bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0214833

Disparate effects of antibiotic-induced microbiome change and enhanced fitness in Daphnia magna
Cited by: 27
Author(s): Asa Motiei, Björn Brindefalk, Martin Ogonowski, Rehab El-Shehawy, Paulina Pastuszek, Karin Ek, Birgitta Liewenborg, Klas I. Udekwu, Elena Gorokhova
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12870-017-1043-1

The common transcriptional subnetworks of the grape berry skin in the late stages of ripening
Cited by: 38
Author(s): Ryan Ghan, Juli Petereit, Richard L. Tillett, Karen Schlauch, David Toubiana, Aaron Fait, Grant R. Cramer
Software Mentions: 5
Published: over 7 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 3 years ago

10.1155/2021/9998697

Comprehensive Analysis of the Systemic Transcriptomic Alternations and Inflammatory Response during the Occurrence and Progress of COVID-19
Cited by: 12
Author(s): Shaocong Mo, Leijie Dai, Yulin Wang, Biao Song, Zongcheng Yang, Wenchao Gu
Software Mentions: 5
Published: over 3 years ago

10.1093/femsyr/foab011

Transcriptomic response of Saccharomyces cerevisiae to octanoic acid production
Cited by: 2
Author(s): Leonie Baumann, Tyler W. Doughty, Verena Siewers, Jens Nielsen, Eckhard Boles, Mislav Oreb
Software Mentions: 5
Published: almost 4 years ago

10.3390/genes11050499

Unmasking Intra-Tumoral Heterogeneity and Clonal Evolution in NF1-MPNST
Cited by: 2
Author(s): Chang In Moon, William Tompkins, Yuxi Wang, Abigail Godec, Xiaochun Zhang, Patrik Pipkorn, Christopher A. Miller, Carina Dehner, Sonika Dahiya, Angela C. Hirbe
Software Mentions: 5
Published: over 4 years ago

10.3390/nu8100660

Effect of Bifidobacterium breve on the Intestinal Microbiota of Coeliac Children on a Gluten Free Diet: A Pilot Study
Cited by: 92
Author(s): Andrea Quagliariello, Irene Aloisio, Nicole Bozzi Cionci, Donata Luiselli, Giuseppe D’Auria, Llúcia Martínez-Priego, David Pérez-Villarroya, Tomaž Langerholc, Maša Primec, Dušanka Mičetić-Turk, Diana Di Gioia
Software Mentions: 5
Published: about 8 years ago

10.1186/s12866-020-01938-w

A comprehensive analysis of the microbiota composition and gene expression in colorectal cancer
Cited by: 15
Author(s): Qian Zhang, Huan Zhao, Dedong Wu, D Y Cao, Wei Ma
Software Mentions: 5
Published: about 4 years ago

10.3390/genes11050504

Pitfalls in Single Clone CRISPR-Cas9 Mutagenesis to Fine-Map Regulatory Intervals
Cited by: 5
Author(s): Ruoyu Tian, Yidan Pan, Thomas H A Etheridge, Harshavardhan Deshmukh, Dalia Gulick, Greg Gibson, Gang Bao, Ciaran M. Lee
Software Mentions: 5
Published: over 4 years ago

10.1186/s13041-021-00835-1

Altered hippocampal transcriptome dynamics following sleep deprivation
Cited by: 14
Author(s): Marie E. Gaine, Ethan Bahl, Snehajyoti Chatterjee, Jacob J. Michaelson, Ted Abel, Lisa C. Lyons
Software Mentions: 5
Published: over 3 years ago

10.1093/jxb/eraa124

Transcriptomics in Erigeron canadensis reveals rapid photosynthetic and hormonal responses to auxin herbicide application
Cited by: 19
Author(s): Cara L. McCauley, Scott A. M. McAdam, Ketaki P. Bhide, Jyothi Thimmapuram, Jo Ann Banks, Bryan G. Young
Software Mentions: 5
Published: almost 5 years ago

10.3389/fimmu.2018.02406

Molecular Signature of Aluminum Hydroxide Adjuvant in Ovine PBMCs by Integrated mRNA and microRNA Transcriptome Sequencing
Cited by: 15
Author(s): Endika Varela-Martínez, Naiara Abendaño, Javier Asín, Maialen Sistiaga-Poveda, Marta Pérez, Ramsés Reina, D. de Andrés, Lluís Luján, Begoña M. Jugo
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0153925

