Bernd Lethaus
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-58779-w

A Group of Olfactory Receptor Alleles that Encode Full Length Proteins are Down-Regulated as Olfactory Sensory Neurons Mature
Cited by: 1
Author(s): Richard C. Krolewski, Brian M. Lin, Samuel D. Stampfer, Adam Packard, James E. Schwob
Software Mentions: 4
Published: over 6 years ago

10.1186/s12935-021-02090-9

The functions and prognostic values of m6A RNA methylation regulators in thyroid carcinoma
Cited by: 8
Author(s): Zuwei Yu, Shao-Ting Feng, Di Zhang, Xuchen Cao, Yue Yu, Xin Wang
Software Mentions: 4
Published: about 5 years ago

10.1186/s13059-019-1918-6

Enteric infection induces Lark-mediated intron retention at the 5′ end of Drosophila genes
Cited by: 4
Author(s): Maroun Bou Sleiman, Michael Frochaux, Tommaso Andreani, Dani Osman, Roderic Guigó, Bart Deplancke
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2021.680369

Identification of MX2 as a Novel Prognostic Biomarker for Sunitinib Resistance in Clear Cell Renal Cell Carcinoma
Cited by: 27
Author(s): Yuang Wei, Xinglin Chen, Xiaohan Ren, Bao Wang, Qian Zhang, Hengtao Bu, Ji Qian, Pengfei Shao
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2021.684281

A Robust Seven-Gene Signature Associated With Tumor Microenvironment to Predict Survival Outcomes of Patients With Stage III–IV Lung Adenocarcinoma
Cited by: 3
Author(s): Hao Zhao, Xuening Zhang, Liting Guo, Songhe Shi, Ciyong Lu
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-57888-w

Describing the fecal metabolome in cryogenically collected samples from healthy participants
Cited by: 9
Author(s): Kajetan Trošt, Linda Ahonen, Tommi Suvitaival, Nicole Christiansen, Trine Nielsen, Maja Thiele, Suganya Jacobsen, Aleksander Krag, Peter Rossing, Torben Hansen, Lars Ove Dragsted, Cristina Legido‐Quigley
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2020.00294

Methylation-Driven Genes Identified as Novel Prognostic Indicators for Thyroid Carcinoma
Cited by: 12
Author(s): Liting Lv, Liyu Cao, Guoqing Hu, Qinyan Shen, Jiaming Wu
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1006295

Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster
Cited by: 35
Author(s): Hangnoh Lee, Dong-Yeon Cho, Cale Whitworth, Robert C. Eisman, Melissa A. S. Phelps, John Roote, Thomas C. Kaufman, Kevin R. Cook, Steven Russell, Teresa M. Przytycka, Brian Oliver
Software Mentions: 4
Published: about 10 years ago

10.1038/s41419-021-04144-2

LncRNA PCBP1-AS1-mediated AR/AR-V7 deubiquitination enhances prostate cancer enzalutamide resistance
Cited by: 19
Author(s): Boya Zhang, Mingpeng Zhang, Chunyi Shen, Guancong Liu, Fan Zhang, Jingyu Hou, Weitao Yao
Software Mentions: 4
Published: almost 5 years ago

10.1155/2021/6672899

Comparative Transcriptome Analysis Reveals Relationship among mRNAs, lncRNAs, and circRNAs of Slow Transit Constipation
Cited by: 2
Author(s): Shuai Yan, Yinzi Yue, Mingming Sun, Yinghui Chen, Xiaopeng Wang, Haihua Qian
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2018.00321

DECtp: Calling Differential Gene Expression Between Cancer and Normal Samples by Integrating Tumor Purity Information
Cited by: 7
Author(s): Weiwei Zhang, Hang Long, Binsheng He, Jialiang Yang
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-020-57542-5

Large-scale Analyses of Disease Biomarkers and Apremilast Pharmacodynamic Effects
Cited by: 11
Author(s): И. В. Медведева, Matthew E. Stokes, Dominic Eisinger, Samuel T. LaBrie, Jing Ai, Matthew Trotter, Peter Schäfer, Robert Yang
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-00267-9

Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis
Cited by: 12
Author(s): Anthony R. Soltis, Shmulik Motola, Santiago Vérnia, Christopher Ng, Norman J. Kennedy, Simona Dalin, Bryan J. Matthews, Roger J. Davis, Ernest Fraenkel
Software Mentions: 4
Published: over 9 years ago

10.3389/fgene.2012.00161

Identification of DNA methylation biomarkers from Infinium arrays
Cited by: 33
Author(s): Frank Wessely, Richard D. Emes
Software Mentions: 4
Published: over 14 years ago

10.3389/fgene.2020.00253

Integrated Analysis to Evaluate the Prognostic Value of Signature mRNAs in Glioblastoma Multiforme
Cited by: 11
Author(s): Jian Yang, Long Wang, Zhou Xu, Liquan Wu, Baohui Liu, Junmin Wang, Daofeng Tian, Xiaoxing Xiong, Qianxue Chen
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2020.00427

Bioinformatics Analysis Reveals Biomarkers With Cancer Stem Cell Characteristics in Lung Squamous Cell Carcinoma
Cited by: 38
Author(s): Yi Liao, Hua Xiao, Mengqing Cheng, Xiaoxuan Fan
Software Mentions: 4
Published: over 6 years ago

10.1155/2020/4980609

The Important Role of Perituberal Tissue in Epileptic Patients with Tuberous Sclerosis Complex by the Transcriptome Analysis
Cited by: 3
Author(s): Shuqiang Li, Huijie Shao, Liansheng Chang
Software Mentions: 4
Published: almost 6 years ago

10.1111/eva.13142

Transcriptional frontloading contributes to cross‐tolerance between stressors
Cited by: 8
Author(s): Michael T. Collins, Melody S. Clark, John I. Spicer, Manuela Truebano
Software Mentions: 4
Published: almost 6 years ago

10.1080/20013078.2018.1461450

ISEV2018 abstract book
Cited by: 157
Author(s): Clotilde Théry, Kenneth W. Witwer
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pgen.1004642

Regulation of p53 and Rb Links the Alternative NF-κB Pathway to EZH2 Expression and Cell Senescence
Cited by: 80
Author(s): Alessio Iannetti, Adeline Ledoux, Susan J. Tudhope, Hélène Sellier, Bo Zhao, Sophia Mowla, Adam J. Moore, Holger Hummerich, Benjamin E. Gewurz, Simon Cockell, Parmjit Jat, Elaine Willmore, Neil D. Perkins
Software Mentions: 4
Published: almost 12 years ago

10.1155/2019/7518374

Network Pharmacology and Bioinformatics Approach Reveals the Therapeutic Mechanism of Action of Baicalein in Hepatocellular Carcinoma
Cited by: 34
Author(s): Chongyang Ma, Tian Xu, Xiaoguang Sun, Shuang Zhang, Shu-Ling Liu, Shuning Fan, Chaofang Lei, Fei‐Fei Tang, Changming Zhai, Changxiang Li, Jian Luo, Qingguo Wang, Wei Wei, Xueqian Wang, Fang Cheng
Software Mentions: 4
Published: over 7 years ago

10.1186/gm122

Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia
Cited by: 105
Author(s): Nathan Stephens, Iain J. Gallagher, Olav Rooyackers, Richard J.E. Skipworth, Ben Tan, Troels Marstrand, James A. Ross, Denis C. Guttridge, Lars Lundell, Kenneth C. H. Fearon, James A. Timmons
Software Mentions: 4
Published: over 16 years ago

10.3390/ijms22010275

The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function
Cited by: 8
Author(s): Yashwanth Subbannayya, Markus Haug, Sneha M. Pinto, Varshasnata Mohanty, Hany Zakaria Meås, Trude Helen Flo, T. S. Keshava Prasad, Richard K. Kandasamy
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2020.01017

Identification of a Novel Signature and Construction of a Nomogram Predicting Overall Survival in Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Xiangkun Wu, Zhijian Zhao, Aisha Khan, Chao Cai, Daojun Lv, Danan Gu, Yongda Liu
Software Mentions: 4
Published: about 6 years ago

10.1186/s13073-014-0059-5

A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD
Cited by: 21
Author(s): Peter K. Davidsen, John Herbert, Philipp Antczak, Kim Clarke, Elisabet Ferrer, Víctor I. Peinado, C. González, Josep Roca, Stuart Egginton, Joan Albert Barberà, Francesco Falciani
Software Mentions: 4
Published: about 12 years ago

