bioconductor: sva | Projects | Ecosyste.ms: Papers

10.1186/s12967-020-02463-0

Identifying the pattern of immune related cells and genes in the peripheral blood of ischemic stroke
Cited by: 24
Author(s): Zijian Li, Yueran Cui, Juan Feng, Yanxia Guo
Software Mentions: 4
Published: over 4 years ago

10.1186/s13075-020-02195-y

Increased serum calpain activity is associated with HMGB1 levels in systemic sclerosis
Cited by: 9
Author(s): Ji-Na Zheng, Yang Li, Yue-Mei Yan, Yong Yu, Wenqi Shao, Qiang Wang
Software Mentions: 4
Published: over 4 years ago

10.7717/peerj.8763

Identification of key genes and pathways affected in epicardial adipose tissue from patients with coronary artery disease by integrated bioinformatics analysis
Cited by: 6
Author(s): Liao Tan, Qian Xu, Qianchen Wang, Ruizheng Shi, Guogang Zhang
Software Mentions: 4
Published: over 4 years ago

10.3390/ijms20092177

Polysome Profiling of a Human Glioblastoma Reveals Intratumoral Heterogeneity
Cited by: 9
Author(s): Fernanda C. S. Lupinacci, Hellen Kuasne, Martín Roffé, Julia Avian Vassalakis, Fernanda Ferreira da Silva, Tiago G. Santos, Victor Piana de Andrade, Paulo Sanematsu, Vilma R. Martins, Sílvia Regina Rogatto, Glaucia Noeli Maroso Hajj
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-017-1501-7

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

10.7717/peerj.9452

Integrative analysis of competitive endogenous RNA network reveals the regulatory role of non-coding RNAs in high-glucose-induced human retinal endothelial cells
Cited by: 6
Author(s): Nanjue Cao, Henan Liu, Feng Dong, Wei Wang, Wei Sun, Gang Wang
Software Mentions: 4
Published: over 4 years ago

10.1155/2021/7331821

Identification of Neuropeptides as Potential Crosstalks Linking Down Syndrome and Periodontitis Revealed by Transcriptomic Analyses
Cited by: 6
Author(s): Yue Chen, Xiaofei Yu, Jia Kong
Software Mentions: 4
Published: about 3 years ago

10.3389/fgene.2021.634171

Weighted Gene Co-expression Network Analysis Reveals Different Immunity but Shared Renal Pathology Between IgA Nephropathy and Lupus Nephritis
Cited by: 6
Author(s): Niya Jia, Xing-Zi Liu, Zhao Zhang, Hong Zhang
Software Mentions: 4
Published: over 3 years ago

10.1002/cam4.3654

Establishment of a prognostic model of four genes in gastric cancer based on multiple data sets
Cited by: 11
Author(s): Liqun Zhou, Shi H Li, You Wu, Lin Xin
Software Mentions: 4
Published: over 3 years ago

10.1002/cam4.3833

The immune landscape during the tumorigenesis of cervical cancer
Cited by: 18
Author(s): Yiying Wang, Mengdi He, Guodong Zhang, Kankan Cao, Moran Yang, Hongwei Zhang, Haiou Liu
Software Mentions: 4
Published: over 3 years ago

10.1002/cam4.3035

Develop a circular RNA–related regulatory network associated with prognosis of gastric cancer
Cited by: 9
Author(s): Shuxun Wei, Shang‐Hua Teng, Jun Yao, Wenchao Gao, Jiachen Zang, Guangyong Wang, Zhiqian Hu
Software Mentions: 4
Published: about 4 years ago

10.1016/j.stemcr.2020.05.007

Modeling and Rescue of RP2 Retinitis Pigmentosa Using iPSC-Derived Retinal Organoids
Cited by: 100
Author(s): Amelia Lane, Katarina Jovanović, Ciara Shortall, Daniele Ottaviani, Anna Brugulat Panes, Nele Schwarz, Rosellina Guarascio, Matthew J. Hayes, Arpad Palfi, Naomi Chadderton, G. Jane Farrar, Alison J. Hardcastle, Michael E. Cheetham
Software Mentions: 4
Published: over 4 years ago

10.7717/peerj.7313

Bioinformatics analysis of microarray data to identify the candidate biomarkers of lung adenocarcinoma
Cited by: 37
Author(s): Tingting Guo, Hongwen Ma, Yuting Zhou
Software Mentions: 4
Published: over 5 years ago

10.1186/s13045-017-0462-7

Posttranslationally modified progesterone receptors direct ligand-specific expression of breast cancer stem cell-associated gene programs
Cited by: 56
Author(s): Todd P. Knutson, Thu H. Truong, Shihong Ma, Nicholas J. Brady, Megan Sullivan, Ganesh V. Raj, Kathryn L. Schwertfeger, Carol A. Lange
Software Mentions: 4
Published: over 7 years ago

