bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3389/fnins.2020.591196

Anticonvulsants and Chromatin-Genes Expression: A Systems Biology Investigation
Cited by: 1
Author(s): Thayne Woycinck Kowalski, João Luiz Ellera Gomes, Mariléa Furtado Feira, Ágata de Vargas Dupont, Mariana Recamonde‐Mendoza, Fernanda Sales Luiz Vianna
Software Mentions: 3
Published: almost 6 years ago

10.3389/fonc.2020.585980

Discovery and Validation of a Metastasis-Related Prognostic and Diagnostic Biomarker for Melanoma Based on Single Cell and Gene Expression Datasets
Cited by: 16
Author(s): Qi Wan, Chengxiu Liu, Chang Liu, Weiqin Liu, Xiaoran Wang, Zhichong Wang
Software Mentions: 3
Published: almost 6 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: over 5 years ago

10.3389/fonc.2021.612952

A 13-Gene Metabolic Prognostic Signature Is Associated With Clinical and Immune Features in Stomach Adenocarcinoma
Cited by: 17
Author(s): Zaisheng Ye, Miao Zheng, Yi Zeng, Shenghong Wei, He Huang, Yi Wang, Qinying Liu, Zhitao Lin, Chen Shu, Qinqin Zheng, Luchuan Chen
Software Mentions: 3
Published: about 5 years ago

10.3389/fonc.2020.00788

The Landscape of Iron Metabolism-Related and Methylated Genes in the Prognosis Prediction of Clear Cell Renal Cell Carcinoma
Cited by: 15
Author(s): Yanhua Mou, Yao Zhang, Jinchun Wu, Busheng Hu, Chunfang Zhang, Chaojun Duan, Bin Li
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2021.641289

Bioinformatics Analysis of a Prognostic miRNA Signature and Potential Key Genes in Pancreatic Cancer
Cited by: 15
Author(s): Shuoling Chen, Chang Gao, Tao Yu, Yueyang Qu, Gary Guishan Xiao, Zunnan Huang
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2021.615963

Identification of Genes Related to Immune Infiltration in the Tumor Microenvironment of Cutaneous Melanoma
Cited by: 10
Author(s): Rujia Qin, Wen Peng, Xuemin Wang, Chunyan Li, Yan Xi, Zhaoming Zhong, Chuanzheng Sun
Software Mentions: 3
Published: over 5 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 5 years ago

10.3389/fonc.2021.595259

A Voxel-Based Radiographic Analysis Reveals the Biological Character of Proneural-Mesenchymal Transition in Glioblastoma
Cited by: 3
Author(s): Tengfei Qi, Xiangqi Meng, Zhenyu Wang, Xinyu Wang, Nan Sun, Jianguang Ming, Lejia Ren, Chuanlu Jiang, Jinquan Cai
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2021.677609

Characterization of the Immune Cell Infiltration Profile in Pancreatic Carcinoma to Aid in Immunotherapy
Cited by: 6
Author(s): De Luo, Fei Li Kuang, Juan Du, Mimi Zhou, Fangyi Peng, Yu Gan, Cheng Fang, Xiaoli Yang, Bo Li, Song Su
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2020.00504

Targeted Deep Sequencing Uncovers Cryptic KIT Mutations in KIT/PDGFRA/SDH/RAS-P Wild-Type GIST
Cited by: 14
Author(s): Annalisa Astolfi, Valentina Indio, Margherita Nannini, Maristella Saponara, Angela Schipani, Antonio De Leo, Annalisa Altimari, Bruno Vincenzi, Danila Comandini, Giovanni Grignani, Paola Secchiero, Milena Urbini, Maria Abbondanza Pantaleo
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2021.644612

The Diagnostic and Immunotherapeutic Value of CD248 in Renal Cell Carcinoma
Cited by: 10
Author(s): Keying Zhang, Chao Xu, Shaojie Li, Yao Jiang, Xiaolong Zhao, Shanjin Ma, Yu Liu, Yang Fa, Yan Wang, Ping Meng, Changhong Shi, Donghui Han, Weihong Wen, Weijun Qin
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2020.00845

Multi-Omic Regulation of the PAM50 Gene Signature in Breast Cancer Molecular Subtypes
Cited by: 14
Author(s): Soledad Ochoa, Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2020.577530

GPR115 Contributes to Lung Adenocarcinoma Metastasis Associated With LAMC2 and Predicts a Poor Prognosis
Cited by: 13
Author(s): Yingjing Wang, Muqi Shi, Nan Yang, Xiaoyu Zhou, Liqin Xu
Software Mentions: 3
Published: almost 6 years ago