Molecular Characterization and Global Expression Analysis of Lectin Receptor Kinases in Bread Wheat (Triticum aestivum)
Cited by: 66
Author(s): . Shumayla, Shailesh Sharma, Ajay Kumar Pandey, Kashmir Singh, Santosh Kumar Upadhyay
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0123658

A Powerful Statistical Approach for Large-Scale Differential Transcription Analysis
Cited by: 4
Author(s): Ying Tan, Anita M. Chandler, Arindam Chaudhury, Joel R. Neilson
Software Mentions: 5
Published: over 9 years ago

10.1098/rsos.200792

Tissue-specific developmental regulation and isoform usage underlie the role ofdoublesexin sex differentiation and mimicry inPapilioswallowtails
Cited by: 13
Author(s): Riddhi Deshmukh, Dhanashree Lakhe, Krushnamegh Kunte
Software Mentions: 5
Published: over 4 years ago

10.1101/2020.04.24.059527

Consensus transcriptional regulatory networks of coronavirus-infected human cells
Cited by: 1
Author(s): Scott A. Ochsner, Rudolf T. Pillich, Neil J. McKenna
Software Mentions: 5
Published: over 4 years ago

10.1073/pnas.2005330117

Nuclear receptor REVERBα is a state-dependent regulator of liver energy metabolism
Cited by: 31
Author(s): Louise Hunter, Charlotte E Pelekanou, Antony Adamson, Polly Downton, Nichola J Barron, Thomas Cornfield, Toryn Poolman, Neil Humphreys, Peter Cunningham, Leanne Hodson, A. S. I. Loudon, Mudassar Iqbal, David A. Bechtold, David Ray
Software Mentions: 5
Published: about 4 years ago

10.1073/pnas.1822046116

Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination
Cited by: 47
Author(s): Diógenes Saulo de Lima, Lucas Esteves Cardozo, Vinicius Maracaja‐Coutinho, Andreas Suhrbier, Karim Mane, David Jeffries, Eduardo Lani Volpe da Silveira, Paulo Amaral, Rino Rappuoli, Thushan I. de Silva, Helder I. Nakaya
Software Mentions: 5
Published: over 5 years ago

10.1186/s13229-020-00359-w

IGF-1 treatment causes unique transcriptional response in neurons from individuals with idiopathic autism
Cited by: 17
Author(s): Sara B. Linker, Ana Paula Mendes, Maria C. Marchetto
Software Mentions: 5
Published: over 4 years ago

10.1186/s13100-018-0138-z

Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis
Cited by: 33
Author(s): Gavin Pereira, Laura Sánchez, Paul Schaughency, Alejandro Rubio-Roldán, Justin Choi, Evarist Planet, Ranjan Batra, Priscilla Turelli, Didier Trono, Lyle W. Ostrow, John Ravits, Haig H. Kazazian, Sarah J. Wheelan, Sara R. Heras, Jens Mayer, José L. García‐Pérez, John Goodier
Software Mentions: 5
Published: about 6 years ago

10.1186/s13100-021-00236-0

Transcriptional activity of transposable elements along an elevational gradient in Arabidopsis arenosa
Cited by: 26
Author(s): Guillaume Wos, Rimjhim Roy Choudhury, Filip Kolář, Christian Parisod
Software Mentions: 5
Published: almost 4 years ago

10.1128/mBio.01193-19

Determination of an Interaction Network between an Extracellular Bacterial Pathogen and the Human Host
Cited by: 23
Author(s): Brad Griesenauer, Tuan M. Tran, Kate R. Fortney, Diane M. Janowicz, Paula A. Johnson, Hongyu Gao, Stephen Barnes, Landon Wilson, Yunlong Liu, Stanley M. Spinola
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1009213

Gene regulatory effects of a large chromosomal inversion in highland maize
Cited by: 38
Author(s): Taylor M. Crow, James Ta, Saghi Nojoomi, M. Rocío Aguilar-Rangel, Jorge Vladimir Torres Rodríguez, David M. Gates, Rubén Rellán‐Álvarez, Ruairidh J. H. Sawers, Daniel E. Runcie
Software Mentions: 5
Published: about 4 years ago

10.1186/s12920-020-00838-2

Genome-wide transcriptome study using deep RNA sequencing for myocardial infarction and coronary artery calcification
Cited by: 5
Author(s): Xiaoling Zhang, Jeroen G.J. van Rooij, Y. Wakabayashi, Shih‐Jen Hwang, Yanqin Yang, Mohsen Ghanbari, Daniël Bos, Daniel Levy, Andrew D. Johnson, Joyce B. J. van Meurs, Maryam Kavousi, Jun Zhu, Christopher J. O’Donnell
Software Mentions: 5
Published: almost 4 years ago

