bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s40168-017-0237-y

Normalization and microbial differential abundance strategies depend upon data characteristics
Cited by: 1,253
Author(s): Sophie Weiss, Zhenjiang Zech Xu, Shyamal D. Peddada, Amir Almasi‐Hashiani, Kyle Bittinger, Antonio González, Catherine Lozupone, Jesse Zaneveld, Yoshiki Vázquez-Baeza, Amanda Birmingham, Embriette R. Hyde, Rob Knight
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pgen.1008420

Physiological and genomic evidence that selection on the transcription factor Epas1 has altered cardiovascular function in high-altitude deer mice
Cited by: 50
Author(s): Rena M. Schweizer, Jonathan P. Velotta, Catherine M. Ivy, Matthew R. Jones, Sarah M. Muir, Gideon S. Bradburd, Jay F. Storz, Graham R. Scott, Zachary A. Cheviron
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12920-018-0391-5

Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine
Cited by: 5
Author(s): Naresh Prodduturi, Aditya Bhagwate, Jean Pierre A. Kocher, Zhifu Sun
Software Mentions: 5
Published: almost 8 years ago

10.1155/2020/3817573

Diet Modifies Pioglitazone’s Influence on Hepatic PPARγ-Regulated Mitochondrial Gene Expression
Cited by: 5
Author(s): Sakil Kulkarni, Jiansheng Huang, Eric Tycksen, Paul Cliften, David A. Rudnick
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2019.01207

Thermal Manipulation During Embryogenesis Impacts H3K4me3 and H3K27me3 Histone Marks in Chicken Hypothalamus
Cited by: 26
Author(s): Sarah-Anne David, Anaïs Vitorino Carvalho, Coralie Gimonnet, Aurélien Brionne, Christelle Hennequet-Antier, Benoît Piégu, Sabine Crochet, Nathalie Couroussé, Thierry Bordeau, Yves Bigot, Anne Collin, Vincent Coustham
Software Mentions: 5
Published: over 6 years ago

10.1093/hmg/ddab031

Sexual dimorphism in cancer: insights from transcriptional signatures in kidney tissue and renal cell carcinoma
Cited by: 10
Author(s): Ruhina Shirin Laskar, Peng Li, Szilvia Ecsedi, Behnoush Abedi‐Ardekani, G. Durand, Nivonirina Robinot, Jean-Noël Hubert, Vladimír Janout, Давид Заридзе, Anush Mukeria, Dana Mateș, Ivana Holcátová, Lenka Foretová, Beata Świątkowska, Zoran Džamić, Saša Milosavljević, Robert Olaso, Anne Boland, Jean‐François Deleuze, David C. Muller, James McKay, Paul Brennan, Florence Le Calvez-Kelm, Ghislaine Scélo, Estelle Chanudet
Software Mentions: 5
Published: over 5 years ago

10.1186/s12936-019-2659-4

A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites
Cited by: 7
Author(s): Abhinay Ramaprasad, Amit Kumar Subudhi, Richard Culleton, Arnab Pain
Software Mentions: 5
Published: over 7 years ago

10.3390/cells9091924

Microcurrent Stimulation Triggers MAPK Signaling and TGF-β1 Release in Fibroblast and Osteoblast-Like Cell Lines
Cited by: 14
Author(s): Evangelia Konstantinou, Zoi Zagoriti, Anastasia Pyriochou, Konstantinos Poulas
Software Mentions: 5
Published: about 6 years ago

10.1155/2021/6648093

Integrated Analysis to Identify a Redox-Related Prognostic Signature for Clear Cell Renal Cell Carcinoma
Cited by: 16
Author(s): Yue Wu, Wa Xian, Huan Feng, Bintao Hu, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Jihong Liu, Tao Wang
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-020-00966-y

Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation
Cited by: 10
Author(s): Rajesh Kaushal, Peng Li, Sunil Kumar Singh, Mengrui Zhang, Xinlian Zhang, Juan Ignacio Vílchez, Zhen Wang, Danxia He, Yu Ye, Suhui Lv, Zhongtian Xu, Rafael J. L. Morcillo, Wei Wang, Wei-Chang Huang, Paul W. Paré, Chun‐Peng Song, Jian‐Kang Zhu, Renyi Liu, Wenxuan Zhong, Ping Ma, Huiming Zhang
Software Mentions: 5
Published: over 5 years ago

10.1186/s12870-015-0661-8

A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit
Cited by: 51
Author(s): Noam Chayut, Hui Yuan, Shachar Ohali, Ayala Meir, Yelena Yeselson, Vitaly Portnoy, Yi Zheng, Zhangjun Fei, Efraim Lewinsohn, Nurit Katzir, Arthur A. Schaffer, Shimon Gepstein, Joseph Burger, L i Li, Yaakov Tadmor
Software Mentions: 4
Published: almost 11 years ago