10.1186/s12935-021-01928-6

Construction of a prognostic model with histone modification-related genes and identification of potential drugs in pancreatic cancer
Cited by: 8
Author(s): Chen Yuan, Ruiyuan Xu, Rexiati Ruze, Jinshou Yang, Huanyu Wang, Jianlu Song, Lei You, Yuming Wang, Yupei Zhao
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-76347-0

Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue
Cited by: 7
Author(s): Rachel Hodos, Matthew D. Strub, Shyam Ramachandran, Li Li, Paul B. McCray, Joel T. Dudley
Software Mentions: 4
Published: about 4 years ago

10.3389/fimmu.2021.704655

An Immune-Associated Genomic Signature Effectively Predicts Pathologic Complete Response to Neoadjuvant Paclitaxel and Anthracycline-Based Chemotherapy in Breast Cancer
Cited by: 4
Author(s): Changfang Fu, Yu Liu, Xinghua Han, Yueyin Pan, Hongqiang Wang, Hongzhi Wang, Haiming Dai, Wulin Yang
Software Mentions: 4
Published: over 3 years ago

10.3390/nu11112804

DNA Methylation Signatures of Breastfeeding in Buccal Cells Collected in Mid-Childhood
Cited by: 16
Author(s): Veronika V. Odintsova, Fiona A. Hagenbeek, Matthew Suderman, Doretta Caramaschi, Catharina E. M. van Beijsterveldt, Noah A. Kallsen, Erik A. Ehli, Gareth E. Davies, Г. Т. Сухих, Vassilios Fanos, Caroline L Relton, Meike Bartels, Dorret I. Boomsma, Jenny van Dongen
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2020.590618

A TP53-Associated Immune Prognostic Signature for the Prediction of Overall Survival and Therapeutic Responses in Muscle-Invasive Bladder Cancer
Cited by: 32
Author(s): Xiangkun Wu, Daojun Lv, Chao Cai, Zhijian Zhao, Ming Wang, Wenzhe Chen, Yongda Liu
Software Mentions: 4
Published: almost 4 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: about 4 years ago

10.3389/fimmu.2018.00699

Clec9a-Mediated Ablation of Conventional Dendritic Cells Suggests a Lymphoid Path to Generating Dendritic Cells In Vivo
Cited by: 18
Author(s): Johanna Salvermoser, Janneke van Blijswijk, Nikos E. Papaioannou, Stephan Rambichler, Mária Pásztói, Dalia Pakalniškytė, Neil C. Rogers, Selina J. Keppler, Tobias Straub, Caetano Reis e Sousa, Barbara U. Schraml
Software Mentions: 4
Published: over 6 years ago

10.4161/epi.27806

Epigenomic and transcriptomic signatures of a Klinefelter syndrome (47,XXY) karyotype in the brain
Cited by: 41
Author(s): Joana Viana, Ruth Pidsley, Claire Troakes, Helen Spiers, Chloe Wong, Safa Al‐Sarraj, Ian W. Craig, Leonard C. Schalkwyk, Jonathan Mill
Software Mentions: 4
Published: almost 11 years ago

10.1042/BSR20203235

Mining the key genes for ventilator-induced lung injury using co-expression network analysis
Cited by: 2
Author(s): Li Zhao, Yajun Xiao, Li Xu, Qingxiu Wang
Software Mentions: 4
Published: almost 4 years ago

10.3390/biom10091207

Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder
Cited by: 24
Author(s): Dongmei Ai, Yuduo Wang, Xiaoxin Li, Hongfei Pan
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2021.705511

Screening and Validation of the Hypoxia-Related Signature of Evaluating Tumor Immune Microenvironment and Predicting Prognosis in Gastric Cancer
Cited by: 27
Author(s): Jun‐Peng Pei, Chundong Zhang, Maimaititusun Yusupu, Dong‐Qiu Dai
Software Mentions: 4
Published: over 3 years ago

10.3390/biomedicines9010034

Shared Blood Transcriptomic Signatures between Alzheimer’s Disease and Diabetes Mellitus
Cited by: 14
Author(s): Taesic Lee, Hyunju Lee
Software Mentions: 4
Published: almost 4 years ago

10.1155/2021/6656622

Profiles of Innate Immune Cell Infiltration and Related Core Genes in Psoriasis
Cited by: 11
Author(s): Xiaoting Gong, Wei Wang
Software Mentions: 4
Published: almost 4 years ago