10.1128/mBio.03042-19

Quantitative Framework for Model Evaluation in Microbiology Research Using Pseudomonas aeruginosa and Cystic Fibrosis Infection as a Test Case
Cited by: 83
Author(s): Daniel M. Cornforth, Frances L. Diggle, Jeffrey A. Melvin, Jennifer M. Bomberger, Marvin Whiteley
Software Mentions: 5
Published: almost 5 years ago

10.3390/genes10070552

Transcriptome Analysis of Landrace Pig Subcutaneous Preadipocytes during Adipogenic Differentiation
Cited by: 14
Author(s): Xitong Zhao, Shaokang Chen, Zhen Tan, Yuan Wang, Fengxia Zhang, Ting Yang, Yibing Liu, Ai Hong, Kai Xing, Chuduan Wang
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-36471-4

Astrocytoma progression scoring system based on the WHO 2016 criteria
Cited by: 12
Author(s): Zhen-Hang Li, Yanlei Guan, Qiang Liu, Yao Wang, Run Cui, Yunjie Wang
Software Mentions: 5
Published: almost 6 years ago

10.1002/evl3.166

Artificial selection reveals the role of transcriptional constraints in the maintenance of life history variation
Cited by: 6
Author(s): Joel L. Pick, Masaomi Hatakeyama, Kate E. Ihle, Julien Gasparini, Claudy Haussy, Satoshi Ishishita, Yoichi Matsuda, Takashi Yoshimura, Masahiro M. Kanaoka, Rie Shimizu‐Inatsugi, Kentaro Shimizu, Barbara Tschirren
Software Mentions: 5
Published: over 4 years ago

10.1128/mSystems.00053-18

Balances: a New Perspective for Microbiome Analysis
Cited by: 173
Author(s): Javier Rivera Pinto, J. J. Egozcue, Vera Pawlowsky‐Glahn, Roger Paredes, Marc Noguera‐Julian, M. Luz Calle
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0236586

Transcriptome analysis of contrasting resistance to herbivory by Empoasca fabae in two shrub willow species and their hybrid progeny
Cited by: 5
Author(s): Wanyan Wang, Craig H. Carlson, Lawrence B. Smart, John E. Carlson
Software Mentions: 5
Published: over 4 years ago

10.1111/eva.12278

Patterns of differential gene expression in adult rotation‐resistant and wild‐type western corn rootworm digestive tracts
Cited by: 10
Author(s): Chia‐Ching Chu, Jorge A. Zavala, Joseph L. Spencer, M. Curzi, Christopher J. Fields, Jenny Drnevich, Blair D. Siegfried, Manfredo J. Seufferheld
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-018-29993-4

Analysis of diet-induced differential methylation, expression, and interactions of lncRNA and protein-coding genes in mouse liver
Cited by: 10
Author(s): José P. Silva, Derek Van Booven
Software Mentions: 5
Published: over 6 years ago

10.1186/s12860-020-00295-w

Molecular docking and machine learning analysis of Abemaciclib in colon cancer
Cited by: 14
Author(s): José Liñares-Blanco, Cristian R. Munteanu, Alejandro Pazos, Carlos Fernández-Lozano
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1007981

Disruption of the Caenorhabditis elegans Integrator complex triggers a non-conventional transcriptional mechanism beyond snRNA genes
Cited by: 29
Author(s): Eva Gómez-Orte, Beatriz Sáenz-Narciso, Angelina Zheleva, Begoña Ezcurra, María de Toro, Rosa López, Irene Gastaca, Hilde Nilsen, María P. Sacristán, Ralf Schnabel, Juan Cabello
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13041-020-00603-7

Ocular hypertension suppresses homeostatic gene expression in optic nerve head microglia of DBA/2 J mice
Cited by: 28
Author(s): James R. Tribble, Jeffrey M. Harder, Pete A. Williams, Simon W. M. John
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0226575

Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis
Cited by: 17
Author(s): Toni Berger, Magnus Dehli Vigeland, Hanne Sagsveen Hjorthaug, Lars Etholm, Cecilie G. Nome, Erik Taubøll, Kjell Heuser, Kaja Kristine Selmer
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12920-021-00905-2

Bioinformatic analysis reveals an exosomal miRNA-mRNA network in colorectal cancer
Cited by: 17
Author(s): Jun Ma, Peilong Wang, Lei Huang, Jianxia Qiao, Jianhong Li
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12934-015-0226-4

