bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1080/20013078.2018.1461450

ISEV2018 abstract book
Cited by: 157
Author(s): Clotilde Théry, Kenneth W. Witwer
Software Mentions: 4
Published: over 6 years ago

Identification of key genes and miRNAs markers of papillary thyroid cancer
Cited by: 31
Author(s): Jie Qiu, Wenwei Zhang, Chuanshan Zang, Xiaomin Liu, Fuxue Liu, Ruifeng Ge, Yan Sun, Qingsheng Xia
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pcbi.1006760

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data
Cited by: 6
Author(s): Vikash Pandey, Vassily Hatzimanikatis
Software Mentions: 4
Published: over 5 years ago

10.1084/jem.20200137

PDGFA-associated protein 1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification
Cited by: 6
Author(s): Verónica Delgado-Benito, Maria Berruezo-Llacuna, Robert Altwasser, Wiebke Winkler, Devakumar Sundaravinayagam, Sandhya Balasubramanian, Marieta Caganova, Robin Graf, Ali Rahjouei, Marie-Thérèse Henke, Madlen Driesner, Lisa Keller, Alessandro Prigione, Martin Janz, Altuna Akalin, Michela Di Virgilio
Software Mentions: 4
Published: over 4 years ago

10.1186/s13046-020-01752-2

MiRNA-340-5p mediates the functional and infiltrative promotion of tumor-infiltrating CD8+ T lymphocytes in human diffuse large B cell lymphoma
Cited by: 9
Author(s): Yangyang Xu, Zhenchuan Liu, Lixin Lv, Ping Li, Bing Xu, Wenbin Qian, Aibin Liang
Software Mentions: 4
Published: about 4 years ago

10.1186/s13046-020-1541-0

FKBP9 promotes the malignant behavior of glioblastoma cells and confers resistance to endoplasmic reticulum stress inducers
Cited by: 16
Author(s): Huizhe Xu, Peng Liu, Yumei Yan, Kun Fang, Dapeng Liang, Yangcheng Liu, Xiaohong Zhang, Songyan Wu, Jin Ma, Ruoyu Wang, Tao Li, Haozhe Piao, Meng Shao
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12918-016-0344-6

A method for automated pathogenic content estimation with application to rheumatoid arthritis
Cited by: 9
Author(s): Xiaoyuan Zhou, Christine Nardini
Software Mentions: 4
Published: about 8 years ago

10.1186/s12870-016-0926-x

Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seq
Cited by: 9
Author(s): Nikolay A. Shmakov, Gennady V. Vasiliev, Natalya V. Shatskaya, А. В. Дорошков, Е. И. Гордеева, D. A. Afonnikov, Е. К. Хлесткина
Software Mentions: 4
Published: about 8 years ago

10.1186/s13046-019-1254-4

Long noncoding RNA MYOSLID promotes invasion and metastasis by modulating the partial epithelial-mesenchymal transition program in head and neck squamous cell carcinoma
Cited by: 74
Author(s): Hong‐Gang Xiong, Hao Li, Yao Xiao, Qi‐Chao Yang, Leilei Yang, Lei Chen, Lin‐Lin Bu, Wenfeng Zhang, Jiali Zhang, Zhi‐Jun Sun
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22157939

Comparative Transcriptome Analysis of Human Adipose-Derived Stem Cells Undergoing Osteogenesis in 2D and 3D Culture Conditions
Cited by: 5
Author(s): Byung Chul Kim, Kyu Hwan Kwack, Jeewan Chun, Jae Hyung Lee
Software Mentions: 4
Published: over 3 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: about 8 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: about 8 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: almost 7 years ago

10.1186/s12918-018-0582-x

A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test
Cited by: 6
Author(s): Qingyang Zhang
Software Mentions: 4
Published: over 6 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: almost 10 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: about 7 years ago

