bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fgene.2021.720421

Identification of a Novel Glycolysis-Related LncRNA Signature for Predicting Overall Survival in Patients With Bladder Cancer
Cited by: 9
Author(s): Zhaoqiang Zheng, Cong Lai, Wenshuang Li, Caixia Zhang, Kaiqun Ma, Yousheng Yao
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0184185

TSS-Seq analysis of low pH-induced gene expression in intercalated cells in the renal collecting duct
Cited by: 4
Author(s): Izumi Yokoyama, Hideki Inoue, Yushi Nakayama, Koji Eguchi, Yukiko Yasuoka, Naomi Matsuo, Hiroshi Nonoguchi, Yutaka Kakizoe, Tomohiko Kuwabara, Masashi Mukoyama
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0176290

Novel genes associated with enhanced motility of Escherichia coli ST131
Cited by: 30
Author(s): Asha Kakkanat, Minh-Duy Phan, Alvin W. Lo, Scott A. Beatson, Mark A. Schembri
Software Mentions: 2
Published: over 9 years ago

10.3389/fgene.2020.570094

Enhanced Activity of Genes Associated With Photosynthesis, Phytohormone Metabolism and Cell Wall Synthesis Is Involved in Gibberellin-Mediated Sugarcane Internode Growth
Cited by: 12
Author(s): Rongfa Chen, Yanting Fan, Haifeng Yan, Huiwen Zhou, Zhongfeng Zhou, Mengling Weng, Xing Huang, Prakash Lakshmanan, Yang–Rui Li, Lihang Qiu, Jianming Wu
Software Mentions: 2
Published: about 6 years ago

10.1186/s13287-021-02509-0

Age-related alteration in characteristics, function, and transcription features of ADSCs
Cited by: 7
Author(s): Keya Li, Guiying Shi, Xuepei Lei, Yiying Huang, Xinyue Li, Lin Bai, Chuan Qin
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.27192

Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions
Cited by: 56
Author(s): Amy E. Brinegar, Zheng Xia, James A. Loehr, Wei Li, George G. Rodney, Thomas A. Cooper
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0214520

Differential changes in bone strength of two inbred mouse strains following administration of a sclerostin-neutralizing antibody during growth
Cited by: 1
Author(s): Noah J. Mathis, Emily N. Adaniya, Lauren Smith, Alexander G. Robling, Karl J. Jepsen, Stephen H. Schlecht
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0227011

A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize
Cited by: 2
Author(s): Clément Cuello, Aurélie Baldy, Véronique Brunaud, Johann Joets, Étienne Delannoy, Marie‐Pierre Jacquemot, Lucy Botran, Yves Griveau, Cécile Guichard, Ludivine Soubigou‐Taconnat, Marie‐Laure Martin‐Magniette, Philippe Leroy, Valérie Méchin, Matthieu Reymond, Sylvie Coursol
Software Mentions: 2
Published: almost 7 years ago

10.1523/ENEURO.0397-19.2019

Identification of a Sacral, Visceral Sensory Transcriptome in Embryonic and Adult Mice
Cited by: 18
Author(s): Casey J. A. Smith-Anttila, Elizabeth A. Mason, Christine Wells, Bruce J. Aronow, Peregrine B. Osborne, Janet R. Keast
Software Mentions: 2
Published: almost 7 years ago

10.3389/fgene.2019.00097

Pan-Cancer Analysis of TCGA Data Revealed Promising Reference Genes for qPCR Normalization
Cited by: 34
Author(s): George S. Krasnov, Anna V. Kudryavtseva, Anastasiya V. Snezhkina, Valentina A. Lakunina, А. Д. Бениаминов, Nataliya V. Melnikova, Alexey A. Dmitriev
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0055817

Alterations in the Colonic Microbiota in Response to Osmotic Diarrhea
Cited by: 105
Author(s): Gregor Gorkiewicz, Gerhard G. Thallinger, Slave Trajanoski, Sonja Lackner, Gernot Stocker, Thomas Hinterleitner, Christian Gülly, Christoph Högenauer
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0237463

Bio-activating ultrafine grain titanium: RNA sequencing reveals enhanced mechano-activation of osteoconduction on nanostructured substrates
Cited by: 4
Author(s): Rebecca A. Reiss, Terry C. Lowe, Johnny A. Sena, Oleg Makhnin, Melanie C. Connick, Patrick Erik Illescas, Casey F. Davis
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0106858

Systemic Suppression of the Shoot Metabolism upon Rice Root Nematode Infection
Cited by: 13
Author(s): Tina Kyndt, Simon Denil, Lander Bauters, Wim Van Criekinge, Tim De Meyer
Software Mentions: 2
Published: about 12 years ago

10.1155/2015/831314

Integrative Analysis with Monte Carlo Cross-Validation Reveals miRNAs Regulating Pathways Cross-Talk in Aggressive Breast Cancer
Cited by: 27
Author(s): Antonio Colaprico, Claudia Cava, Gloria Bertoli, Gianluca Bontempi, Isabella Castiglioni
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0200783

Amino acid deprivation triggers a novel GCN2-independent response leading to the transcriptional reactivation of non-native DNA sequences
Cited by: 6
Author(s): Annarosaria De Vito, Massimo Lazzaro, Ilaria Palmisano, Davide Cittaro, Michela Riba, Dejan Lazarevic, Makoto Bannai, Davide Gabellini, Maria Vittoria Schiaffino
Software Mentions: 2
Published: over 8 years ago