An analysis of the changes in soluble hydrogenase and global gene expression in Cupriavidus necator (Ralstonia eutropha) H16 grown in heterotrophic diauxic batch culture
Cited by: 17
Author(s): Bat-Erdene Jugder, Zhiliang Chen, Darren Tan Tek Ping, Hélène Lebhar, Jeffrey Welch, Christopher P. Marquis
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pgen.1007431

Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development
Cited by: 18
Author(s): Timothy M. Johanson, Hannah D. Coughlan, Aaron T. L. Lun, Naiara G. Bediaga, Gaetano Naselli, Alexandra L. Garnham, Leonard C. Harrison, Rhys S. Allan
Software Mentions: 5
Published: over 6 years ago

10.1155/2021/6642939

Identification of a Potential PPAR-Related Multigene Signature Predicting Prognosis of Patients with Hepatocellular Carcinoma
Cited by: 7
Author(s): Wenfang Xu, Zhe Chen, Gang Liu, Yong Dai, Xuanfu Xu, Duan Ma, Lei Liu
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-018-36768-4

Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets
Cited by: 10
Author(s): Stefan Wyder, Michael T. Raissig, Ueli Grossniklaus
Software Mentions: 5
Published: almost 6 years ago

10.17305/bjbms.2020.5096

Bionformatics analysis reveals TSPAN1 as a candidate biomarker of progression and prognosis in pancreatic cancer
Cited by: 5
Author(s): Chenhui Ma, Zelong Cui, YiChao Wang, Lei Zhang, Jiaxin Wen, Huaibin Guo, Na Li, Wanxing Zhang
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-020-76991-6

Salivary microbiome composition changes after bariatric surgery
Cited by: 11
Author(s): Mária Džunková, Róbert Lipták, Barbora Vlková, Roman Gardlík, M Cierny, Andrés Moya, Peter Celec
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-015-2135-7

Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish
Cited by: 27
Author(s): Candida Vaz, Choon Wei Wee, Gek Ping Serene Lee, Philip W. Ingham, Vivek Tanavde, Sinnakaruppan Mathavan
Software Mentions: 5
Published: about 9 years ago

10.1038/s41598-020-76769-w

GIANT: galaxy-based tool for interactive analysis of transcriptomic data
Cited by: 8
Author(s): Jimmy Vandel, Céline Gheeraert, Bart Staels, Jérôme Eeckhoute, Philippe Lefèbvre, Julie Dubois-Chevalier
Software Mentions: 5
Published: about 4 years ago

10.3389/fcell.2021.664178

Differential Transcriptomes and Methylomes of Trophoblast Stem Cells From Naturally-Fertilized and Somatic Cell Nuclear-Transferred Embryos
Cited by: 0
Author(s): Jin Sun, Weisheng Zheng, Wenqiang Liu, Xiaochen Kou, Yanhong Zhao, Zehang Liang, Lu Wang, Zihao Zhang, Jing Xiao, Rui Gao, Shaorong Gao, Cizhong Jiang
Software Mentions: 5
Published: over 3 years ago

10.1155/2013/481545

Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies
Cited by: 13
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith
Software Mentions: 5
Published: over 11 years ago

10.18632/oncotarget.25330

Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma
Cited by: 14
Author(s): Michael Hamilton, Thomas Girke, Ernest Martinez
Software Mentions: 5
Published: over 6 years ago

10.1038/srep25668

Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy
Cited by: 76
Author(s): Konrad J. Dębski, Asla Pitkänen, Noora Puhakka, Anna Bot, Ishant Khurana, K N Harikrishnan, Mark Ziemann, Antony Kaspi, Assam El‐Osta, Katarzyna Łukasiuk, Katja Kobow
Software Mentions: 5
Published: over 8 years ago

10.1111/acel.13320

BiT age: A transcriptome‐based aging clock near the theoretical limit of accuracy
Cited by: 45
Author(s): David Meyer, Björn Schumacher
Software Mentions: 5
Published: almost 4 years ago

10.1038/srep29647

Tracking Cancer Genetic Evolution using OncoTrack
Cited by: 4
Author(s): Asoke K. Talukder, Mahima Agarwal, Kenneth H. Buetow, Patrice Denèfle
Software Mentions: 5
Published: over 8 years ago

10.1186/s12859-019-2947-6

Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis
Cited by: 3
Author(s): Mohamed K. Gunady, Stephen M. Mount, Héctor Corrada Bravo
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2020.00639

DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
Cited by: 14
Author(s): Anne M. Hahn, Daniel Pensold, Cathrin Bayer, Jessica Tittelmeier, Lourdes González-Bermúdez, Lisa Marx-Blümel, Jenice Linde, Jonas Groß, Gabriela Salinas-Riester, Thomas Lingner, Julia von Maltzahn, Marc Spehr, Tomas Pieler, Anja Urbach, Geraldine Zimmer-Bensch
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-63275-2

Modulation of stress and immune response by Amblyomin-X results in tumor cell death in a horse melanoma model
Cited by: 9
Author(s): Flávio Lichtenstein, Asif Iqbal, Sonia Elisabete Alves de Lima Will, Rosemary Viola Bösch, Carlos DeOcesano-Pereira, Maurício Barbugiani Goldfeder, Roger Chammas, Carlos Eduardo Madureira Trufen, Kátia L.P. Morais, Jean Gabriel de Souza, Renato José Mendonça Natalino, Inácio L.M. Junqueira-de-Azevedo, Milton Yutaka Nishiyama-Jr, Úrsula Castro de Oliveira, F Alves, Jaqueline Mayara Araujo, Aline Ramos Maia Lobba, Ana Marisa Chudzinski‐Tavassi
Software Mentions: 5
Published: over 4 years ago

10.1186/s13068-021-01975-1

Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172
Cited by: 14
Author(s): Monika Tõlgo, Silvia Hüttner, Peter Rugbjerg, Nguyễn Thanh Thủy, Vu Nguyen Thanh, Johan Larsbrink, Lisbeth Olsson
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-74705-6

Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method
Cited by: 5
Author(s): Marta Lucchetta, Marco Pellegrini
Software Mentions: 5
Published: about 4 years ago

10.3389/fcell.2020.588041

Identification of Differential Gene Groups From Single-Cell Transcriptomes Using Network Entropy
Cited by: 3
Author(s): Yanglan Gan, Shanshan Liang, Qingting Wei, Guobing Zou
Software Mentions: 5
Published: about 4 years ago

10.3389/fonc.2021.691372

Prognostic Signature of Hepatocellular Carcinoma and Analysis of Immune Infiltration Based on m6A-Related lncRNAs
Cited by: 6
Author(s): Ting Guo, Kun He, Yifei Wang, Jingjing Sun, Yong Chen, Zelong Yang
Software Mentions: 5
Published: over 3 years ago

10.1042/BSR20203231

Identification of an autophagy-related gene signature predicting overall survival for hepatocellular carcinoma
Cited by: 5
Author(s): Wenfang Xu, Wenxiu Guo, Ping Lü, Ding Ma, Lei Liu, Fudong Yu
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-020-67690-3

Transcriptomic analysis of the mechanisms of alleviating renal interstitial fibrosis using the traditional Chinese medicine Kangxianling in a rat model
Cited by: 13
Author(s): Yufeng Jiang, Yaohan Zhu, Timing Zhen, Jie Li, Kaichen Xing, Liqun He, Sibo Zhu
Software Mentions: 5
Published: over 4 years ago

10.1111/acel.13280

Modeling the human aging transcriptome across tissues, health status, and sex
Cited by: 23
Author(s): Maxim N. Shokhirev, Adiv A. Johnson
Software Mentions: 5
Published: about 4 years ago

10.1038/srep37393

Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer
Cited by: 84
Author(s): Stephan H. Bernhart, Helene Kretzmer, Lesca M. Holdt, Frank Jühling, Ole Ammerpohl, Anke Bergmann, Bernd H. Northoff, Gero Doose, Reiner Siebert, Peter F. Stadler, Steve Hoffmann
Software Mentions: 5
Published: about 8 years ago

10.3389/fcimb.2016.00136

The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection
Cited by: 22
Author(s): Caroline Poyntner, Barbara Blasi, Elsa Arcalís, Ursula Mirastschijski, Katja Sterflinger, Hakim Tafer
Software Mentions: 5
Published: about 8 years ago

10.3389/fcell.2021.624711

Single-Cell RNA Sequencing With Combined Use of Bulk RNA Sequencing to Reveal Cell Heterogeneity and Molecular Changes at Acute Stage of Ischemic Stroke in Mouse Cortex Penumbra Area
Cited by: 22
Author(s): Kang Guo, Jianing Luo, Dayun Feng, Lin Wu, Xin Wang, Xia Li, Kai Tao, Xun Wu, Wenxing Cui, Yijie He, Bing Wang, Zhenwei Zhao, Zhiguo Zhang
Software Mentions: 5
Published: almost 4 years ago