10.3389/fonc.2019.00729

Development of a 21-miRNA Signature Associated With the Prognosis of Patients With Bladder Cancer
Cited by: 39
Author(s): Xiaohong Yin, Yinghui Jin, Yue Cao, York Wong, Hong Weng, Chao Sun, Junhao Deng, Xian‐Tao Zeng
Software Mentions: 3
Published: about 7 years ago

10.3389/fped.2020.00032

Hydrolyzed Fat Formula Increases Brain White Matter in Small for Gestational Age and Appropriate for Gestational Age Neonatal Piglets
Cited by: 5
Author(s): Megan P. Caputo, Jennifer N. Williams, Jenny Drnevich, Emily C. Radlowski, Ryan J. Larsen, Bradley P. Sutton, Brian J. Leyshon, Jamal Hussain, Manabu Nakamura, Matthew J. Kuchan, Tapas Das, Rodney W. Johnson
Software Mentions: 3
Published: over 6 years ago

10.3389/fphar.2021.632206

LINC01116 Promotes Doxorubicin Resistance in Osteosarcoma by Epigenetically Silencing miR-424-5p and Inducing Epithelial-Mesenchymal Transition
Cited by: 11
Author(s): Ran Li, Qing Ruan, Jia Zheng, Butian Zhang, Hongliang Yang
Software Mentions: 3
Published: over 5 years ago

10.3389/fphar.2018.00583

DeCoST: A New Approach in Drug Repurposing From Control System Theory
Cited by: 15
Author(s): Thanh Nguyen, Syed Aun Muhammad, Sara Ibrahim, Lin Ma, Jinchao Guo, Baogang Bai, Bixin Zeng
Software Mentions: 3
Published: over 8 years ago

10.3389/fphar.2020.572627

Identification of Mutations Related to Cisplatin-Resistance and Prognosis of Patients With Lung Adenocarcinoma
Cited by: 9
Author(s): Rui Li, Junfang Liu, Ze-Kui Fang, Zhenyu Liang, Xin Chen
Software Mentions: 3
Published: almost 6 years ago

10.3389/fphar.2021.657486

Caspase-11-Gasdermin D-Mediated Pyroptosis Is Involved in the Pathogenesis of Atherosclerosis
Cited by: 34
Author(s): Mengqing Jiang, Xuejing Sun, Suzhen Liu, Tao Yan, Yunming Shi, Yuanyuan Bai, Yujie Wang, Qiong Yang, Qize Yang, Weihong Jiang, Hong Yuan, Qixia Jiang, Jingjing Cai
Software Mentions: 3
Published: over 5 years ago

10.3389/fphar.2020.00544

Identification of Prognostic miRNA Signature and Lymph Node Metastasis-Related Key Genes in Cervical Cancer
Cited by: 27
Author(s): Shuoling Chen, Chang Gao, Yangyuan Wu, Zunnan Huang
Software Mentions: 3
Published: over 6 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: about 5 years ago

10.1186/s13059-019-1701-8

Detection of circular RNA expression and related quantitative trait loci in the human dorsolateral prefrontal cortex
Cited by: 47
Author(s): Zelin Liu, Yuan Ran, Changyu Tao, Sichen Li, Jian Chen, Ence Yang
Software Mentions: 3
Published: over 7 years ago

10.1186/s13059-019-1814-0

The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation
Cited by: 26
Author(s): Andrea Hildebrandt, Mirko Brüggemann, Cornelia Rücklé, Susan Boerner, Jan B. Heidelberger, Anke Busch, Heike Hänel, Andrea Voigt, Martin Möckel, Stefanie Ebersberger, Anica Scholz, Annabelle Dold, Tobias Schmid, Ingo Ebersberger, Jean‐Yves Roignant, Kathi Zarnack, Julian König, Petra Beli
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13059-020-02125-w

Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits
Cited by: 24
Author(s): Kevin J. Gleason, Fan Yang, Brandon L. Pierce, Xin He, Lin S. Chen
Software Mentions: 3
Published: about 6 years ago

10.1093/gbe/evu272

Evolutionary Dynamics of GLD-1–mRNA Complexes in Caenorhabditis Nematodes
Cited by: 7
Author(s): Alana V. Beadell, Eric S. Haag
Software Mentions: 3
Published: almost 12 years ago

10.1093/gbe/evab160

Comparative Transcriptomics Reveals Distinct Patterns of Gene Expression Conservation through Vertebrate Embryogenesis
Cited by: 2
Author(s): Megan Chan, Pranav S. Bhamidipati, Heather J. Goldsby, Arend Hintze, Hans A. Hofmann, Rebecca L. Young
Software Mentions: 3
Published: about 5 years ago