10.1093/jhered/esaa021

X-Linked Signature of Reproductive Isolation in Humans is Mirrored in a Howler Monkey Hybrid Zone
Cited by: 6
Author(s): Marcella D. Baiz, Priscilla K. Tucker, Jacob L. Mueller, Liliana Cortés‐Ortiz
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0137461

Dynamic Change and Target Prediction of Axon-Specific MicroRNAs in Regenerating Sciatic Nerve
Cited by: 27
Author(s): Monichan Phay, Hak Hee Kim, Soonmoon Yoo
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0094555

Genetic Control of Differential Acetylation in Diabetic Rats
Cited by: 7
Author(s): Pamela J. Kaisaki, G. Otto, Joanna F. McGouran, Amine Toubal, Karène Argoud, Helen Waller-Evans, Clare Finlay, Sophie Caldérari, Marie-Thérèse Bihoreau, Benedikt M. Kessler, Dominique Guyader, Richard Mott
Software Mentions: 2
Published: over 12 years ago

10.1155/2019/9749751

P4HB, a Novel Hypoxia Target Gene Related to Gastric Cancer Invasion and Metastasis
Cited by: 31
Author(s): Jun Zhang, Shuai Guo, Yue Wu, Zhichao Zheng, Yue Wang, Yan Zhao
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0120791

Transcriptomic Analysis of the Primary Roots of Alhagi sparsifolia in Response to Water Stress
Cited by: 13
Author(s): Huanian Wu, Yongqiang Zhang, Wangbin Zhang, Xinwu Pei, Chao Zhang, Sun Jia, Weimin Liu
Software Mentions: 2
Published: over 11 years ago

10.1155/2020/7165893

Profiling and Bioinformatics Analysis of Differentially Expressed circRNAs in Spinal Ligament Tissues of Patients with Ankylosing Spondylitis
Cited by: 16
Author(s): Jianqiang Kou, Guoming Liu, Xiangyun Liu, LI Tian-mi, Ying Wei, Yuanliang Sun, Ting Wang, Yingzhen Wang, Xiujun Zheng
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0184167

De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech
Cited by: 26
Author(s): Markus Müller, Stefan Seifert, Torben Lübbe, Christoph Leuschner, Reiner Finkeldey
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0191213

Transcriptome analysis revealed the possible regulatory pathways initiating female geese broodiness within the hypothalamic-pituitary-gonadal axis
Cited by: 13
Author(s): Hehe Liu, Jiwen Wang, Li Liang, Chunchun Han, Hua He, Hengyong Xu
Software Mentions: 2
Published: over 8 years ago

10.1155/2014/969768

Stratification of Gene Coexpression Patterns and GO Function Mining for a RNA-Seq Data Series
Cited by: 2
Author(s): Haoqiang Zhao, Fenglin Cao, Yuanfeng Gong, Huafeng Xu, Yiping Fei, Longyue Wu, Xiangmei Ye, Dongguang Yang, Xiuhua Li, Xia Li, Jin Zhang
Software Mentions: 2
Published: almost 13 years ago

10.3390/biology10060462

Metatranscriptomic Analysis Reveals an Imbalance of Hepatopancreatic Flora of Chinese Mitten Crab Eriocheir sinensis with Hepatopancreatic Necrosis Disease
Cited by: 10
Author(s): Zeen Shen, Dhiraj Kumar, Xunmeng Liu, Bingyu Yan, Ping Fang, Yuchao Gu, Manyun Li, Meiping Xie, Rui Yuan, Yongjie Feng, Xiaolong Hu, Guangwen Cao, Renyu Xue, Hui Chen, Xiaohan Liu, Chengliang Gong
Software Mentions: 2
Published: over 5 years ago

10.3390/biology10060500

Gene Expression Profiles Associated with Radio-Responsiveness in Locally Advanced Rectal Cancer
Cited by: 9
Author(s): Jeeyong Lee, Joshua Kwon, Dayeon Kim, Misun Park, Kwang‐Seok Kim, In-Hwa Bae, Hyunkyung Kim, Joonseog Kong, Younjoo Kim, Ui-Sup Shin, EunJu Kim
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0204033

Transcriptional profiling reveals that a MYB transcription factor MsMYB4 contributes to the salinity stress response of alfalfa
Cited by: 27
Author(s): Dong Wang, Xijiang Liu, Donglei Li, Tianxue Gao, Yuhan Song
Software Mentions: 2
Published: about 8 years ago

10.1111/acel.12952

Cell‐type‐specific role of lamin‐B1 in thymus development and its inflammation‐driven reduction in thymus aging
Cited by: 18
Author(s): Sibiao Yue, Xiaobin Zheng, Yixian Zheng
Software Mentions: 2
Published: over 7 years ago

10.3390/biology9120470

Inhibition of FGF and TGF-β Pathways in hESCs Identify STOX2 as a Novel SMAD2/4 Cofactor
Cited by: 2
Author(s): Peter F. Renz, Daniel Spies, Panagiota Tsikrika, Anton Wutz, Tobias A. Beyer, Constance Ciaudo
Software Mentions: 2
Published: almost 6 years ago