10.18632/aging.102923

Integrative analysis of DNA methylation and gene expression reveals distinct hepatocellular carcinoma subtypes with therapeutic implications
Cited by: 10
Author(s): Xiaowen Huang, Chen Yang, Jilin Wang, Tiantian Sun, Hua Xiong
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.62850

Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks
Cited by: 24
Author(s): Beryl M. Jones, Vikyath D. Rao, Tim Gernat, Tobias Jagla, Amy Cash Ahmed, Rubin Be, Troy J. Comi, Shounak Bhogale, Syed Sameed Husain, Charles Blatti, Martin Middendorf, Saurabh Sinha, Sriram Chandrasekaran, Gene E. Robinson
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-020-6665-2

The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice
Cited by: 37
Author(s): Lei Xu, Anil Surathu, Isaac Raplee, Ashok Chockalingam, Sharron Stewart, Lacey Walker, Leonard Sacks, Vikram Patel, Zhihua Li, Rodney Rouse
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-68949-5

Capsidiol-related genes are highly expressed in response to Colletotrichum scovillei during Capsicum annuum fruit development stages
Cited by: 10
Author(s): Viviane Yumi Baba, Adrian F. Powell, Suzana Tiemi Ivamoto, Luiz Filipe Protásio Pereira, André Luís Laforga Vanzela, Renata Mussoi Giacomin, Susan R. Strickler, Lukas A. Mueller, Rosana Rodrigues, Leandro Simões Azeredo Gonçalves
Software Mentions: 5
Published: over 4 years ago

10.3390/biom11020291

Determination of Genotoxicity Attributed to Diesel Exhaust Particles in Normal Human Embryonic Lung Cell (WI-38) Line
Cited by: 4
Author(s): Joong Won Lee, Hee Jae Lee, Young Joo Lee, Yong Beom Lim, Woo Jong Sim, Ji Hye Jang, Hye Ryeon Heo, Hyunwoo Lim, Ji Won Jung, Jin Sik Kim
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-019-5887-7

Refinement of breast cancer molecular classification by miRNA expression profiles
Cited by: 59
Author(s): Rolf Søkilde, Helena Persson, Anna Ehinger, Anna Chiara Pirona, Mårten Fernö, Cecilia Hegardt, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Lao H. Saal, Åke Borg, Johan Vallon-Christerson, Carlos Rovira
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-72511-8

Burn resuscitation strategy influences the gut microbiota-liver axis in swine
Cited by: 11
Author(s): Wayne Muraoka, Jose C. Granados, Belinda I. Gómez, Susannah E. Nicholson, Kevin K. Chung, Jeffrey W. Shupp, James A. Bynum, Michael A. Dubick, David M. Burmeister
Software Mentions: 5
Published: about 4 years ago

10.1186/s12859-020-03691-3

Analysis of genomic and transcriptomic variations as prognostic signature for lung adenocarcinoma
Cited by: 31
Author(s): Talip Zengin, Tuğba Önal-Süzek
Software Mentions: 5
Published: over 4 years ago

10.1038/s42003-020-01398-y

Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation
Cited by: 2
Author(s): Michal Schwartz, Avital Sarusi Portugez, Bracha Zukerman Attia, Miriam Tannenbaum, Leslie E. Cohen, Olga Loza, Emily Chase, Yousef Turman, Tommy Kaplan, Zaidoun Salah, Ofir Hakim
Software Mentions: 5
Published: about 4 years ago

10.1038/srep33813

Contrasting diets reveal metabolic plasticity in the tree-killing beetle, Anoplophora glabripennis (Cerambycidae: Lamiinae)
Cited by: 20
Author(s): Charles J. Mason, Erin D. Scully, Scott M. Geib, Kelli Hoover
Software Mentions: 5
Published: about 8 years ago

10.1155/2020/6034670

Bioinformatics Analysis to Screen the Key Prognostic Genes in Tumor Microenvironment of Bladder Cancer
Cited by: 6
Author(s): Zhao Zhang, Dongshan Chen, Zeyan Li, Zhao Liu, Lei Yan, Zhonghua Xu
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-015-2174-0

Extensive variation between tissues in allele specific expression in an outbred mammal
Cited by: 67
Author(s): Amanda J. Chamberlain, Christy J. Vander Jagt, Ben J. Hayes, Majid Khansefid, L. C. Marett, Catriona A. Millen, Thuy Thi Thu Nguyen, Michael E. Goddard
Software Mentions: 5
Published: about 9 years ago