10.1186/gm130

Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in type 2 diabetes
Cited by: 228
Author(s): Iain J. Gallagher, Camilla Schéele, Pernille Keller, Annemette Nielsen, Judit Reményi, Christian P. Fischer, Karim Roder, John Babraj, Claes Wahlestedt, György Hutvágner, Bente Klarlund Pedersen, James A. Timmons
Software Mentions: 3
Published: over 16 years ago

10.1186/s13073-015-0180-0

The oxidative demethylase ALKBH3 marks hyperactive gene promoters in human cancer cells
Cited by: 14
Author(s): Robert Liefke, Indra M. Windhof-Jaidhauser, Jochen Gaedcke, Gabriela Salinas-Riester, Feizhen Wu, Michael Ghadimi, Sebastian Dango
Software Mentions: 3
Published: about 11 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: almost 11 years ago

10.1186/s13073-016-0310-3

Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factors in tumorigenesis
Cited by: 18
Author(s): Valeriya Malysheva, Marco Antonio Mendoza-Parra, Mohamed-Ashick M. Saleem, Hinrich Gronemeyer
Software Mentions: 3
Published: over 10 years ago

10.1186/s13073-018-0557-y

Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells
Cited by: 27
Author(s): Ksenia S. Anufrieva, Victoria О. Shender, Georgij Arapidi, Marat S. Pavlyukov, M. I. Shakhparonov, Polina V. Shnaider, Ivan Butenko, Maria A. Lagarkova, Vadim M. Govorun
Software Mentions: 3
Published: about 8 years ago

10.1186/s13073-019-0674-2

Inflammatory cytokines and organ dysfunction associate with the aberrant DNA methylome of monocytes in sepsis
Cited by: 52
Author(s): Clara Lorente-Sorolla, Antonio García-Gómez, Francesc Català-Moll, Víctor Toledano, Laura Ciudad, José Avendaño-Ortíz, Charbel Maroun Eid, Alejandro Martín-Quirós, Mónica Martínez-Gallo, Adolfo Ruiz-Sanmartín, Álvaro García del Campo, Ricard Ferrer, Juan Carlos Ruiz‐Rodríguez, Damiana Álvarez-Errico, Eduardo López-Collazo, Esteban Ballestar
Software Mentions: 3
Published: almost 7 years ago

10.1080/19490976.2020.1854639

Personalized B cell response to the <i>Lactobacillus rhamnosus GG</i> probiotic in healthy human subjects: a randomized trial
Cited by: 4
Author(s): Jette Bornholdt, Christa Broholm, Yun Chen, Alfredo Rago, Stine Sloth, Jakob Hendel, Cathrine Melsæther, Christina V Müller, Mads Eggert Nielsen, Jesper A.B. Strickertsson, Lars H. Engelholm, Kristoffer Vitting-Seerup, Kim B. Jensen, Adam Baker, Albin Sandelin
Software Mentions: 3
Published: almost 6 years ago

10.1186/s41065-021-00187-9

Identification of potential biomarkers for pathogenesis of Alzheimer’s disease
Cited by: 10
Author(s): Huimin Wang, Xiujiang Han, Sheng Gao
Software Mentions: 3
Published: about 5 years ago

10.1038/s41438-021-00572-5

Tissue and regional expression patterns of dicistronic tRNA–mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants
Cited by: 4
Author(s): Pastor Jullian Fabres, Lakshay Anand, Na Sai, Stephen Pederson, Fei Zheng, Alexander A. Stewart, Benjamin Clements, Edwin R. Lampugnani, James Breen, Matthew Gilliham, Penny J. Tricker, Carlos M. Rodríguez López, Rakesh David
Software Mentions: 3
Published: over 5 years ago

10.1038/s41438-020-0249-9

Application of an antibody chip for screening differentially expressed proteins during peach ripening and identification of a metabolon in the SAM cycle to generate a peach ethylene biosynthesis model
Cited by: 10
Author(s): Wenfang Zeng, Liang Niu, Zhaohui Wang, Xiaobei Wang, Yan Wang, Lei Pan, Zhenhua Lü, Guochao Cui, Weining Weng, Mingqiao Wang, Xianghong Meng, Zhiqiang Wang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12979-015-0038-8

Hormetic effect of rotenone in primary human fibroblasts
Cited by: 13
Author(s): Shiva Marthandan, Stefan Priebe, Marco Groth, Reinhard Guthke, Matthias Platzer, Peter Hemmerich, Stephan Diekmann
Software Mentions: 3
Published: about 11 years ago

10.1002/iid3.379

Prognostic value of lipid metabolism‐related genes in head and neck squamous cell carcinoma
Cited by: 13
Author(s): Ying Xiong, Shaohua Yu, Yisi Feng, Shipei Zhuo, Bozhen Cui, Zhigang Zhang
Software Mentions: 3
Published: almost 6 years ago