10.1534/g3.118.200810

Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression
Cited by: 13
Author(s): Stephen J. Bush, Mary E. B. McCulloch, Charity Muriuki, Mazdak Salavati, Gemma M. Davis, Iseabail L. Farquhar, Zofia M. Lisowski, Alan Archibald, David Hume, Emily L. Clark
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1004261

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation
Cited by: 329
Author(s): Guilhem Janbon, Kate L. Ormerod, Damien Paulet, Edmond J. Byrnes, Vikas Yadav, Gautam Chatterjee, Nandita Mullapudi, Chung-Chau Hon, R. Blake Billmyre, François Brunel, Yong-Sun Bahn, Weidong Chen, Yuan Chen, Eve W. L. Chow, Jean Yves Coppée, Anna Floyd-Averette, Claude Gaillardin, Kimberly J. Gerik, Jonathan M. Goldberg, Sara Gonzalez-Hilarion, Sharvari Gujja, Joyce L. Hamlin, Yu-Ting Hsueh, Giuseppe Ianiri, Steven J.M. Jones, Chinnappa D. Kodira, Lukasz Kozubowski, Woei C. Lam, Marco A. Marra, Larry D. Mesner, Piotr A. Mieczkowski, Frédérique Moyrand, Kirsten Nielsen, Caroline Proux, Tristan Rossignol, Jacqueline E. Schein, Sheng Sun, Carolin Wollschlaeger, Ian Wood, Qiandong Zeng, Cécile Neuvéglise, Carol S. Newlon, John R. Perfect, Jennifer K. Lodge, Alexander Idnurm, Jason E. Stajich, James W. Kronstad, Kaustuv Sanyal, Joseph Heitman, James A. Fraser, Christina A. Cuomo, Fred S. Dietrich
Software Mentions: 4
Published: over 12 years ago

10.7554/eLife.24570

EED orchestration of heart maturation through interaction with HDACs is H3K27me3-independent
Cited by: 36
Author(s): Shanshan Ai, Yong Peng, Chen Li, Fei Gu, Xianhong Yu, Yanzhu Yue, Qing Ma, Jinghai Chen, Zhiqiang Lin, Pingzhu Zhou, Huafeng Xie, Terence Prendiville, Wen Zheng, Yuli Liu, Stuart H. Orkin, Dazhi Wang, Jia Yu, William T. Pu, Aibin He
Software Mentions: 4
Published: over 9 years ago

10.3390/ijms21124470

Differences between Well-Differentiated Neuroendocrine Tumors and Ductal Adenocarcinomas of the Pancreas Assessed by Multi-Omics Profiling
Cited by: 8
Author(s): Teresa Starzyńska, Jakub Karczmarski, Agnieszka Paziewska, Maria Kulecka, Katarzyna Kuśnierz, Natalia Żeber‐Lubecka, Filip Ambrożkiewicz, Michał Mikula, Beata Kos‐Kudła, Jerzy Ostrowski
Software Mentions: 4
Published: about 6 years ago

10.1534/g3.118.200516

Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
Cited by: 6
Author(s): Cathy Boscarino, Thomas Nalpathamkalam, Giovanna Pellecchia, Weili Li, Bhooma Thiruvahindrapuram, Daniele Merico
Software Mentions: 4
Published: over 7 years ago

10.1534/g3.118.200677

Genotype-by-Environment-by-Environment Interactions in the Saccharomyces cerevisiae Transcriptomic Response to Alcohols and Anaerobiosis
Cited by: 5
Author(s): Maria Sardi, Molly Krause, Justin Heilberger, Audrey P. Gasch
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.53237

Rapid sex-specific adaptation to high temperature in Drosophila
Cited by: 20
Author(s): Sheng‐Kai Hsu, Ana Marija Jakšić, Viola Nolte, Manolis Lirakis, Robert Kofler, Neda Barghi, Elisabetta Versace, Christian Schlötterer
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1008181

Hepatitis C virus leaves an epigenetic signature post cure of infection by direct-acting antivirals
Cited by: 101
Author(s): Shira Perez, Antony Kaspi, Tom Domovitz, Ateret Davidovich, Anat Lavi-Itzkovitz, Tomer Meirson, Jacinta A Holmes, Chia Yen Dai, Chung Feng Huang, Raymond T. Chung, Nimer Assy, Assam El‐Osta, Gur Yaari, Salomon M. Stemmer, Ming‐Lung Yu, Izhak Haviv, Meital Gal-Tanamy
Software Mentions: 4
Published: about 7 years ago

10.1534/g3.117.300245

Genome-Wide Screen forSaccharomyces cerevisiaeGenes Contributing to Opportunistic Pathogenicity in an Invertebrate Model Host
Cited by: 7
Author(s): Sujal Phadke, Calum J. Maclean, Serena Zhao, Emmi A. Mueller, Lucas A. Michelotti, Kaitlyn L. Norman, Anuj Kumar, Timothy Y. James
Software Mentions: 4
Published: over 8 years ago