10.1155/2019/2725192

In Silico Integration Approach Reveals Key MicroRNAs and Their Target Genes in Follicular Thyroid Carcinoma
Cited by: 10
Author(s): Shengqing Hu, Yunfei Liao, Juan Zheng, Luoning Gou, Anita Regmi, Mohammad Ishraq Zafar, Lulu Chen
Software Mentions: 4
Published: over 5 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: over 4 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: almost 7 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: about 5 years ago

10.1523/JNEUROSCI.0860-21.2021

Spinal Cord Injury Induces Permanent Reprogramming of Microglia into a Disease-Associated State Which Contributes to Functional Recovery
Cited by: 21
Author(s): Ramil Hakim, Vasilios Zachariadis, Sreenivasa Raghavan Sankavaram, Jinming Han, Robert A. Harris, Lou Brundin, Martin Enge, Mikael Svensson
Software Mentions: 4
Published: over 3 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: almost 8 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: about 10 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: over 9 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 9 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 4 years ago

10.1371/journal.pone.0238420

Construction and analysis of a competing endogenous RNA network to reveal potential prognostic biomarkers for Oral Floor Squamous Cell Carcinoma
Cited by: 1
Author(s): Wenjing Zhang, Shuai Xu, Laner Shi, Zhangzhi Zhu, Xinying Xie
Software Mentions: 4
Published: over 4 years ago

10.1186/s12870-019-1968-7

Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australe
Cited by: 40
Author(s): Shouli Feng, Min Xu, Fujie Liu, Changjiang Cui, Baoliang Zhou
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0081809

Next Generation Sequencing Analysis of Human Platelet PolyA+ mRNAs and rRNA-Depleted Total RNA
Cited by: 55
Author(s): Antheia Kissopoulou, Jon Jonasson, Tomas Lindahl, Abdimajid Osman
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0091918

RNA-Sequence Analysis of Primary Alveolar Macrophages after In Vitro Infection with Porcine Reproductive and Respiratory Syndrome Virus Strains of Differing Virulence
Cited by: 34
Author(s): Bouabid Badaoui, Teresa Rutigliano, Anna Anselmo, Merijn Vanhee, Hans Nauwynck, Elisabetta Giuffra, Sara Botti
Software Mentions: 4
Published: almost 11 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: almost 4 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: almost 4 years ago

10.1371/journal.pone.0141910

Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be?
Cited by: 25
Author(s): Shanrong Zhao, Li Xi, Baohong Zhang
Software Mentions: 4
Published: about 9 years ago

10.1016/j.isci.2021.102751

The effects of aging on molecular modulators of human embryo implantation
Cited by: 6
Author(s): Panagiotis Ntostis, Grace Swanson, Georgia Kokkali, David Iles, John Huntriss, Agni Pantou, Maria Tzetis, Konstantinos Pantos, Helen M. Picton, Stephen A. Krawetz, D. H. Miller
Software Mentions: 4
Published: over 3 years ago

10.1186/s12917-020-02373-9

Transcriptome profiling of porcine testis tissue reveals genes related to sperm hyperactive motility
Cited by: 5
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Dag Inge Våge, Teklu Tewoldebrhan Zeremichael, Frøydis Deinboll Myromslien, Eli Grindflek
Software Mentions: 4
Published: over 4 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: about 8 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: almost 4 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: about 4 years ago

10.1007/s00395-021-00862-y

Fibroblast GATA-4 and GATA-6 promote myocardial adaptation to pressure overload by enhancing cardiac angiogenesis
Cited by: 29
Author(s): Gesine M. Dittrich, Natali Froese, Xue Wang, Hannah Kröger, Honghui Wang, Malgorzata Szaroszyk, Mona Malek Mohammadi, Julio Cordero, Merve Keles, Mortimer Korf‐Klingebiel, Kai C. Wollert, Robert Geffers, Manuel Mayr, Simon J. Conway, Gergana Dobreva, Johann Bauersachs, Joerg Heineke
Software Mentions: 4
Published: over 3 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: about 5 years ago

