bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1186/s12935-021-02073-w

Identification of autophagy-related risk signatures for the prognosis, diagnosis, and targeted therapy in cervical cancer
Cited by: 9
Author(s): Dan Meng, Hua Jin, Xing Zhang, Wenjing Yan, Qianqian Xia, Siyuan Shen, Shuqian Xie, Mengjing Cui, Bo Ding, Yun Gu, Shizhi Wang
Software Mentions: 3
Published: about 5 years ago

10.3389/fcell.2021.580834

Construction of circRNA-miRNA-mRNA Network for Exploring Underlying Mechanisms of Lubrication Disorder
Cited by: 2
Author(s): Shengnan Cong, Jinlong Li, Jingjing Zhang, Jingyi Feng, Aixia Zhang, Lianjun Pan, Jianhua Ma
Software Mentions: 3
Published: over 5 years ago

10.1186/s13148-020-00895-5

H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts
Cited by: 17
Author(s): Jiayi Pei, Magdaléna Harakaľová, Thomas A. Treibel, R Thomas Lumbers, Bastiaan J. Boukens, Igor R. Efimov, Jip T. van Dinter, Arantxa González, Begoña López, Hamid el Azzouzi, Noortje van den Dungen, Christian G.M. van Dijk, Merle M. Krebber, Hester M. den Ruijter, Gérard Pasterkamp, Dirk J. Duncker, Edward E. S. Nieuwenhuis, Roel de Weger, Manon M. H. Huibers, Aryan Vink, Jason H. Moore, James Moon, Marianne C. Verhaar, Georgios Kararigas, Michal Mokrý, Folkert W. Asselbergs, Caroline Cheng
Software Mentions: 3
Published: about 6 years ago

10.3389/fimmu.2019.02736

Exacerbation of Chikungunya Virus Rheumatic Immunopathology by a High Fiber Diet and Butyrate
Cited by: 28
Author(s): Natalie A. Prow, Thiago Dominguez Crespo Hirata, Bing Tang, Thibaut Larcher, Pamela Mukhopadhyay, Tiago Lubiana Alves, Thuy T. Le, Joy Gardner, Yee Suan Poo, Eri Nakayama, Viviana P. Lutzky, Helder I. Nakaya, Andreas Suhrbier
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-37411-y

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

10.3390/ijms19113351

Age- and Genotype-Specific Effects of the Angiotensin-Converting Enzyme Inhibitor Lisinopril on Mitochondrial and Metabolic Parameters in Drosophila melanogaster
Cited by: 14
Author(s): Karis A. Ederer, Kelly Jin, Sarah Bouslog, Lu Wang, Gregory S. Gorman, Glenn C. Rowe, Peter M. Abadir, Daniel Raftery, Douglas R. Moellering, Daniel Promislow, Patricia Jumbo-Lucioni, María De Luca
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-35868-5

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

10.3389/fcimb.2017.00512

Toxoplasma gondii Infection Is Associated with Mitochondrial Dysfunction in-Vitro
Cited by: 33
Author(s): Genevieve Syn, Denise Anderson, Jenefer M. Blackwell, Sarra E. Jamieson
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0044255

System Wide Analysis of the Evolution of Innate Immunity in the Nematode Model Species Caenorhabditis elegans and Pristionchus pacificus
Cited by: 49
Author(s): Amit Sinha, Robbie Rae, Igor Iatsenko, Ralf J. Sommer
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pone.0142037

Impact of Statins on Gene Expression in Human Lung Tissues
Cited by: 4
Author(s): Jackson Lane, Stephan F. van Eeden, Ma’en Obeidat, Don D. Sin, Scott J. Tebbutt, Wim Timens, Dirkje S. Postma, Michel Laviolette, Peter D. Paré, Yohan Bossé
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13148-017-0335-5

DNA methylation profiling in peripheral lung tissues of smokers and patients with COPD
Cited by: 72
Author(s): Isaac K. Sundar, Qin Yin, Brian S. Baier, Li Yan, Witold Mazur, Dongmei Li, Martha Susiarjo, Irfan Rahman
Software Mentions: 3
Published: over 9 years ago

10.1186/s12935-021-01871-6

Identifying SLC27A5 as a potential prognostic marker of hepatocellular carcinoma by weighted gene co-expression network analysis and in vitro assays
Cited by: 9
Author(s): Fan Zhang, Mengzhou Xue, Xin Jiang, Huiyuan Yu, Yixuan Qiu, J. Yu, Fan Yang, Zhijun Bao
Software Mentions: 3
Published: over 5 years ago