10.1155/2015/621690

The Impact of Normalization Methods on RNA-Seq Data Analysis
Cited by: 81
Author(s): Joanna Zyprych-Walczak, Alicja Szabelska, Luiza Handschuh, Katarzyna Górczak, Kamila Klamecka, Marek Figlerowicz, Idzi Siatkowski
Software Mentions: 4
Published: almost 10 years ago

10.3390/ijms22052669

Additive Role of Immune System Infiltration and Angiogenesis in Uveal Melanoma Progression
Cited by: 18
Author(s): Sandra García-Mulero, M. Henar Alonso, L.P. del Carpio, Rebeca Sanz‐Pamplona, Josep María Piulats
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-60595-1

Prediction of Alzheimer’s disease using blood gene expression data
Cited by: 55
Author(s): Taesic Lee, Hyunju Lee
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0148818

Meta-Analysis of Tumor Stem-Like Breast Cancer Cells Using Gene Set and Network Analysis
Cited by: 14
Author(s): Wonjun Lee, Sang Cheol Kim, Jong Ho Yoon, Sang Jun Yoon, Jong-Tae Lim, You Sun Kim, Sung Won Kwon, Jeong Hill Park
Software Mentions: 4
Published: almost 9 years ago

10.3390/ijms21010292

Identification of Novel Pathways Associated with Patterned Cerebellar Purkinje Neuron Degeneration in Niemann-Pick Disease, Type C1
Cited by: 16
Author(s): Kyle B. Martin, Ian M. Williams, Céline Cluzeau, Antony Cougnoux, Ryan Dale, James R. Iben, Niamh X. Cawley, Christopher A. Wassif, Forbes D. Porter
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41389-019-0150-2

The epigenetic factor BORIS (CTCFL) controls the androgen receptor regulatory network in ovarian cancer
Cited by: 16
Author(s): Marisol Salgado-Albarrán, Rodrigo González‐Barrios, Lissania Guerra-Calderas, Nicolás Alcaraz, Thalía Estefanía Sánchez-Correa, Clementina Castro-Hernández, Yesennia Sánchez-Pérez, Elena Aréchaga-Ocampo, Alejandro García‐Carrancá, David Cantú de León, Luis A. Herrera, Jan Baumbach, Ernesto Soto-Reyes
Software Mentions: 3
Published: over 5 years ago

10.1186/s13148-019-0618-0

A randomized controlled trial of folic acid intervention in pregnancy highlights a putative methylation-regulated control element at ZFP57
Cited by: 32
Author(s): Rachelle E Irwin, Sara-Jayne Thursby, Miroslava Ondičová, Kristina Pentieva, Helene McNulty, Rebecca C Richmond, Aoife Caffrey, Diane J. Lees-Murdock, Marian McLaughlin, Tony Cassidy, Matthew Suderman, Caroline L Relton, Colum P. Walsh
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13148-020-00925-2

Loss-of-function maternal-effect mutations of PADI6 are associated with familial and sporadic Beckwith-Wiedemann syndrome with multi-locus imprinting disturbance
Cited by: 37
Author(s): Maria Vittoria Cubellis, Laura Pignata, Ankit Verma, Ángela Sparago, Rosita Del Prete, Maria Monticelli, Luciano Calzari, Vincenzo Antona, Daniela Melis, Romano Tenconi, Silvia Russo, Flavia Cerrato, Andrea Riccio
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.17915

A genomic lifespan program that reorganises the young adult brain is targeted in schizophrenia
Cited by: 40
Author(s): Nathan G. Skene, Marcia Roy, Seth G. N. Grant
Software Mentions: 3
Published: about 7 years ago

10.1016/j.csbj.2021.04.044

protGear: A protein microarray data pre-processing suite
Cited by: 1
Author(s): Kennedy Mwai, Nelson Kibinge, James Tuju, Gathoni Kamuyu, Rinter Kimathi, James Mburu, Emily Chepsat, Lydia Nyamako, Timothy Chege, Irene Nkumama, Samson Kinyanjui, Eustasius Musenge, Faith Osier
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.dib.2015.05.007

Prenatal alcohol exposure alters gene expression in the rat brain: Experimental design and bioinformatic analysis of microarray data
Cited by: 2
Author(s): Alexandre A. Lussier, Katarzyna Stępień, Joanne Weinberg, Michæl S. Kobor
Software Mentions: 3
Published: over 9 years ago

10.7717/peerj.11627

Development and validation of ferroptosis-related lncRNAs signature for hepatocellular carcinoma
Cited by: 20
Author(s): Jingang Liang, Yaofeng Zhi, Wenhui Deng, Weige Zhou, Xuejun Li, Zheyou Cai, Zengtai Zhu, Jinxiang Zeng, Wanlan Wu, Ying Dong, Jin Huang, Yuzhuo Zhang, Shichao Xu, Yixin Feng, Fuping Ding, Zhang Jin
Software Mentions: 3
Published: over 3 years ago