10.1007/s12088-019-00847-5

Identification of Key Candidate Genes and Pathways of Candida albicans-Infected Human Umbilical Vein Endothelial Cells and Drug Screening
Cited by: 1
Author(s): Wei Jiang, Ping Liu, Jianlei Zhang, Wenjie Yang
Software Mentions: 3
Published: almost 7 years ago

10.1128/IAI.00331-18

Genome Plasticity of <i>agr</i> -Defective Staphylococcus aureus during Clinical Infection
Cited by: 45
Author(s): Deena R. Altman, Mitchell J. Sullivan, Kieran I. Chacko, Divya Balasubramanian, Theodore R. Pak, William E. Sause, Krishan Kumar, Robert Sebra, Gintaras Deikus, Oliver Attie, Hannah Rose, Martha Lewis, Yi Fulmer, Ali Kashif Bashir, Andrew Kasarskis, Eric E. Schadt, Anthony R. Richardson, Victor J. Torres, Bo Shopsin, Harm van Bakel
Software Mentions: 3
Published: almost 8 years ago

10.1093/ibd/izy119

Discovery and Validation of Methylation Biomarkers for Ulcerative Colitis Associated Neoplasia
Cited by: 8
Author(s): Andrew D Beggs, Jonathan James, Germaine Caldwell, Toby Prout, Mark Dilworth, Philippe Taniere, Tariq Iqbal, Dean Morton, Glenn Matthews
Software Mentions: 3
Published: over 8 years ago

10.1590/S1677-5538.IBJU.2020.1104

Exploration of the core genes in ulcerative interstitial cystitis/bladder pain syndrome
Cited by: 4
Author(s): Hao Wu, Qiuju Su, Ziyi Zhang, Ze Zhang, Shenglin Gao, Chen Lü, Li Zuo, Lifeng Zhang
Software Mentions: 3
Published: about 5 years ago

10.1111/jcmm.16502

Novel COL4A1‐VEGFD gene fusion in myofibroma
Cited by: 5
Author(s): Guillaume Dachy, Sylvie Fraïtag, Boutaina Boulouadnine, Sabine Cordi, Jean‐Baptiste Demoulin
Software Mentions: 3
Published: over 5 years ago

10.1111/jcmm.16536

FABP5 enhances malignancies of lower‐grade gliomas via canonical activation of NF‐κB signaling
Cited by: 19
Author(s): Yichang Wang, Alafate Wahafu, Wei Wu, Jianyang Xiang, Longwei Huo, Xudong Ma, Ning Wang, Hao Líu, Xia Bai, Dongze Xu, Wei Xie, Maode Wang, Jia Wang
Software Mentions: 3
Published: over 5 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: about 9 years ago

10.1172/JCI97007

Hypothalamic loss of Snord116 recapitulates the hyperphagia of Prader-Willi syndrome
Cited by: 73
Author(s): Joseph Polex-Wolf, Brian Lam, Rachel Larder, John Tadross, Debra Rimmington, Fàtima Bosch, Verónica Jiménez Cenzano, Eduard Ayuso, Marcella Kl, Kara Rainbow, Anthony P. Coll, Stephen O’Rahilly, Giles S.H. Yeo
Software Mentions: 3
Published: over 8 years ago

10.3390/jcm10051057

Gene Expression Landscape of SDH-Deficient Gastrointestinal Stromal Tumors
Cited by: 9
Author(s): Valentina Indio, Angela Schipani, Margherita Nannini, Milena Urbini, Alessandro Rizzo, Antonio De Leo, Annalisa Altimari, Valerio Di Scioscio, Daria Messelodi, Giuseppe Tarantino, Annalisa Astolfi, Maria Abbondanza Pantaleo
Software Mentions: 3
Published: over 5 years ago

10.1093/jxb/ery062

Thermopriming triggers splicing memory in Arabidopsis
Cited by: 91
Author(s): Lexiang Yu, Natalia Serrano, Ge Gao, Mohamed A. M. Atia, Morad M. Mokhtar, Yong Woo, Jérémie Bazin, Alaguraj Veluchamy, Moussa Benhamed, Martín Crespi, Chris Gehring, Anireddy S. N. Reddy, Magdy M. Mahfouz
Software Mentions: 3
Published: over 8 years ago

10.1093/jxb/eraa264

The chromatin-modifying protein HUB2 is involved in the regulation of lignin composition in xylem vessels
Cited by: 4
Author(s): Bo Zhang, Bernadette Sztojka, Carolin Seyfferth, Sacha Escamez, Pál Miskolczi, Maxime Chantreau, L. Bako, Nicolas Delhomme, András Gorzsás, Rishikesh P. Bhalerao, Hannele Tuominen
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1000154