10.1016/j.bbr.2017.04.007

Recognition memory-induced gene expression in the perirhinal cortex: A transcriptomic analysis
Cited by: 6
Author(s): Hannah Scott, Mark F. Rogers, Helen L. Scott, Colin Campbell, E. Clea Warburton, James B. Uney
Software Mentions: 4
Published: over 7 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: over 8 years ago

10.1155/2021/6616434

Weighted Gene Coexpression Network Analysis Uncovers Critical Genes and Pathways for Multiple Brain Regions in Parkinson’s Disease
Cited by: 4
Author(s): Jianjun Huang, Li Liu, Lingling Qin, Hehua Huang, Li Xue
Software Mentions: 4
Published: almost 4 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: about 4 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: over 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: about 4 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 3 years ago

10.1186/s12870-018-1602-0

Dual RNA-seq analysis provides new insights into interactions between Norway spruce and necrotrophic pathogen Heterobasidion annosum s.l.
Cited by: 31
Author(s): Andriy Kovalchuk, Zhen Zeng, Rajendra P. Ghimire, Minna Kivimäenpää, Tommaso Raffaello, Mengxia Liu, Mukrimin Mukrimin, Risto Kasanen, Hui Sun, Riitta Julkunen‐Tiitto, Jarmo K. Holopainen, Fred O. Asiegbu
Software Mentions: 4
Published: almost 6 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 3 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: 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: almost 4 years ago

10.1016/j.celrep.2021.109032

Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome
Cited by: 17
Author(s): Alejandro Brenes, Harunori Yoshikawa, Dalila Bensaddek, Bogdan Mirauta, Daniel D Seaton, Jens Hukelmann, Hao Jiang, Oliver Stegle, Angus I. Lamond
Software Mentions: 4
Published: over 3 years ago

10.1016/j.stem.2017.03.003

H3K4 Methylation-Dependent Memory of Somatic Cell Identity Inhibits Reprogramming and Development of Nuclear Transfer Embryos
Cited by: 85
Author(s): Eva Hörmanseder, Angela Simeone, George E. Allen, Charles R. Bradshaw, Magdalena Figlmüller, J. B. Gurdon, Jérôme Jullien
Software Mentions: 4
Published: over 7 years ago

10.1016/j.stem.2019.09.008

Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal
Cited by: 71
Author(s): Stephanie Z. Xie, Laura García‐Prat, Véronique Voisin, Raffaele Ferrari, Olga I. Gan, Elvin Wagenblast, Kerstin B. Kaufmann, Andy G.X. Zeng, Shin‐ichiro Takayanagi, Ishita Patel, Esther K. Lee, Joseph Jargstorf, Gareth D. Holmes, Guy Romm, Kristele Pan, Michelle Shoong, Aditi Vedi, Chiara Luberto, Mark D. Minden, Gary D. Bader, Elisa Laurenti, John E. Dick
Software Mentions: 4
Published: about 5 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: over 4 years ago

10.3390/cells7120275

Activation of Polyamine Catabolism by N1,N11-Diethylnorspermine in Hepatic HepaRG Cells Induces Dedifferentiation and Mesenchymal-Like Phenotype
Cited by: 12
Author(s): О. Н. Иванова, Anastasiya V. Snezhkina, George S. Krasnov, Vladimir T. Valuev-Elliston, Olga A. Khomich, Alexey Khomutov, Tuomo A. Keinänen, Leena Alhonen, Birke Bartosch, Anna V. Kudryavtseva, Sergey N. Kochetkov, Alexander Ivanov
Software Mentions: 4
Published: about 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: over 4 years ago

10.3390/cells10030692

CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
Cited by: 2
Author(s): Sweta Talyan, Samantha Filipów, Michael Ignarski, Magdalena Smieszek, He Chen, Lucas Kühne, Linus Butt, Heike Göbel, Karla Johanna Ruth Hoyer-Allo, Felix C. Koehler, Janine Altmüller, Paul Brinkkötter, Bernhard Schermer, Thomas Benzing, Martin Kann, Roman‐Ulrich Müller, Christoph Dieterich
Software Mentions: 4
Published: almost 4 years ago

