bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3389/fgene.2020.00045

Identification of Core Gene Expression Signature and Key Pathways in Colorectal Cancer
Cited by: 45
Author(s): Xiang Ding, Houyu Duan, Haitao Luo
Software Mentions: 2
Published: over 6 years ago

Identification of a Ubiquitination-Related Gene Risk Model for Predicting Survival in Patients With Pancreatic Cancer
Cited by: 8
Author(s): Hao Zuo, Luojun Chen, Na Li, Qing Song
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2021.741226

Construction and Validation of an Immune Cell Signature Score to Evaluate Prognosis and Therapeutic Efficacy in Hepatocellular Carcinoma
Cited by: 2
Author(s): Linfeng Xu, Xingxing Jian, Zhenhao Liu, Jingjing Zhao, Siwen Zhang, Yong Lin, Lu Xie
Software Mentions: 2
Published: almost 5 years ago

10.3389/fgene.2020.00382

Expression Profiling and Cell Type Classification Analysis in Periodontitis Reveal Dysregulation of Multiple lncRNAs in Plasma Cells
Cited by: 16
Author(s): Donglei Wu, Peng Zhou, Fengdi Cao, Zhengshen Lin, Defeng Liang, Xiong Zhou
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2020.00070

Hippocampal DNA Methylation in a Mouse Model of Fetal Alcohol Spectrum Disorder That Includes Maternal Separation Stress Only Partially Explains Changes in Gene Expression
Cited by: 11
Author(s): Bonnie Alberry, Shiva M. Singh
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.101005

Huntington's disease accelerates epigenetic aging of human brain and disrupts DNA methylation levels
Cited by: 174
Author(s): Steve Horvath, Peter Langfelder, Seung Kwak, Jeff Aaronson, Jim Rosinski, Thomas Vogt, M Eszes, Richard L.M. Faull, Maurice A. Curtis, Henry J. Waldvogel, Oi-Wa Choi, Steve Tung, Harry V. Vinters, Giovanni Coppola, X. William Yang
Software Mentions: 2
Published: about 10 years ago

10.3389/fgene.2019.00180

Identification of Triple-Negative Breast Cancer Genes and a Novel High-Risk Breast Cancer Prediction Model Development Based on PPI Data and Support Vector Machines
Cited by: 12
Author(s): Ming Li, Yu Guo, Yuanming Feng, Ning Zhang
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-13-160

Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma
Cited by: 32
Author(s): Elana J. Fertig, Qing Ren, Haixia Cheng, Hyōe Hatakeyama, Adam P. Dicker, Ulrich Rodeck, Michael Considine, Michael F. Ochs, Christine H. Chung
Software Mentions: 2
Published: over 14 years ago

10.18632/aging.102397

Identifying hub genes of clear cell renal cell carcinoma associated with the proportion of regulatory T cells by weighted gene co-expression network analysis
Cited by: 11
Author(s): Ye‐Hui Chen, Shao‐Hao Chen, Jian Hou, Zhi‐Bin Ke, Yupeng Wu, Tingting Lin, Yong Wei, Xue-Yi Xue, Qing‐Shui Zheng, Jiaofeng Huang, Ning Xu
Software Mentions: 2
Published: almost 7 years ago

10.3389/fimmu.2021.651619

A Comprehensive View on the Human Antibody Repertoire Against Staphylococcus aureus Antigens in the General Population
Cited by: 18
Author(s): Tanja Meyer, Stephan Michalik, Silva Holtfreter, Stefan Weiß, Nele Friedrich, Henry Völzke, Thomas Kocher, Christian Köhler, Frank Schmidt, Barbara M. Bröker, Uwe Völker
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2019.00261

Aberrant Expressions of Co-stimulatory and Co-inhibitory Molecules in Autoimmune Diseases
Cited by: 11
Author(s): Wei He, Bin Wang, Qian Li, Qiuming Yao, Xi Jia, Ronghua Song, Sheli Li, Jinan Zhang
Software Mentions: 2
Published: over 7 years ago

10.18632/aging.203194

Shifting epigenetic contexts influence regulatory variation and disease risk
Cited by: 1
Author(s): Daniel Richard, Terence D. Capellini
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2021.709164

Defining a Methylation Signature Associated With Operational Tolerance in Kidney Transplant Recipients
Cited by: 5
Author(s): Ramón María Alvargonzález Rodríguez, María P. Hernández-Fuentes, Viviana Corte-Iglesias, María Laura Sáiz, Juan José Lozano, Ana R. Cortázar, Isabel Mendizabal, María Luisa Suárez-Fernández, Eliécer Coto, Antonio López-Vázquez, Carmen Díaz‐Corte, Ana M. Aransay, Carlos López‐Larrea, Beatriz Suárez-Álvarez
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-8-96

Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays
Cited by: 48
Author(s): Ann Hess, Hari Iyer
Software Mentions: 2
Published: over 19 years ago