10.1186/s13073-014-0125-z

Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia
Cited by: 51
Author(s): Simone Ecker, Véra Pancaldi, Daniel Rico, Alfonso Valencia
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pgen.1007473

RES complex is associated with intron definition and required for zebrafish early embryogenesis
Cited by: 23
Author(s): Juan Pablo Fernández, Miguel A. Moreno-Mateos, André Gohr, Liyun Miao, Shun Hang Chan, Manuel Irimia, Antonio J. Giráldez
Software Mentions: 4
Published: about 8 years ago

10.1186/s12935-018-0681-1

Identification of RPL5 and RPL10 as novel diagnostic biomarkers of Atypical teratoid/rhabdoid tumors
Cited by: 6
Author(s): Yanming Ren, Chuanmin Tao, Xiliang Wang, Yan Ju
Software Mentions: 4
Published: almost 8 years ago

10.1186/1471-2164-15-133

Virus-independent and common transcriptome responses of leafhopper vectors feeding on maize infected with semi-persistently and persistent propagatively transmitted viruses
Cited by: 33
Author(s): Bryan J. Cassone, Saranga Wijeratne, Andrew P. Michel, Lucy R. Stewart, Yuting Chen, Pearlly S. Yan, Margaret G. Redinbaugh
Software Mentions: 4
Published: over 12 years ago

10.1038/s41431-021-00854-5

Regional heritability mapping identifies several novel loci (STAT4, ULK4, and KCNH5) for primary biliary cholangitis in the Japanese population
Cited by: 6
Author(s): Olivier Gervais, Kazuko Ueno, Yosuke Kawai, Yuki Hitomi, Yoshihiro Aiba, Mayumi Ueta, Minoru Nakamura, Katsushi Tokunaga, Masao Nagasaki
Software Mentions: 4
Published: over 5 years ago

10.3389/fnmol.2021.672614

Bisulfite Amplicon Sequencing Can Detect Glia and Neuron Cell-Free DNA in Blood Plasma
Cited by: 11
Author(s): Zac Chatterton, Natalia Mendelev, Sean Chen, Walter Carr, Gary H. Kamimori, Yongchao Ge, Andrew J. Dwork, Fatemeh Haghighi
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2164-11-50

Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data
Cited by: 17
Author(s): Jun Yin, Sarah McLoughlin, Ian B. Jeffery, Antonino Glaviano, Breandán N. Kennedy, Desmond G. Higgins
Software Mentions: 4
Published: over 16 years ago

10.1371/journal.pgen.1002589

A Genome-Wide Association Study Identifies Variants Underlying the Arabidopsis thaliana Shade Avoidance Response
Cited by: 90
Author(s): Daniele Filiault, Julin N. Maloof
Software Mentions: 4
Published: over 14 years ago

10.3390/ijms20236040

Whole Genome Expression Analyses of miRNAs and mRNAs Suggest the Involvement of miR-320a and miR-155-3p and their Targeted Genes in Lithium Response in Bipolar Disorder
Cited by: 27
Author(s): Claudia Pisanu, Eleni Merkouri Papadima, Carla Melis, Donatella Congiu, Annalisa Loizedda, Nicola Orrù, Stefano Calza, Sandro Orrù, Carlo Carcassi, Giovanni Severino, Raffaella Ardau, Caterina Chillotti, Maria Del Zompo, Alessio Squassina
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pgen.1007891

Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation
Cited by: 47
Author(s): A. Callegari, Christian Sieben, Alexander Benke, David M. Suter, Beat Fierz, Davide Mazza, Suliana Manley
Software Mentions: 4
Published: over 7 years ago

10.1186/1756-8935-7-26

Protection of CpG islands against de novo DNA methylation during oogenesis is associated with the recognition site of E2f1 and E2f2
Cited by: 23
Author(s): Heba Saadeh, Reiner Schulz
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2164-12-64

Pre-processing and differential expression analysis of Agilent microRNA arrays using the AgiMicroRna Bioconductor library
Cited by: 118
Author(s): Pedro López-Romero
Software Mentions: 4
Published: over 15 years ago