10.1016/j.celrep.2021.108860

COX2 regulates senescence secretome composition and senescence surveillance through PGE2
Cited by: 30
Author(s): S. Goncalves, Kai Yin, Yoko Itō, Adelyne Chan, Ioana Olan, Sarah Gough, Liam Cassidy, Eva M. Serrao, Stephen Smith, Andrew Young, Masashi Narita, Matthew Hoare
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2019.01605

De Novo Transcriptome Analysis of Durum Wheat Flag Leaves Provides New Insights Into the Regulatory Response to Elevated CO2 and High Temperature
Cited by: 26
Author(s): Rubén Vicente, Anthony Bolger, Rafael Martínez‐Carrasco, Pilar Pérez Pérez, Elena Gutiérrez, Björn Usadel, Rosa Morcuende
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1009349

Acetyltransferase Enok regulates transposon silencing and piRNA cluster transcription
Cited by: 3
Author(s): Shih-Ying Tsai, Fu Huang
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2021.727302

Identification of Genes and MicroRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses
Cited by: 4
Author(s): Minsu Park, Wookap Choi, Sang Yoon Shin, Hongman Moon, Dowhan Lee, Yun Shil Gho, Ki Hong Jung, Jong Seong Jeon, Chanseok Shin
Software Mentions: 4
Published: about 5 years ago

10.1016/j.celrep.2016.06.096

Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins
Cited by: 60
Author(s): Christian Hauer, Jana Sieber, Thomas Schwarzl, Ina Hollerer, Tomaž Curk, Anne-Marie Alleaume, Matthias W. Hentze, Andreas E. Kulozik
Software Mentions: 4
Published: about 10 years ago

10.3389/fpls.2018.00204

Transcriptome and Cell Physiological Analyses in Different Rice Cultivars Provide New Insights Into Adaptive and Salinity Stress Responses
Cited by: 55
Author(s): Elide Formentin, Cristina Sudiro, Giorgio Perin, Samantha Riccadonna, Elisabetta Barizza, Elena Baldoni, Enrico Lavezzo, Piergiorgio Stevanato, Gian Attilio Sacchi, Paolo Fontana, Stefano Toppo, Tomas Morosinotto, Michela Zottini, Fiorella Lo Schiavo
Software Mentions: 4
Published: over 8 years ago

10.3389/fpls.2016.01431

Quantitative Resistance to Verticillium Wilt in Medicago truncatula Involves Eradication of the Fungus from Roots and Is Associated with Transcriptional Responses Related to Innate Immunity
Cited by: 13
Author(s): Maoulida Toueni, Cécile Ben, Aurélie Le Ru, Laurent Gentzbittel, Martina Rickauer
Software Mentions: 4
Published: almost 10 years ago

10.3389/fphys.2020.588313

High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress
Cited by: 21
Author(s): Heather Ikert, Michael Lynch, Andrew C. Doxey, John P. Giesy, Mark R. Servos, Barbara A. Katzenback, Paul M. Craig
Software Mentions: 4
Published: over 5 years ago

10.3389/fphys.2021.707116

Transcriptional Time Course After Rotator Cuff Tear
Cited by: 3
Author(s): Laura S Vasquez-Bolanos, Michael C. Gibbons, Severin Ruoss, Isabella T. Wu, Mario Vargas-Vila, Sydnee A Hyman, Mary C. Esparza, Donald C. Fithian, Joseph R. Lane, Anshuman Singh, Chanond A. Nasamran, Kathleen M. Fisch, Samuel R. Ward
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2021.605015

RNA-Seq Profiling of Circular RNAs During Development of Hindgut in Rat Embryos With Ethylenethiourea-Induced Anorectal Malformations
Cited by: 5
Author(s): Si Ying Li, Chen Yi Wang, Yun Xiao, Xiao Tang, Zheng Wei Yuan, Yu Bai
Software Mentions: 4
Published: over 5 years ago

10.3389/fphar.2021.678256

Dysregulated lncRNAs are Involved in the Progress of Sepsis by Constructing Regulatory Networks in Whole Blood Cells
Cited by: 5
Author(s): Yanwei Cheng, Xue Cao, Jiange Zhang, Dong Chen, Juan Zhu, Lijun Xu, Lijie Qin
Software Mentions: 4
Published: about 5 years ago

10.3390/ijerph18157975

Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data
Cited by: 6
Author(s): Yongjun Piao, Wanxue Xu, Kwang Ho Park, Keun Ho Ryu, Rong Xiang
Software Mentions: 4
Published: about 5 years ago

