bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0128041

Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions
Cited by: 85
Author(s): Lei Gong, Hongxia Zhang, Xiaoyan Gan, Li Zhang, Yuchao Chen, Fengjie Nie, Lei Shi, Miao Li, Zhiqian Guo, Guohui Zhang, Song Yao
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0188285

DEclust: A statistical approach for obtaining differential expression profiles of multiple conditions
Cited by: 7
Author(s): Yoshimasa Aoto, Tsuyoshi Hachiya, Kazuhiro Okumura, Sumitaka Hase, Kengo Sato, Yuichi Wakabayashi, Yasubumi Sakakibara
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0238594

High accuracy gene expression profiling of sorted cell subpopulations from breast cancer PDX model tissue
Cited by: 1
Author(s): Warren Porter, Eileen Snowden, Friedrich Hahn, Mitchell Ferguson, Frances Tong, W. Shannon Dillmore, Rainer Blaesius
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0251868

Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem
Cited by: 3
Author(s): Stephanie Lam, Arun Kommadath, Ó. López-Campos, Nuria Prieto, J. L. Aalhus, M. Juárez, M. E. R. Dugan, Payam Vahmani
Software Mentions: 3
Published: over 5 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

10.1371/journal.pone.0237400

Whole-blood transcriptome profiling reveals signatures of metformin and its therapeutic response
Cited by: 14
Author(s): Monta Ustinova, Laura Ansone, Ivars Silamiķelis, Vita Rovīte, Ilze Elbere, Laila Silamiķele, Ineta Kalniņa, Dāvids Fridmanis, Jeļizaveta Sokolovska, Ilze Konrāde, Valdis Pīrāgs, Jānis Kloviņš
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0178281

Gene and metabolite time-course response to cigarette smoking in mouse lung and plasma
Cited by: 18
Author(s): Mikaela Miller, Thomas Danhorn, Charmion Cruickshank‐Quinn, Sonia M. Leach, Sean Jacobson, Matthew Strand, Nichole Reisdorph, Russell P. Bowler, Irina Petrache, Katerina Kechris
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0115717

Melanocytes in the Skin – Comparative Whole Transcriptome Analysis of Main Skin Cell Types
Cited by: 42
Author(s): Paula Reemann, Ene Reimann, Sten Ilmjärv, Orm Porosaar, Helgi Silm, Viljar Jaks, Eero Vasar, Külli Kingo, Sulev Kõks
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0079874

Phenotypic and Transcriptional Fidelity of Patient-Derived Colon Cancer Xenografts in Immune-Deficient Mice
Cited by: 31
Author(s): Jeffrey Chou, Matthew Fitzgibbon, Christie-Lynn Mortales, Andrea M. H. Towlerton, Melissa P. Upton, Raymond S. Yeung, Martin W. McIntosh, Edus H. Warren
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0250758

Comprehensive at-arrival transcriptomic analysis of post-weaned beef cattle uncovers type I interferon and antiviral mechanisms associated with bovine respiratory disease mortality
Cited by: 9
Author(s): Matthew A. Scott, Amelia R. Woolums, Cyprianna E. Swiderski, Andy D. Perkins, Bindu Nanduri, David R. Smith, Brandi B. Karisch, William B. Epperson, J. R. Blanton
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0210358

Ocean acidification at a coastal CO2 vent induces expression of stress-related transcripts and transposable elements in the sea anemone Anemonia viridis
Cited by: 11
Author(s): Ilona Urbárová, Sylvain Forêt, Mikael Dahl, Åse Emblem, Marco Milazzo, Jason M. Hall‐Spencer, Steinar Johansen
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0173094

Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response
Cited by: 6
Author(s): Alex Yi‐Lin Tsai, Kin Chan, Chi-Yip Ho, Thomas Canam, Resmi Capron, Emma R. Master, Katharina Bräutigam
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0031526

The Transcriptome of Compatible and Incompatible Interactions of Potato (Solanum tuberosum) with Phytophthora infestans Revealed by DeepSAGE Analysis
Cited by: 55
Author(s): Gabor Gyetvai, Mads Sønderkær, Ulrike Göbel, Rico Basekow, Agim Ballvora, Maren Imhoff, Birgit Kersten, Kåre Lehmann Nielsen, Christiane Gebhardt
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0236395

The effect of compound kushen injection on cancer cells: Integrated identification of candidate molecular mechanisms
Cited by: 12
Author(s): Jingang Cui, Zhibo Qu, Yuka Harata-Lee, Hao Shen, Thazin Nwe Aung, Wei Wang, R. Daniel Kortschak, David L. Adelson
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0207715