10.3389/fcimb.2018.00160

Group A Streptococcus M1T1 Intracellular Infection of Primary Tonsil Epithelial Cells Dampens Levels of Secreted IL-8 Through the Action of SpyCEP
Cited by: 20
Author(s): Amelia T. Soderholm, Timothy C. Barnett, Othmar Korn, Tania Rivera-Hernandez, Lisa M. Seymour, Benjamin L. Schulz, Victor Nizet, Christine A. Wells, Matthew J. Sweet, Mark J. Walker
Software Mentions: 3
Published: over 8 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 5 years ago

10.1038/s41598-018-34292-z

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

10.3389/fimmu.2018.03106

Expression of the Plasma Cell Transcriptional Regulator Blimp-1 by Dark Zone Germinal Center B Cells During Periods of Proliferation
Cited by: 31
Author(s): Daniel Radtke, Oliver Bannard
Software Mentions: 3
Published: over 7 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 10 years ago

10.1186/s12967-018-1650-0

p53 modeling as a route to mesothelioma patients stratification and novel therapeutic identification
Cited by: 8
Author(s): Kun Tian, Emyr Bakker, Michelle Hussain, Alice Guazzelli, Hasen Alhebshi, Parisa Meysami, Constantinos Demonacos, Jean-Marc Schwartz, Luciano Mutti, Marija Krstic‐Demonacos
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12935-021-02173-7

Xanthine dehydrogenase as a prognostic biomarker related to tumor immunology in hepatocellular carcinoma
Cited by: 5
Author(s): Zhen Lin, Yizhao Xie, Ming-Chun Zhao, Pin-Pin Hou, Juan Tang, Guang-Liang Chen
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-33897-8

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

10.3389/fncel.2014.00148

Deregulated expression of cytoskeleton related genes in the spinal cord and sciatic nerve of presymptomatic SOD1G93A Amyotrophic Lateral Sclerosis mouse model
Cited by: 24
Author(s): Jéssica Ruivo Maximino, Gilson Pereira de Oliveira, Chrystian Junqueira Alves, Gerson Chadi
Software Mentions: 3
Published: over 12 years ago

10.1186/s12870-017-1143-y

Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes
Cited by: 80
Author(s): Tan Ming, Dan Cheng, Yunhai Yang, Guoqiang Zhang, Mengjie Qin, Jun Chen, Yahua Chen, Mingyi Jiang
Software Mentions: 3
Published: almost 9 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: about 5 years ago

10.1111/jcmm.15595

Mining TCGA database for genes of prognostic value in gastric cancer microenvironment
Cited by: 10
Author(s): Qingzhi Lan, Peng Wang, Shan Tian, Weiguo Dong
Software Mentions: 3
Published: about 6 years ago

10.3389/fpls.2021.624365

A Multi-OMICs Approach Sheds Light on the Higher Yield Phenotype and Enhanced Abiotic Stress Tolerance in Tobacco Lines Expressing the Carrot lycopene β-cyclase1 Gene
Cited by: 13
Author(s): Juan C. Moreno, Silvia Martínez-Jaime, Monika Kosmacz, Ewelina Sokołowska, Philipp Schulz, Axel Fischer, Urszula Luzarowska, Michel Havaux, Aleksandra Skirycz
Software Mentions: 3
Published: over 5 years ago

10.1002/cam4.3474

Molecular and immunological associations of elevated serum lactate dehydrogenase in metastatic melanoma patients: A fresh look at an old biomarker
Cited by: 8
Author(s): Grant M. Fischer, Fernando Carapeto, Aron Y. Joon, Lauren E. Haydu, Huiqin Chen, Fuchenchu Wang, John S. Van Arnam, Jennifer L. McQuade, Khalida Wani, John M. Kirkwood, John F. Thompson, Michael T. Tetzlaff, Alexander J. Lazar, Hussein A. Tawbi, Jeffrey E. Gershenwald, Richard A. Scolyer, Georgina V. Long
Software Mentions: 3
Published: almost 6 years ago

10.7717/peerj.7413

Identification of a novel four-lncRNA signature as a prognostic indicator in cirrhotic hepatocellular carcinoma
Cited by: 17
Author(s): Linkun Ma, Chao Deng
Software Mentions: 3
Published: about 7 years ago