Sub-Telomere Directed Gene Expression during Initiation of Invasive Aspergillosis
Cited by: 227
Author(s): Andrew McDonagh, Natalie D. Fedorova, Jonathan Crabtree, Yu Yan, Heenam Stanley Kim, Dan Chen, Omar Loss, Timothy C. Cairns, Gustavo H. Goldman, Darius Armstrong‐James, Ken Haynes, Hubertus Haas, Markus Schrettl, Gregory S. May, William C. Nierman, Elaine Bignell
Software Mentions: 3
Published: about 18 years ago

10.1371/journal.ppat.1000781

Genome-Wide mRNA Expression Correlates of Viral Control in CD4+ T-Cells from HIV-1-Infected Individuals
Cited by: 166
Author(s): Margalida Rotger, Kristen K. Dang, Jacques Fellay, Erin L. Heinzen, Sheng Feng, Patrick Descombes, Kevin V. Shianna, Dongliang Ge, Huldrych F Günthard, David B. Goldstein, Amalio Telenti, Aids Immunology
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.ppat.1002861

Exon Level Transcriptomic Profiling of HIV-1-Infected CD4+ T Cells Reveals Virus-Induced Genes and Host Environment Favorable for Viral Replication
Cited by: 46
Author(s): Michaël Imbeault, Katia Giguère, Michel Ouellet, Michel J. Tremblay
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.ppat.1002864

Genome-Wide Analysis of Germline Signaling Genes Regulating Longevity and Innate Immunity in the Nematode Pristionchus pacificus
Cited by: 24
Author(s): Robbie Rae, Amit Sinha, Ralf J. Sommer
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.ppat.1003920

Group B Streptococcal Infection of the Choriodecidua Induces Dysfunction of the Cytokeratin Network in Amniotic Epithelium: A Pathway to Membrane Weakening
Cited by: 44
Author(s): Jeroen Vanderhoeven, Craig J. Bierle, Raj P. Kapur, Ryan M. McAdams, Richard P. Beyer, Theo K. Bammler, Federico M. Farin, Aasthaa Bansal, Min Spencer, Mei Deng, Michael G. Gravett, Craig E. Rubens, Lakshmi Rajagopal, Kristina M. Adams Waldorf
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.ppat.1005943

Cathelicidin Insufficiency in Patients with Fatal Leptospirosis
Cited by: 21
Author(s): Janet C. Lindow, Elsio A. Wunder, Stephen J. Popper, Jinsoo Min, Praveen Mannam, Anup Srivastava, Yi Yao, Kathryn P. Hacker, Khadir Raddassi, Patty J Lee, Ruth R. Montgomery, Albert C. Shaw, José E. Hagan, Guilherme C. Araújo, Nívison Nery, David A. Relman, Charles C. Kim, Mitermayer Galvão dos Reis, Albert I. Ko
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.ppat.1006664

EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells
Cited by: 23
Author(s): Laura V. Glaser, Simone Rieger, Sybille Thumann, Sophie Beer, Cornelia Kuklik-Roos, Dietmar E. Martin, Kerstin Maier, Marie L. Harth-Hertle, Björn Grüning, Rolf Backofen, Stefan Krebs, Helmut Blum, Ralf Zimmer, Florian Erhard, Bettina Kempkes
Software Mentions: 3
Published: almost 9 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 7 years ago

10.1371/journal.ppat.1008155

The alternative cap-binding complex is required for antiviral defense in vivo
Cited by: 18
Author(s): Anna Gebhardt, Valter Bergant, Daniel Schnepf, Markus Moser, Arno Meiler, Dieudonnée Togbe, Claire Mackowiak, Line S. Reinert, Søren R. Paludan, Bernhard Ryffel, Alexey Stukalov, Peter Staeheli, Andreas Pichlmair
Software Mentions: 3
Published: over 6 years ago

10.1038/srep26020

The N-end rule pathway regulates pathogen responses in plants
Cited by: 37
Author(s): Rémi de Marchi, Maud Sorel, Brian Mooney, Isabelle Fudal, Kevin Goslin, Kamila Kwaśniewska, Patrick T. Ryan, Marina Pfalz, Juergen Kroymann, Stephan Pollmann, Angela Feechan, Frank Wellmer, Susana Rivas, Emmanuelle Graciet
Software Mentions: 3
Published: over 10 years ago

10.1038/srep27392

Transcriptional reprogramming and phenotypic switching associated with the adaptation of Lactobacillus plantarum C2 to plant niches
Cited by: 31
Author(s): Pasquale Filannino, Raffaella Di Cagno, Carmine Crecchio, Caterina De Virgilio, Maria De Angelis, Marco Gobbetti
Software Mentions: 3
Published: over 10 years ago