10.1155/2021/8886897

Integrated Analysis of lncRNA-Associated ceRNA Network Identifies Two lncRNA Signatures as a Prognostic Biomarker in Gastric Cancer
Cited by: 7
Author(s): Shuyan Zhang, Shanshan Li, Jiuxin Guo, Ningyi Li, Caining Zhang, Jie Liu
Software Mentions: 3
Published: about 3 years ago

10.1186/s12989-019-0309-1

Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation
Cited by: 25
Author(s): Marit Ilves, Pia Anneli Sofia Kinaret, Joseph Ndika, Piia Karisola, Veer Singh Marwah, Vittorio Fortino, Yuri Fedutik, Manuel Correia, Nicky Ehrlich, Katrin Loeschner, Alexandros Besinis, Joanne Vassallo, Richard D. Handy, Henrik Wolff, Kai Savolainen, Dario Greco, Harri Alenius
Software Mentions: 3
Published: over 5 years ago

10.1017/S0031182020002176

A <i>Trypanosoma cruzi</i> zinc finger protein that is implicated in the control of epimastigote-specific gene expression and metacyclogenesis
Cited by: 9
Author(s): Thais S. Tavares, Fernanda L. B. Mügge, Viviane Grazielle-Silva, Bruna M. Valente, Wanessa Moreira Goes, Antônio Edson Rocha Oliveira, Ashton T. Belew, Alessandra A. Guarneri, Fabiano Sviatopolk-Mirsky Pais, Najib M. El-Sayed, Santuza Maria Ribeiro Teixeira
Software Mentions: 3
Published: about 4 years ago

10.1186/s12957-021-02387-z

Comprehensive analysis of the cancer driver genes in breast cancer demonstrates their roles in cancer prognosis and tumor microenvironment
Cited by: 6
Author(s): Xinyue Du, Li Gao, Juan Liu, Chunyan Zhang, Qiong Liu, Hao Wang, Tingsong Chen
Software Mentions: 3
Published: about 3 years ago

10.1093/eurheartj/ehaa794

Hypertension and renin-angiotensin system blockers are not associated with expression of angiotensin-converting enzyme 2 (ACE2) in the kidney
Cited by: 37
Author(s): Xiao Jiang, James Eales, David Scannali, Alicja Nazgiewicz, Priscilla Prestes, Michelle Maier, Matthew Denniff, Xiaoguang Xu, Sushant Saluja, Eddie Cano-Gamez, Wojciech Wystrychowski, Monika Szulińska, Andrzej Antczak, Sean G. Byars, Damian Skrypnik, Maciej Głyda, Robert Król, Joanna Żywiec, E Żukowska-Szczechowska, Louise M Burrell, Adrian S. Woolf, Adam Greenstein, Paweł Bogdański, Bernard Keavney, Andrew P. Morris, Anthony M. Heagerty, Bryan Williams, Stephen Harrap, Gosia Trynka, Nilesh J. Samani, Tomasz J. Guzik, Fadi J. Charchar, Maciej Tomaszewski
Software Mentions: 3
Published: about 4 years ago

10.1002/1878-0261.12309

Specific breast cancer prognosis‐subtype distinctions based on<scp>DNA</scp>methylation patterns
Cited by: 62
Author(s): Shumei Zhang, Yihan Wang, Yue Gu, Jiang Zhu, Ce Ci, Zhongfu Guo, Chuangeng Chen, Yanjun Wei, Wenhua Lv, Hongbo Liu, Dongwei Zhang, Yan Zhang
Software Mentions: 3
Published: over 6 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: almost 7 years ago

10.1186/s13229-020-00384-9

Ribosome profiling in mouse hippocampus: plasticity-induced regulation and bidirectional control by TSC2 and FMRP
Cited by: 10
Author(s): Annie Hien, Gemma Molinaro, Botao Liu, Kimberly M. Huber, Joel D. Richter
Software Mentions: 3
Published: about 4 years ago

10.3389/fcell.2021.703629

N6-Methylandenosine-Related lncRNA Signature Is a Novel Biomarkers of Prognosis and Immune Response in Colon Adenocarcinoma Patients
Cited by: 14
Author(s): Peiling Zhang, Guolong Liu, Lin Lü
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.19531

Evolution of herbivore-induced early defense signaling was shaped by genome-wide duplications in Nicotiana
Cited by: 24
Author(s): Wenwu Zhou, Thomas Brockmöller, Zhihao Ling, Ashton Omdahl, Ian Thomas Baldwin, Shuqing Xu
Software Mentions: 3
Published: about 8 years ago