10.3390/biology10090830

Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis
Cited by: 6
Author(s): Jing Li, Shaowen Bao, Chongnv Wang, Changwei Shao, Xuezhou Liu, Daiqiang Zhang
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0213796

Exploring integument transcriptomes, cuticle ultrastructure, and cuticular hydrocarbons profiles in eusocial and solitary bee species displaying heterochronic adult cuticle maturation
Cited by: 16
Author(s): Tiago Falcón, Daniel Guariz Pinheiro, M. J. Ferreira-Caliman, Izabel Cristina Casanova Turatti, Fabiano Carlos Pinto de Abreu, Juliana Stephanie Galaschi Teixeira, Juliana Ramos Martins, Moysés Elias-Neto, Michelle Soares, Marcela B. Laure, V.L.P. Figueiredo, Norberto Peporine Lopes, Zilá Luz Paulino Simões, Carlos Alberto Garófalo, M. M. G. Bitondi
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0086856

Urine MicroRNA as Potential Biomarkers of Autosomal Dominant Polycystic Kidney Disease Progression: Description of miRNA Profiles at Baseline
Cited by: 86
Author(s): Iddo Z. Ben‐Dov, Ying-Cai Tan, Pavel Morozov, Patricia D. Wilson, Hanna Rennert, Jon D. Blumenfeld, Thomas Tuschl
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0215729

Reference genes selection for Calotropis procera under different salt stress conditions
Cited by: 6
Author(s): Maria Reis Valois Coêlho, Rebeca Rivas, José Ribamar Costa Ferreira‐Neto, Valesca Pandolfi, João Pacífico Bezerra-Neto, Ana Maria Benko‐Iseppon, Mariana Santos
Software Mentions: 2
Published: over 7 years ago

10.1111/acel.13180

Impaired phagocytic function in CX3CR1 + tissue‐resident skeletal muscle macrophages prevents muscle recovery after influenza A virus‐induced pneumonia in old mice
Cited by: 17
Author(s): Constance E. Runyan, Lynn C. Welch, Emilia Lecuona, Masahiko Shigemura, Luciano Amarelle, Hiam Abdala‐Valencia, Nikita Joshi, Ziyan Lu, Ki-Won Nam, Nikolay S. Markov, Alexandra C. McQuattie‐Pimentel, Raul Piseaux‐Aillon, Yuliya Politanska, Lango Sichizya, Satoshi Watanabe, Kibileri Williams, G. R. Scott Budinger, Jacob I. Sznajder, Alexander V. Misharin
Software Mentions: 2
Published: over 6 years ago

10.3390/cancers13163976

USP19 and RPL23 as Candidate Prognostic Markers for Advanced-Stage High-Grade Serous Ovarian Carcinoma
Cited by: 10
Author(s): Haeyoun Kang, Min Chul Choi, Sewha Kim, Jooyeon Jeong, Ah-Young Kwon, Tae-Hoen Kim, Gwangil Kim, Won Duk Joo, Hyun Park, Chan Lee, Seung Hun Song, Sang Geun Jung, Sohyun Hwang, Hee Jung An
Software Mentions: 2
Published: about 5 years ago

10.1186/s40659-016-0095-2

Conserved genes and pathways in primary human fibroblast strains undergoing replicative and radiation induced senescence
Cited by: 29
Author(s): Shiva Marthandan, Uwe Menzel, Stefan Priebe, Marco Groth, Reinhard Guthke, Matthias Platzer, Peter Hemmerich, Christoph Kaether, Stephan Diekmann
Software Mentions: 2
Published: over 10 years ago

10.3390/cancers12092541

Combination Treatment with GSK126 and Pomalidomide Induces B-Cell Differentiation in EZH2 Gain-of-Function Mutant Diffuse Large B-Cell Lymphoma
Cited by: 5
Author(s): Sungryul Park, Seunghyun Jo, Jong-Hwan Kim, Seon‐Young Kim, Jae Du Ha, Jong Yeon Hwang, Myeong Youl Lee, Jong Soon Kang, Tae-Su Han, Sung Goo Park, Sunhong Kim, Byoung Chul Park, Jeong-Hoon Kim
Software Mentions: 2
Published: about 6 years ago

10.3390/cancers11020208

ORAI1 and ORAI3 in Breast Cancer Molecular Subtypes and the Identification of ORAI3 as a Hypoxia Sensitive Gene and a Regulator of Hypoxia Responses
Cited by: 42
Author(s): Iman Azimi, Michael J. G. Milevskiy, Silke B. Chalmers, Kunsala T. D. S. Yapa, Mélanie Robitaille, Christopher Henry, Gregory J. Baillie, Erik W. Thompson, Sarah J. Roberts‐Thomson, Gregory R. Monteith
Software Mentions: 2
Published: over 7 years ago

10.1242/bio.037937

Physiological profile of undifferentiated bovine blastocyst-derived trophoblasts
Cited by: 13
Author(s): Viju Vijayan Pillai, L. G. B. Siqueira, Moubani Das, Tiffany G. Kei, Lan N. Tu, Anthony W. Herren, Brett S. Phinney, Soon Hon Cheong, Peter J. Hansen, Vimal Selvaraj
Software Mentions: 2
Published: almost 8 years ago