10.1038/srep27514

Cross-talk between AMPK and EGFR dependent Signaling in Non-Small Cell Lung Cancer
Cited by: 8
Author(s): Paurush Praveen, H. Hülsmann, Holger Sültmann, Ruprecht Kuner, Holger Fröhlich
Software Mentions: 3
Published: over 10 years ago

10.1038/srep28998

The RNA binding protein HuR determines the differential translation of autism-associated FoxP subfamily members in the developing neocortex
Cited by: 33
Author(s): Tatiana Popovitchenko, Kevin J. Thompson, Barbara Viljetić, Xuan Jiao, D. L. Kontonyiannis, Megerditch Kiledjian, Ronald P. Hart, Mladen-Roko Rašin
Software Mentions: 3
Published: about 10 years ago

10.1038/srep28851

Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules
Cited by: 17
Author(s): Isar Nassiri, Rosario Lombardo, Mario Lauria, Melissa J. Morine, Petros Moyseos, Vijayalakshmi Varma, Greg T. Nolen, Bridgett Knox, Daniel T. Sloper, Jim Kaput, Corrado Priami
Software Mentions: 3
Published: about 10 years ago

10.1038/srep29334

Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness
Cited by: 31
Author(s): Christopher J. Walsh, Jane Batt, Margaret S. Herridge, Sunita Mathur, Gary D. Bader, Pingzhao Hu, Claudia C. dos Santos
Software Mentions: 3
Published: about 10 years ago

10.1038/srep37651

Immune signatures of protective spleen memory CD8 T cells
Cited by: 11
Author(s): Lilia Brinza, Sophia Djebali, Martine Tomkowiak, Julien Mafille, Céline Loiseau, Pierre Emmanuel Jouve, Simon Bernard, Laurent Buffat, Bruno Lina, Michèle Ottmann, Manuel Rosa‐Calatrava, Stéphane Schicklin, Nathalie Bonnefoy, Grégoire Lauvau, Morgan Grau, Mélanie Wencker, Christophe Arpin, Thierry Walzer, Yann Leverrier, Jacqueline Marvel
Software Mentions: 3
Published: almost 10 years ago

10.1038/srep40775

Disrupting Hepatocyte Cyp51 from Cholesterol Synthesis Leads to Progressive Liver Injury in the Developing Mouse and Decreases RORC Signalling
Cited by: 24
Author(s): Žiga Urlep, Gregor Lorbek, Martina Perše, Jera Jeruc, Peter Juvan, Madlen Matz‐Soja, Rolf Gebhardt, Ingemar Björkhem, Jason A. Hall, Richard Bonneau, Dan R. Littman, Damjana Rozman
Software Mentions: 3
Published: over 9 years ago

10.1038/srep42060

Integrative analysis of copy number and transcriptional expression profiles in esophageal cancer to identify a novel driver gene for therapy
Cited by: 26
Author(s): Gaochao Dong, Qixing Mao, Decai Yu, Yi Zhang, Mantang Qiu, Gaoyue Dong, Qiang Chen, Wenjie Xia, Jie Wang, Lin Xu, Feng Jiang
Software Mentions: 3
Published: over 9 years ago

10.1038/srep42633

Transcriptomic responses of the olive fruit fly Bactrocera oleae and its symbiont Candidatus Erwinia dacicola to olive feeding
Cited by: 40
Author(s): Nena Pavlidi, Αnastasia Gioti, Nicky Wybouw, Wannes Dermauw, Michael Ben-Yosef, Boaz Yuval, Edouard Jurkevich, Anastasia Kampouraki, Thomas Van Leeuwen, John Vontas
Software Mentions: 3
Published: over 9 years ago

10.1038/srep43478

The influence of haemoglobin and iron on in vitro mycobacterial growth inhibition assays
Cited by: 29
Author(s): Rachel Tanner, Matthew K. O’Shea, Andrew Dickson White, Julius Müller, Rachel Harrington-Kandt, Magali Matsumiya, Mike Dennis, Eneida Abreu Parizotto, Stephanie A. Harris, Elena Stylianou, Vivek Naranbhai, Paulo Bettencourt, Hal Drakesmith, Sally Sharpe, Helen A. Fletcher, Helen McShane
Software Mentions: 3
Published: over 9 years ago

10.1038/srep44131

Vascular transcriptome profiling identifies Sphingosine kinase 1 as a modulator of angiotensin II-induced vascular dysfunction
Cited by: 36
Author(s): Mateusz Siedliński, Ryszard Nosalski, Piotr Szczepaniak, Agnieszka H. Ludwig-Gałęzowska, T. Mikołajczyk, Magdalena Filip, Grzegorz Osmenda, G. Wilk, Michał Nowak, Paweł Wołkow, Tomasz J. Guzik
Software Mentions: 3
Published: over 9 years ago