10.7554/eLife.65331

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

10.3389/fcell.2021.739509

Integrated Analysis of Stemness-Related LncRNAs Helps Predict the Immunotherapy Responsiveness of Gastric Cancer Patients
Cited by: 1
Author(s): Quan Jiang, Lingli Chen, Hao Chen, Zhaoqing Tang, Fenglin Liu, Yihong Sun
Software Mentions: 3
Published: about 5 years ago

10.1523/ENEURO.0287-18.2018

Overweight Mice Show Coordinated Homeostatic and Hedonic Transcriptional Response across Brain
Cited by: 0
Author(s): Ilario De Toma, Ilona Grabowicz, Marta Fructuoso, Daniel Trujillano, Bartek Wilczyński, Mara Dierssen
Software Mentions: 3
Published: almost 8 years ago

10.1186/1752-0509-8-12

Influence networks based on coexpression improve drug target discovery for the development of novel cancer therapeutics
Cited by: 10
Author(s): Nadia M. Penrod, Jason H. Moore
Software Mentions: 3
Published: over 12 years ago

10.1186/s12918-017-0520-3

Linking physiologically-based pharmacokinetic and genome-scale metabolic networks to understand estradiol biology
Cited by: 13
Author(s): Joanna H. Sier, Alfred E. Thumser, Nick Plant
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12935-020-01587-z

Identified IGSF9 association with prognosis and hypoxia in nasopharyngeal carcinoma by bioinformatics analysis
Cited by: 6
Author(s): Danxia Huang, Qianqian Liu, Weijun Zhang, Chunyue Huang, Ronghui Zheng, Gaoqiang Xie, Hongmei Wang, Baochang Jia, Jianjun Shi, Yawei Yuan, Min Deng
Software Mentions: 3
Published: almost 6 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 5 years ago

10.3389/fpsyt.2021.628361

A Potential Autophagy-Related Competing Endogenous RNA Network and Corresponding Diagnostic Efficacy in Schizophrenia
Cited by: 12
Author(s): Rongjie Li, Qiaoye Wang, Yufen Qiu, Youshi Meng, Lei Wei, Hao Wang, Ruikang Mo, Donghua Zou, Chunbin Liu
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-34191-3

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

10.3389/fimmu.2019.00708

Immunological Molecular Responses of Human Retinal Pigment Epithelial Cells to Infection With Toxoplasma gondii
Cited by: 15
Author(s): Shervi Lie, E Rochet, Erik Segerdell, Yuefang Ma, Liam M. Ashander, Audra Shadforth, Timothy A. Blenkinsop, Michael Michael, Binoy Appukuttan, Beth Wilmot, Justine R. Smith
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2021.622599

DNA Methylation Analysis to Unravel Altered Genetic Pathways Underlying Early Onset and Late Onset Neonatal Sepsis. A Pilot Study
Cited by: 12
Author(s): Sheila Lorente-Pozo, Paula Navarrete, María José Garzón, Inmaculada Lara-Cantón, Jesús Beltrán-García, Rebeca Osca-Verdegal, Salvador Mena-Mollá, Eva García-López, Máximo Vento, Federico V. Pallardó, José Luis García‐Gimenez
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-021-02185-3

Calculated identification of mutator-derived lncRNA signatures of genomic instability to predict the clinical outcome of muscle-invasive bladder cancer
Cited by: 1
Author(s): Yingchun Liang, Fangdie Ye, Cheng Zhang, Yuxi Ou, Lina Zou, Yun Hu, Jimeng Hu, Haowen Jiang
Software Mentions: 3
Published: about 5 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: about 6 years ago

10.1371/journal.pone.0225080

Identifying candidate diagnostic markers for early stage of non-small cell lung cancer
Cited by: 1
Author(s): Zhen Wu, Xu Zhang, Zhijun He, Liyun Hou
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.57068

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

10.1038/s41598-018-33807-y

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

10.1186/s12870-020-2260-6

Transcriptomic study of pedicels from GA3-treated table grape genotypes with different susceptibility to berry drop reveals responses elicited in cell wall yield, primary growth and phenylpropanoids synthesis
Cited by: 6
Author(s): Marco Meneses, Miguel García-Rojas, Claudia Muñoz-Espinoza, Tomás Carrasco-Valenzuela, Bruno G. Defilippi, Mauricio González-Agüero, Claudio Meneses, Rodrigo Infante, Patricio Hinrichsen
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-33478-9