10.3390/cancers12040786

A Novel Role for the Tumor Suppressor Gene ITF2 in Tumorigenesis and Chemotherapy Response
Cited by: 9
Author(s): Olga Pernía, Ana Sastre-Perona, Carlos Rodriguez-Antolín, Álvaro García-Guede, María Palomares‐Bralo, Rocío Rosas, Darío Sánchez-Cabrero, Patricia Cruz, Carmen Rodrı́guez, MDolores Diestro, Rubén Martín‐Arenas, Verónica Pulido, Pilar Santisteban, Javier de Castro, Olga Vera, Inmaculada Ibáñez de Cáceres
Software Mentions: 2
Published: over 6 years ago

10.1242/bio.023473

Reprogramming towards totipotency is greatly facilitated by synergistic effects of small molecules
Cited by: 27
Author(s): Kazuaki Miyamoto, Yosuke Tajima, Koki Yoshida, Mami Oikawa, Rika Azuma, George E. Allen, Tomomi Tsujikawa, Tomomasa Tsukaguchi, Charles R. Bradshaw, Jérôme Jullien, Kazuya Yamagata, Kazuya Matsumoto, Masayuki Anzai, Hiroshi Imai, J. B. Gurdon, Masao Yamada
Software Mentions: 2
Published: over 9 years ago

10.1242/bio.050260

RNA-seq analysis and compound screening highlight multiple signalling pathways regulating secondary cell death after acute CNS injury in vivo
Cited by: 2
Author(s): Chiara Herzog, David Greenald, Juan Larraz, Marcus Keatinge, Leah Herrgen
Software Mentions: 2
Published: over 6 years ago

10.1242/bio.020891

Early molecular events during retinoic acid induced differentiation of neuromesodermal progenitors
Cited by: 38
Author(s): Thomas J. Cunningham, Alexandre R. Colas, Gregg Duester
Software Mentions: 2
Published: about 10 years ago

10.1242/bio.043372

Unanchored ubiquitin chains do not lead to marked alterations in gene expression inDrosophila melanogaster
Cited by: 6
Author(s): Jessica R. Blount, Danielle Meyer, Camille Akemann, Sean L. Johnson, Katherine Gurdziel, Tracie R. Baker, Sokol V. Todi
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13062-018-0205-x

Genes sharing the protein family domain decrease the performance of classification with RNA-seq genomic signatures
Cited by: 2
Author(s): Anna Leśniewska, Joanna Zyprych-Walczak, Alicja Szabelska‐Berȩsewicz, Michał Okoniewski
Software Mentions: 2
Published: over 8 years ago

10.1186/s40425-019-0503-6

Combined treatment with HMGN1 and anti-CD4 depleting antibody reverses T cell exhaustion and exerts robust anti-tumor effects in mice
Cited by: 8
Author(s): Chang Yu Chen, Satoshi Ueha, Yoichi Ishiwata, Shoji Yokochi, De Yang, Joost J. Oppenheim, Haru Ogiwara, Shigeyuki Shichino, Shungo Deshimaru, Francis H.W. Shand, Sotaro Shibayama, Kouji Matsushima
Software Mentions: 2
Published: almost 8 years ago

10.3390/cancers12020353

Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of Cancer
Cited by: 22
Author(s): Martin Metzenmacher, Renáta Váraljai, Balázs Hegedűs, Igor Cima, Jan Förster, Alexander Schramm, Björn Scheffler, Peter A. Horn, Christoph A. Klein, Tibor Szarvas, Henning Reis, Nicola Bielefeld, Alexander Roesch, Clemens Aigner, Volker Kunzmann, Marcel Wiesweg, Jens T. Siveke, Martin Schüler, Smiths Lueong
Software Mentions: 2
Published: over 6 years ago

10.3390/cancers13092012

Inhibition of the Myocardin-Related Transcription Factor Pathway Increases Efficacy of Trametinib in NRAS-Mutant Melanoma Cell Lines
Cited by: 5
Author(s): Kathryn M. Appleton, Charuta C. Palsuledesai, Sean A. Misek, Maja K. Blake, Joseph Zagorski, Kathleen A. Gallo, Thomas S. Dexheimer, Richard R. Neubig
Software Mentions: 2
Published: over 5 years ago

10.1093/bioinformatics/btaa735

FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts
Cited by: 1
Author(s): Rajinder K. Gupta, Yannick Schrooders, Marcha Verheijen, Adrian Roth, Jos Kleinjans, Florian Caiment
Software Mentions: 2
Published: about 6 years ago

10.3390/cancers10110403

Simultaneous Inhibition of MEK and Hh Signaling Reduces Pancreatic Cancer Metastasis
Cited by: 13
Author(s): Dongsheng Gu, Hai Lin, Xiaoli Zhang, Qipeng Fan, Shaoxiong Chen, Safi Shahda, Yunlong Liu, Jie Sun, Jingwu Xie
Software Mentions: 2
Published: about 8 years ago

10.3390/cancers12092674

Direct Antiviral Treatments for Hepatitis C Virus Have Off-Target Effects of Oncologic Relevance in Hepatocellular Carcinoma
Cited by: 11
Author(s): Catia Giovannini, Francesca Fornari, Valentina Indio, Davide Treré, Matteo Renzulli, Francesco Vasuri, Matteo Cescon, Matteo Ravaioli, Alessia Perrucci, Annalisa Astolfi, Fabio Piscaglia, Laura Gramantieri
Software Mentions: 2
Published: about 6 years ago