Distinct genes and pathways associated with transcriptome differences in early cardiac development between fast- and slow-growing broilers
Cited by: 9
Author(s): J. Zhang, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0233064

Transcriptome analysis of Catarina scallop (Argopecten ventricosus) juveniles treated with highly-diluted immunomodulatory compounds reveals activation of non-self-recognition system
Cited by: 9
Author(s): Jesús Antonio López‐Carvallo, José Manuel Mazón‐Suástegui, Miguel Ángel Hernández‐Oñate, Dariel Tovar‐Ramírez, Fernando Abasolo‐Pacheco, Rosa María Morelos‐Castro, Guadalupe Fabiola Arcos‐Ortega
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0160168

New Cell Adhesion Molecules in Human Ischemic Cardiomyopathy. PCDHGA3 Implications in Decreased Stroke Volume and Ventricular Dysfunction
Cited by: 14
Author(s): Ana Ortega, Carolina Gil-Cayuela, Estefanía Tarazón, María García‐Manzanares, José Montero, Juan Cinca, Manuel Portolés, Miguel Rivera, Esther Roselló‐Lletí
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0239450

Integrative analysis of long non-coding RNA and mRNA in broilers with valgus-varus deformity
Cited by: 10
Author(s): Hehe Tang, Yaping Guo, Zhenzhen Zhang, Zhuanjian Li, Yanhua Zhang, Yuanfang Li, Xiangtao Kang, Ruili Han
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0201851

Small RNAs detected in exosomes derived from the MH7A synovial fibroblast cell line with TNF-α stimulation
Cited by: 19
Author(s): Yosuke Takamura, Wataru Aoki, Atsushi Satomura, Seiji Shibasaki
Software Mentions: 3
Published: about 8 years ago

10.3389/fnagi.2017.00064

Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease
Cited by: 9
Author(s): Francisco Altimiras, Barbara Uszczyńska-Ratajczak, Francisco Câmara, Anna Vlasova, Emilio Palumbo, Stephen Newhouse, Robert M. J. Deacon, Leandro A. E. Farias, Michael Hurley, David E. Loyola, Rodrigo A. Vásquez, Richard Dobson, Roderic Guigó, Patricia Cogram
Software Mentions: 3
Published: over 9 years ago

10.3389/fnagi.2019.00101

Transcriptional Dysregulation Study Reveals a Core Network Involving the Progression of Alzheimer's Disease
Cited by: 22
Author(s): Guofeng Meng, Hongkang Mei
Software Mentions: 3
Published: over 7 years ago

10.3389/fbioe.2020.611701

Efficient Production of Pyruvate Using Metabolically Engineered Lactococcus lactis
Cited by: 5
Author(s): Fan Suo, Jianming Liu, Jun Chen, Xuanji Li, Peter Ruhdal Jensen
Software Mentions: 3
Published: almost 6 years ago

10.3389/fcell.2020.00807

The Pathogenic Effects of Fusobacterium nucleatum on the Proliferation, Osteogenic Differentiation, and Transcriptome of Osteoblasts
Cited by: 8
Author(s): Hui Gao, Tianyong Sun, Fanghong Yang, Jiakan Yuan, Mei Yang, Wenyan Kang, Di Tang, Jun Zhang, Qiang Feng
Software Mentions: 3
Published: about 6 years ago

10.3389/fcell.2021.685494

Novel Functional Genes Involved in Transdifferentiation of Canine ADMSCs Into Insulin-Producing Cells, as Determined by Absolute Quantitative Transcriptome Sequencing Analysis
Cited by: 2
Author(s): Pengxiu Dai, Jiakai Li, Yijing Chen, Luwen Zhang, Xinke Zhang, Jinglu Wang, Guixiang Qi, Yihua Zhang
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2021.727183

A Novel Pyroptosis-Associated Long Non-coding RNA Signature Predicts Prognosis and Tumor Immune Microenvironment of Patients With Breast Cancer
Cited by: 29
Author(s): Liqin Ping, Kaiming Zhang, Xueqi Ou, Xingsheng Qiu, Xia Xiao
Software Mentions: 3
Published: about 5 years ago

10.3389/fcell.2020.583434

Human Fetal Scalp Dermal Papilla Enriched Genes and the Role of R-Spondin-1 in the Restoration of Hair Neogenesis in Adult Mouse Cells
Cited by: 9
Author(s): Elizabeth Weber, Yung-Chih Lai, Mingxing Lei, Ting‐Xin Jiang, Cheng‐Ming Chuong
Software Mentions: 3
Published: almost 6 years ago