10.3389/fpls.2021.632033

The Genomic Impact of Mycoheterotrophy in Orchids
Cited by: 8
Author(s): Marcin Jąkalski, Julita Minasiewicz, José Caïus, Michał May, Marc‐André Selosse, Étienne Delannoy
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2019.00606

Inactivation of Prostaglandin E2 as a Mechanism for UGT2B17-Mediated Adverse Effects in Chronic Lymphocytic Leukemia
Cited by: 10
Author(s): Éric P. Allain, Michèle Rouleau, Trang Le, Katrina Vanura, Lyne Villeneuve, Patrick Caron, Véronique Turcotte, Éric Lévesque, Chantal Guillemette
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0226128

Fecal transplant prevents gut dysbiosis and anxiety-like behaviour after spinal cord injury in rats
Cited by: 70
Author(s): Emma K.A. Schmidt, Abel Torres-Espín, Pamela Raposo, Karen Madsen, Kristina A. Kigerl, Phillip G. Popovich, Keith K. Fenrich, Karim Fouad
Software Mentions: 4
Published: over 6 years ago

10.1186/s13072-021-00393-9

H3K36 methylation reprograms gene expression to drive early gametocyte development in Plasmodium falciparum
Cited by: 10
Author(s): Jessica Connacher, Gabrielle A. Josling, Lindsey M. Orchard, Janette Reader, Manuel Llinás, Lyn‐Marié Birkholtz
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1006593

Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer’s disease
Cited by: 99
Author(s): Fiona Kerr, Oyinkan Sofola-Adesakin, Dobril Ivanov, Jemma Gatliff, Beatriz Gomez Perez‐Nievas, Hélène Bertrand, Pedro Martı́nez, Rebecca Callard, Inge Snoeren, Helena M. Cochemé, Jennifer Adcott, Mobina Khericha, Jorge Iván Castillo-Quan, Geoff Wells, Wendy Noble, Janet M. Thornton, Linda Partridge
Software Mentions: 4
Published: over 9 years ago

10.1186/s12935-019-0953-4

Effect of hyperoside on cervical cancer cells and transcriptome analysis of differentially expressed genes
Cited by: 22
Author(s): Guo Wei, Hui Yu, Lu Zhang, Xiuwei Chen, Yunduo Liu, Yaoxian Wang, Yunyan Zhang
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pgen.1002074

Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex
Cited by: 53
Author(s): Tomoko M. Tabuchi, Bart Deplancke, Naoki Osato, Lihua Julie Zhu, Inmaculada M. Barrasa, Melissa M. Harrison, Robert Horvitz, Albertha J.M. Walhout, Kirsten Hagstrom
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pgen.1005211

Early Lineage Priming by Trisomy of Erg Leads to Myeloproliferation in a Down Syndrome Model
Cited by: 12
Author(s): Ashley P Ng, Yifang Hu, Donald Metcalf, Craig D. Hyland, Helen Ierino, Belinda Phipson, Di Wu, Tracey M. Baldwin, Maria Kauppi, Hiu Kiu, Ladina Di Rago, Douglas J. Hilton, Gordon K. Smyth, Warren S. Alexander
Software Mentions: 4
Published: over 11 years ago

10.1186/s13073-016-0355-3

Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer’s disease
Cited by: 191
Author(s): Minghui Wang, Panos Roussos, Andrew McKenzie, Xianxiao Zhou, Yuji Kajiwara, Kristen J. Brennand, Gabriele C. DeLuca, John F. Crary, Patrizia Casaccia, Joseph D. Buxbaum, Michelle E. Ehrlich, Sam Gandy, Alison M. Goate, Pavel Katsel, Eric E. Schadt, Vahram Haroutunian, Bin Zhang
Software Mentions: 4
Published: almost 10 years ago

10.3389/fnmol.2018.00288

Dysregulation of MicroRNAs and Target Genes Networks in Peripheral Blood of Patients With Sporadic Amyotrophic Lateral Sclerosis
Cited by: 84
Author(s): Maria Liguori, Nicoletta Nuzziello, Alessandro Introna, Arianna Consiglio, Flavio Licciulli, Eustachio D’Errico, Antonio Scarafino, Eugenio Distaso, Isabella Laura Simone
Software Mentions: 4
Published: about 8 years ago