10.1186/s12864-018-4618-9

DNA Methylation variability among individuals is related to CpGs cluster density and evolutionary signatures
Cited by: 19
Author(s): Domenico Palumbo, Ornella Affinito, Antonella Monticelli, Sérgio Cocozza
Software Mentions: 2
Published: over 8 years ago

10.18632/aging.102667

Systematic analysis of lncRNA and microRNA dynamic features reveals diagnostic and prognostic biomarkers of myocardial infarction
Cited by: 6
Author(s): Hang Shi, Haoran Sun, Jiayao Li, Ziyi Bai, Jie Wu, Xiuhong Li, Yingli Lv, Guangde Zhang
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2017.00489

Heterogeneity of Phenotype and Function Reflects the Multistage Development of T Follicular Helper Cells
Cited by: 18
Author(s): Marta Trüb, Tom A. Barr, Vicky L. Morrison, Sheila Brown, Stefano Caserta, Jordan Rixon, Alasdair Ivens, David Gray
Software Mentions: 2
Published: over 9 years ago

10.3389/fimmu.2021.636614

Integrative Transcriptomic, Proteomic and Functional Analysis Reveals ATP1B3 as a Diagnostic and Potential Therapeutic Target in Hepatocellular Carcinoma
Cited by: 12
Author(s): Shanshan Lu, Shenglan Cai, Peng Xu, Ruochan Cheng, Yiya Zhang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-018-5259-8

PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli
Cited by: 15
Author(s): Clémentine Dressaire, Vânia Pobre, Sandrine Laguerre, Laurence Girbal, Cecília M. Arraiano, Muriel Cocaign‐Bousquet
Software Mentions: 2
Published: almost 8 years ago

10.3389/fped.2021.617298

Differential Expression Profiles and Functional Analysis of Long Non-coding RNAs in Children With Dilated Cardiomyopathy
Cited by: 0
Author(s): Dongxiao Cai, Bo Han, Wei Sun, Li Zhang, Jing Wang, Diandong Jiang, Honglei Jia
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2021.634441

ERAP2 Increases the Abundance of a Peptide Submotif Highly Selective for the Birdshot Uveitis-Associated HLA-A29
Cited by: 16
Author(s): Wouter J. Venema, Sanne Hiddingh, Joke H. de Boer, Frans H.J. Claas, Arend Mulder, Anneke I. den Hollander, Efstratios Stratikos, Siranush Sarkizova, Lars T. van der Veken, George M.C. Janssen, Peter A. van Veelen, Jonas J.W. Kuiper
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2021.682415

Integrative Analysis of Neuregulin Family Members-Related Tumor Microenvironment for Predicting the Prognosis in Gliomas
Cited by: 16
Author(s): Wenjin Zhao, Guan‐Yong Ou, Wen–Jen Lin
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-12-330

MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters
Cited by: 23
Author(s): Bas Jansen, Iziah E. Sama, Dagmar Eleveld-Trancikova, Maaike A. van Hout-Kuijer, Joop H. Jansen, Martijn A. Huynen, Gosse J. Adema
Software Mentions: 2
Published: about 15 years ago

10.3389/fimmu.2019.01661

Lnc-C/EBPβ Modulates Differentiation of MDSCs Through Downregulating IL4i1 With C/EBPβ LIP and WDR5
Cited by: 22
Author(s): Yuan Gao, Wencong Shang, Dan Zhang, Shiwu Zhang, Xipeng Zhang, Yuan Zhang, Rongcun Yang
Software Mentions: 2
Published: about 7 years ago

10.18632/aging.202494

Identification of novel candidate biomarkers for pancreatic adenocarcinoma based on TCGA cohort
Cited by: 5
Author(s): Jie Yang, Peng Wang, Yuanyuan Li
Software Mentions: 2
Published: over 5 years ago

10.3389/fped.2021.576585

Identification of Potential Diagnostic Gene Targets for Pediatric Sepsis Based on Bioinformatics and Machine Learning
Cited by: 2
Author(s): Ying Qiao, Bo Zhang, Ying Liu
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2021.658341

Exploration of the Shared Gene Signatures and Molecular Mechanisms Between Systemic Lupus Erythematosus and Pulmonary Arterial Hypertension: Evidence From Transcriptome Data
Cited by: 31
Author(s): Meng Yao, Chunyi Zhang, Congcong Gao, Qianqian Wang, Mengmeng Dai, Runzhi Yue, Wenbo Sun, Wenfang Liang, Zhaohui Zheng
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2021.735643

Tissue-Resident-Memory CD8+ T Cells Bridge Innate Immune Responses in Neighboring Epithelial Cells to Control Human Genital Herpes
Cited by: 14
Author(s): Tao Peng, Khamsone Phasouk, Catherine Sodroski, Sijie Sun, Yon Hwangbo, Erik D. Layton, Lei Jin, Alexis Klock, Kurt Diem, Amalia Magaret, Lichen Jing, Kerry J. Laing, Alvason Li, Meei‐Li Huang, Max E. Mertens, Christine Johnston, Keith R. Jerome, David M. Koelle, Anna Wald, David M. Knipe, Lawrence Corey, Jia Zhu
Software Mentions: 2
Published: about 5 years ago