10.3389/fcell.2020.603815

Genome-Wide Integrated Analysis Revealed Functions of lncRNA–miRNA–mRNA Interaction in Growth of Intermuscular Bones in Megalobrama amblycephala
Cited by: 14
Author(s): Yulong Chen, Shiming Wan, Qing Li, Xiaoru Dong, Jinghan Diao, Qing Liao, Guiying Wang, Zexia Gao
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2020.602493

The Identification of Plasma Exosomal miR-423-3p as a Potential Predictive Biomarker for Prostate Cancer Castration-Resistance Development by Plasma Exosomal miRNA Sequencing
Cited by: 29
Author(s): Tianyu Guo, Yang Wang, Jing Jia, Xueying Mao, Elżbieta Stankiewicz, Glenda Scandura, Edwina Burke, Lei Xu, Jacek Marzec, Caitlin R. Davies, Jiaying Lu, Prabhakar Rajan, Alistair Grey, K. H. Tipples, John Hines, Sakunthala C. Kudahetti, Tim Oliver, Thomas Powles, Constantine Alifrangis, Manish Kohli, Greg Shaw, Wen Wang, Na Feng, Jonathan Shamash, Daniel M. Berney, Liang Wang, Yong‐Jie Lu
Software Mentions: 3
Published: almost 6 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

10.3389/fcell.2020.00520

Multi-Omic Approach to Identify Phenotypic Modifiers Underlying Cerebral Demyelination in X-Linked Adrenoleukodystrophy
Cited by: 11
Author(s): Phillip A. Richmond, Frans van der Kloet, Frédéric M. Vaz, David T.S. Lin, Anuli Uzozie, Emma Graham, Michael S. Kobor, Sara Mostafavi, Perry D. Moerland, Philipp F. Lange, Antoine H. C. van Kampen, Wyeth W. Wasserman, Marc Engelen, Stephan Kemp, Clara van Karnebeek
Software Mentions: 3
Published: over 6 years ago

10.3389/fcell.2021.663032

Phenotypically Anchored mRNA and miRNA Expression Profiling in Zebrafish Reveals Flame Retardant Chemical Toxicity Networks
Cited by: 6
Author(s): Subham Dasgupta, Cheryl L. Dunham, Lisa Truong, Michael T. Simonich, Christopher Sullivan, Robyn L Tanguay
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2021.615098

Transcriptome Analysis of Dnmt3l Knock-Out Mice Derived Multipotent Mesenchymal Stem/Stromal Cells During Osteogenic Differentiation
Cited by: 2
Author(s): Chih-Yi Yang, Rita Jui-Hsien Lu, Ming-Kang Lee, Felix Shih-Hsian Hsiao, Ya-Ping Yen, Chi‐Feng Cheng, Pu-Sheng Hsu, Yi-Tzang Tsai, Shih‐Kuo Chen, I-Hsuan Liu, Pao‐Yang Chen, Shau-Ping Lin
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2021.671211

Identification of ZNF26 as a Prognostic Biomarker in Colorectal Cancer by an Integrated Bioinformatic Analysis
Cited by: 2
Author(s): Jiaqi Liu, Yimin Li, Yaqi Gan, Qing Xiao, Ruotong Tian, Guang Shu, Gang Yin
Software Mentions: 3
Published: over 5 years ago

10.3389/fcimb.2019.00254

Probiotic Supplementation During Human Pregnancy Affects the Gut Microbiota and Immune Status
Cited by: 19
Author(s): Yuyi Chen, Zhe Li, Kian Deng Tye, Huijuan Luo, Xiaomei Tang, Yu-Chieh Liao, Dongju Wang, Juan Zhou, Ping Yang, Yimi Li, Yingbing Su, Xiaomin Xiao
Software Mentions: 3
Published: over 7 years ago

10.3389/fcimb.2020.00082

Francisella novicida Two-Component System Response Regulator BfpR Modulates iglC Gene Expression, Antimicrobial Peptide Resistance, and Biofilm Production
Cited by: 6
Author(s): Scott N. Dean, Morgan E. Milton, John Cavanagh, Monique L. van Hoek
Software Mentions: 3
Published: over 6 years ago

10.3389/fendo.2018.00245

Drosophila Insulin-Like Peptides DILP2 and DILP5 Differentially Stimulate Cell Signaling and Glycogen Phosphorylase to Regulate Longevity
Cited by: 65
Author(s): Stephanie Post, Galina Karashchuk, John D. Wade, Waseem Sajid, Pierre De Meyts, Marc Tatar
Software Mentions: 3
Published: over 8 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