10.1186/s12944-020-01299-3

Ubiquitin-specific protease as the underlying gene biomarker for aortic stenosis
Cited by: 3
Author(s): Yin Yuan, Lianqun Wang, Bo-Chen Yao, Zhigang Guo
Software Mentions: 3
Published: over 4 years ago

10.3389/fcell.2021.705291

Autophagy-Related Genes and Long Noncoding RNAs Signatures as Predictive Biomarkers for Osteosarcoma Survival
Cited by: 8
Author(s): Jian Zhang, Rui Ding, Tianlong Wu
Software Mentions: 3
Published: over 3 years ago

10.1002/cam4.3946

WGCNA identification of TLR7 as a novel diagnostic biomarker, progression and prognostic indicator, and immunotherapeutic target for stomach adenocarcinoma
Cited by: 16
Author(s): Qihang Yuan, Qi Zhou, Jie Ren, Guan Wang, Chunlai Yin, Dong Shang, Shilin Xia
Software Mentions: 3
Published: over 3 years ago

10.3389/fncel.2018.00112

Environmental Enrichment Prevents Transcriptional Disturbances Induced by Alpha-Synuclein Overexpression
Cited by: 26
Author(s): Zinah Wassouf, Thomas Hentrich, Sebastian Samer, Carola Rotermund, Philipp J. Kahle, Ingrid Ehrlich, Olaf Rieß, Nicolas Casadei, Julia M. Schulze‐Hentrich
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.00016

Genome-Wide DNA Methylation Patterns in Persistent Attention-Deficit/Hyperactivity Disorder and in Association With Impulsive and Callous Traits
Cited by: 25
Author(s): Michiel Meijer, Marieke Klein, Eilís Hannon, Dennis van der Meer, Catharina A. Hartman, Jaap Oosterlaan, Dirk J. Heslenfeld, Pieter J. Hoekstra, Jan K. Buitelaar, Jonathan Mill, Barbara Franke
Software Mentions: 3
Published: almost 5 years ago

10.3389/fgene.2020.00671

Methylation Data Processing Protocol and Comparison of Blood and Cerebral Spinal Fluid Following Aneurysmal Subarachnoid Hemorrhage
Cited by: 7
Author(s): Annie I. Arockiaraj, Dongjing Liu, John R. Shaffer, Theresa A. Koleck, Elizabeth Crago, Daniel E. Weeks, Yvette P. Conley
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms21010317

The Use of PTI-Marker Genes to Identify Novel Compounds that Establish Induced Resistance in Rice
Cited by: 16
Author(s): Jonas De Kesel, Ramsés Gómez-Rodríguez, Eli Bonneure, Sven Mangelinckx, Tina Kyndt
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms21218115

Fluid Shear Stress Induces EMT of Circulating Tumor Cells via JNK Signaling in Favor of Their Survival during Hematogenous Dissemination
Cited by: 28
Author(s): Ying Xiao, Keming Li, Mo Yang, Youhua Tan
Software Mentions: 3
Published: about 4 years ago

10.1186/s12935-021-01982-0

Identification of collagen genes related to immune infiltration and epithelial-mesenchymal transition in glioma
Cited by: 25
Author(s): Yin Wu, Hecheng Zhu, Jun Tan, Zhaoqi Xin, Quanwei Zhou, Yudong Cao, Zhaoping Wu, Lei Wang, Ming Zhao, Xingjun Jiang, Chao Ren, Guihua Tang
Software Mentions: 3
Published: over 3 years ago

10.1186/s12935-020-01675-0

SLC39A1 contribute to malignant progression and have clinical prognostic impact in gliomas
Cited by: 12
Author(s): Peng Wang, Jingjing Zhang, Shuai He, Boan Xiao, Xiaobin Peng
Software Mentions: 3
Published: about 4 years ago

10.1186/s12935-020-1104-7

Immune-related gene signature for predicting the prognosis of head and neck squamous cell carcinoma
Cited by: 47
Author(s): Yangyang She, Xiangbo Kong, Yaping Ge, Ping Yin, Yong Li, Jieyu Chen, Feng Gao, Si-Lian Fang
Software Mentions: 3
Published: almost 5 years ago

10.3389/fgene.2018.00346

Stable Histone Methylation Changes at Proteoglycan Network Genes Following Ethanol Exposure
Cited by: 9
Author(s): David P. Gavin, Joel G. Hashimoto, Nathan H. Lazar, Lucia Carbone, John C. Crabbe, Marina Guizzetti
Software Mentions: 3
Published: over 6 years ago

10.3389/fimmu.2021.629854

Investigation of a Hypoxia-Immune-Related Microenvironment Gene Signature and Prediction Model for Idiopathic Pulmonary Fibrosis
Cited by: 13
Author(s): Xinyu Li, Haozheng Cai, Yi Cai, Quyan Zhang, Yinghe Ding, Quan Zhuang
Software Mentions: 3
Published: over 3 years ago