10.3389/fonc.2021.711736

A Novel Prognostic Model Based on Autophagy-Related Long Non-Coding RNAs for Clear Cell Renal Cell Carcinoma
Cited by: 11
Author(s): Xinyuan Li, Haitao Yu, Zongjie Wei, Xin Gou, Simin Liang, Fu Liu
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2021.643036

Diagnostic and Predictive Value of Immune-Related Genes in Crohn’s Disease
Cited by: 15
Author(s): Bing Yu, Yuqing Yin, Yanping Tang, Kang‐Lai Wei, Zhigang Pan, Kezhi Li, Xianwen Guo, Bang-li Hu
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2020.575737

Combination of T-Cell Bispecific Antibodies With PD-L1 Checkpoint Inhibition Elicits Superior Anti-Tumor Activity
Cited by: 25
Author(s): Johannes Sam, Sara Colombetti, Tanja Fauti, Andreas Roller, Marlene Biehl, Linda Fahrni, Valeria Nicolini, Mario Perro, Tapan K. Nayak, Esther Bommer, Anne Schoenle, Μaria Karagianni, Marine Le Clech, Nathalie Steinhoff, Christian Klein, Pablo Umaña, Marina Bacac
Software Mentions: 2
Published: almost 6 years ago

10.3389/fimmu.2017.01146

Genomic Programming of Human Neonatal Dendritic Cells in Congenital Systemic and In Vitro Cytomegalovirus Infection Reveal Plastic and Robust Immune Pathway Biology Responses
Cited by: 9
Author(s): Widad Dantoft, Pablo Martínez-Vicente, James Jafali, Lara Pérez-Martínez, Kimberly Martin, Konstantinos Kotzamanis, Marie Craigon, Manfred Auer, N. J. Young, Paul Walsh, Arnaud Marchant, Ana Angulo, Thorsten Forster, Peter Ghazal
Software Mentions: 2
Published: almost 9 years ago

10.3389/fimmu.2016.00088

TLR3 Signaling Promotes the Induction of Unique Human BDCA-3 Dendritic Cell Populations
Cited by: 23
Author(s): Nicholas Colletti, Hong Liu, Adam C. Gower, Yuriy O. Alekseyev, Christopher Arendt, Michael H. Shaw
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-8-307

Living with an imperfect cell wall: compensation of femAB inactivation in Staphylococcus aureus
Cited by: 34
Author(s): Judith Hübscher, Andrea Jansen, Oliver Kotte, Juliane Schäfer, Paul Majcherczyk, Llinos G. Harris, Gabriele Bierbaum, Matthias Heinemann, Brigitte Berger‐Bächi
Software Mentions: 2
Published: about 19 years ago

10.1186/s12864-018-5108-9

Developing specific molecular biomarkers for thermal stress in salmonids
Cited by: 83
Author(s): Arash Akbarzadeh, Oliver P. Günther, Aimee Lee S. Houde, Shaorong Li, Tobi J. Ming, Kenneth M. Jeffries, Scott G. Hinch, Kristina M. Miller
Software Mentions: 2
Published: almost 8 years ago

10.3389/fonc.2021.692774

An Adaptive Transfer-Learning-Based Deep Cox Neural Network for Hepatocellular Carcinoma Prognosis Prediction
Cited by: 7
Author(s): Hua Chai, Xia Long, Lei Zhang, Jiarui Yang, Zhongyue Zhang, Xiangjun Qian, Yuedong Yang, Weidong Pan
Software Mentions: 2
Published: almost 5 years ago

10.3389/fonc.2020.00605

LUM Expression and Its Prognostic Significance in Gastric Cancer
Cited by: 32
Author(s): Xiaowei Chen, Xin Li, Xin Hu, Fei Jiang, Yan Shen, Rui Xu, Leilei Wu, Pingmin Wei, Xiaobing Shen
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2020.586124

Immune Profiles Identification by Vaccinomics After MVA Immunization in Randomized Clinical Study
Cited by: 6
Author(s): Jorge Sánchez, Eléna Gonçalves, Anuska Llano, Pedro Gonzáles, María Fernández-Maldonado, Annika Vogt, Angèle Soria, Susana Cedrés Pérez, Samandhy Cedeño, Marco A. Fernández, Julien Nourikyan, Simon Bernard, Carmela Ganoza, Eric Pédruzzi, Olivia Bonduelle, Beatriz Mothe, Carmen Elena Gómez, Mariano Esteban, Felipe García, Javier R. Lama, Christian Berthou, Béhazine Combadière
Software Mentions: 2
Published: almost 6 years ago