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

10.1371/journal.pone.0191932

Integrated micro/messenger RNA regulatory networks in essential thrombocytosis
Cited by: 8
Author(s): Lu Zhao, Song Wu, Erya Huang, Dimitri Gnatenko, Wadie F. Bahou, Wei Zhu
Software Mentions: 3
Published: over 8 years ago

10.3389/fimmu.2020.582358

Transcriptional Memory-Like Imprints and Enhanced Functional Activity in γδ T Cells Following Resolution of Malaria Infection
Cited by: 7
Author(s): Rasika Kumarasingha, Lisa J Ioannidis, Waruni Abeysekera, Stephanie I Studniberg, Dinidu S Wijesurendra, Ramin Mazhari, Daniel P. Poole, Ivo Müeller, Louis Schofield, Diana S. Hansen, Emily M. Eriksson
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-33272-7

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

10.3390/cells9091966

Explorative Combined Lipid and Transcriptomic Profiling of Substantia Nigra and Putamen in Parkinson’s Disease
Cited by: 24
Author(s): Helena Xicoy, Jos F. Brouwers, Bé Wieringa, Gerard J.M. Martens
Software Mentions: 3
Published: about 6 years ago

10.3389/fncel.2020.00239

The CNS Myelin Proteome: Deep Profile and Persistence After Post-mortem Delay
Cited by: 46
Author(s): Olaf Jahn, Sophie B Siems, Kathrin Kusch, Dörte Hesse, Ramona B. Jung, Thomas Liepold, Marina Uecker, Ting Sun, Hauke Werner
Software Mentions: 3
Published: about 6 years ago

10.3389/fimmu.2021.747020

Integrated Analysis of Prognostic Genes Associated With Ischemia–Reperfusion Injury in Renal Transplantation
Cited by: 5
Author(s): Di Zhang, Yicun Wang, Song Zeng, Min Zhang, Xin Zhang, Yuxuan Wang, Zijian Zhang, Xi Wang, Xiaosong Hu
Software Mentions: 3
Published: about 5 years ago

10.1186/1752-0509-7-52

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum
Cited by: 21
Author(s): Katherine Lawler, K. E. Hammond‐Kosack, Alvis Brāzma, Richard M. R. Coulson
Software Mentions: 3
Published: over 13 years ago

10.1186/1471-2180-7-78

Identification of human pathogens isolated from blood using microarray hybridisation and signal pattern recognition
Cited by: 48
Author(s): Herbert Wiesinger-Mayr, Klemens Vierlinger, Rudolf Pichler, Albert Kriegner, Alexander M. Hirschl, Elisabeth Presterl, Levente Bodrossy, Christa Noehammer
Software Mentions: 3
Published: over 19 years ago

10.3390/cells10020387

Long-Term Effects of Very Low Dose Particle Radiation on Gene Expression in the Heart: Degenerative Disease Risks
Cited by: 8
Author(s): Venkata Naga Srikanth Garikipati, Arsen Arakelyan, Eleanor A. Blakely, Polly Y. Chang, May Truongcao, Maria Cimini, Vandana Malaredy, Anamika Bajpai, Sankar Addya, Malik Bisserier, Agnieszka Brojakowska, Abrisham Eskandari, Mary Khlgatian, Lahouaria Hadri, Kenneth Fish, Raj Kishore, David A. Goukassian
Software Mentions: 3
Published: over 5 years ago

10.1186/s12957-021-02196-4

Comprehensive analyses of correlation and survival reveal informative lncRNA prognostic signatures in colon cancer
Cited by: 13
Author(s): Meng Gao, Yang Guo, Yifu Xiao, Xuequn Shang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0191452

Developmental profiling of microRNAs in the human embryonic inner ear
Cited by: 16
Author(s): Duncan M. Chadly, Jennifer M. Best, Cong Ran, M Bruska, W Woźniak, Bartosz Kempisty, Mark W. Schwartz, Bonnie LaFleur, Billie‐Jo M. Kerns, John A. Kessler, Akihiro Matsuoka
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-32579-9

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

10.1371/journal.pone.0227455

Concurrent lipidomics and proteomics on malignant plasma cells from multiple myeloma patients: Probing the lipid metabolome
Cited by: 15
Author(s): Ahmed Mohamed, Joel Collins, Hui Jiang, Jeffrey Molendijk, Thomas Stoll, Federico Torta, Markus R. Wenk, Robert Bird, Paula Marlton, Peter Mollee, Kate A. Markey, Michelle M. Hill
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2021.729261