10.1093/biostatistics/kxv027

Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses
Cited by: 235
Author(s): Vegard Nygaard, Einar Andreas Rødland, Eivind Hovig
Software Mentions: 3
Published: over 9 years ago

10.1042/BSR20192546

Genetic interactions between INPP4B and RAD50 is prognostic of breast cancer survival
Cited by: 1
Author(s): Xiao Chen, Rutaganda Theobard, Jianying Zhang, Xiaofeng Dai
Software Mentions: 3
Published: almost 5 years ago

10.3390/biomedicines9010013

DNA Methylomes and Epigenetic Age Acceleration Associations with Poor Metabolic Control in T1D
Cited by: 2
Author(s): Raúl Fernández Pérez, Juan Luís Fernández-Morera, Judit Romano-García, Edelmiro Menéndez-Torre, Elías Delgado, Mario F. Fraga, Agustín F. Fernández
Software Mentions: 3
Published: almost 4 years ago

10.3389/fnins.2018.01033

Distinct Stress Response and Altered Striatal Transcriptome in Alpha-Synuclein Overexpressing Mice
Cited by: 8
Author(s): Zinah Wassouf, Thomas Hentrich, Nicolas Casadei, Mirko Jaumann, Marlies Knipper, Olaf Rieß, Julia M. Schulze‐Hentrich
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms22136958

Level of Murine DDX3 RNA Helicase Determines Phenotype Changes of Hepatocytes In Vitro and In Vivo
Cited by: 2
Author(s): Olga V. Sergeeva, Tatiana O. Abakumova, Ilia Kurochkin, Renata Ialchina, А. М. Косырева, Tatiana Prikazchikova, Varvara Varlamova, Evgeniya Shcherbinina, Timofei S. Zatsepin
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2021.626748

PD-L2 Is Constitutively Expressed in Normal and Malignant Urothelium
Cited by: 6
Author(s): Alexander C. Dowell, Haydn Munford, Ankit Goel, Naheema S. Gordon, Nicholas D. James, Kar Keung Cheng, Maurice P. Zeegers, Douglas G. Ward, Richard T. Bryan
Software Mentions: 3
Published: almost 4 years ago

10.1155/2020/7573689

Identification of Three lncRNAs as Potential Predictive Biomarkers of Lung Adenocarcinoma
Cited by: 14
Author(s): Donghui Jin, Yuxuan Song, Yuan Chen, Peng Zhang
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12974-020-01781-w

Transcriptomic analysis of brain tissues identifies a role for CCAAT enhancer binding protein β in HIV-associated neurocognitive disorder
Cited by: 11
Author(s): Saranya Canchi, Mary Swinton, Robert A. Rissman, Jerel Adam Fields
Software Mentions: 3
Published: over 4 years ago

10.1186/s13104-021-05741-2

An effective processing pipeline for harmonizing DNA methylation data from Illumina’s 450K and EPIC platforms for epidemiological studies
Cited by: 9
Author(s): Lauren A. Vanderlinden, Randi K. Johnson, Patrick M. Carry, Fran Dong, Dawn L. DeMeo, Ivana V. Yang, Jill M. Norris, Katerina Kechris
Software Mentions: 3
Published: about 3 years ago

10.3389/fonc.2021.657466

m5C RNA Methylation Regulators Predict Prognosis and Regulate the Immune Microenvironment in Lung Squamous Cell Carcinoma
Cited by: 51
Author(s): Junfan Pan, Zhidong Huang, Yiquan Xu
Software Mentions: 3
Published: over 3 years ago

10.18632/aging.101028

Ischemic stroke patients are biologically older than their chronological age
Cited by: 46
Author(s): Carolina Soriano‐Tárraga, Eva Giralt-Steinhauer, Marina Mola-Caminal, Rosa María Vivanco-Hidalgo, Ángel Ois, Ana Rodríguez-Campello, Elisa Cuadrado-Godia, Sergi Sayols-Baixeras, Roberto Elosúa, Jaume Roquer, Jordi Jiménez‐Conde
Software Mentions: 3
Published: over 8 years ago

10.3389/fphar.2021.638622

Large-Scale Transcriptome Analysis Identified a Novel Cancer Driver Genes Signature for Predicting the Prognostic of Patients With Hepatocellular Carcinoma
Cited by: 4
Author(s): Li Gao, Xinyue Du, Xiaoxiong Wu, Shen Wu, Yufei Zhang, Jianing Xu, Hao Wang, Tingsong Chen
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2020.00908