10.3389/fimmu.2020.02128

The Oncometabolite 5′-Deoxy-5′-Methylthioadenosine Blocks Multiple Signaling Pathways of NK Cell Activation
Cited by: 6
Author(s): Bénédikt Jacobs, Sebastian Schlögl, Carolin Dorothea Strobl, Simon Völkl, Andrew L. Stoll, Dimitrios Mougiakakos, Karl‐Johan Malmberg, Andréas Mackensen, Michael Aigner
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2164-15-1001

Transcriptomics of the late gestation ovine fetal brain: modeling the co-expression of immune marker genes
Cited by: 11
Author(s): María Belén Rabaglino, Maureen Keller‐Wood, Charles E. Wood
Software Mentions: 2
Published: over 12 years ago

10.3389/fimmu.2018.02893

Human Hookworm Infection Enhances Mycobacterial Growth Inhibition and Associates With Reduced Risk of Tuberculosis Infection
Cited by: 20
Author(s): Matthew K. O’Shea, Tom Fletcher, Julius Müller, Rachel Tanner, Magali Matsumiya, J. W. Bailey, Jayne Jones, Steven G. Smith, Gavin Koh, William Horsnell, Nicholas J. Beeching, James Dunbar, David E. Wilson, Adam F. Cunningham, Helen McShane
Software Mentions: 2
Published: almost 8 years ago

10.18632/aging.103486

Characterization of aberrant pathways activation and immune microenviroment of BK virus associated nephropathy
Cited by: 5
Author(s): Yongguang Liu, Song Zhou, Jianmin Hu, Wentao Xu, Ding Liu, Jun Liu, Guorong Liao, Zhiqiang Guo, Yuzhu Li, Siqiang Yang, Shichao Li, Hua Chen, Ying Guo, Ming Li, Li‐pei Fan, Liuyang Li, Anqi Lin, Ming Zhao
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2164-13-369

Jasmonate and ethylene dependent defence gene expression and suppression of fungal virulence factors: two essential mechanisms of Fusarium head blight resistance in wheat?
Cited by: 103
Author(s): Sven Gottwald, Birgit Samans, Stefanie Lück, Wolfgang Friedt
Software Mentions: 2
Published: about 14 years ago

10.3389/fonc.2020.547942

CircRNA_000864 Upregulates B-cell Translocation Gene 2 Expression and Represses Migration and Invasion in Pancreatic Cancer Cells by Binding to miR-361-3p
Cited by: 20
Author(s): Lei Huang, Junxiang Han, Huifan Yu, Jialing Liu, Lili Gui, Zhengkun Wu, Xinxu Zhao, Shiqi Su, Gaohang Fu, Fēi Li
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-015-2160-6

Genome-wide miR-155 and miR-802 target gene identification in the hippocampus of Ts65Dn Down syndrome mouse model by miRNA sponges
Cited by: 30
Author(s): Xavier Bofill-De Ros, Mónica Santos, María Vila-Casadesús, Eneko Villanueva, Núria Andreu, Mara Dierssen, Cristina Fillat
Software Mentions: 2
Published: almost 11 years ago

10.3389/fimmu.2020.599647

Regulation of Decay Accelerating Factor Primes Human Germinal Center B Cells for Phagocytosis
Cited by: 6
Author(s): Andy Dernstedt, Jana Leidig, Anna Holm, Priscilla F Kerkman, Jenny Mjösberg, Clas Ahlm, Johan Henriksson, Magnus Hultdin, Mattias N.E. Forsell
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-13-323

Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio)
Cited by: 50
Author(s): Robert E. Drew, Matthew L. Settles, Erin Churchill, Shayna M Williams, Soniya Balli, Barrie D. Robison
Software Mentions: 2
Published: about 14 years ago

10.1038/s41598-020-71328-9

Genome characteristics of Kordia antarctica IMCC3317T and comparative genome analysis of the genus Kordia
Cited by: 7
Author(s): Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-71997-6

Identification of miRNA signatures for kidney renal clear cell carcinoma using the tensor-decomposition method
Cited by: 13
Author(s): Ka-Lok Ng, Y-h. Taguchi
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-72399-4

Translation elongation factor 2 depletion by siRNA in mouse liver leads to mTOR-independent translational upregulation of ribosomal protein genes
Cited by: 10
Author(s): Maxim V. Gerashchenko, Mikhail V. Nesterchuk, Elena M. Smekalova, João A. Paulo, Piotr S. Kowalski, Kseniya A. Akulich, Roman L. Bogorad, Sergey E. Dmitriev, Steven P. Gygi, Timofei S. Zatsepin, Daniel G. Anderson, Vadim N. Gladyshev, Victor Koteliansky
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-72172-7

Hepatic lipocalin 2 promotes liver fibrosis and portal hypertension
Cited by: 25
Author(s): Jiegen Chen, Josepmaria Argemí, Gemma Òdena, Mingjiang Xu, Yan Cai, Veronica Massey, Austin Parrish, Rajanikanth Vadigepalli, José Altamirano, Joaquín Cabezas, Pere Ginès, Juan Caballería, Natasha T. Snider, Pau Sancho‐Bru, Shizuo Akira, Ivan Rusyn, Bin Gao, R. Bataller
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-72068-6