10.3389/fimmu.2021.656846

Expression of Senescence Marker TIGIT Identifies Polyfunctional Donor-Reactive CD4+ T Cells Preferentially Lost After Kidney Transplantation
Cited by: 12
Author(s): Amy C. J. van der List, Nicolle H.R. Litjens, Mariska Klepper, M. Betjes
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2021.678699

The Zinc Nutritional Immunity of Epinephelus coioides Contributes to the Importance of znuC During Pseudomonas plecoglossicida Infection
Cited by: 12
Author(s): Lixing Huang, Yanfei Zuo, Yingxue Qin, Lingmin Zhao, Mao Lin, Qingpi Yan
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2019.01960

Differential Impact of Co-expressed SP-A1/SP-A2 Protein on AM miRNome; Sex Differences
Cited by: 16
Author(s): Nithyananda Thorenoor, Yuka Imamura Kawasawa, Chintan K. Gandhi, Xuesheng Zhang, Joanna Floros
Software Mentions: 3
Published: about 7 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: about 6 years ago

10.3389/fimmu.2018.03071

Protection Against Marburg Virus Using a Recombinant VSV-Vaccine Depends on T and B Cell Activation
Cited by: 34
Author(s): Andrea Marzi, Andrea Menicucci, Flora Engelmann, Julie Callison, Eva Horne, Friederike Feldmann, Allen Jankeel, Heinz Feldmann, Ilhem Messaoudi
Software Mentions: 3
Published: almost 8 years ago

10.3389/fmed.2020.00056

A Robust 6-lncRNA Prognostic Signature for Predicting the Prognosis of Patients With Colorectal Cancer Metastasis
Cited by: 22
Author(s): Shuyuan Li, Shuo Chen, Boxue Wang, Lin Zhang, Yinan Su, Xipeng Zhang
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2020.01921

The Role of Testosterone and Gibberellic Acid in the Melanization of Cryptococcus neoformans
Cited by: 4
Author(s): Jamila S Tucker, Tiffany Guess, Erin E. McClelland
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2017.02121

Different Non-Saccharomyces Yeast Species Stimulate Nutrient Consumption in S. cerevisiae Mixed Cultures
Cited by: 57
Author(s): José Antonio Curiel, Pilar Morales, Ramón González, Jordi Tronchoni
Software Mentions: 3
Published: about 9 years ago

10.3389/fmicb.2018.01026

Comparative Methylome Analysis Reveals Perturbation of Host Epigenome in Chestnut Blight Fungus by a Hypovirus
Cited by: 10
Author(s): Ru Li, Sisi Zhou, Yongbing Li, Xiaorui Shen, Qinnan Wang, Baoshan Chen
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2020.00518

Depth Influences Symbiodiniaceae Associations Among Montastraea cavernosa Corals on the Belize Barrier Reef
Cited by: 24
Author(s): Ryan J. Eckert, Ashley M Reaume, Alexis B. Sturm, Michael S. Studivan, Joshua D. Voss
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2020.00163

Synthesis, Regulation and Degradation of Carotenoids Under Low Level UV-B Radiation in the Filamentous Cyanobacterium Chlorogloeopsis fritschii PCC 6912
Cited by: 26
Author(s): Carole A. Llewellyn, Ruth L. Airs, Garry Farnham, Carolyn Greig
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2019.01568

A Novel Two-Component System, Encoded by the sco5282/sco5283 Genes, Affects Streptomyces coelicolor Morphology in Liquid Culture
Cited by: 6
Author(s): Erick Eligio Arroyo-Pérez, Gabriela González‐Cerón, Gloria Soberón‐Chávez, Dimitris Georgellis, Luis Servı́n‐González
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2021.643679

Understanding the Shift in the Microbiome of Composts That Are Optimized for a Better Fit-for-Purpose in Growing Media
Cited by: 13
Author(s): Steffi Pot, Caroline De Tender, Sarah Ommeslag, Ilse Delcour, Johan Ceusters, E. Gorrens, Jane Debode, Bart Vandecasteele, Karen Vancampenhout
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2017.00732

A Meta-Transcriptomics Survey Reveals Changes in the Microbiota of the Chinese Mitten Crab Eriocheir sinensis Infected with Hepatopancreatic Necrosis Disease
Cited by: 30
Author(s): Huangxuan Shen, Yanan Zang, Kun Song, Yuanchao Ma, Tianhao Dai, Ali Serwadda
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2021.724042

Transcriptomic Profile of Mycobacterium smegmatis in Response to an Imidazo[1,2-b][1,2,4,5]tetrazine Reveals Its Possible Impact on Iron Metabolism
Cited by: 0
Author(s): Aleksey A. Vatlin, Egor Shitikov, Mohd Shahbaaz, Dmitry Bespiatykh, Ksenia M. Klimina, Alan Christoffels, В. Н. Даниленко, Д. А. Маслов
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2021.725403