10.1038/srep25948

Integrated metabolomic and transcriptome analyses reveal finishing forage affects metabolic pathways related to beef quality and animal welfare
Cited by: 58
Author(s): José A. Carrillo, Yanghua He, Yaokun Li, Jianan Liu, R.A. Erdman, Tad S. Sonstegard, Jiuzhou Song
Software Mentions: 5
Published: over 8 years ago

10.3389/fcell.2021.684643

Development of an Individualized Ubiquitin Prognostic Signature for Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Yue Wu, Xi Zhang, Wa Xian, Huan Feng, Bintao Hu, Zhiyao Deng, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Jihong Liu, Tao Wang
Software Mentions: 5
Published: over 3 years ago

10.1038/s42003-021-01716-y

Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp
Cited by: 28
Author(s): Jianbo Yuan, Xiaojun Zhang, Min Wang, Yamin Sun, Xianhui Qin, Shihao Li, Yang Yu, Yi Gao, Fei Liu, Jie Kong, Guangyi Fan, Chengsong Zhang, Lu Feng, Jianhai Xiang, Fuhua Li
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12859-016-1248-6

Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering
Cited by: 11
Author(s): Lydia Müller, Daniel Gerighausen, Mariam R. Farman, Dirk Zeckzer
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-020-74748-9

Dynamic changes in the brain protein interaction network correlates with progression of Aβ42 pathology in Drosophila
Cited by: 6
Author(s): Harry M. Scholes, Adam Cryar, Fiona Kerr, David Sutherland, Lee A. Gethings, Johannes P.C. Vissers, Jonathan G. Lees, Christine A. Orengo, Linda Partridge, Konstantinos Thalassinos
Software Mentions: 5
Published: about 4 years ago

10.1002/cti2.1093

Machine learning applied to whole‐blood RNA‐sequencing data uncovers distinct subsets of patients with systemic lupus erythematosus
Cited by: 39
Author(s): William A. Figgett, Katherine Monaghan, Milica Ng, Monther Alhamdoosh, Eugene Maraskovsky, Nicholas J. Wilson, Alberta Hoi, Eric F Morand, Fabienne Mackay
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12859-019-3324-1

Lag penalized weighted correlation for time series clustering
Cited by: 8
Author(s): Thevaa Chandereng, Anthony Gitter
Software Mentions: 5
Published: over 4 years ago

10.1038/sdata.2018.290

Transcriptome profiling of a beach-adapted wild legume for dissecting novel mechanisms of salinity tolerance
Cited by: 5
Author(s): Hengyou Zhang, Christine Zuelsdorf, Darin S. Penneys, Shoujin Fan, Janice Kofsky, Bao‐Hua Song
Software Mentions: 5
Published: about 6 years ago

10.1186/s12863-020-00852-4

Transcriptome analysis identifies genes and co-expression networks underlying heat tolerance in pigs
Cited by: 9
Author(s): Yuqing He, Christian Maltecca, Francesco Tiezzi, Emmanuel Lozada Soto, W. L. Flowers
Software Mentions: 5
Published: over 4 years ago

10.1186/s13148-020-00879-5

G9a regulates tumorigenicity and stemness through genome-wide DNA methylation reprogramming in non-small cell lung cancer
Cited by: 25
Author(s): Rajendra P. Pangeni, Lu Yang, Keqiang Zhang, Jinhui Wang, Wendong Li, Chao Guo, Xinwei Yun, Ting Sun, Jami Wang, Dan J. Raz
Software Mentions: 5
Published: over 4 years ago

10.1186/s12916-020-01806-4

ADAM22/LGI1 complex as a new actionable target for breast cancer brain metastasis
Cited by: 7
Author(s): Sara Charmsaz, Ben Doherty, Sinéad Cocchiglia, Damir Varešlija, Attilio Marino, Nicola Cosgrove, Ricardo Marques, Nolan Priedigkeit, Siobhan Purcell, Fiona T. Bane, Jarlath Bolger, Christopher Byrne, Philip J. O’Halloran, Francesca Brett, Katherine M. Sheehan, Kieran Brennan, Ann M. Hopkins, Stephen Keelan, Petra Jagušt, Stephen F. Madden, Chiara Martinelli, Matteo Battaglini, Steffi Oesterreich, Adrian V. Lee, Gianni Ciofani, Arnold D. Hill, Leonie S. Young
Software Mentions: 5
Published: about 4 years ago