Heterogeneous ozone effects on the DNA methylome of bronchial cells observed in a crossover study
Cited by: 11
Author(s): Marie‐Abèle Bind, Donald B. Rubin, Andrés Cárdenas, Radhika Dhingra, Cavin Ward‐Caviness, Liu Z, Jaime E. Mirowsky, Joel Schwartz, David Díaz-Sánchez, Robert B. Devlin
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2229-11-1

Haplotyping, linkage mapping and expression analysis of barley genes regulated by terminal drought stress influencing seed quality
Cited by: 84
Author(s): Sebastian Worch, Rajesh Kalladan, Vokkaliga T. Harshavardhan, Christof Pietsch, Viktor Korzun, L. Kuntze, Andreas Börner, Ulrich Wobus, Marion S. Röder, Nese Sreenivasulu
Software Mentions: 2
Published: over 15 years ago

10.1038/s41598-020-72864-0

Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures
Cited by: 21
Author(s): Julian Wolf, Claudia Auw-Haedrich, Anja Schlecht, Stefaniya Boneva, Hans Mittelviefhaus, Thabo Lapp, Hansjürgen Agostini, Thomas Reinhard, Günther Schlunck, Clemens Lange
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-70244-2

Obesity and ethnicity alter gene expression in skin
Cited by: 5
Author(s): Joseph R. Walker, Sandra Garcet, José O. Alemán, Christopher E. Mason, David Danko, Simone Zuffa, Jonathan R. Swann, James G. Krueger, Jan L. Breslow, Peter R. Holt
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-74276-6

Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis
Cited by: 6
Author(s): Gaojianyong Wang, Dimitris Anastassiou
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-74973-2

Gene expression profile of CD14+ blood monocytes following lifestyle-induced weight loss in individuals with metabolic syndrome
Cited by: 3
Author(s): Ronald Biemann, Kirsten Roomp, Nosheen Fatima, Shruthi Krishnan, Zhen Li, K. Shahzad, Katrin Borucki, Claus Luley, Jochen G. Schneider, Berend Isermann
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12903-015-0086-7

Genes related to inflammation and bone loss process in periodontitis suggested by bioinformatics methods
Cited by: 31
Author(s): Liang Song, Jueqi Yao, Zhijing He, Bin Xu
Software Mentions: 2
Published: about 11 years ago

10.1038/s41598-020-76879-5

The effect of Rbfox2 modulation on retinal transcriptome and visual function
Cited by: 6
Author(s): Lin Gu, Riki Kawaguchi, Joseph Caprioli, Natik Piri
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-70541-w

Changes in the plasma microvesicle proteome during the ovarian hyperstimulation phase of assisted reproductive technology
Cited by: 1
Author(s): Nina Olausson, Fariborz Mobarrez, Roman A. Zubarev, Alexey Chernobrovkin, Dorothea Rutishauser, Katarina Bremme, Eli Westerlund, Outi Hovatta, Håkan Wallén, Peter Henriksson
Software Mentions: 2
Published: about 6 years ago

10.1186/s12870-017-1032-4

Transcriptomic analysis links gene expression to unilateral pollen-pistil reproductive barriers
Cited by: 6
Author(s): Amanda K. Broz, Rafael F. Guerrero, April M. Randle, You Soon Baek, Matthew W. Hahn, Patricia A. Bedinger
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-020-77601-1

Loss of FOXF1 expression promotes human lung-resident mesenchymal stromal cell migration via ATX/LPA/LPA1 signaling axis
Cited by: 10
Author(s): Pengxiu Cao, Neff Walker, Russell R. Braeuer, Serina Mazzoni-Putman, Yoshiro Aoki, Keizo Misumi, David Wheeler, Ragini Vittal, Vibha N. Lama
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-78866-2

Rho-GTPase pathways may differentiate treatment response to TNF-alpha and IL-17A inhibitors in psoriatic arthritis
Cited by: 4
Author(s): Sara Rahmati, Darren D. O’Rielly, Quan Li, D. Codner, A. Dohey, Kari Jenkins, Igor Jurišica, Dafna D. Gladman, Vinod Chandran, Proton Rahman
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-79165-6

Lipid metabolism in Calanus finmarchicus is sensitive to variations in predation risk and food availability
Cited by: 0
Author(s): Elise Skottene, Ann M. Tarrant, Dag Altin, Rolf Erik Olsen, Marvin Choquet, Kristina Øie Kvile
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12870-021-02970-2

BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon
Cited by: 7
Author(s): Kaori Sakai, Sylvie Citerne, Sébastien Antelme, Philippe Le Bris, Sylviane Daniel, Axelle Bouder, Angélina D’Orlando, Amy Cartwright, Frédérique Tellier, Stéphanie Pateyron, Étienne Delannoy, Debbie Laudencia‐Chingcuanco, Grégory Mouille, Jean-Christophe Palauqui, John P. Vogel, Richard Sibout
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-80509-5