Revealing Shared and Distinct Genes Responding to JA and SA Signaling in Arabidopsis by Meta-Analysis
Cited by: 30
Author(s): Nailou Zhang, Shuang Zhou, Dongyan Yang, Fan Zhang
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-017-3808-1

Fast and robust adjustment of cell mixtures in epigenome-wide association studies with SmartSVA
Cited by: 51
Author(s): Jun Chen, Ehsan Behnam, Jinyan Huang, Miriam F. Moffatt, Daniel J. Schaid, Liming Liang, Xihong Lin
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-018-5091-1

Transcriptional defects and reprogramming barriers in somatic cell nuclear reprogramming as revealed by single-embryo RNA sequencing
Cited by: 23
Author(s): Yong Liu, Fengrui Wu, Ling Zhang, Xiaoqing Wu, Dengkun Li, Xin Jing, Juan Xie, Feng Kong, Wenying Wang, Qiaoqin Wu, Di Zhang, Rong Wang, Shaorong Gao, Wenyong Li
Software Mentions: 3
Published: about 6 years ago

10.1186/s13059-020-02102-3

Splicing-accessible coding 3′UTRs control protein stability and interaction networks
Cited by: 10
Author(s): Marco Preußner, Qingsong Gao, Eliot Morrison, Olga Herdt, Florian Finkernagel, Michael Schümann, Eberhard Krause, Christian Freund, Wei Chen
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-018-5000-7

Murine host response to Neisseria gonorrhoeae upper genital tract infection reveals a common transcriptional signature, plus distinct inflammatory responses that vary between reproductive cycle phases
Cited by: 11
Author(s): Ian Francis, Epshita A. Islam, Adam C. Gower, Yazdani B. Shaik‐Dasthagirisaheb, Scott D. Gray-Owen, Lee M. Wetzler
Software Mentions: 3
Published: over 6 years ago

10.1186/s13073-015-0227-2

Dynamic tracking of functional gene modules in treated juvenile idiopathic arthritis
Cited by: 12
Author(s): Nan Du, Kaiyu Jiang, Ashley Sawle, Mark Barton Frank, Carol A. Wallace, Aidong Zhang, James N. Jarvis
Software Mentions: 3
Published: about 9 years ago

10.1186/s13073-017-0419-z

Unique DNA methylation signature in HPV-positive head and neck squamous cell carcinomas
Cited by: 59
Author(s): Davide Degli Esposti, Athéna Sklias, Sheila Coelho Soares Lima, Stéphanie Beghelli-de la Forest Divonne, Vincent Cahais, Nora Fernández-Jiménez, Marie-Pierre Cros, Szilvia Ecsedi, Cyrille Cuenin, Liacine Bouaoun, Graham Byrnes, Rosita Accardi, Anne Sudaka, Valérie Giordanengo, Héctor Hernandez-Vargas, Luís Felipe Ribeiro Pinto, Ellen Van Obberghen-Schilling, Zdenko Herceg
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-1176

Distinct gene signatures in aortic tissue from ApoE-/-mice exposed to pathogens or Western diet
Cited by: 8
Author(s): Carolyn D. Kramer, Ellen O. Weinberg, Adam C. Gower, Xianbao He, Samrawit Mekasha, Connie Slocum, Lea M. Beaulieu, Lee M. Wetzler, Yuriy O. Alekseyev, Frank C. Gibson, Jane E. Freedman, Robin R. Ingalls, Caroline A. Genco
Software Mentions: 3
Published: about 10 years ago

10.1186/s12863-021-00988-x

DNA methylation changes in African American women with a history of preterm birth from the InterGEN study
Cited by: 3
Author(s): Veronica Barcelona, Janitza L. Montalvo-Ortiz, Michelle L. Wright, Sheila Tiemi Nagamatsu, Caitlin Dreisbach, Cindy A. Crusto, Yan V. Sun, Jacquelyn Y. Taylor
Software Mentions: 3
Published: about 3 years ago

10.1210/jc.2017-00881

Prognostic Classifier Based on Genome-Wide DNA Methylation Profiling in Well-Differentiated Thyroid Tumors
Cited by: 42
Author(s): Mariana Bisarro dos Reis, Mateus Camargo Barros-Filho, Fábio Albuquerque Marchi, Caroline Moraes Beltrami, Hellen Kuasne, Clóvis Antônio Lopes Pinto, Srikant Ambatipudi, Zdenko Herceg, Luiz Paulo Kowalski, Sílvia Regina Rogatto
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.ppat.1007802

Strength of T cell signaling regulates HIV-1 replication and establishment of latency
Cited by: 20
Author(s): Matthew Gagné, Daniel Michaels, Gillian M. Schiralli Lester, Suryaram Gummuluru, Wilson Wong, Andrew J. Henderson
Software Mentions: 3
Published: over 5 years ago