10.1186/s12916-020-01898-y

Development and validation of a novel circular RNA as an independent prognostic factor in acute myeloid leukemia
Cited by: 9
Author(s): Jinghan Wang, Jiajia Pan, Shujuan Huang, Fenglin Li, Jiansong Huang, Xia Li, Qing Ling, Wenle Ye, Yungui Wang, Wenjuan Yu, Jie Jin
Software Mentions: 5
Published: almost 4 years ago

10.1038/sdata.2016.4

DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing
Cited by: 10
Author(s): Anneleen Decock, Maté Ongenaert, Wim Van Criekinge, Franki Speleman, Jo Vandesompele
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2105-15-S9-S6

BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data
Cited by: 10
Author(s): Jin Gu, Wang Xiao, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-021-84667-y

Neuron-specific spinal cord translatomes reveal a neuropeptide code for mouse dorsal horn excitatory neurons
Cited by: 15
Author(s): Rebecca R Das Gupta, Louis Scheurer, Paweł Pelczar, Hendrik Wildner, Hanns Ulrich Zeilhofer
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12967-018-1707-0

Evaluation of the prognostic value of paraoxonase 1 in the recurrence and metastasis of hepatocellular carcinoma and establishment of a liver-specific predictive model of survival
Cited by: 18
Author(s): Zhenzhen Yu, Qifeng Ou, Chongxi Fan, Jiong Bi, Wen Li, Jiachi Ma, Rongchang Wang, Xiaohui Huang
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-019-5838-3

Genome-wide profiling of the alternative splicing provides insights into development in Plutella xylostella
Cited by: 6
Author(s): Qian Zhao, Weimin Zhong, Weiyi He, Yiying Li, Yaqing Li, Tianpu Li, Liette Vasseur, Minsheng You
Software Mentions: 5
Published: over 5 years ago

10.1038/s41438-021-00606-y

Integrative genomics reveals paths to sex dimorphism in Salix purpurea L
Cited by: 8
Author(s): Brennan Hyden, Craig H. Carlson, Fred E. Gouker, Jeremy Schmutz, Kerrie Barry, Anna Lipzen, Aarti Sharma, Laura Sandor, Gerald A. Tuskan, Guanying Feng, Matthew S. Olson, Stephen P. DiFazio, Lawrence B. Smart
Software Mentions: 5
Published: over 3 years ago

10.1038/s41597-020-0352-7

Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L.
Cited by: 69
Author(s): Won-Hee Kang, Young Mi Sim, Namjin Koo, Jae Do Nam, Junesung Lee, Nayoung Kim, Hakgi Jang, Yongmin Kim, Seon-In Yeom
Software Mentions: 5
Published: almost 5 years ago

10.18632/aging.102185

Prognostic value of long non-coding RNA signatures in bladder cancer
Cited by: 30
Author(s): Anbang He, Shiming He, Peng Ding, Yonghao Zhan, Yifan Li, Zhicong Chen, Yanqing Gong, Xuesong Li, Liqun Zhou
Software Mentions: 5
Published: over 5 years ago

10.1177/1759091419843393

Global Brain Transcriptome Analysis of a Tpp1 Neuronal Ceroid Lipofuscinoses Mouse Model
Cited by: 11
Author(s): Miriam S. Domowicz, Wen-Ching Chan, Patricia Claudio-Vázquez, Judith Henry, Christopher B. Ware, Jorge Andrade, Glyn Dawson, Nancy B. Schwartz
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41438-021-00529-8

Chromatin accessibility and translational landscapes of tea plants under chilling stress
Cited by: 21
Author(s): Pengjie Wang, Shan Jin, Xuejin Chen, Lihua Wu, Yuanrun Zheng, Chuan Yue, Yan Guo, Xingtan Zhang, Jing Yang, Naixing Ye
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.51796

A MAC2-positive progenitor-like microglial population is resistant to CSF1R inhibition in adult mouse brain
Cited by: 44
Author(s): Lihong Zhan, Li Fan, Lay Kodama, Peter Sohn, Man Ying Wong, Gergey Alzaem Mousa, Yungui Zhou, Yaqiao Li, Li Gan
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-020-07228-z

Differential gene expression analysis reveals pathways important in early post-traumatic osteoarthritis in an equine model
Cited by: 6
Author(s): Annette M. McCoy, Ann M. Kemper, M. Boyce, M. P. Brown, Troy N. Trumble
Software Mentions: 5
Published: about 4 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568