10.3390/cells9112452

Photochemotherapy Induces Interferon Type III Expression via STING Pathway
Cited by: 0
Author(s): Edyta Biskup, Brian D. Larsen, Leonor Rib, Lasse Folkersen, Omid Niazi, Maria R. Kamstrup, Claus Storgaard Sørensen
Software Mentions: 4
Published: about 4 years ago

10.3390/cells9081846

Caenorhabditis elegans Deficient in DOT-1.1 Exhibit Increases in H3K9me2 at Enhancer and Certain RNAi-Regulated Regions
Cited by: 6
Author(s): Ruben Esse, Alla Grishok
Software Mentions: 4
Published: over 4 years ago

10.3390/cells9122593

Induced Pluripotent Stem Cells to Understand Mucopolysaccharidosis. I: Demonstration of a Migration Defect in Neural Precursors
Cited by: 3
Author(s): Silvin Lito, Adama Sidibé, Sten Ilmjärv, Patricie Burda, Matthias R. Baumgartner, Bernhard Wehrle-Haller, Karl‐Heinz Krause, Antoine Marteyn
Software Mentions: 4
Published: about 4 years ago

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: about 6 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: over 4 years ago

10.1186/s13148-021-01050-4

Epigenetic evidence of an Ac/Dc axis by VPA and SAHA
Cited by: 10
Author(s): Sebastian Lunke, Scott Maxwell, Ishant Khurana, K N Harikrishnan, Jun Okabe, Keith Al-Hasani, Assam El‐Osta
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13148-015-0086-0

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis
Cited by: 26
Author(s): Warwick J. Locke, Elena Zotenko, Clare Stirzaker, Mark D. Robinson, Rebecca A. Hinshelwood, Andrew Stone, Roger R. Reddel, Lily I. Huschtscha, Susan J. Clark
Software Mentions: 4
Published: over 9 years ago

10.1186/s13148-020-00836-2

Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer
Cited by: 15
Author(s): Mitchell G. Lawrence, Ruth Pidsley, Birunthi Niranjan, Melissa Papargiris, Brooke A. Pereira, Michelle Richards, Linda Teng, Sam Norden, Andrew Ryan, Mark Frydenberg, Clare Stirzaker, Renea A. Taylor, Gail P. Risbridger, Susan J. Clark
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13148-020-00989-0

Identification and validation of methylated differentially expressed miRNAs and immune infiltrate profile in EBV-associated gastric cancer
Cited by: 4
Author(s): Man-Sheng Zhu, Qi Liang, Tao Chen, Qian Kong, Gengtai Ye, Shitong Yu, Xunjun Li, Qinglie He, Hao Líu, Yanfeng Hu, Jiang Yu, Guoxin Li
Software Mentions: 4
Published: almost 4 years ago

10.3390/ijms22105066

The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa
Cited by: 10
Author(s): Karolina Kotecka, Adam Kawałek, Kamil Kobyłecki, Aneta Agnieszka Bartosik
Software Mentions: 4
Published: over 3 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 3 years ago

10.1186/s40169-017-0150-9

Single‐cell RNA‐sequencing of the brain
Cited by: 46
Author(s): Raquel Durán, Haichao Wei, Jia Qian Wu
Software Mentions: 4
Published: over 7 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: about 4 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: almost 4 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: over 4 years ago

10.15252/embr.201846557

Tamoxifen mechanically reprograms the tumor microenvironment via <scp>HIF</scp> ‐1A and reduces cancer cell survival
Cited by: 55
Author(s): Ernesto Cortés, Dariusz Lachowski, Benjamin Robinson, Müge Sarper, Jaakko Teppo, Stephen D. Thorpe, Tyler J Lieberthal, Kenji Iwamoto, David A. Lee, Mariko Okada‐Hatakeyama, Markku Varjosalo, Armando E. del Río Hernández
Software Mentions: 4
Published: about 6 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: almost 5 years ago