Genome-Wide Characterization of the MLO Gene Family in Cannabis sativa Reveals Two Genes as Strong Candidates for Powdery Mildew Susceptibility
Cited by: 9
Author(s): Noémi Pépin, François Hébert, David L. Joly
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-32549-1

Integrative metabolic and transcriptomic profiling of prostate cancer tissue containing reactive stroma
Cited by: 45
Author(s): Maria Andersen, Kjersti Rise, Guro F. Giskeødegård, Elin Richardsen, Helena Bertilsson, Øystein Størkersen, Tone Frost Bathen, Morten Rye, May‐Britt Tessem
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0075213

Otitis Media Impacts Hundreds of Mouse Middle and Inner Ear Genes
Cited by: 29
Author(s): Carol J. MacArthur, Fran Hausman, J. Beth Kempton, Dongseok Choi, Dennis R. Trune
Software Mentions: 3
Published: almost 13 years ago

10.7554/eLife.24265

Transcription factor TFCP2L1 patterns cells in the mouse kidney collecting ducts
Cited by: 55
Author(s): Max Werth, Kai M. Schmidt‐Ott, Thomas Leete, Andong Qiu, Christian Hinze, Mélanie Viltard, Neal Paragas, Carrie J. Shawber, Wenqiang Yu, Peter Lee, Xia Chen, Abby Sarkar, Weiyi Mu, Alexander Rittenberg, Chyuan Sheng Lin, Jan Kitajewski, Qais Al‐Awqati, Jonathan Barasch
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0102185

Embryonic miRNA Profiles of Normal and Ectopic Pregnancies
Cited by: 30
Author(s): Francisco Domı́nguez, Juan Manuel Moreno-Moya, Teresa Lozoya, Ainhoa Romero, Sebastián Martínez, Mercedes Monterde, Marta Gurrea, Blanca Ferri, Marı́a José Núñez, Carlos Simón, António Pellicer
Software Mentions: 3
Published: about 12 years ago

10.7554/eLife.26851

Molecular architecture underlying fluid absorption by the developing inner ear
Cited by: 35
Author(s): Keiji Honda, Sung Huhn Kim, Michael C. Kelly, J. C. Burns, Laura A. Constance, Xiangming Li, Fei Zhou, Michael Hoa, Matthew W. Kelley, Philine Wangemann, Robert J. Morell, Andrew J. Griffith
Software Mentions: 3
Published: almost 9 years ago

10.7150/jca.30336

Prognostic Value of Survival of MicroRNAs Signatures in Non-small Cell Lung Cancer
Cited by: 20
Author(s): Bin Chen, Tianshun Gao, Weiwei Yuan, Weihong Zhao, Tza‐Huei Wang, Jianqing Wu
Software Mentions: 3
Published: over 7 years ago

10.3389/fcell.2020.584232

HS-5 and HS-27A Stromal Cell Lines to Study Bone Marrow Mesenchymal Stromal Cell-Mediated Support to Cancer Development
Cited by: 24
Author(s): Annalisa Adamo, Pietro Delfino, Alessandro Gatti, Alice Bonato, Paul Takam Kamga, Ilaria Tanasi, Stefano Ugel, Angela Mercuri, Simone Caligola, Mauro Krampera
Software Mentions: 3
Published: almost 6 years ago

10.3390/cells8020133

MiRNAs from DLK1-DIO3 Imprinted Locus at 14q32 are Associated with Multiple Sclerosis: Gender-Specific Expression and Regulation of Receptor Tyrosine Kinases Signaling
Cited by: 19
Author(s): Natalia Baulina, German Osmak, Ivan Kiselev, Е. В. Попова, Alexey Boyко, О. Г. Кулакова, О. О. Фаворова
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.31126