The Perception of Rhizosphere Bacterial Communication Signals Leads to Transcriptome Reprogramming in Lysobacter capsici AZ78, a Plant Beneficial Bacterium
Cited by: 1
Author(s): Ana Bejarano, Michele Perazzolli, I. Pertot, Gerardo Puopolo
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2021.656589

Transcriptome Analysis Reveals Cr(VI) Adaptation Mechanisms in Klebsiella sp. Strain AqSCr
Cited by: 2
Author(s): Paloma Lara, Leticia Vega‐Alvarado, Diana X. Sahonero‐Canavesi, Michel Koenen, Laura Villanueva, Fernando Riveros-Mckay, Enrique Morett, Katy Juárez
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2019.00826

Identifying Gut Microbiota Associated With Colorectal Cancer Using a Zero-Inflated Lognormal Model
Cited by: 98
Author(s): Dongmei Ai, Hongfei Pan, Xiaoxin Li, Yingxin Gao, Gang Liu, Xia Li
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2021.684664

Basidiomycetes Are Particularly Sensitive to Bacterial Volatile Compounds: Mechanistic Insight Into the Case Study of Pseudomonas protegens Volatilome Against Heterobasidion abietinum
Cited by: 12
Author(s): Maria Isabella Prigigallo, A. De Stradis, Abhishek Anand, Francesco Mannerucci, Floriane L’Haridon, Laure Weisskopf, Giovanni Bubici
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2020.596472

Effect of Two Different Sugarcane Cultivars on Rhizosphere Bacterial Communities of Sugarcane and Soybean Upon Intercropping
Cited by: 22
Author(s): Yue Liu, Hao Yang, Qi Liu, Xue Zhao, Sasa Xie, Ziting Wang, Ronghui Wen, Muqing Zhang, Baoshan Chen
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2017.01036

RNA-Seq Reveals Enhanced Sugar Metabolism in Streptococcus mutans Co-cultured with Candida albicans within Mixed-Species Biofilms
Cited by: 66
Author(s): Jinzhi He, Dongyeop Kim, Xuedong Zhou, Sang‐Joon Ahn, Robert A. Burne, Vincent P. Richards, Hyun Koo
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2016.00636

Transcriptomic Analysis Reveals Adaptive Responses of an Enterobacteriaceae Strain LSJC7 to Arsenic Exposure
Cited by: 17
Author(s): Yingjiao Zhang, Songcan Chen, Xiuli Hao, Jian‐Qiang Su, Xudong Xue, Yu Yan, Yan Zhu, Jun Ye
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2020.00482

Comparative Metatranscriptomics of Periodontitis Supports a Common Polymicrobial Shift in Metabolic Function and Identifies Novel Putative Disease-Associated ncRNAs
Cited by: 15
Author(s): Nikhil Ram-Mohan, Michelle M. Meyer
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2017.00716

Effects of Inhibitors on the Transcriptional Profiling of Gluconobater oxydans NL71 Genes after Biooxidation of Xylose into Xylonate
Cited by: 16
Author(s): Yuanyuan Miao, Yi Shen, Yong Xu
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2017.01830

A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro
Cited by: 18
Author(s): J. Wallis Marsh, Michael S. Humphrys, Garry Myers
Software Mentions: 3
Published: about 9 years ago

10.3389/fmicb.2018.02259

The MADS-box Transcription Factor PsMAD1 Is Involved in Zoosporogenesis and Pathogenesis of Phytophthora sojae
Cited by: 19
Author(s): Long Lin, Wenwu Ye, Jiawei Wu, Mingrun Xuan, Yufei Li, Jian Gao, Yonglin Wang, Yan Wang, Suomeng Dong, Yuanchao Wang
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2019.02084

YtrASa, a GntR-Family Transcription Factor, Represses Two Genetic Loci Encoding Membrane Proteins in Sulfolobus acidocaldarius
Cited by: 9
Author(s): Liesbeth Lemmens, Laurentijn Tilleman, Ezra De Koning, K. Valegård, Ann-Christin Lindås, Filip Van Nieuwerburgh, Dominique Maes, Eveline Peeters
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2017.01784

Analyzing the Complex Regulatory Landscape of Hfq – an Integrative, Multi-Omics Approach
Cited by: 14
Author(s): Lucia Grenga, Govind Chandra, Gerhard Saalbach, Carla V. Galmozzi, Günter Krämer, Jacob G. Malone
Software Mentions: 3
Published: about 9 years ago