10.1186/s13619-021-00083-7

Defining cell identity beyond the premise of differential gene expression
Cited by: 2
Author(s): Hani Jieun Kim, Patrick Tam, Pengyi Yang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pntd.0008424

Differential gene expression elicited by ZIKV infection in trophoblasts from congenital Zika syndrome discordant twins
Cited by: 17
Author(s): Murilo Sena Amaral, Ernesto Goulart, Luiz C. Caires-Júnior, David A. Morales-Vicente, Alessandra Soares‐Schanoski, Roselane P. Gomes, Giovanna Gonçalves de Oliveira Olberg, Renato Mancini Astray, Jorge Kalil, Mayana Zatz, Sérgio Verjovski-Almeida
Software Mentions: 4
Published: about 6 years ago

10.1038/s42003-021-01823-w

Shared associations identify causal relationships between gene expression and immune cell phenotypes
Cited by: 2
Author(s): Christiane Gasperi, Sung Chun, Shamil Sunyaev, Chris Cotsapas
Software Mentions: 4
Published: over 5 years ago

10.1007/s00018-021-03822-w

Immune cells lacking Y chromosome show dysregulation of autosomal gene expression
Cited by: 43
Author(s): Jan P. Dumanski, Jonatan Halvardson, Hanna Davies, Edyta Rychlicka-Buniowska, Jonas Mattisson, Behrooz Torabi Moghadam, Noémi Nagy, Kazimierz Węglarczyk, Karolina Bukowska-Straková, Marcus Danielsson, Paweł Olszewski, Arkadiusz Piotrowski, Erin Oerton, Aleksandra Ambicka, Marcin Przewoźnik, Łukasz Bełch, Tomasz Grodzicki, Piotr Chłosta, Stefan Imreh, Vilmantas Giedraitis, Lena Kilander, Jessica Nordlund, Adam Ameur, Ulf Gyllensten, Åsa Johansson, Alicja Józkowicz, Maciej Siedlar, Alicja Klich-Rączka, Janusz Jaszczyński, Stefan Enroth, Jarosław Baran, Martin Ingelsson, John Perry, Janusz Ryś, Lars A. Forsberg
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.576615

Integrated Analysis of Distant Metastasis-Associated Genes and Potential Drugs in Colon Adenocarcinoma
Cited by: 6
Author(s): Min Wu, Weiyang Lou, Meng Lou, Peifen Fu, Xiaofang Yu
Software Mentions: 4
Published: almost 6 years ago

10.3390/nu12123858

Effects of Daily Raspberry Consumption on Immune-Metabolic Health in Subjects at Risk of Metabolic Syndrome: A Randomized Controlled Trial
Cited by: 18
Author(s): Maximilien Franck, Juan de Toro‐Martín, Véronique Garneau, Valérie Guay, Michèle Kearney, Geneviève Pilon, Denis Roy, Patrick Couture, Charles Couillard, André Marette, Marie‐Claude Vohl
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2019.00149

The Neuronal Overexpression of Gclc in Drosophila melanogaster Induces Life Extension With Longevity-Associated Transcriptomic Changes in the Thorax
Cited by: 8
Author(s): Alexey Moskalev, Zulfiya G. Guvatova, Mikhail Shaposhnikov, Ekaterina Lashmanova, Ekaterina Proshkina, Liubov Koval, Alex Zhavoronkov, George S. Krasnov, Anna V. Kudryavtseva
Software Mentions: 4
Published: over 7 years ago

10.7150/ijms.51297

Heat shock factor 5 correlated with immune infiltration serves as a prognostic biomarker in lung adenocarcinoma
Cited by: 5
Author(s): Aizemaiti Rusidanmu, Zhigang Wu, Jie Tang, Haimeng Yan, Xiaoshu Lv
Software Mentions: 4
Published: over 5 years ago

10.1038/s41421-018-0030-5

Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation
Cited by: 64
Author(s): Yuli Li, Ruijia Wang, Xiaogang Xun, Jing Wang, Lisui Bao, Ramesha Thimmappa, Jun Ding, Jingwei Jiang, Liheng Zhang, Tianqi Li, Jia Lv, Chuang Mu, Xiaoli Hu, Lingling Zhang, Jing Liu, Yuqiang Li, Lijie Yao, Wenqian Jiao, Yangfan Wang, Shanshan Lian, Zelong Zhao, Yaoyao Zhan, Xiaoting Huang, Huan Liao, Wang Jia, Hongzhen Sun, Xue Mi, Yu Xia, Qiang Xing, Wei Lü, Anne Osbourn, Zunchun Zhou, Yaqing Chang, Zhenmin Bao, Shi Wang
Software Mentions: 4
Published: about 8 years ago