Neuropathological and transcriptomic characteristics of the aged brain
Cited by: 74
Author(s): Jeremy A. Miller, Angela L. Guillozet-Bongaarts, Laura E. Gibbons, Nadia Postupna, Anne Renz, Allison Beller, Susan M. Sunkin, Lydia Ng, Shannon Rose, Kimberly A. Smith, Aaron Szafer, Chris Barber, Darren Bertagnolli, Kristopher Bickley, Krissy Brouner, Shiella Caldejon, Mike Chapin, Melvin L.K. Chua, Natalie M Coleman, Eiron Cudaback, Christine Cuhaciyan, Rachel Dalley, Nick Dee, Tsega Desta, Tim Dolbeare, Nadezhda Dotson, Michael Fisher, Nathalie Gaudreault, Garrett Gee, Terri L. Gilbert, Jeff Goldy, Fiona Griffin, Caroline Habel, Zeb Haradon, Nika Hejazinia, Leanne L Hellstern, Steve Horvath, Kim Howard, Robert Howard, Justin Johal, Nikolas L. Jorstad, Samuel R Josephsen, Chihchau Kuan, Florence Lai, Eric Lee, Felix Lee, Tracy Lemon, Xianwu Li, Desiree A. Marshall, J.L Melchor, Shubhabrata Mukherjee, Julie Nyhus, Julie Pendergraft, Lydia Potekhina, Elizabeth Rha, Samantha Rice, David Rosen, Abharika Sapru, Aimee M. Schantz, Elaine Shen, Emily Sherfield, Shi Shu, Andy J. Sodt, Nivretta Thatra, Michael Tieu, Angela Wilson, Thomas J. Montine, Eric B. Larson, Amy Bernard, Paul K. Crane, Richard G. Ellenbogen, C. Dirk Keene, Ed Lein
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.10809

An aspartyl protease defines a novel pathway for export of Toxoplasma proteins into the host cell
Cited by: 93
Author(s): Michael Coffey, Brad E. Sleebs, Alessandro D. Uboldi, Alexandra L. Garnham, Magdalena Franco, Nicole D. Marino, Michael W. Panas, David J. P. Ferguson, Marta Enciso, Matthew T O'Neill, Sash Lopaticki, Rebecca J. Stewart, Grant Dewson, Gordon K. Smyth, Brian J. Smith, Seth L. Masters, John C. Boothroyd, Justin A Boddey, Christopher J. Tonkin
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2202-15-11

Genes showing altered expression in the medial preoptic area in the highly social maternal phenotype are related to autism and other disorders with social deficits
Cited by: 33
Author(s): Terri M. Driessen, Brian E. Eisinger, Changjiu Zhao, Sharon A. Stevenson, Michael C. Saul, Stephen C. Gammie
Software Mentions: 3
Published: over 12 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 8 years ago

10.1186/s12886-020-01365-5

Identification of lncRNA–miRNA–mRNA regulatory network associated with primary open angle glaucoma
Cited by: 24
Author(s): Minwen Zhou, Bing Lu, Wei Tan, Mingshui Fu
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2016.01692

A Developmental and Molecular View of Formation of Auxin-Induced Nodule-Like Structures in Land Plants
Cited by: 19
Author(s): Ryan Hiltenbrand, Jacklyn Thomas, Hannah McCarthy, Karl Dykema, Ashley Spurr, Hamilton Newhart, Mary E. Winn, Arijit Mukherjee
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0221143

The effect of H1N1 vaccination on serum miRNA expression in children: A tale of caution for microRNA microarray studies
Cited by: 7
Author(s): Ruth Drury, Andrew J. Pollard, Daniel O’Connor
Software Mentions: 3
Published: about 7 years ago

10.1155/2017/2913648

Differential Analysis of Genetic, Epigenetic, and Cytogenetic Abnormalities in AML
Cited by: 7
Author(s): Mirazul Islam, Zahurin Mohamed, Yassen Assenov
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0159177

Immunophenotypic and Ultrastructural Analysis of Mast Cells in Hermansky-Pudlak Syndrome Type-1: A Possible Connection to Pulmonary Fibrosis
Cited by: 11
Author(s): Arnold S. Kirshenbaum, Glenn Cruse, Avanti Desai, Geethani Bandara, Maarten Leerkes, Chyi‐Chia Richard Lee, Elizabeth R. Fischer, Kevin O’Brien, Bernadette R. Gochuico, Kelly D. Stone, William A. Gahl, Dean D. Metcalfe
Software Mentions: 3
Published: about 10 years ago

10.3390/v11060549

Lnc-ITM2C-1 and GPR55 Are Proviral Host Factors for Hepatitis C Virus
Cited by: 14
Author(s): Pan Hu, Jochen Wilhelm, Gesche K. Gerresheim, Lyudmila Shalamova, Michael Niepmann
Software Mentions: 3
Published: over 7 years ago