Nuclear IL-33 restrains the early conversion of fibroblasts to an extracellular matrix-secreting phenotype
Cited by: 16
Author(s): Francesca Gatti, Sobuj Mia, Clara Hammarström, Nadine Frerker, Bjarte Fosby, Junbai Wang, Wojciech Pietka, Olav Sundnes, Johanna Hol, Monika Kasprzycka, Guttorm Haraldsen
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2229-9-50

A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences
Cited by: 54
Author(s): Martin Trick, Foo Cheung, Nizar Drou, F C Fråser, Edward K. Lobenhofer, Patrick Hurban, Andreas Magusin, Christopher D. Town, Ian Bancroft
Software Mentions: 2
Published: over 17 years ago

10.1038/s41598-020-79356-1

Late p65 nuclear translocation in glioblastoma cells indicates non-canonical TLR4 signaling and activation of DNA repair genes
Cited by: 6
Author(s): Isabele Fattori Moretti, Antônio M. Lerário, Marina Trombetta-Lima, Paula R. Sola, Roseli da Silva Soares, Sueli Mieko Oba-Shinjo, Suely Kazue Nagahashi Marie
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-77636-4

Investigation of MicroRNA and transcription factor mediated regulatory network for silicosis using systems biology approach
Cited by: 9
Author(s): Jyoti Kant Choudhari, Mukesh Verma, Jyotsna Choubey, Biju Prava Sahariah
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-80941-7

Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients
Cited by: 8
Author(s): Teresa Rubio, Vicente Felipo, Sonia Tarazona, Roberta Pastorelli, Desamparados Escudero‐García, Joan Tosca, Amparo Urios, Ana Conesa, Carmina Montoliú
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-79769-y

Integrative multiomics analysis of Premolis semirufa caterpillar venom in the search for molecules leading to a joint disease
Cited by: 2
Author(s): Giselle Pidde, Milton Yutaka Nishiyama, Úrsula Castro de Oliveira, Isadora Maria Villas-Boas, Adriana F. Paes‐Leme, Inácio L.M. Junqueira-de-Azevedo, Rafael Marques-Porto, Carla Cristina Squaiella-Baptistão, Denise V. Tambourgi
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-69695-4

Identification of differentially expressed genes profiles in a combined mouse model of Parkinsonism and colitis
Cited by: 7
Author(s): Ana-Luisa Gil-Martínez, Lorena Cuenca‐Bermejo, Ana González-Cuello, Consuelo Sánchez-Rodrigo, Antonio Parrado, Sheela Vyas, Emiliano Fernández-Villalba, María Teófila Vicente Herrero
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-021-81794-4

Valproic acid influences the expression of genes implicated with hyperglycaemia-induced complement and coagulation pathways
Cited by: 17
Author(s): Marina Barreto Felisbino, Mark Ziemann, Ishant Khurana, Jun Okabe, Keith Al-Hasani, Scott Maxwell, K N Harikrishnan, C. Oliveira, Maria Luiza S. Mello, Assam El‐Osta
Software Mentions: 2
Published: over 5 years ago

10.3389/fmolb.2021.598427

An Extracellular Matrix-Based Signature Associated With Immune Microenvironment Predicts the Prognosis and Therapeutic Responses of Patients With Oesophageal Squamous Cell Carcinoma
Cited by: 8
Author(s): Hongpan Zhang, Qi Shi, Zhihao Yang, Kaige Wang, Zhe Zhang, Zheng Huang, Xiaobin Cui, Feng Li
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-82802-3

Transgenic inhibition of interleukin-6 trans-signaling does not prevent skeletal pathologies in mucolipidosis type II mice
Cited by: 1
Author(s): Lena Marie Westermann, Anke Baranowsky, Giorgia Di Lorenzo, Tatyana Danyukova, Jamie Soul, Jean-Marc Schwartz, Gretl Hendrickx, Michael Amling, Stefan Rose‐John, Christoph Garbers, Thorsten Schinke, Sandra Pohl
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-82252-x

Inhibition of androgen/AR signaling inhibits diethylnitrosamine (DEN) induced tumour initiation and remodels liver immune cell networks
Cited by: 8
Author(s): Timothy H. Helms, Riley Mullins, Jennifer M. Thomas‐Ahner, Samuel K. Kulp, Moray J. Campbell, Fabienne Lucas, Nathan W. Schmidt, D. Lemoine, Surafel Getaneh, Zhiliang Xie, Mitch A. Phelps, Steven K. Clinton, Christopher C. Coss
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-83345-3

Altered non-coding RNA expression profile in F1 progeny 1 year after parental irradiation is linked to adverse effects in zebrafish
Cited by: 4
Author(s): Leonardo Martín, Jorke H. Kamstra, Selma Hurem, Leif C. Lindeman, Dag Anders Brede, Håvard Aanes, Igor Babiak, Amílcar Arenal, Deborah Oughton, Brit Salbu, Jan Ludvig Lyche, Peter Alestrøm
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-80662-x