10.3390/cancers13092009

Distinct mRNAs in Cancer Extracellular Vesicles Activate Angiogenesis and Alter Transcriptome of Vascular Endothelial Cells
Cited by: 5
Author(s): Pan Zhang, Su Bin Lim, Kuan Jiang, Ti Weng Chew, Boon Chuan Low, Chwee Teck Lim
Software Mentions: 2
Published: over 5 years ago

10.1093/bioinformatics/btx049

FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions
Cited by: 7
Author(s): Koji Iwayama, Yuri Aisaka, Natsumaro Kutsuna, Atsushi J. Nagano
Software Mentions: 2
Published: almost 10 years ago

10.1093/bioinformatics/btu333

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series
Cited by: 254
Author(s): María José Nueda, Sonia Tarazona, Ana Conesa
Software Mentions: 2
Published: over 12 years ago

10.3390/cancers13050957

Bifidobacterium Strain-Specific Enhances the Efficacy of Cancer Therapeutics in Tumor-Bearing Mice
Cited by: 23
Author(s): Young‐In Yoon, Gihyeon Kim, Bu‐Nam Jeon, Sungsoon Fang, Hansoo Park
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers11050673

SIRT2 Contributes to the Resistance of Melanoma Cells to the Multikinase Inhibitor Dasatinib
Cited by: 19
Author(s): Iwona Karwaciak, Anna Sałkowska, Kaja Karaś, Marta Sobalska‐Kwapis, Aurelia Walczak‐Drzewiecka, Łukasz Pułaski, Dominik Strapagiel, Jarosław Dastych, Marcin Ratajewski
Software Mentions: 2
Published: over 7 years ago

10.3390/cancers12113169

Id1 and PD-1 Combined Blockade Impairs Tumor Growth and Survival of KRAS-mutant Lung Cancer by Stimulating PD-L1 Expression and Tumor Infiltrating CD8+ T Cells
Cited by: 8
Author(s): Iosune Baraibar, Marta Cimavilla Román, María Rodríguez‐Remírez, Inés López, Anna Vilalta, Elizabeth Guruceaga, Margarita Ecay, María Collantes, Teresa Lozano, Diego Alignani, A. Puyalto, Carolina Oliver, Sergio Ortiz‐Espinosa, Haritz Moreno, María Dolores Torregrosa, Christian Rolfo, Christian Caglevic, David García-Ros, María Villalba-Esparza, Carlos de Andrea, Silvestre Vicent, Rubén Pı́o, Juan José Lasarte, Alfonso Calvo, Daniel Ajona, Ignacio Gil‐Bazo
Software Mentions: 2
Published: about 6 years ago

10.1186/s13040-015-0050-8

Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study
Cited by: 2
Author(s): Jiang Gui, Casey S. Greene, Claire Sullivan, W. Rowland Taylor, Jason H. Moore, Carol H. Kim
Software Mentions: 2
Published: over 11 years ago

10.3390/cancers13061433

Epigenetic Mechanisms Are Involved in the Oncogenic Properties of ZNF518B in Colorectal Cancer
Cited by: 3
Author(s): Francisco Gimeno-Valiente, Ángela L. Riffo‐Campos, Luís Torres, Noelia Tarazona, Gerardo López-Rodas, Luís Franco, Josefa Castillo
Software Mentions: 2
Published: over 5 years ago

10.1186/s13040-019-0204-1

ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
Cited by: 83
Author(s): Aurélien Brionne, Amélie Juanchich, Christelle Hennequet-Antier
Software Mentions: 2
Published: about 7 years ago

10.18632/aging.202168

Plasma cytokines for predicting diabetic retinopathy among type 2 diabetic patients via machine learning algorithms
Cited by: 3
Author(s): Bin Cao, Ning Zhang, Yuanyuan Zhang, Ying Fu, Dong Zhao
Software Mentions: 2
Published: almost 6 years ago

10.1007/s00395-021-00846-y

AMPKα1 deletion in myofibroblasts exacerbates post-myocardial infarction fibrosis by a connexin 43 mechanism
Cited by: 19
Author(s): Cécile Dufeys, Evangelos-Panagiotis Daskalopoulos, Diego Castanares-Zapatero, Simon J. Conway, Audrey Ginion, Caroline Bouzin, Jérôme Ambroise, Bertrand Bearzatto, Jean‐Luc Gala, Stéphane Heymans, Anna-Pia Papageorgiou, Stefan Vinckier, Julien Cumps, Jean‐Luc Balligand, Maarten Vanhaverbeke, Peter Sinnaeve, Stefan Janssens, Luc Bertrand, Christophe Beauloye, Sandrine Horman
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.202373

Microglia exosomal miRNA-137 attenuates ischemic brain injury through targeting Notch1
Cited by: 46
Author(s): Dianquan Zhang, Guoliang Cai, Kai Li, Zhe Zhuang, Kunping Jia, Siying Pei, Xiuzhen Wang, Hong Wang, Shengnan Xu, Cheng Cui, Manchao Sun, Sihui Guo, Wenli Song, Guofeng Cai
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12917-018-1583-0

Novel insights into the host immune response of chicken Harderian gland tissue during Newcastle disease virus infection and heat treatment
Cited by: 19
Author(s): Perot Saelao, Ying Wang, Rodrigo A. Gallardo, Susan J. Lamont, Jack Dekkers, T. Ross Kelly, Huaijun Zhou
Software Mentions: 2
Published: about 8 years ago