10.3389/fonc.2020.00681

Identification of Hub Genes Associated With Development of Head and Neck Squamous Cell Carcinoma by Integrated Bioinformatics Analysis
Cited by: 50
Author(s): Chia‐Ying Li, Jia-Hua Cai, Jeffrey J. P. Tsai, Charles C.N. Wang
Software Mentions: 4
Published: about 6 years ago

10.3389/fgene.2014.00035

The analytical landscape of static and temporal dynamics in transcriptome data
Cited by: 26
Author(s): Sangwon Oh, Seongho Song, Nupur Dasgupta, Gregory A. Grabowski
Software Mentions: 4
Published: over 12 years ago

10.1186/s12870-017-1108-1

Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription
Cited by: 17
Author(s): Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino, Serena Varotto
Software Mentions: 4
Published: almost 9 years ago

10.3389/fgene.2020.00478

Bioinformatics Analysis of Prognostic miRNA Signature and Potential Critical Genes in Colon Cancer
Cited by: 25
Author(s): Weigang Chen, Chang Gao, Yong Liu, Ying Wen, Xiaoling Hong, Zunnan Huang
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2019.01269

An Integrated Three-Long Non-coding RNA Signature Predicts Prognosis in Colorectal Cancer Patients
Cited by: 27
Author(s): Yuhang Liu, Bingxin Liu, Guoying Jin, Jia Zhang, Xue Wang, Yuyang Feng, Zehua Bian, Bojian Fei, Yuan Yin, Zhaohui Huang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0157022

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data
Cited by: 660
Author(s): Hugo Varet, Loraine Brillet-Guéguen, Jean‐Yves Coppée, Marie‐Agnès Dillies
Software Mentions: 4
Published: about 10 years ago

10.1186/s12870-018-1293-6

Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch)
Cited by: 20
Author(s): Marco Cirilli, D. Giovannini, Angelo Ciacciulli, Remo Chiozzotto, Stefano Gattolin, Laura Rossini, A. Liverani, D. Bassi
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0164766

RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process
Cited by: 1
Author(s): Thanh Nguyen, Asim Bhatti, Samuel Yang, Saeid Nahavandi
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0164461

Responses of Bovine Innate Immunity to Mycobacterium avium subsp. paratuberculosis Infection Revealed by Changes in Gene Expression and Levels of MicroRNA
Cited by: 40
Author(s): M. Malvisi, Fiorentina Palazzo, Nicola Morandi, Barbara Lazzari, J. L. Williams, G. Pagnacco, Giulietta Minozzi
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0190456

Mitochondrial DNA depletion by ethidium bromide decreases neuronal mitochondrial creatine kinase: Implications for striatal energy metabolism
Cited by: 18
Author(s): Emily B. Warren, Aidan Aicher, Joshua P. Fessel, Christine Konradi
Software Mentions: 4
Published: over 8 years ago

10.3389/fgene.2021.670405

Construction of a Nine-MicroRNA-Based Signature to Predict the Overall Survival of Esophageal Cancer Patients
Cited by: 2
Author(s): Xiaobin Zhang, Yi He, Haiyong Gu, Zhichao Liu, Bin Li, Yang Yang, Jie Hao, Hua Ren
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2016.00225

Extending the R Library PROPER to Enable Power Calculations for Isoform-Level Analysis with EBSeq
Cited by: 2
Author(s): Amadou Thierno Gaye
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0115964

A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments
Cited by: 12
Author(s): Asta Laiho, Laura L. Elo
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0188264

Wnt co-receptors Lrp5 and Lrp6 differentially mediate Wnt3a signaling in osteoblasts
Cited by: 25
Author(s): Aimy Sebastian, Nicholas R. Hum, Deepa K. Murugesh, Sarah Hatsell, Aris N. Economides, Gabriela G. Loots
Software Mentions: 4
Published: over 8 years ago

10.3389/fonc.2020.00615

Long Non-coding RNA LINC02195 as a Regulator of MHC I Molecules and Favorable Prognostic Marker for Head and Neck Squamous Cell Carcinoma
Cited by: 29
Author(s): Hao Li, Hong‐Gang Xiong, Yao Xiao, Qi‐Chao Yang, Shao‐Chen Yang, Hongchao Tang, Wenfeng Zhang, Zhi‐Jun Sun
Software Mentions: 4
Published: over 6 years ago

10.1186/s40303-016-0017-9

αT-catenin in restricted brain cell types and its potential connection to autism
Cited by: 20
Author(s): Stephen Sai Folmsbee, Douglas R. Wilcox, Koen Tyberghein, Pieter De Bleser, Warren G. Tourtellotte, Jolanda van Hengel, Frans van Roy, Cara J. Gottardi
Software Mentions: 4
Published: about 10 years ago

10.3389/fgene.2020.599292

Hybrid Incompatibilities and Transgressive Gene Expression Between Two Closely Related Subspecies of Drosophila
Cited by: 10
Author(s): Alwyn C. Go, Alberto Civetta
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2014.00312

Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension
Cited by: 33
Author(s): Gang Wang, Ence Yang, Kerri J. Smith, Yong Zeng, Guoli Ji, Richard E. Connon, Nann A. Fangue, James J. Cai
Software Mentions: 4
Published: almost 12 years ago

10.3389/fgene.2018.00321

DECtp: Calling Differential Gene Expression Between Cancer and Normal Samples by Integrating Tumor Purity Information
Cited by: 7
Author(s): Weiwei Zhang, Hang Long, Binsheng He, Jialiang Yang
Software Mentions: 4
Published: almost 8 years ago

10.3389/fgene.2017.00052

Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs
Cited by: 25
Author(s): Andrew D. L. Nelson, Upendra Kumar Devisetty, Kyle Palos, Asher Haug-Baltzell, Eric Lyons, Mark A. Beilstein
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0166862

Drosophila DDX3/Belle Exerts Its Function Outside of the Wnt/Wingless Signaling Pathway
Cited by: 1
Author(s): Fabian H. Jenny, Konrad Basler
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0114461

Inference of the Oxidative Stress Network in Anopheles stephensi upon Plasmodium Infection
Cited by: 10
Author(s): Jatin Shrinet, Umesh K. Nandal, T. Adak, Raj K. Bhatnagar, Sujatha Sunil
Software Mentions: 4
Published: over 11 years ago

10.3389/fgene.2020.563954

Identification of Critical Genes and Proteins for Stent Restenosis Induced by Esophageal Benign Hyperplasia in Esophageal Cancer
Cited by: 4
Author(s): Li Weng, Shanshan Shen, Shaoqiu Wu, Xiaoxing Yin, Bingyan Liu, Ming Shang, Xiaoping Zou, Aiwu Mao
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0166944

Transcriptomic Analysis Shows Decreased Cortical Expression of NR4A1, NR4A2 and RXRB in Schizophrenia and Provides Evidence for Nuclear Receptor Dysregulation
Cited by: 23
Author(s): Susan M. Corley, Shan-Yuan Tsai, Marc R. Wilkins, Cynthia Shannon Weickert
Software Mentions: 4
Published: over 9 years ago

10.3389/fgene.2019.01081

Characterization of Hepatocellular Carcinoma Cell Lines Using a Fractionation-Then-Sequencing Approach Reveals Nuclear-Enriched HCC-Associated lncRNAs
Cited by: 12
Author(s): Elaine Chow, Jizhou Zhang, Hao Qin, Ting‐Fung Chan
Software Mentions: 4
Published: almost 7 years ago

10.3389/fgene.2020.559074

Transcriptomic Changes in Young Japanese Males After Exposure to Acute Hypobaric Hypoxia
Cited by: 8
Author(s): Yoshiki Yasukochi, Sora Shin, Hisao Wakabayashi, Takafumi Maeda
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0225382

Biomarker discovery in inflammatory bowel diseases using network-based feature selection
Cited by: 17
Author(s): Mostafa M. Abbas, John Matta, Thanh Le, Halima Bensmail, Tayo Obafemi-Ajayi, Vasant Honavar, Yasser EL-Manzalawy
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0125224

An Iterative Leave-One-Out Approach to Outlier Detection in RNA-Seq Data
Cited by: 31
Author(s): Nysia I. George, John F. Bowyer, Nathaniel M. Crabtree, Ching‐Wei Chang
Software Mentions: 4
Published: about 11 years ago

10.1038/s41598-020-78364-5

Hdac3 deletion in myeloid progenitor cells enhances bone healing in females and limits osteoclast fusion via Pmepa1
Cited by: 7
Author(s): David H. H. Molstad, Elizabeth L. Zars, Andrew Norton, Kim C. Mansky, Jennifer J. Westendorf, Elizabeth W. Bradley
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-79704-1

Data-driven detection of subtype-specific differentially expressed genes
Cited by: 9
Author(s): Lulu Chen, Yingzhou Lu, Chiung Ting Wu, Robert Clarke, Guoqiang Yu, Jennifer E. Van Eyk, David M. Herrington, Yue Wang
Software Mentions: 4
Published: over 5 years ago

10.1099/mgen.0.000319

Landscape of gene expression variation of natural isolates of Cryptococcus neoformans in response to biologically relevant stresses
Cited by: 22
Author(s): Yu Chen, Chen Yuan, Christopher A. Desjardins, Jennifer L. Tenor, Dena L. Toffaletti, Charles Giamberardino, Anastasia P. Litvintseva, John R. Perfect, Christina A. Cuomo
Software Mentions: 4
Published: over 6 years ago