10.3389/fmicb.2019.01914

Soil Metatranscriptomes Under Long-Term Experimental Warming and Drying: Fungi Allocate Resources to Cell Metabolic Maintenance Rather Than Decay
Cited by: 28
Author(s): Adriana L. Romero‐Olivares, Germán Meléndrez-Carballo, Asunción Lago‐Lestón, Kathleen K. Treseder
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2018.00445

Comparative mRNA-Seq Analysis Reveals the Improved EPS Production Machinery in Streptococcus thermophilus ASCC 1275 During Optimized Milk Fermentation
Cited by: 25
Author(s): Qinglong Wu, Nagendra P. Shah
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2020.01978

Sound Vibration-Triggered Epigenetic Modulation Induces Plant Root Immunity Against Ralstonia solanacearum
Cited by: 7
Author(s): Jihye Jung, Seon‐Kyu Kim, Sung‐Hee Jung, Mi‐Jeong Jeong, Choong-Min Ryu
Software Mentions: 3
Published: about 6 years ago

10.3389/fmolb.2021.625608

P23 Acts as Functional RBP in the Macrophage Inflammation Response
Cited by: 6
Author(s): Sebastian de Vries, Vladimı́r Beneš, Isabel S. Naarmann-de Vries, Cornelia Rücklé, Kathi Zarnack, Gernot Marx, Dirk H. Ostareck, Antje Ostareck-Lederer
Software Mentions: 3
Published: over 5 years ago

10.3389/fmolb.2021.678877

A Ferroptosis-Related lncRNAs Signature Predicts Prognosis and Immune Microenvironment for Breast Cancer
Cited by: 42
Author(s): Kaiming Zhang, Liqin Ping, Tian Du, Gehao Liang, Yun Huang, Zhiling Li, Rong Deng, Jun Tang
Software Mentions: 3
Published: over 5 years ago

10.3389/fmolb.2020.00030

Coexisting EGFR and TP53 Mutations in Lung Adenocarcinoma Patients Are Associated With COMP and ITGB8 Upregulation and Poor Prognosis
Cited by: 17
Author(s): Chang Zheng, Xuelian Li, Yong Ren, Zhihua Yin, Baosen Zhou
Software Mentions: 3
Published: over 6 years ago

10.3389/fmolb.2021.720370

Hydroxychloroquine Induces Apoptosis in Cholangiocarcinoma via Reactive Oxygen Species Accumulation Induced by Autophagy Inhibition
Cited by: 8
Author(s): Jiaqi Chen, Qiaoya Pan, Yang Bai, Xuepeng Chen, Yi Zhou
Software Mentions: 3
Published: about 5 years ago

10.3389/fneur.2015.00045

Long Non-Coding RNA Expression during Aging in the Human Subependymal Zone
Cited by: 37
Author(s): Guy Barry, Boris Guennewig, Samantha J. Fung, Dominik C. Kaczorowski, Cynthia Shannon Weickert
Software Mentions: 3
Published: over 11 years ago

10.3389/fneur.2020.573575

Differential Glial Activation in Early Epileptogenesis—Insights From Cell-Specific Analysis of DNA Methylation and Gene Expression in the Contralateral Hippocampus
Cited by: 4
Author(s): Toni Berger, Magnus Dehli Vigeland, Hanne Sagsveen Hjorthaug, Cecilie G. Nome, Erik Taubøll, Kaja Kristine Selmer, Kjell Heuser
Software Mentions: 3
Published: almost 6 years ago

10.3389/fnins.2020.00538

Brainstem Organoids From Human Pluripotent Stem Cells
Cited by: 42
Author(s): Nobuyuki Eura, Takeshi K. Matsui, Joachim Luginbühl, Masaya Matsubayashi, Hitoki Nanaura, T. Shiota, Kaoru Kinugawa, Naohiko Iguchi, Takao Kiriyama, Canbin Zheng, Tsukasa Kouno, Yan Lan, Pornparn Kongpracha, Pattama Wiriyasermkul, Yoshihiko Sakaguchi, Riko Nagata, Tomoya Komeda, Naritaka Morikawa, Fumika Kitayoshi, Miyong Jong, Shinko Kobashigawa, Mari Nakanishi, Masatoshi Hasegawa, Yasuhiko Saito, Takashi Shiromizu, Yuhei Nishimura, Takahiko Kasai, Maiko Takeda, Hiroshi Kobayashi, Yusuke Inagaki, Yasuhito Tanaka, Manabu Makinodan, Toshifumi Kishimoto, Hiroki Kuniyasu, Shushi Nagamori, Alysson R. Muotri, Jay W. Shin, Kazuma Sugie, Eiichiro Mori
Software Mentions: 3
Published: over 6 years ago