10.1186/s12935-021-02045-0

Identification and validation of a novel glycolysis-related gene signature for predicting the prognosis in ovarian cancer
Cited by: 17
Author(s): Jing Yu, Tingting Liu, Leilei Liang, Jing Liu, Hong‐Qing Cai, Jia Zeng, Tiantian Wang, Jian Li, Lin Xiu, Ning Li, Lingying Wu
Software Mentions: 4
Published: about 5 years ago

10.1186/s13073-020-00754-1

Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults
Cited by: 20
Author(s): Robert F. Hillary, Daniel Trejo Baños, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, Sven Erik Ojavee, Qian Zhang, David C. Liewald, Craig W. Ritchie, Kathryn Evans, Elliot M. Tucker‐Drob, Naomi R. Wray, Allan F. McRae, Peter M. Visscher, Ian J. Deary, Matthew R. Robinson, Riccardo E. Marioni
Software Mentions: 4
Published: about 6 years ago

10.1186/s13073-020-00787-6

Molecular correlates and therapeutic targets in T cell-inflamed versus non-T cell-inflamed tumors across cancer types
Cited by: 21
Author(s): Riyue Bao, Daniel Stapor, Jason J. Luke
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpls.2019.00235

Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs
Cited by: 49
Author(s): Cristiane P. G. Calixto, Nikoleta A. Τzioutziou, Allan B. James, Csaba Hornyik, Wenbin Guo, Runxuan Zhang, Hugh G. Nimmo, John W. Brown
Software Mentions: 4
Published: over 7 years ago

10.1186/s40659-018-0188-1

Identification of key genes and miRNAs markers of papillary thyroid cancer
Cited by: 31
Author(s): Jie Qiu, Wenwei Zhang, Chuanshan Zang, Xiaomin Liu, Fuxue Liu, Ruifeng Ge, Yan Sun, Qingsheng Xia
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41419-018-1141-5

Plau and Tgfbr3 are YAP-regulated genes that promote keratinocyte proliferation
Cited by: 18
Author(s): Susan M. Corley, Veronica Mendoza-Reinoso, Nichole Giles, Emma Suwanun Singer, John E.A. Common, Marc R. Wilkins, Annemiek Beverdam
Software Mentions: 4
Published: almost 8 years ago

10.3389/fpls.2019.01098

Identification of Candidate Adaxial–Abaxial-Related Genes Regulating Petal Expansion During Flower Opening in Rosa chinensis “Old Blush”
Cited by: 10
Author(s): Yu Han, Yong Xue, Jiayao Yu, Tangren Cheng, Jia Wang, Weiru Yang, Huitang Pan, Qixiang Zhang
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-53471-0

Feature selection with the Fisher score followed by the Maximal Clique Centrality algorithm can accurately identify the hub genes of hepatocellular carcinoma
Cited by: 31
Author(s): Chengzhang Li, Jiucheng Xu
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13073-021-00948-1

An epigenetic and transcriptomic signature of immune tolerance in human monocytes through multi-omics integration
Cited by: 9
Author(s): Xanthe Brands, Bastiaan W. Haak, Augustijn M. Klarenbeek, Joe Butler, Fabrice Uhel, Wanhai Qin, Natasja A. Otto, Marja E. Jakobs, Daniel Faber, René Lutter, W. Joost Wiersinga, Tom van der Poll, Brendon P. Scicluna
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-5767-1

Transcriptomic responses to diet quality and viral infection in Apis mellifera
Cited by: 23
Author(s): Lindsay Rutter, Jimena Carrillo-Tripp, Bryony C. Bonning, Dianne Cook, Amy L. Toth, Adam Doležal
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1009390

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition
Cited by: 11
Author(s): Luis Enrique Cabrera-Quio, Alexander Schleiffer, Karl Mechtler, Andrea Pauli
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2019.00159

A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures
Cited by: 22
Author(s): Adib Shafi, Tin Nguyen, Azam Peyvandipour, Hung Son Nguyen, Sorin Drăghici
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2021.648329