10.3390/metabo10120513

Single-Cell Transcriptional Profiling of Mouse Islets Following Short-Term Obesogenic Dietary Intervention
Cited by: 12
Author(s): Annie R. Piñeros, Hongyu Gao, Wenting Wu, Yunlong Liu, Sarah A. Tersey, Raghavendra G. Mirmira
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0123569

XomAnnotate: Analysis of Heterogeneous and Complex Exome- A Step towards Translational Medicine
Cited by: 5
Author(s): Asoke K. Talukder, Shashidhar Ravishankar, Krittika Sasmal, Santhosh Gandham, Jyothsna Prabhukumar, Prahalad Achutharao, Debmalya Barh, Francesco Blasi
Software Mentions: 4
Published: over 11 years ago

10.1038/s41598-020-74128-3

Magnetic separation of peripheral nerve-resident cells underscores key molecular features of human Schwann cells and fibroblasts: an immunochemical and transcriptomics approach
Cited by: 18
Author(s): Kangqiang Peng, David W. Sant, Natalia Denise Andersen, Risset Silvera, Vladimir Camarena, Gonzalo Piñero, Regina M. Graham, Aisha Khan, Xiao Ming Xu, Gaofeng Wang, Paula V. Monje
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-75060-2

Differential immune gene expression associated with contemporary range expansion in two invasive rodents in Senegal
Cited by: 1
Author(s): Nathalie Charbonnel, Maxime Galan, Caroline Tatard, Anne Loiseau, Christophe Diagne, Ambroise Dalecky, Hugues Parrinello, Stéphanie Rialle, Dany Séverac, Carine Brouat
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2020.00650

Genome Regulation and Gene Interaction Networks Inferred From Muscle Transcriptome Underlying Feed Efficiency in Pigs
Cited by: 9
Author(s): Victor Adriano Okstoft Carmelo, Haja N. Kadarmideen
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-80682-7

TIM29 is required for enhanced stem cell activity during regeneration in the flatworm Macrostomum lignano
Cited by: 2
Author(s): Stijn Mouton, Kirill Ustyantsev, Frank W. Beltman, Lisa Glazenburg, Eugène Berezikov
Software Mentions: 4
Published: over 5 years ago

10.3390/metabo11050329

Iron-Bound Lipocalin-2 Protects Renal Cell Carcinoma from Ferroptosis
Cited by: 19
Author(s): Julia K. Meier, Matthias Schnetz, Susanne Beck, Tobias Schmid, Monica Dominguez, Sanela Kalinovic, Andreas Daiber, Bernhard Brüne, Michaela Jung
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-81689-4

Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression
Cited by: 19
Author(s): Hollis Wright, Carlos F. Aylwin, Carlos A. Toro, Sergio R. Ojeda, Alejandro Lomniczi
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0230566

Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease
Cited by: 35
Author(s): Elena Buglo, Evan Sarmiento, Nicole Belliard Martuscelli, David W. Sant, Matt C. Danzi, A. Jeanine Abrams, Julia E. Dallman, Stephan Züchner
Software Mentions: 4
Published: over 6 years ago

10.1186/s12866-020-01979-1

Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog
Cited by: 14
Author(s): Randall R. Jiménez, Gilbert Alvarado, José Luís Sandoval, Simone Sommer
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40168-015-0136-z

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries
Cited by: 43
Author(s): Joel D. Rudney, Pratik Jagtap, Cavan Reilly, Ruoqiong Chen, Todd W. Markowski, LeeAnn Higgins, James E. Johnson, Timothy J. Griffin
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-020-72291-1

SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng
Cited by: 9
Author(s): Dan Zhang, Wei Li, Zhongjian Chen, Fang Wei, Yunlong Liu, Li‐Zhi Gao
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijms21061910

NR2F2 Orphan Nuclear Receptor is Involved in Estrogen Receptor Alpha-Mediated Transcriptional Regulation in Luminal A Breast Cancer Cells
Cited by: 8
Author(s): Edina Erdős, Bálint László Bálint
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-71889-9

Gene expression is stable in a complete CIB1 knockout keratinocyte model
Cited by: 2
Author(s): Elias Imahorn, Magomet Aushev, Stefan Herms, Per Hoffmann, Sven Cichon, Julia Reichelt, Peter Itin, Bettina Burger
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40168-017-0356-5

Indoor microbiota in severely moisture damaged homes and the impact of interventions
Cited by: 38
Author(s): Balamuralikrishna Jayaprakash, Rachel I. Adams, Pirkka V. Kirjavainen, Anne M. Karvonen, Asko Vepsäläinen, Maria Valkonen, Kati Järvi, Michael Sulyok, Juha Pekkanen, Anne Hyvärinen, Martin Täubel
Software Mentions: 4
Published: almost 9 years ago

10.3389/fgene.2021.662468

Hypoxia-Induced miR-148a Downregulation Contributes to Poor Survival in Colorectal Cancer
Cited by: 15
Author(s): Stepan Nersisyan, A. V. Galatenko, Milena Chekova, Alexander G. Tonevitsky
Software Mentions: 4
Published: about 5 years ago