Identification of LINC00665-miR-let-7b-CCNA2 competing endogenous RNA network associated with prognosis of lung adenocarcinoma
Cited by: 12
Author(s): Yu‐Sheng Huang, Zhong Li, Kechao Nie, Lijuan Li, Shaohua Song, Fengbin Liu, Peiwu Li, Deliang Cao, Yufeng Liu
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-83366-y

Elevation in viral entry genes and innate immunity compromise underlying increased infectivity and severity of COVID-19 in cancer patients
Cited by: 4
Author(s): Jennifer Kwan, Liang Lin, Rachel Bell, Jeffrey P. Bruce, Christopher T. Richardson, Trevor J. Pugh, Fei‐Fei Liu
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-83668-1

Novel gene signatures for stage classification of the squamous cell carcinoma of the lung
Cited by: 3
Author(s): Ángel Juárez-Flores, Gabriel S. Zamudio, Marco V. José
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2229-9-29

Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants
Cited by: 46
Author(s): Debra J. Skinner, Charles S. Gasser
Software Mentions: 2
Published: over 17 years ago

10.1038/s41598-021-84350-2

Epithelial to mesenchymal transition and microRNA expression are associated with spindle and apocrine cell morphology in triple-negative breast cancer
Cited by: 13
Author(s): Markéta Kolečková, Jiří Ehrmann, Jan Bouchal, Mária Janíková, Aneta Brisudova, Josef Srovnal, Kateřina Štaffová, Marek Svoboda, Ondřej Slabý, Lenka Radová, Katherine Vomáčková, Bohuslav Melichar, L Veverková, Zdeněk Kolář
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-69978-w

Immune outcomes of Zika virus infection in nonhuman primates
Cited by: 5
Author(s): Blake Schouest, Marissa Fahlberg, Elizabeth A. Scheef, Matthew J. Ward, Kyra Headrick, Dawn Szeltner, Robert V Blair, Margaret H. Gilbert, Lara A. Doyle-Meyers, Victoria W. Danner, Myrna C. Bonaldo, Dawn M. Wesson, Antonito T. Panganiban, Nicholas J. Maness
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2229-11-149

Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening
Cited by: 123
Author(s): Ana Margarida Fortes, Ana Patrícia, Marta S. Silva, Kashif Ali, Lisete Sousa, Federica Maltese, Young Hae Choi, Jérôme Grimplet, J. M. Martínez-Zapater, Robert Verpoorte, M. S. Pais
Software Mentions: 2
Published: over 15 years ago

10.18632/aging.102790

LncRNA MEG3 targeting miR-424-5p via MAPK signaling pathway mediates neuronal apoptosis in ischemic stroke
Cited by: 58
Author(s): Yuzhi Xiang, Yayun Zhang, Yanni Xia, Hua Zhao, Anchang Liu, Yuguo Chen
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-021-84824-3

DBnorm as an R package for the comparison and selection of appropriate statistical methods for batch effect correction in metabolomic studies
Cited by: 9
Author(s): Nasim Bararpour, Federica Gilardi, Cristian Carmeli, Jonathan Sidibé, Julijana Ivanišević, Tiziana Caputo, Marc Augsburger, Silke Grabherr, Béatrice Desvergne, Nicolas Guex, Murielle Bochud, Aurélien Thomas
Software Mentions: 2
Published: over 5 years ago

10.1186/s12903-020-01266-5

Diagnostic biomarker candidates for pulpitis revealed by bioinformatics analysis of merged microarray gene expression datasets
Cited by: 17
Author(s): Ming Chen, Junkai Zeng, Yeqing Yang, Buling Wu
Software Mentions: 2
Published: almost 6 years ago

10.1155/2016/3605302

A Cross-Study Biomarker Signature of Human Bronchial Epithelial Cells Infected with Respiratory Syncytial Virus
Cited by: 7
Author(s): Luiz Gustavo Gardinassi
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2229-12-185

Grape berry ripening delay induced by a pre-véraison NAA treatment is paralleled by a shift in the expression pattern of auxin- and ethylene-related genes
Cited by: 84
Author(s): F. Ziliotto, Massimiliano Corso, Fabio Massimo Rizzini, Angela Rasori, Alessandro Botton, Claudio Bonghi
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2229-12-100

Reprogramming of gene expression during compression wood formation in pine: Coordinated modulation of S-adenosylmethionine, lignin and lignan related genes
Cited by: 56
Author(s): David P. Villalobos, Sara M. Díaz-Moreno, El-Sayed S Said, Rafael A. Cañas, Daniel Osuna, Sonia H E Van Kerckhoven, Rocío Bautista, M. Gonzalo Claros, Francisco M. Cánovas, Francisco R. Cantón
Software Mentions: 2
Published: about 14 years ago