10.3390/cancers11081179

Papillary Thyroid Carcinoma Variants are Characterized by Co-dysregulation of Immune and Cancer Associated Genes
Cited by: 14
Author(s): Jaideep Chakladar, Wei Tse Li, Michael Bouvet, Eric Y. Chang, Jessica Wang‐Rodriguez, Weg M. Ongkeko
Software Mentions: 2
Published: about 7 years ago

10.1523/JNEUROSCI.2571-18.2019

The Spinal Transcriptome after Cortical Stroke: In Search of Molecular Factors Regulating Spontaneous Recovery in the Spinal Cord
Cited by: 22
Author(s): Julia Kaiser, Martina A. Maibach, Iris Salpeter, Niels Hagenbuch, Vladimir B. C. de Souza, Mark D. Robinson, Martin E. Schwab
Software Mentions: 2
Published: over 7 years ago

10.1186/s12918-017-0466-5

Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma
Cited by: 8
Author(s): Xinan Yang, Fangming Tang, Jisu Shin, John M. Cunningham
Software Mentions: 2
Published: about 9 years ago

10.1186/s12918-019-0699-6

A fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data
Cited by: 15
Author(s): Shuang Sun, Yabo Chen, Liu Yang, Xuequn Shang
Software Mentions: 2
Published: over 7 years ago

10.1186/s13104-021-05624-6

Effects of FUdR on gene expression in the C. elegans bacterial diet OP50
Cited by: 3
Author(s): Grace McIntyre, Justin Wright, Hoi Tong Wong, Regina Lamendella, Jason P. Chan
Software Mentions: 2
Published: over 5 years ago

10.1186/1756-0500-6-503

Impact of RNA-seq attributes on false positive rates in differential expression analysis of de novo assembled transcriptomes
Cited by: 18
Author(s): Emmanuel González, Simon Joly
Software Mentions: 2
Published: almost 13 years ago

10.1016/j.cell.2017.11.042

Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner
Cited by: 497
Author(s): Morgane Sonia Thion, Donovan Low, Aymeric Silvin, Jinmiao Chen, Pauline Grisel, Jonas Schulte-Schrepping, Ronnie Blecher‐Gonen, Thomas Ulas, Paola Squarzoni, Guillaume Hoeffel, Fanny Coulpier, Eleni Siopi, Friederike S. David, Claus‐Jürgen Scholz, Shihui Foo, Josephine Lum, Arlaine Anne Amoyo, Anis Larbi, Michael Poidinger, Anne Buttgereit, Pierre-Marie Lledo, Melanie Greter, Jerry Kok Yen Chan, Ido Amit, Marc Beyer, Joachim L. Schultze, Andreas Schlitzer, Sven Pettersson, Florent Ginhoux, Sonia Garel
Software Mentions: 2
Published: almost 9 years ago

10.1007/s10565-020-09516-6

Estrogen receptor alpha (ERα)–mediated coregulator binding and gene expression discriminates the toxic ERα agonist diethylstilbestrol (DES) from the endogenous ERα agonist 17β-estradiol (E2)
Cited by: 10
Author(s): Aziza Hussein Bakheit Adam, L.H.J. de Haan, Ignacio Miro Estruch, Guido Hooiveld, Jochem Louisse, Ivonne M.C.M. Rietjens
Software Mentions: 2
Published: over 6 years ago

10.1038/s41388-020-01593-5

C-terminal truncated HBx initiates hepatocarcinogenesis by downregulating TXNIP and reprogramming glucose metabolism
Cited by: 45
Author(s): Yu Zhang, Qian Yan, Lanqi Gong, Hang Xu, Beilei Liu, Xiaona Fang, Dandan Yu, Lei Li, Ting Wei, Ying Wang, Ching Ngar Wong, Zhaojie Lyu, Ying Tang, Pak C. Sham, Xin‐Yuan Guan
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13104-018-3154-7

Use of DAVID algorithms for clustering custom annotated gene lists in a non-model organism, rainbow trout
Cited by: 3
Author(s): Hao Ma, Guangtu Gao, Gregory M. Weber
Software Mentions: 2
Published: almost 9 years ago

10.1038/oncsis.2017.30

Epigenetic pathway inhibitors represent potential drugs for treating pancreatic and bronchial neuroendocrine tumors
Cited by: 33
Author(s): Kate E Lines, Mark Stevenson, P. Filippakopoulos, Susanne Müller, Helen Lockstone, Benjamin Wright, Simona Grozinsky‐Glasberg, Ashley Grossman, S. Knapp, David Buck, C. Bountra, R V Thakker
Software Mentions: 2
Published: over 9 years ago

10.1038/s41418-020-0541-0

Targeting triple-negative breast cancers with the Smac-mimetic birinapant
Cited by: 27
Author(s): Najoua Lalaoui, Delphine Mérino, Göknur Giner, François Vaillant, Diep Chau, Lin Liu, Tobias Kratina, Bhupinder Pal, James R. Whittle, Nima Etemadi, Jean Berthelet, Julius Gräsel, Cathrine Hall, Matthew E. Ritchie, Matthias Ernst, Gordon K. Smyth, David Vaux, Jane E. Visvader, Geoffrey J. Lindeman, John Silke
Software Mentions: 2
Published: over 6 years ago