10.1038/s41396-019-0508-7

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)
Cited by: 53
Author(s): Adrien Assié, Nikolaus Leisch, Dimitri V. Meier, Harald R. Gruber‐Vodicka, Halina E. Tegetmeyer, Anke Meyerdierks, Manuel Kleiner, Tjorven Hinzke, Samantha B. Joye, Matthew Saxton, Nicole Dubilier, Jillian M. Petersen
Software Mentions: 4
Published: almost 7 years ago

10.3389/fgene.2015.00331

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line
Cited by: 12
Author(s): Marina Lizio, Yuri Ishizu, Masayoshi Itoh, Timo Lassmann, Akira Hasegawa, Atsutaka Kubosaki, Jessica Severin, Hideya Kawaji, Yukio Nakamura, Harukazu Suzuki, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41396-017-0043-3

Energy limitation of cyanophage development: implications for marine carbon cycling
Cited by: 54
Author(s): Richard John Puxty, David J. Evans, Andrew Millard, David J. Scanlan
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-020-68373-9

Increased predominance of the matured ventricular subtype in embryonic stem cell-derived cardiomyocytes in vivo
Cited by: 22
Author(s): Hajime Ichimura, Shin Kadota, Toshihide Kashihara, Mitsuhiko Yamada, Kyoko Ito, Hideki Kobayashi, Yuki Tanaka, Naoko Shiba, Shinichiro Chuma, Shugo Tohyama, Takashi Seto, Kenji Okada, Koichiro Kuwahara, Yuji Shiba
Software Mentions: 4
Published: about 6 years ago

10.1038/s41396-020-0729-9

Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens
Cited by: 35
Author(s): Pilar Vesga, Pascale Flury, Jordan Vacheron, Christoph Keel, Daniel Croll, M. Maurhofer
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-67432-5

Differential expression of polyamine biosynthetic pathways in skin lesions and in plasma reveals distinct profiles in diffuse cutaneous leishmaniasis
Cited by: 7
Author(s): Hayna Malta‐Santos, Jaqueline França‐Costa, Amanda Ferreira Macedo, Artur T. L. Queiroz, Kiyoshi F. Fukutani, Sandra Márcia Muxel, Ricardo Khouri, Johan Van Weyenbergh, Viviane Boaventura, Aldina Barral, Jackson Maurício Lopes Costa, Eny Iochevet Segal Floh, Bruno B. Andrade, Lucile Maria Floeter‐Winter, Valéria M. Borges
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms21218333

Transcriptional Effects of Psychoactive Drugs on Genes Involved in Neurogenesis
Cited by: 7
Author(s): Chiara C. Bortolasci, Briana Spolding, Srisaiyini Kidnapillai, Timothy Connor, Trang T. T. Truong, Zoe Liu, Bruna Panizzutti, Mark F. Richardson, Laura J. Gray, Michael Berk, Olivia Dean, Ken Walder
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-66309-x

Comparative targeting analysis of KLF1, BCL11A, and HBG1/2 in CD34+ HSPCs by CRISPR/Cas9 for the induction of fetal hemoglobin
Cited by: 35
Author(s): Andrés Lamsfus‐Calle, Alberto Daniel‐Moreno, Justin S. Antony, Thomas Epting, Lukas Heumos, Praveen Baskaran, Jakob Admard, Nicolas Casadei, Ngadhnjim Latifi, Darina M. Siegmund, Michael Kormann, Rupert Handgretinger, Markus Mezger
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms21082800

Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides)
Cited by: 13
Author(s): Xi Wu, Yang Yang, Chaoyue Zhong, Yin Guo, Tengyu Wei, Shuisheng Li, Haoran Lin, Xiaochun Liu
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-66556-y

WNT and inflammatory signaling distinguish human Fallopian tube epithelial cell populations
Cited by: 9
Author(s): Ian M. Rose, Mallikarjun Bidarimath, Alex Webster, Andrew K. Godwin, Andrea Flesken‐Nikitin, Alexander Yu. Nikitin
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-64514-2

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype
Cited by: 12
Author(s): Sharon A. McGrath‐Morrow, Roland Ndeh, Kathryn A. Helmin, Basil Khuder, Cynthia Rothblum-Oviatt, Joseph M. Collaco, Jonathan H. Wright, Paul A. Reyfman, Howard M. Lederman, Benjamin D. Singer
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-61177-x

RNA-seq analysis reveals TRPC genes to impact an unexpected number of metabolic and regulatory pathways
Cited by: 10
Author(s): Karina Formoso, Sebastián Susperreguy, Marc Freichel, Lutz Birnbaumer
Software Mentions: 4
Published: over 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568