10.18632/aging.103145

Exosomal miR-183-5p promotes angiogenesis in colorectal cancer by regulation of FOXO1
Cited by: 58
Author(s): Anquan Shang, Xuan Wang, Chenzheng Gu, Wenfang Liu, Junjun Sun, Bingjie Zeng, Chen Chen, Ping Ji, Junlu Wu, Wenqiang Quan, Yiwen Yao, Weiwei Wang, Zujun Sun, Li Dong
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-735

Parallel selection on gene copy number variations through evolution of three-spined stickleback genomes
Cited by: 25
Author(s): Shotaro Hirase, Haruka Ozaki, Wataru Iwasaki
Software Mentions: 2
Published: over 12 years ago

10.1038/s41598-021-86284-1

Ibuprofen alters epoxide hydrolase activity and epoxy-oxylipin metabolites associated with different metabolic pathways in murine livers
Cited by: 4
Author(s): Shuchita Tiwari, Jun Yang, Christophe Morisseau, Blythe Durbin‐Johnson, Bruce D. Hammock, Aldrin V. Gomes
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-86671-8

Toward the discovery of biological functions associated with the mechanosensor Mtl1p of Saccharomyces cerevisiae via integrative multi-OMICs analysis
Cited by: 3
Author(s): Nelson Martinez‐Matias, Nataliya Chorna, Sahily González-Crespo, Lilliam Villanueva, Ingrid M. Montes-Rodríguez, Loyda M. Melendez-Aponte, Abiel Roche-Lima, Kelvin Carrasquillo-Carrión, Ednalise Santiago‐Cartagena, Brian C. Rymond, Mohan Babu, Igor Štagljar, José R. Rodríguez‐Medina
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-86879-8

Transcriptomic signals in blood prior to lung cancer focusing on time to diagnosis and metastasis
Cited by: 4
Author(s): Therese Haugdahl Nøst, Matthew T. G. Holden, Tom Dønnem, Hege Bøvelstad, Charlotta Rylander, Eiliv Lund, Torkjel M. Sandanger
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-017-14314-y

Promoter DNA methylation analysis reveals a novel diagnostic CpG-based biomarker and RAB25 hypermethylation in clear cell renel cell carcinoma
Cited by: 12
Author(s): Yinmin Gu, Yi Ming Zou, Danqing Lei, Yuanjie Huang, Weidong Li, Zengnan Mo, Yanling Hu
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-017-14440-7

Dysregulated gene expressions of MEX3D, FOS and BCL2 in human induced-neuronal (iN) cells from NF1 patients: a pilot study
Cited by: 12
Author(s): Noriyuki Sagata, Takahiro A. Kato, Shin-ichi Kano, Masahiro Ohgidani, Norihiro Shimokawa, Mina Sato-Kasai, Kohei Hayakawa, Nobuki Kuwano, Ana Wilson, Koko Ishizuka, Shiori Kato, Takeshi Nakahara, Makiko Nakahara-Kido, Daiki Setoyama, Yasunari Sakai, Shouichi Ohga, Masutaka Furue, Akira Sawa, Shigenobu Kanba
Software Mentions: 2
Published: almost 9 years ago

10.18632/aging.102780

Immune-related key gene CLDN10 correlates with lymph node metastasis but predicts favorable prognosis in papillary thyroid carcinoma
Cited by: 16
Author(s): Zhaoyin Xiang, Cheng Zhong, Aoshuang Chang, Junjun Ling, Hou-Yu Zhao, Wei Zhou, Xianlu Zhuo
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-019-1935-3

Rpv3–1 mediated resistance to grapevine downy mildew is associated with specific host transcriptional responses and the accumulation of stilbenes
Cited by: 35
Author(s): Birgit Eisenmann, Stefan Czemmel, Tobias Ziegler, Günther Buchholz, A. Kortekamp, Oliver Trapp, Thomas Rausch, Ian B. Dry, Jochen Bogs
Software Mentions: 2
Published: about 7 years ago

10.1007/s00401-019-02056-2

MYCN amplification drives an aggressive form of spinal ependymoma
Cited by: 87
Author(s): David R. Ghasemi, Martin Sill, Konstantin Okonechnikov, Andrey Korshunov, Stephen Yip, Peter W. Schütz, David Scheie, Andreas Kruse, Patrick N. Harter, Marina Kastelan, Marlies Wagner, Christian Hartmann, Julia Benzel, Kendra K. Maaß, Mustafa Khasraw, Ronald Sträter, Christian Thomas, Werner Paulus, Christian P. Kratz, Hendrik Witt, Daisuke Kawauchi, Christel Herold‐Mende, Felix Sahm, Sebastian Brandner, Marcel Kool, David Jones, Andreas von Deimling, Stefan M. Pfister, David Reuß, Kristian W. Pajtler
Software Mentions: 2
Published: about 7 years ago

Projects: bioconductor: limma

Science Score: 78/100

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Papers Mentioning limma 7,776