10.1002/ece3.6946

Genomic analysis of Asian honeybee populations in China reveals evolutionary relationships and adaptation to abiotic stress
Cited by: 6
Author(s): Peng Shi, Jun Zhou, Huali Song, Yujuan Wu, Lan Lan, Xiangyou Tang, Zhengang Ma, Charles R. Vossbrinck, Bettina Vossbrinck, Zeyang Zhou, Jianlong Xu
Software Mentions: 4
Published: about 4 years ago

10.1093/bioinformatics/bts394

An accurate paired sample test for count data
Cited by: 58
Author(s): Thang V. Pham, Connie R. Jiménez
Software Mentions: 4
Published: over 12 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: over 4 years ago

10.1530/ERC-19-0448

Effects of epigenetic pathway inhibitors on corticotroph tumour AtT20 cells
Cited by: 5
Author(s): Kate E Lines, P. Filippakopoulos, Mark Stevenson, Susanne Müller, Helen Lockstone, Benjamin Wright, Stefan Knapp, David Buck, C. Bountra, R V Thakker
Software Mentions: 4
Published: almost 5 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: over 4 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 4 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 4 years ago

10.1111/1462-2920.15554

Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi
Cited by: 7
Author(s): Baojun Wu, Murray P. Cox
Software Mentions: 4
Published: over 3 years ago

10.1186/s13072-018-0246-5

Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus
Cited by: 54
Author(s): Adam J. Bewick, Zachary Sanchez, Elizabeth C. McKinney, Allen J. Moore, Patricia J. Moore, Robert J. Schmitz
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13072-019-0319-0

Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells
Cited by: 29
Author(s): Ryuichiro Nakato, Youichiro Wada, Ryo Nakaki, Genta Nagae, Yuki Katou, Sadami Tsutsumi, N. Nakajima, Hiroshi Fukuhara, Atsushi Iguchi, Takahide Kohro, Yasuharu Kanki, Yutaka Saitô, Mika Kobayashi, Akashi Izumi-Taguchi, Naoki Osato, Kenji Tatsuno, Asuka Kamio, Yoko Hayashi‐Takanaka, Hiromi Wada, Shinzo Ohta, Masamichi Aikawa, Hiroyuki Nakajima, Masaki Nakamura, Rebecca C. McGee, Kyle W. Heppner, Tatsuo Kawakatsu, Michiru Genno, Hiroshi Yanase, Haruki Kume, Takaaki Senbonmatsu, Yukio Homma, Shigeyuki Nishimura, Toutai Mitsuyama, Hiroyuki Aburatani, Hiroshi Kimurâ, Katsuhiko Shirahige
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms22073674

Can miRNA Indicate Risk of Illness after Continuous Exposure to M. tuberculosis?
Cited by: 3
Author(s): Cleonardo Augusto Silva, André M. Ribeiro-dos-Santos, Wanderson Gonçalves e Gonçalves, Pablo Diego do Carmo Pinto, Rafael Pompeu Pantoja, Tatiana Vinasco-Sandoval, André M. Ribeiro-dos-Santos, Mara H. Hutz, Amanda Ferreira Vidal, Gilderlanio Santana de Araújo, Sidney Emanuel Batista dos Santos
Software Mentions: 4
Published: over 3 years ago

10.1186/s13072-018-0186-0

Transient reduction of DNA methylation at the onset of meiosis in male mice
Cited by: 36
Author(s): Valeriya Gaysinskaya, Brendan Miller, Chiara De Luca, Godfried W. van der Heijden, Kasper D. Hansen, Alex Bortvin
Software Mentions: 4
Published: over 6 years ago

10.1186/s13072-017-0142-4

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure
Cited by: 18
Author(s): Sergey V. Ulianov, Aleksandra A. Galitsyna, Ilya M. Flyamer, Arkadiy K. Golov, Ekaterina E. Khrameeva, Maxim Imakaev, Nezar Abdennur, Mikhail S. Gelfand, А. В. Гаврилов, Sergey V. Razin
Software Mentions: 4
Published: over 7 years ago