Deep Learning Reveals Key Immunosuppression Genes and Distinct Immunotypes in Periodontitis
Cited by: 10
Author(s): Wanchen Ning, Aneesha Acharya, Zhenjie Sun, Anthony Chukwunonso Ogbuehi, Cong Liu, Shiting Hua, Qiyun Ou, Muhui Zeng, Xiangqiong Liu, Yupei Deng, Rainer Haak, Dirk Ziebolz, Gerhard Schmalz, George Pelekos, Yan Wang, Xianda Hu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1007961

A genetic variant associated with multiple sclerosis inversely affects the expression of CD58 and microRNA-548ac from the same gene
Cited by: 17
Author(s): Michael Hecker, Nina Boxberger, Nicole Illner, Brit Fitzner, I Schröder, Alexander Winkelmann, Aleš Dudešek, Stefanie Meister, Dirk Koczan, Peter Lorenz, Hans‐Jürgen Thiesen, Uwe K. Zettl
Software Mentions: 4
Published: over 7 years ago

10.1016/j.gpb.2018.08.002

PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System
Cited by: 19
Author(s): Huan Qi, Zhenhong Jiang, Kang Zhang, Shiping Yang, Fei He, Ziding Zhang
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pgen.1003188

Suv4-20h Histone Methyltransferases Promote Neuroectodermal Differentiation by Silencing the Pluripotency-Associated Oct-25 Gene
Cited by: 29
Author(s): Dario Nicetto, Matthias Hahn, Julia Jeannine Jung, Tobias D. Schneider, Tobias Straub, Róbert Dávid, Gunnar Schotta, Ralph A.W. Rupp
Software Mentions: 4
Published: over 13 years ago

10.1038/s41419-020-03020-9

Intracellular amyloid toxicity induces oxytosis/ferroptosis regulated cell death
Cited by: 51
Author(s): Ling Huang, Daniel B. McClatchy, Pamela Maher, Zhibin Liang, Jolene K. Diedrich, David Soriano-Castell, Joshua Goldberg, Maxim N. Shokhirev, John R. Yates, David Schubert, António Currais
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1008537

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation
Cited by: 33
Author(s): Gregory R. Keele, Bryan C. Quach, Jennifer W. Israel, Grace A. Chappell, Lauren Lewis, Alexias Safi, Jeremy M. Simon, Paul Cotney, Gregory E. Crawford, William Valdar, Ivan Rusyn, Terrence S. Furey
Software Mentions: 4
Published: over 6 years ago

10.1155/2020/4348371

DHX36, BAX, and ARPC1B May Be Critical for the Diagnosis and Treatment of Tuberculosis
Cited by: 3
Author(s): Yunli Zhang, Yanming Liu, Hongling Li, Qingxia Liu, Wei Wang, Zijuan Jian, Wenen Liu
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2020.560229

A Molecular Subtype Model for Liver HBV-Related Hepatocellular Carcinoma Patients Based on Immune-Related Genes
Cited by: 5
Author(s): Qiyao Zhang, Xiao Yu, Qingyuan Zheng, Yuting He, Wenzhi Guo
Software Mentions: 4
Published: almost 6 years ago

10.15252/emmm.202013131

Synaptic disruption and CREB‐regulated transcription are restored by K + channel blockers in ALS
Cited by: 19
Author(s): Alberto Catanese, Sandeep Rajkumar, Daniel Sommer, Dennis Freisem, Alexander Wirth, Amr Aly, David Massa-López, Andrea Olivieri, Federica Torelli, Valentin Ioannidis, Joanna Lipecka, Ida Chiara Guerrera, Daniel Zytnicki, Albert C. Ludolph, Edor Kabashi, Medhanie Mulaw, Francesco Roselli, Tobias M. Böckers
Software Mentions: 4
Published: over 5 years ago

10.15252/emmm.201911659

<scp>FBXL</scp> 4 deficiency increases mitochondrial removal by autophagy
Cited by: 34
Author(s): David Alsina, Oleksandr Lytovchenko, Aleksandra Schab, Ilian Atanassov, F. Schober, Min Jiang, Camilla Koolmeister, Anna Wedell, Robert W. Taylor, Anna Wredenberg, Nils-Göran Larsson
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2020.517637

The Landscape of Immune Cells Infiltrating in Prostate Cancer
Cited by: 54
Author(s): Zhicong Wu, Hua Chen, Wenyang Luo, Hanyun Zhang, Guihuan Li, Fanning Zeng, Fan Deng
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-50873-y