10.1038/srep44219

Variability in statin-induced changes in gene expression profiles of pancreatic cancer
Cited by: 30
Author(s): Helena Gbelcová, Silvie Rimpelová, Tomáš Ruml, Marie Fenclová, Vít Kosek, Jana Hajšlová, Hynek Strnad, Michal Kolář, Libor Vı́tek
Software Mentions: 3
Published: over 9 years ago

10.1038/srep44232

Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue
Cited by: 73
Author(s): Jarrett Morrow, Xiaobo Zhou, Taotao Lao, Zhiqiang Jiang, Dawn L. DeMeo, Michael H. Cho, Weiliang Qiu, Suzanne M. Cloonan, Víctor Pinto-Plata, B Celli, Nathaniel Marchetti, Gerard J. Criner, Raphael Bueno, George R. Washko, Kimberly Glass, John Quackenbush, Augustine M.K. Choi, Edwin K. Silverman, Craig P. Hersh
Software Mentions: 3
Published: over 9 years ago

10.1038/srep44497

Glycol porphyrin derivatives and temoporfin elicit resistance to photodynamic therapy by different mechanisms
Cited by: 18
Author(s): Jarmila Králová, Michal Kolář, Michal Kahle, Jaroslav Truksa, Sandra Lettlová, Kamila Balušíková, Petr Bartůněk
Software Mentions: 3
Published: over 9 years ago

10.1038/srep45101

Profiling the MAPK/ERK dependent and independent activity regulated transcriptional programs in the murine hippocampus in vivo
Cited by: 40
Author(s): Nils Blüthgen, Mirjam van Bentum, Barbara Merz, Dietmar Kuhl, Guido Hermey
Software Mentions: 3
Published: over 9 years ago

10.1038/srep45657

Acute effects of focused ultrasound-induced increases in blood-brain barrier permeability on rat microvascular transcriptome
Cited by: 89
Author(s): Dallan McMahon, Reina Bendayan, Kullervo Hynynen
Software Mentions: 3
Published: over 9 years ago

10.1038/srep46533

A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential Biomarkers
Cited by: 7
Author(s): Yuan Yang, Lan‐Juan Zhao, Bo Huang, Guoqing Hou, Beibei Zhou, Jin Qian, Shengxian Yuan, Huasheng Xiao, Minghui Li, Weiping Zhou
Software Mentions: 3
Published: over 9 years ago

10.1038/srep46695

Pathways and Genes Associated with Immune Dysfunction in Sheep Paratuberculosis
Cited by: 16
Author(s): Anton Gossner, Craig Watkins, Francesca Chianini
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-017-01526-5

Gene co-expression network analysis identifies porcine genes associated with variation in metabolizing fenbendazole and flunixin meglumine in the liver
Cited by: 8
Author(s): Jeremy Howard, M.S. Ashwell, Ronald E. Baynes, James D. Brooks, James L. Yeatts, Christian Maltecca
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-017-03133-w

PCDH18 is frequently inactivated by promoter methylation in colorectal cancer
Cited by: 15
Author(s): Dan Zhou, Weiwei Tang, Guoqiang Su, Mingquan Cai, Han‐Xiang An, Yun Zhang
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-017-04961-6

A Novel Unsupervised Algorithm for Biological Process-based Analysis on Cancer
Cited by: 3
Author(s): Tianci Song, Sha Cao, Sheng Ce Tao, Shuhua Liang, Wei Du, Yanchun Liang
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-06569-2

KDM4B-mediated reduction of H3K9me3 and H3K36me3 levels improves somatic cell reprogramming into pluripotency
Cited by: 29
Author(s): Jingwei Wei, Jisha Antony, Fei Meng, Paul Maclean, Rebekah Rhind, Götz Laible, Björn Oback
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-09490-w

The epigenetic modifier Fam208a is required to maintain epiblast cell fitness
Cited by: 6
Author(s): Shohag Bhargava, Brian Cox, Christiana Polydorou, Veronika Gresakova, Vladimír Kořínek, Hynek Strnad, Radislav Sedláček, Trevor Epp, Kallayanee Chawengsaksophak
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-11520-6

Identification of prognostic genes through expression differentiation during metastatic process in lung adenocarcinoma
Cited by: 2
Author(s): Ning An, Xue Yang
Software Mentions: 3
Published: about 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

10.1038/s41598-020-71875-1

Investigating the influence of perinatal nicotine and alcohol exposure on the genetic profiles of dopaminergic neurons in the VTA using miRNA–mRNA analysis
Cited by: 15
Author(s): Tina Kazemi, Shuyan Huang, Naze G. Avci, Charlotte Mae K. Waits, Yasemin M. Akay, Metin Akay
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-74051-7