10.1038/s41597-019-0331-z

Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media
Cited by: 7
Author(s): Abhishek Rajput, Saugat Poudel, Hannah Tsunemoto, Michael J. Meehan, Richard Szubin, Connor A. Olson, Anne Lamsa, Yara Seif, Nicholas Dillon, Alison Vrbanac, Joseph Sugie, Samira Dahesh, Jonathan M. Monk, Pieter C. Dorrestein, Rob Knight, Victor Nizet, Bernhard Ø. Palsson, Adam M. Feist, Joe Pogliano
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12859-018-2263-6

Alternative empirical Bayes models for adjusting for batch effects in genomic studies
Cited by: 45
Author(s): Yuqing Zhang, D. Graham Jenkins, Solaiappan Manimaran, W. Evan Johnson
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-017-08134-3

Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs
Cited by: 46
Author(s): Anna García-Elías, Leonor Alloza, Eulàlia Puigdecanet, Lara Nonell, Marta Tajes, João Curado, Cristina Enjuanes, Óscar Díaz, Jordi Bruguera, Julio Martí‐Almor, Josep Comín‐Colet, Begoña Benito
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-24219-z

A mega-analysis of expression quantitative trait loci (eQTL) provides insight into the regulatory architecture of gene expression variation in liver
Cited by: 51
Author(s): Tobias Strunz, Felix Graßmann, Javier Gayán, Satu Nahkuri, Débora C. Souza-Costa, Cyrille Maugeais, Sascha Fauser, Everson Nogoceke, Bernhard H. F. Weber
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-31132-y

RNA-Seq Analysis of Spinal Cord Tissues from hPFN1G118V Transgenic Mouse Model of ALS at Pre-symptomatic and End-Stages of Disease
Cited by: 11
Author(s): Caroline Barham, Daniel Fil, Stephanie D. Byrum, Yasir Rahmatallah, Galina Glazko, Mahmoud Kiaei
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-46491-3

Transcriptome Network Analysis Identifies CXCL13-CXCR5 Signaling Modules in the Prostate Tumor Immune Microenvironment
Cited by: 21
Author(s): Adaugo Q. Ohandjo, Zongzhi Liu, Eric B. Dammer, Courtney D. Dill, Tiara Griffen, Kaylin Carey, Denise E. Hinton, Robert Meller, James W. Lillard
Software Mentions: 3
Published: about 5 years ago

10.1080/21623945.2020.1789283

Identification of differentially expressed mRNA and the Hub mRNAs modulated by lncRNA Meg3 as a competing endogenous RNA in brown adipose tissue of mice on a high-fat diet
Cited by: 5
Author(s): Yemin Zhang, Yalin Fu, Yuyang Zheng, Zhongyuan Wen, Changhua Wang
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-78402-2

SARS-CoV-2 receptor ACE2 is co-expressed with genes related to transmembrane serine proteases, viral entry, immunity and cellular stress
Cited by: 29
Author(s): Wasco Wruck, James Adjaye
Software Mentions: 3
Published: almost 4 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: over 11 years ago

10.1038/s41598-021-82609-2

Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells
Cited by: 4
Author(s): Gina Eagle, John Herbert, Jianguo Zhuang, Melanie Oates, Umair Khan, Neil R. Kitteringham, Kim Clarke, B Kevin Park, Andrew R. Pettitt, Rosalind E. Jenkins, Francesco Falciani
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-020-80857-2

Sperm DNA methylation mediates the association of male age on reproductive outcomes among couples undergoing infertility treatment
Cited by: 18
Author(s): Oladele A. Oluwayiose, Haotian Wu, Hachem Saddiki, Brian W. Whitcomb, Laura B. Balzer, Nicole Brandon, Alexander Suvorov, Tayyab Rahil, Cynthia K. Sites, Lisa Hill, Chelsea Marcho, J. Richard Pilsner
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12967-016-0913-x

Longitudinal study of DNA methylation during the first 5 years of life
Cited by: 29
Author(s): Rocío G. Urdinguio, María Isabel Torró, Gustavo F. Bayón, Julio Álvarez, Agustín F. Fernández, P. Redon, Mario F. Fraga, Empar Lurbe
Software Mentions: 3
Published: over 8 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: over 4 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: about 4 years ago

10.18632/aging.202958

Identification of a novel glycolysis-related gene signature for predicting the prognosis of osteosarcoma patients
Cited by: 16
Author(s): Mengkai Yang, Xiao‐Jun Ma, Zhuoying Wang, Tao Zhang, Yingqi Hua, Zhengdong Cai
Software Mentions: 3
Published: over 3 years ago

Projects: bioconductor: sva

Papers Mentioning sva 511