Airway epithelial cell isolation techniques affect DNA methylation profiles with consequences for analysis of asthma related perturbations to DNA methylation
Cited by: 9
Author(s): Rachel L. Clifford, J. Patel, Julia L. MacIsaac, Lisa M. McEwen, Simon R. Johnson, Dominick Shaw, Alan J. Knox, Tillie-Louise Hackett, Michæl S. Kobor
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0163344

Differing Alterations of Two Esca Associated Fungi, Phaeoacremonium aleophilum and Phaeomoniella chlamydospora on Transcriptomic Level, to Co-Cultured Vitis vinifera L. calli
Cited by: 6
Author(s): Jochen Fischer, Stéphane Compant, Romain Pierron, Markus Gorfer, Alban Jacques, Eckhard Thines, Harald Berger
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pgen.1005184

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans
Cited by: 111
Author(s): Li Zhao, Janneke Wit, Nicolas Svetec, David J. Begun
Software Mentions: 4
Published: over 11 years ago

10.1155/2014/145243

Integration of High-Volume Molecular and Imaging Data for Composite Biomarker Discovery in the Study of Melanoma
Cited by: 7
Author(s): Κωνσταντίνος Μούτσελος, Ilias Maglogiannis, Aristotelis Chatziioannou
Software Mentions: 4
Published: over 12 years ago

10.15252/emmm.202013074

Impairment of the ER/mitochondria compartment in human cardiomyocytes with PLN p.Arg14del mutation
Cited by: 25
Author(s): Friederike Cuello, Anika E. Knaust, Umber Saleem, Malte Loos, Janice Raabe, Diogo Mosqueira, Sandra D. Laufer, Michaela Schweizer, Petra van der Kraak, Frederik Flenner, Bärbel Ulmer, Ingke Braren, Xiaoke Yin, Konstantinos Theofilatos, Jorge Ruiz-Orera, Giannino Patone, Birgit Klampe, Thomas G. Schulze, Angelika Piasecki, Yigal M. Pinto, Aryan Vink, Norbert Hübner, Siân E. Harding, Manuel Mayr, Chris Denning, Thomas Eschenhagen, Arne Hansen
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms21228749

Dysregulation of Transcription Factor Activity during Formation of Cancer-Associated Fibroblasts
Cited by: 6
Author(s): Przemysław Kapusta, Joanna Dulińska-Litewka, Justyna Totoń‐Żurańska, A. Borys, Paweł Konieczny, Paweł Wołkow, Michał Seweryn
Software Mentions: 4
Published: almost 6 years ago

10.1038/srep29477

Limits of Peripheral Blood Mononuclear Cells for Gene Expression-Based Biomarkers in Juvenile Idiopathic Arthritis
Cited by: 18
Author(s): Lai-Ping Wong, Kaiyu Jiang, Yanmin Chen, Teresa Hennon, Lucy C Holmes, Carol A. Wallace, James N. Jarvis
Software Mentions: 4
Published: about 10 years ago

10.3389/fneur.2021.576382

Potential Molecular Mechanism of TNF Superfamily-Related Genes in Glioblastoma Multiforme Based on Transcriptome and Epigenome
Cited by: 6
Author(s): Hui Xie, Ce Yuan, Jinjiang Li, Zhaoyang Li, Wei-Cheng Lu
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-50217-w

Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection
Cited by: 28
Author(s): Abhijeet R. Sonawane, Tian Liang, Chin Yi Chu, Xing Qiu, Lu Wang, Jeanne Holden‐Wiltse, Alex Grier, Steven R. Gill, Mary T. Caserta, Ann R. Falsey, David J. Topham, Edward E. Walsh, Thomas J. Mariani, Scott T. Weiss, Edwin K. Silverman, Kimberly Glass, Yang Yu Liu
Software Mentions: 4
Published: almost 7 years ago

10.1155/2019/5437531

Long Noncoding RNA ASB16-AS1 Promotes Proliferation, Migration, and Invasion in Glioma Cells
Cited by: 26
Author(s): Delong Zhang, Huanggui Zhou, Jun Liu, Jie Mao
Software Mentions: 4
Published: over 7 years ago

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Papers Mentioning limma 7,776