10.1038/s41418-020-00653-3

HDAC inhibition ameliorates cone survival in retinitis pigmentosa mice
Cited by: 21
Author(s): Marijana Samardzija, Andrea Corna, Raquel Gómez‐Sintes, Mohamed Ali Jarboui, Angela Armento, Jérôme E. Roger, Eleni Petridou, Wadood Haq, François Paquet-Durand, Eberhart Zrenner, Pedro de la Villa, Günther Zeck, Christian Grimm, Patricia Boya, Marius Ueffing, Dragana Trifunović
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41419-020-2435-y

CCL5 derived from tumor-associated macrophages promotes prostate cancer stem cells and metastasis via activating β-catenin/STAT3 signaling
Cited by: 131
Author(s): Renlun Huang, Shengqi Wang, Neng Wang, Yifeng Zheng, Jianfu Zhou, Bowen Yang, Xuan Wang, Juping Zhang, Lang Guo, Shusheng Wang, Zhiqiang Chen, Zhiyu Wang, Shulin Xiang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41419-021-04005-y

ETV7 regulates breast cancer stem-like cell features by repressing IFN-response genes
Cited by: 11
Author(s): Laura Pezzè, Erna Marija Meškytė, Mattia Forcato, Stefano Pontalti, Kalina Aleksandra Badowska, Dario Rizzotto, Ira Skvortsova, Silvio Bicciato, Yari Ciribilli
Software Mentions: 2
Published: over 5 years ago

10.1038/s41419-021-04076-x

Toll-like receptor 4 is a master regulator for colorectal cancer growth under high-fat diet by programming cancer metabolism
Cited by: 6
Author(s): Xianjing Hu, Sarwat Fatima, Minting Chen, Keyang Xu, Chunhua Huang, Rui Gong, Tao Su, Hoi Leong Xavier Wong, Zhaoxiang Bian, Hiu Yee Kwan
Software Mentions: 2
Published: about 5 years ago

10.1038/s41419-019-1938-x

TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP
Cited by: 22
Author(s): Janin Knop, Lisanne M. Spilgies, Stefanie Rufli, Ramona Reinhart, Lazaros Vasilikos, Monica Yabal, Erika Owsley, Philipp J. Jost, Rebecca Marsh, Harald Wajant, Mark D. Robinson, Thomas Kaufmann, Wendy Wei-Lynn Wong
Software Mentions: 2
Published: about 7 years ago

10.1186/s12870-016-0831-3

RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways
Cited by: 54
Author(s): Stephen Pearce, Néstor Kippes, Andrew Chen, Juan M. Debernardi, Jorge Dubcovsky
Software Mentions: 2
Published: over 10 years ago

10.1186/s40478-020-00903-y

Altered secretory and neuroprotective function of the choroid plexus in progressive multiple sclerosis
Cited by: 29
Author(s): Sabela Rodríguez‐Lorenzo, David Francisco, Ricardo Vos, Bert van het Hof, Merel Rijnsburger, Horst Schroten, Hiroshi Ishikawa, Wissam Beaino, Rémy Bruggmann, Gijs Kooij, Helga E. de Vries
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-015-0598-y

A transcriptomic analysis of bermudagrass (Cynodon dactylon) provides novel insights into the basis of low temperature tolerance
Cited by: 39
Author(s): Chen Liang, Jibiao Fan, Longxing Hu, Zhengrong Hu, Yan Xie, Yingzi Zhang, Yanhong Lou, Eviatar Nevo, Jinmin Fu
Software Mentions: 2
Published: about 11 years ago

10.1038/s41419-019-1696-9

FGF1ΔHBS ameliorates chronic kidney disease via PI3K/AKT mediated suppression of oxidative stress and inflammation
Cited by: 48
Author(s): Dezhong Wang, Mengyun Jin, Xinyu Zhao, Tianyang Zhao, Wei Lin, Zhengle He, Miaojuan Fan, Wei Jin, Jie Zhou, Lingwei Jin, Chao Zheng, Hui Jin, Yushuo Zhao, Xiaokun Li, Ying Lei, Yang Wang, Guo‐Qing Zhu, Zhifeng Huang
Software Mentions: 2
Published: over 7 years ago

10.1038/s41419-020-2589-7

BCL-xL/BCL2L1 is a critical anti-apoptotic protein that promotes the survival of differentiating pancreatic cells from human pluripotent stem cells
Cited by: 19
Author(s): Larry Sai Weng Loo, Andreas Alvin Purnomo Soetedjo, Hwee Hui Lau, Natasha Hui Jin Ng, Soumita Ghosh, Linh Nguyen, Vidhya G. Krishnan, Hyungwon Choi, Xavier Roca, Shawn Hoon, Adrian Kee Keong Teo
Software Mentions: 2
Published: over 6 years ago

10.1038/s41419-020-2704-9

Reduced replication origin licensing selectively kills KRAS-mutant colorectal cancer cells via mitotic catastrophe
Cited by: 4
Author(s): Bastian Gastl, Kathleen Klotz-Noack, Bertram Klinger, Sylvia Ispasanie, Krenoula Hani Fouad Salib, Johannes Zuber, Soulafa Mamlouk, Natalie Bublitz, Nils Blüthgen, David Horst, Markus Morkel, Reinhold Schäfer, Christine Sers
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-015-0596-0