10.3389/fnins.2021.606926

The Epidemiological and Mechanistic Understanding of the Neurological Manifestations of COVID-19: A Comprehensive Meta-Analysis and a Network Medicine Observation
Cited by: 6
Author(s): Jason Shen, Yuan Hou, Yadi Zhou, Reena Mehra, Lara Jehi, Feixiong Cheng
Software Mentions: 3
Published: over 5 years ago

10.3389/fnins.2019.00297

Regeneration Enhances Metastasis: A Novel Role for Neurovascular Signaling in Promoting Melanoma Brain Metastasis
Cited by: 13
Author(s): Roshini Prakash, Sivan Izraely, Nikita S. Thareja, Rex H. Lee, Maya Rappaport, Riki Kawaguchi, Orit Sagi‐Assif, Shlomit Ben‐Menachem, Tsipi Meshel, Michał Machnicki, Shuichi Ohe, Dave S. B. Hoon, Giovanni Coppola, Isaac P. Witz, S. Thomas Carmichael
Software Mentions: 3
Published: over 7 years ago

10.3389/fonc.2020.554759

Integrated Analysis of lncRNA–Mediated ceRNA Network in Lung Adenocarcinoma
Cited by: 90
Author(s): Xianxian Wu, Zhilin Sui, Hongdian Zhang, Ying Wang, Zhentao Yu
Software Mentions: 3
Published: about 6 years ago

10.3389/fonc.2020.00215

A Novel Long Non-coding RNA, MSTRG.51053.2 Regulates Cisplatin Resistance by Sponging the miR-432-5p in Non-small Cell Lung Cancer Cells
Cited by: 24
Author(s): Jie Zhang, Chuanqin Xu, Y Gao, Yi Wang, Zongli Ding, Yueming Zhang, Wenyi Shen, Yulong Zheng, Yufeng Wan
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2021.553594

Comprehensive In Silico Analysis of a Novel Serum Exosome-Derived Competitive Endogenous RNA Network for Constructing a Prognostic Model for Glioblastoma
Cited by: 9
Author(s): Zihao Wang, Xin Ji, Lu Gao, Xiaopeng Guo, Wei Lian, Kan Deng, Bing Xing
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2020.533616

Expression Profile of Circular RNAs in Oral Squamous Cell Carcinoma
Cited by: 19
Author(s): Yanxiong Shao, Yuhan Song, Shuying Xu, Siyi Li, Huifang Zhou
Software Mentions: 3
Published: almost 6 years ago

10.3389/fonc.2020.602555

Development of an Immune-Related Gene Signature for Prognosis in Melanoma
Cited by: 13
Author(s): Mengli Zhang, Xu Zhou, Dan Huang, Chao Luan, Heng Gu, Ju Mei, Kun Chen
Software Mentions: 3
Published: almost 6 years ago

10.3389/fonc.2020.00871

A Radiosensitivity Gene Signature and XPO1 Predict Clinical Outcomes for Glioma Patients
Cited by: 5
Author(s): Shan Wu, Qiao Qiao, Guang Li
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2018.00374

Prognostic Genes of Breast Cancer Identified by Gene Co-expression Network Analysis
Cited by: 178
Author(s): Jianing Tang, Deguang Kong, Qiuxia Cui, Kun Wang, Dan Zhang, Yan Gong
Software Mentions: 3
Published: about 8 years ago

10.3389/fonc.2020.00780

Identification and Validation of a Prognostic lncRNA Signature for Hepatocellular Carcinoma
Cited by: 36
Author(s): Wang Li, Qifeng Chen, Tao Huang, Peihong Wu, Lujun Shen, Zijing Huang
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2020.550986

MicroRNAs Expression Patterns Predict Tumor Mutational Burden in Colorectal Cancer
Cited by: 5
Author(s): Jiahao Huang, Haizhou Liu, Yang Zhao, Tao Luo, Jungang Liu, Junjie Liu, Xiaoyan Pan, Weizhong Tang
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2020.00601

Circular RNA Expression Profiles in Nasopharyngeal Carcinoma by Sequence Analysis
Cited by: 17
Author(s): Jing Yang, Yongqian Gong, Qingshan Jiang, Lijun Liu, Shuyan Li, Quanjun Zhou, Fang Huang, Zhifeng Liu
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2020.01765

Identification of TYROBP and C1QB as Two Novel Key Genes With Prognostic Value in Gastric Cancer by Network Analysis
Cited by: 26
Author(s): Junjie Jiang, Yongfeng Ding, Mengjie Wu, Xiadong Lyu, Haifeng Wang, Yanyan Chen, Haiyong Wang, Lisong Teng
Software Mentions: 3
Published: about 6 years ago