10.3389/fncel.2016.00230

Altered Expression of Genes Encoding Neurotransmitter Receptors in GnRH Neurons of Proestrous Mice
Cited by: 32
Author(s): Csaba Vastagh, Annie Rodolosse, Norbert Solymosi, Zsolt Liposits
Software Mentions: 3
Published: almost 10 years ago

10.3389/fphys.2020.565240

Identification of Pathways and Key Genes in Venous Remodeling After Arteriovenous Fistula by Bioinformatics Analysis
Cited by: 10
Author(s): Jie Kong, Zhen Wang, Bin Zhao, Maofeng Gong, Jianbin Zhang, Zhaoxuan Lu, Yangyi Zhou, Changhong Liang, Haobo Su, Wensheng Lou, Guoping Chen, Jianping Gu, Xu He, Jianyan Wen
Software Mentions: 3
Published: almost 6 years ago

10.1155/2020/7524057

Construction and Validation of Predictive Model to Identify Critical Genes Associated with Advanced Kidney Disease
Cited by: 4
Author(s): Guangda Xin, Guangyu Zhou, Wenlong Zhang, Xiaofei Zhang
Software Mentions: 3
Published: almost 6 years ago

10.3389/fphys.2018.00618

Coactivation of TLR2 and TLR8 in Primary Human Monocytes Triggers a Distinct Inflammatory Signaling Response
Cited by: 14
Author(s): Korbinian Bösl, Miriam S. Giambelluca, Markus Haug, Marit Bugge, Terje Espevik, Richard K. Kandasamy, Bjarte Bergstrøm
Software Mentions: 3
Published: over 8 years ago

10.1534/g3.112.004127

Natural Variation in the Yeast Glucose-Signaling Network Reveals a New Role for the Mig3p Transcription Factor
Cited by: 19
Author(s): Jeffrey A. Lewis, Audrey P. Gasch
Software Mentions: 3
Published: almost 14 years ago

10.3389/fphys.2019.00214

Understanding Molecular Mechanisms of the Brain Through Transcriptomics
Cited by: 14
Author(s): Wei Wang, Guang-Zhong Wang
Software Mentions: 3
Published: over 7 years ago

10.1155/2018/8929057

The Effect of Citalopram on Genome-Wide DNA Methylation of Human Cells
Cited by: 10
Author(s): Riya R. Kanherkar, Bruk Getachew, Joseph Ben-Sheetrit, Sudhir Varma, Thomas Heinbockel, Yousef Tizabi, Antonei B. Csóka
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-29496-2

Subtle left-right asymmetry of gene expression profiles in embryonic and foetal human brains
Cited by: 47
Author(s): Carolien G.F. de Kovel, Steven Lisgo, Simon E. Fisher, Clyde Francks
Software Mentions: 3
Published: about 8 years ago

10.1186/1743-8977-9-25

Type I interferon and pattern recognition receptor signaling following particulate matter inhalation
Cited by: 12
Author(s): Aaron Erdely, James M. Antonini, Rebecca Salmen‐Muniz, Angie Liston, Tracy Hulderman, Petia P. Simeonova, Michael L. Kashon, Shengqiao Li, Ja K. Gu, Samuel Stone, Bean T. Chen, David G. Frazer, Patti C. Zeidler-Erdely
Software Mentions: 3
Published: over 14 years ago

10.1038/s41598-018-30781-3

Integrative epigenomic analysis in differentiated human primary bronchial epithelial cells exposed to cigarette smoke
Cited by: 11
Author(s): Kimberly Glass, Derek Thibault, Feng Guo, Joseph F. Mitchel, Brandon Pham, Weiliang Qiu, Yan Li, Zhiqiang Jiang, Peter J. Castaldi, Edwin K. Silverman, Benjamin A. Raby, Jin‐Ah Park, Guo‐Cheng Yuan, Xiaobo Zhou
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-29708-9

Loss of function of miR-342-3p results in MCT1 over-expression and contributes to oncogenic metabolic reprogramming in triple negative breast cancer
Cited by: 70
Author(s): Sandra Romero-Córdoba, Sergio Rodríguez‐Cuevas, Verónica Bautista-Piña, Antonio Maffuz‐Aziz, Elvira D’Ippolito, Giulia Cosentino, Sara Baroni, Marilena V. Iorio, Alfredo Hidalgo-Miranda
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-30587-3

A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes
Cited by: 2
Author(s): Brett W. Engelmann, Chiaowen Joyce Hsiao, John Blischak, Yannick Fourne, Zia Khan, Michael J. Ford, Yoav Gilad
Software Mentions: 3
Published: about 8 years ago