10.1093/bioinformatics/btu274

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation
Cited by: 64
Author(s): Tarmo Äijö, Vincent Butty, Zhi Chen, Verna Salo, Subhash Tripathi, Christopher B. Burge, Riitta Lahesmaa, Harri Lähdesmäki
Software Mentions: 4
Published: over 10 years ago

10.3390/ijms22063125

A Transcriptomic Approach to Understanding the Combined Impacts of Supra-Optimal Temperatures and CO2 Revealed Different Responses in the Polyploid Coffea arabica and Its Diploid Progenitor C. canephora
Cited by: 12
Author(s): Isabel Marques, Isabel Fernandes, Octávio S. Paulo, Fernando C. Lidon, Fábio M. DaMatta, José C. Ramalho, Ana I. Ribeiro‐Barros
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13227-019-0135-4

Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes
Cited by: 16
Author(s): Graham A. McCulloch, Andrew Oliphant, Peter K. Dearden, Andrew J. Veale, Charles W. Ellen, Jonathan M. Waters
Software Mentions: 4
Published: over 5 years ago

10.1111/eva.12463

Plasticity in gene transcription explains the differential performance of two invasive fish species
Cited by: 47
Author(s): Kyle Wellband, Daniel D. Heath
Software Mentions: 4
Published: over 7 years ago

10.1038/s12276-020-00538-y

Tumor-promoting macrophages prevail in malignant ascites of advanced gastric cancer
Cited by: 39
Author(s): Hye Hyeon Eum, Minsuk Kwon, Daeun Ryu, Areum Jo, Wingyan Chung, Nayoung Kim, Yourae Hong, Dae‐Soon Son, Seung Tae Kim, Jeeyun Lee, Hae‐Ock Lee, Woong-Yang Park
Software Mentions: 4
Published: about 4 years ago

10.12688/f1000research.16005.3

MSF: Modulated Sub-graph Finder
Cited by: 0
Author(s): Mariam R. Farman, Ivo L. Hofacker, Fabian Amman
Software Mentions: 4
Published: over 5 years ago

10.1096/fj.201600675R

New function of the myostatin/activin type I receptor (ALK4) as a mediator of muscle atrophy and muscle regeneration
Cited by: 22
Author(s): Svitlana Pasteuning-Vuhman, Johanna W Boertje-van der Meulen, Maaike van Putten, Maurice Overzier, Peter ten Dijke, Szymon M. Kiełbasa, Wibowo Arindrarto, Ron Wolterbeek, Ksenia Lezhnina, Ivan V. Ozerov, Aleksandr M Aliper, Willem M.H. Hoogaars, Annemieke Aartsma‐Rus, Cindy J.M. Loomans
Software Mentions: 4
Published: about 8 years ago

10.1002/2211-5463.12983

Identification of modules and novel prognostic biomarkers in liver cancer through integrated bioinformatics analysis
Cited by: 5
Author(s): Bo Shen, Kun Li, Yuting Zhang
Software Mentions: 4
Published: about 4 years ago

10.1186/s12987-021-00269-w

Characterization of the blood–brain barrier in genetically diverse laboratory mouse strains
Cited by: 16
Author(s): Johanna Schaffenrath, Sheng‐Fu Huang, Tania Wyss, Mauro Delorenzi, Annika Keller
Software Mentions: 4
Published: over 3 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: about 9 years ago

10.1038/s41598-017-19072-5

Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs
Cited by: 45
Author(s): Yuliaxis Ramayo-Caldas, María Ballester, Juan Pablo Sánchez, Olga González‐Rodríguez, Manuel Revilla, Henry Reyer, Klaus Wimmers, D. Torrallardona, Raquel Quintanilla
Software Mentions: 4
Published: almost 7 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: almost 11 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568