10.3389/fonc.2021.707066

Cystatin-B Negatively Regulates the Malignant Characteristics of Oral Squamous Cell Carcinoma Possibly Via the Epithelium Proliferation/Differentiation Program
Cited by: 3
Author(s): Tiantian Xu, Xiao‐Wen Zeng, Xinhong Wang, Luxi Yang, Gang Luo, Ting Yu
Software Mentions: 3
Published: about 5 years ago

10.3389/fonc.2021.659201

Prognostic Prediction of Cytogenetically Normal Acute Myeloid Leukemia Based on a Gene Expression Model
Cited by: 4
Author(s): Yang Liu, Houyu Zhang, Xue Yang, Ting Lu, Shihui Ma, Hui Cheng, Kuangyu Yen, Tao Cheng
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2020.01029

Abnormal Food Timing Promotes Alcohol-Associated Dysbiosis and Colon Carcinogenesis Pathways
Cited by: 5
Author(s): Faraz Bishehsari, Shirin Moossavi, Phillip A. Engen, Xiaohan Liu, Yue Zhang
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2018.00368

Integrated Analysis of a Competing Endogenous RNA Network Revealing a Prognostic Signature for Cervical Cancer
Cited by: 11
Author(s): Leilei Xia, Han Wang, Shengyun Cai, Xiaoling Su, Jizi Shen, Meng Qi, Yu Chen, Li Li, Jiuqiong Yan, Caihong Zhang, Man Xu
Software Mentions: 3
Published: about 8 years ago

10.3389/fonc.2020.580276

Transcriptome Based System Biology Exploration Reveals Homogeneous Tumorigenicity of Alimentary Tract Malignancy
Cited by: 2
Author(s): You Lu, Jingqi Shi, Zixin Zhang, Jiayi Zhou, Haikun Zhou, Yuancai Feng, Zhenhua Lu, Shuya Yang, Xi-Yang Zhang, Yang Liu, Zichao Li, Yuanjie Sun, Lianhe Zheng, Duyin Jiang, Kun Yang
Software Mentions: 3
Published: almost 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.2020.01109

Identification of Immune-Related Prognostic Genes and LncRNAs Biomarkers Associated With Osteosarcoma Microenvironment
Cited by: 12
Author(s): Tao Zhang, Yingli Nie, Haifa Xia, Yanbin Zhang, Kailin Cai, Xiangdong Chen, Huili Li, Jiliang Wang
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2019.00613

Identification of Biomarkers for Controlling Cancer Stem Cell Characteristics in Bladder Cancer by Network Analysis of Transcriptome Data Stemness Indices
Cited by: 92
Author(s): Shen Pan, Yunhong Zhan, Xiaonan Chen, Bin Wu, Bitian Liu
Software Mentions: 3
Published: over 7 years ago

10.3389/fonc.2020.00979

High Expression of FAP in Colorectal Cancer Is Associated With Angiogenesis and Immunoregulation Processes
Cited by: 42
Author(s): Mairene Coto‐Llerena, Caner Ercan, Venkatesh Kancherla, Stephanie Taha‐Mehlitz, Serenella Eppenberger‐Castori, Savas D. Soysal, Charlotte K.Y. Ng, Martin Bolli, Markus von Flüe, Guillaume Nicolas, Luigi Terracciano, Melpomeni Fani, Salvatore Piscuoglio
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2021.684396

Adrenomedullin Expression Characterizes Leukemia Stem Cells and Associates With an Inflammatory Signature in Acute Myeloid Leukemia
Cited by: 6
Author(s): Giorgia Simonetti, Davide Angeli, Elisabetta Petracci, Eugenio Fonzi, Susanna Vedovato, Alessandra Sperotto, Antonella Padella, Martina Ghetti, Anna Ferrari, Valentina Robustelli, Rosa Di Liddo, Maria Teresa Conconi, Cristina Papayannidis, Claudio Cerchione, Michela Rondoni, Annalisa Astolfi, Emanuela Ottaviani, Giovanni Martinelli, Michele Gottardi
Software Mentions: 3
Published: over 5 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.2019.00649

Construction and Investigation of a lncRNA-Associated ceRNA Regulatory Network in Cholangiocarcinoma
Cited by: 32
Author(s): Junyu Long, Jianping Xiong, Yi Bai, Jianshan Mao, Jianzhen Lin, Weiyu Xu, Hui Zhang, Shuguang Chen, Hong Zhao
Software Mentions: 3
Published: about 7 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568