10.1186/s12967-016-0886-9

Serum microRNA-1233 is a specific biomarker for diagnosing acute pulmonary embolism
Cited by: 33
Author(s): Thorsten Kessler, Jeanette Erdmann, Baiba Vilne, Petra Bruse, Volkhard Kurowski, Patrick Diemert, Heribert Schunkert, Hendrik B. Sager
Software Mentions: 3
Published: over 10 years ago

10.7554/eLife.40174

Time-resolved mapping of genetic interactions to model rewiring of signaling pathways
Cited by: 19
Author(s): Florian Heigwer, Christian Scheeder, Thilo Miersch, Barbara Schmitt, Claudia Blass, Mischan Vali Pour Jamnani, Michael Boutros
Software Mentions: 3
Published: over 7 years ago

10.1186/s13104-021-05788-1

miRkit: R framework analyzing miRNA PCR array data
Cited by: 0
Author(s): Maria Tsagiopoulou, Anastasis Togkousidis, Nikolaos Pechlivanis, Μαρία Μανιού, Aristea Batsali, Angelos Matheakakis, Charalampos Pontikoglou, Fotis Psomopoulos
Software Mentions: 3
Published: almost 5 years ago

10.3389/fimmu.2018.00879

Cord Blood CD8+ T Cells Have a Natural Propensity to Express IL-4 in a Fatty Acid Metabolism and Caspase Activation-Dependent Manner
Cited by: 11
Author(s): Yuxia Zhang, Jovana Maksimovic, Bing Huang, David P. De Souza, Gaetano Naselli, Huan Chen, Li Zhang, Kai Weng, Hanquan Liang, Yanhui Xu, John M. Wentworth, Nicholas D. Huntington, Alicia Oshlack, Sitang Gong, Axel Kallies, Peter Vuillermin, Min Yang, Leonard C. Harrison
Software Mentions: 3
Published: over 8 years ago

10.1155/2017/2568706

Genomewide Expression and Functional Interactions of Genes under Drought Stress in Maize
Cited by: 34
Author(s): Nepolean Thirunavukkarasu, R.C. Sharma, Nidhi Singh, Kaliyugam Shiriga, Sweta Mohan, Swati Mittal, Mittal Shikha, Mallana Gowdra Mallikarjuna, Atmakuri Ramakrishna Rao, Prasanta K. Dash, Firoz Hossain, H. S. Gupta
Software Mentions: 3
Published: over 9 years ago

10.1186/s12866-021-02110-8

HilE is required for synergistic activation of SPI-1 gene expression in Salmonella enterica serovar Typhimurium
Cited by: 1
Author(s): Selwan Hamed, Riham M. Shawky, Mohamed Emara, James M. Slauch, Christopher V. Rao
Software Mentions: 3
Published: over 5 years ago

10.1186/1749-8546-7-19

Effects of alpha-mangostin on the expression of anti-inflammatory genes in U937 cells
Cited by: 39
Author(s): Szu-Hsiu Liu, Lain-Tze Lee, Nai-Yun Hu, Kuo-Kuei Huange, Ying-Chu Shih, Munekazu Iinuma, Jen-Ming Li, Ting-Yu Chou, Wei‐Hsin Wang, Ting-Shou Chen
Software Mentions: 3
Published: about 14 years ago

10.3389/fcell.2021.668738

Screening for Core Genes Related to Pathogenesis of Alzheimer’s Disease
Cited by: 3
Author(s): Long-Xiu Yang, Yuan Qin, Chongdong Jian
Software Mentions: 3
Published: over 5 years ago

10.7150/jca.49138

LINC00184 involved in the regulatory network of ANGPT2 via ceRNA mediated miR-145 inhibition in gastric cancer
Cited by: 13
Author(s): Haiyan Piao, Shuai Guo, Haoyi Jin, Yue Wang, Jun Zhang
Software Mentions: 3
Published: over 5 years ago

10.1155/2018/8076397

The Influence of Metabolic Syndrome and Sex on the DNA Methylome in Schizophrenia
Cited by: 12
Author(s): Kyle J. Burghardt, Jaclyn M. Goodrich, Brittany N Lines, Vicki L. Ellingrod
Software Mentions: 3
Published: over 8 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: about 7 years ago

Projects: bioconductor: limma

Science Score: 78/100

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Papers Mentioning limma 7,776