Transcriptome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants
Cited by: 59
Author(s): Jillian M. Hagel, Jeremy S. Morris, Eun-Jeong Lee, Isabel Desgagné‐Penix, Crystal D. Bross, Lihong Chang, Xue Chen, Scott C. Farrow, Ye Zhang, Jung Soh, Christoph Wilhelm Sensen, Peter J. Facchini
Software Mentions: 2
Published: about 11 years ago

10.1038/s41419-018-1296-0

Transcriptome profiling of caspase-2 deficient EμMyc and Th-MYCN mouse tumors identifies distinct putative roles for caspase-2 in neuronal differentiation and immune signaling
Cited by: 4
Author(s): Loretta Dorstyn, Emily Hackett-Jones, Andrej Nikolic, Murray D. Norris, Yoon Pin Lim, John Toubia, Michelle Haber, Sharad Kumar
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41419-018-0869-2

LncRNA MIR100HG promotes cell proliferation in triple-negative breast cancer through triplex formation with p27 loci
Cited by: 105
Author(s): Shaowei Wang, Ke Hao, Honglei Zhang, Yujie Ma, Lei Ao, Li Zou, Qin Yang, Huiping Zhu, Jianyun Nie, Chen Wu, Baowei Jiao
Software Mentions: 2
Published: over 8 years ago

10.1038/s41419-020-2372-9

Myofibroblast induces hepatocyte-to-ductal metaplasia via laminin–ɑvβ6 integrin in liver fibrosis
Cited by: 15
Author(s): Ting Xu, Zhijie Lu, Zhuanglong Xiao, Fang Liu, Yuhua Chen, Zhijun Wang, Shenghua Zhu, Yufang Song
Software Mentions: 2
Published: over 6 years ago

10.1038/s41420-020-00295-x

The prognostic value of six survival-related genes in bladder cancer
Cited by: 7
Author(s): Songbai Cheng, Jiang Zhou, Jing Xiao, Huiling Guo, Zhengrong Wang, Yuhui Wang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41420-020-00392-x

Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae
Cited by: 5
Author(s): Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41420-021-00560-7

Identification of a seven-long non-coding RNA signature associated with Jab1/CSN5 in predicting hepatocellular carcinoma
Cited by: 7
Author(s): Weijie Ma, Ye Yao, Gang Xu, Xiaoling Wu, Jinghua Liu, Ganggang Wang, Xi Chen, Kunlei Wang, Yirang Chen, Yonghua Guo, Yongsheng Li, Deli Tan, Hui Guo, Zhisu Liu, Yufeng Yuan, François X. Claret
Software Mentions: 2
Published: over 5 years ago

10.1002/embr.201337642

Extensive regulation of the non‐coding transcriptome by hypoxia: role of <scp>HIF</scp> in releasing paused <scp>RNA</scp> pol2
Cited by: 138
Author(s): Hani Choudhry, Johannes Schödel, Spyros Oikonomopoulos, Carme Camps, Steffen Grampp, Adrian L. Harris, Peter J. Ratcliffe, Jiannis Ragoussis, David R. Mole
Software Mentions: 2
Published: almost 13 years ago

10.15252/embr.201847379

<scp>IL</scp> ‐7‐dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti‐tumour response
Cited by: 35
Author(s): Hung-Chang Chen, Nils Eling, Celia P. Martínez-Jiménez, L. M. O'Brien, Valentina Carbonaro, John C. Marioni, Duncan T. Odom
Software Mentions: 2
Published: over 7 years ago

10.1186/s12870-019-2069-3

Transcriptome analysis of two inflorescence branching mutants reveals cytokinin is an important regulator in controlling inflorescence architecture in the woody plant Jatropha curcas
Cited by: 10
Author(s): Maosheng Chen, Miaomiao Zhao, Guijuan Wang, Hua He, Xue Bai, Bang-Zhen Pan, Qi Fu, Yongfu Tao, Mingyong Tang, Jorge Martínez‐Herrera, Zeng-Fu Xu
Software Mentions: 2
Published: almost 7 years ago

10.15252/embr.201948469

Wnt regulates amino acid transporter Slc7a5 and so constrains the integrated stress response in mouse embryos
Cited by: 21
Author(s): Nadège Poncet, Pamela A. Halley, Christopher Lipina, Marek Gierliński, Alwyn Dady, Gail Singer, Melanie Febrer, Yun‐Bo Shi, Terry P. Yamaguchi, Peter M. Taylor, Kate G. Storey
Software Mentions: 2
Published: almost 7 years ago

10.15252/embr.201948019

The role of Xist ‐mediated Polycomb recruitment in the initiation of X‐chromosome inactivation
Cited by: 72
Author(s): Aurélie Bousard, Ana Raposo, J. Ż̷ylicz, Christel Picard, Vanessa Borges Pires, Yanyan Qi, Cláudia Raquel Estopa Gil, Laurène Syx, Howard Y. Chang, Edith Heard, Simão Teixeira da Rocha
Software Mentions: 2
Published: about 7 years ago

10.1002/ece3.4976

Transcriptomic changes during caste development through social interactions in the termite Zootermopsis nevadensis
Cited by: 15
Author(s): Hajime Yaguchi, Rikako Suzuki, Masatoshi Matsunami, Shuji Shigenobu, Kazuyuki Maekawa
Software Mentions: 2
Published: over 7 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568