Integrative transcriptomic analysis for linking acute stress responses to squamous cell carcinoma development
Cited by: 4
Author(s): Tran Nguyen, Kimal Rajapakshe, Courtney Nicholas, Leticia Tordesillas, Erik A. Ehli, Christel M. Davis, Cristian Coarfa, Elsa R. Flores, Sally E. Dickinson, Clara Curiel‐Lewandrowski, Kenneth Y. Tsai
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-73867-7

Repeated sampling facilitates within- and between-subject modeling of the human sperm transcriptome to identify dynamic and stress-responsive sncRNAs
Cited by: 14
Author(s): Christopher P. Morgan, Amol Shetty, Jackie Chan, David Berger, Seth A. Ament, C. Neill Epperson, Tracy L. Bale
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-77402-6

Mycosporine-like amino acid and aromatic amino acid transcriptome response to UV and far-red light in the cyanobacterium Chlorogloeopsis fritschii PCC 6912
Cited by: 16
Author(s): Carole A. Llewellyn, Carolyn Greig, Alla Silkina, Bethan Kultschar, Matthew D. Hitchings, Garry Farnham
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-78339-6

MACE RNA sequencing analysis of conjunctival squamous cell carcinoma and papilloma using formalin-fixed paraffin-embedded tumor tissue
Cited by: 8
Author(s): Stefaniya Boneva, Anja Schlecht, Peipei Zhang, Daniel Boehringer, Thabo Lapp, Hans Mittelviefhaus, Thomas Reinhard, Claudia Auw-Haedrich, Guenther Schlunck, Julian Wolf, Clemens Lange
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-78809-x

Epigenetic differences at the HTR2A locus in progressive multiple sclerosis patients
Cited by: 8
Author(s): Vicki E. Maltby, Rodney Arthur Lea, Sean M Burnard, Alexandre Xavier, Thao Van Cao, Nicole White, Kira Groen, Katherine Sanders, Rebecca Seeto, Samara Bray, Melissa Gresle, Louise Laverick, Helmut Butzkueven, Rodney J. Scott, Jeannette Lechner‐Scott
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-79235-9

Identifying of biomarkers associated with gastric cancer based on 11 topological analysis methods of CytoHubba
Cited by: 32
Author(s): Hua Ma, Zhijun He, Jing Chen, Xu Zhang, Pingping Song
Software Mentions: 3
Published: over 5 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: over 5 years ago

10.1038/s41598-021-83742-8

Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis
Cited by: 2
Author(s): Hanze Guo, Chun‐Hua Yan, Naiyu Chi
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-84082-3

Pre-therapeutic efficacy of the CDK inhibitor dinaciclib in medulloblastoma cells
Cited by: 8
Author(s): Marta Buzzetti, Sonia Morlando, Dimitrios Solomos, Ammara Mehmood, Alexander W I Cox, Mattia Chiesa, Yuri D’Alessandra, Michela Garofalo, Caroline Topham, Gianpiero Di Leva
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-86230-1

Ionizing radiation exposure of stem cell-derived chondrocytes affects their gene and microRNA expression profiles and cytokine production
Cited by: 2
Author(s): Ewelina Stelcer, Katarzyna Kulcenty, Marcin Ruciński, Marta Kruszyna-Mochalska, A. Skrobała, Agnieszka Sobecka, Karol Jopek, Wiktoria Suchorska
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-87703-z

Evidence of a dysregulated vitamin D endocrine system in SARS-CoV-2 infected patient’s lung cells
Cited by: 11
Author(s): B George, Amjesh Revikumar, Aswathy Mary Paul, T.R. Santhoshkumar, M. Radhakrishna Pillai, Rakesh Kumar
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-88221-8

Investigating the effects of chronic perinatal alcohol and combined nicotine and alcohol exposure on dopaminergic and non-dopaminergic neurons in the VTA
Cited by: 2
Author(s): Tina Kazemi, Shuyan Huang, Naze G. Avci, Yasemin M. Akay, Metin Akay
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-88948-4

Genetic network and gene set enrichment analyses identify MND1 as potential diagnostic and therapeutic target gene for lung adenocarcinoma
Cited by: 4
Author(s): Jinying Wei, Guangping Meng, Jing Wu, Qiang Zhang, Jie Zhang
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-90330-3

ADAMTS12 acts as a tumor microenvironment related cancer promoter in gastric cancer
Cited by: 11
Author(s): Yangming Hou, Yingjuan Xu, Danping Wu
Software Mentions: 3
Published: over 5 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776