bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0094031

Disruption of the Homogentisate Solanesyltransferase Gene Results in Albino and Dwarf Phenotypes and Root, Trichome and Stomata Defects in Arabidopsis thaliana
Cited by: 12
Author(s): Yuehui Chao, Junmei Kang, Tiejun Zhang, Qingchuan Yang, Margaret Y. Gruber, Yan Sun
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-016-2897-6

Detection of high variability in gene expression from single-cell RNA-seq profiling
Cited by: 35
Author(s): Hung I Harry Chen, Yufang Jin, Yufei Huang, Yidong Chen
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-021-07959-7

Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens
Cited by: 7
Author(s): Arnar K. S. Sandholt, Eva Wattrang, Tobias Lilja, Harri Ahola, Anna Lundén, Karin Troell, Staffan G. Svärd, Robert Söderlund
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0172884

Ion channel expression patterns in glioblastoma stem cells with functional and therapeutic implications for malignancy
Cited by: 36
Author(s): Julia Pollak, Goutam Karan, Cory C. Funk, Sonali Arora, Eunjee Lee, Jun Zhu, Nathan D. Price, Patrick J. Paddison, Jan‐Marino Ramirez, Robert Rostomily
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0256319

Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening
Cited by: 4
Author(s): Fernando G. Razo-Mendivil, Fernando Hernández-Godínez, Corina Hayano-Kanashiro, Octavio Martínez
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0083504

RNA Sequencing of the Exercise Transcriptome in Equine Athletes
Cited by: 43
Author(s): Stefano Capomaccio, Nicola Vitulo, Andrea Verini-Supplizi, Gianni Barcaccia, Alessandro Albiero, Michela D’Angelo, Davide Campagna, Giorgio Valle, Michela Felicetti, Maurizio Silvestrelli, Katia Cappelli
Software Mentions: 3
Published: almost 13 years ago

10.18632/aging.101027

Higher expression of somatic repair genes in long-lived ant queens than workers
Cited by: 28
Author(s): Eric R. Lucas, Eyal Privman, Laurent Keller
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0238175

Time-series transcriptomic analysis reveals novel gene modules that control theanine biosynthesis in tea plant (Camellia sinensis)
Cited by: 2
Author(s): Haisheng Cao, Xiaolong He, Jinke Du, Rui Zhang, Ying Chen, Yan Ma, Qi Chen, Congbing Fang, Chi Tang Ho, Shihua Zhang, Xiaochun Wan
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0209535

How to build a fruit: Transcriptomics of a novel fruit type in the Brassiceae
Cited by: 4
Author(s): Shane Carey, Kerrin Mendler, Jocelyn C. Hall
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0111297

Distinct Strains of Toxoplasma gondii Feature Divergent Transcriptomes Regardless of Developmental Stage
Cited by: 26
Author(s): Matthew McKnight Croken, Yanfen Ma, Lye Meng Markillie, Ron Taylor, Galya Orr, Louis M. Weiss, Kami Kim
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0224909

Sequence count data are poorly fit by the negative binomial distribution
Cited by: 28
Author(s): Stijn Hawinkel, J. C. W. Rayner, Luc Bijnens, Olivier Thas
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2018.00368

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

10.3389/fonc.2020.580276

Transcriptome Based System Biology Exploration Reveals Homogeneous Tumorigenicity of Alimentary Tract Malignancy
Cited by: 2
Author(s): You Lu, Jingqi Shi, Zixin Zhang, Jiayi Zhou, Haikun Zhou, Yuancai Feng, Zhenhua Lu, Shuya Yang, Xi-Yang Zhang, Yang Liu, Zichao Li, Yuanjie Sun, Lianhe Zheng, Duyin Jiang, Kun Yang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-015-1254-5

Global transcriptomic profiling demonstrates induction of oxidative stress and of compensatory cellular stress responses in brown trout exposed to glyphosate and Roundup
Cited by: 85
Author(s): Tamsyn M. Uren Webster, Eduarda M. Santos
Software Mentions: 3
Published: almost 12 years ago

10.3389/fonc.2021.641289

Bioinformatics Analysis of a Prognostic miRNA Signature and Potential Key Genes in Pancreatic Cancer
Cited by: 15
Author(s): Shuoling Chen, Chang Gao, Tao Yu, Yueyang Qu, Gary Guishan Xiao, Zunnan Huang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2565-x

Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome
Cited by: 14
Author(s): Aimee Benjamin, Benjamin B. Green, B.A. Crooker, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: over 10 years ago

10.3389/fonc.2020.01109

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

10.3389/fonc.2019.00613

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

10.1186/s12864-017-4296-z

Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews
Cited by: 19
Author(s): Michie Kobayashi, Yukie Hiraka, Akira Abe, Hiroki Yaegashi, Satoshi Natsume, Hideko Kikuchi, Hiroki Takagi, Hiromasa Saitoh, Joe Win, Sophien Kamoun, Ryohei Terauchi
Software Mentions: 3
Published: almost 9 years ago

10.3389/fonc.2020.00979

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

10.1186/s12864-016-2572-y

Genome-wide analysis of ionotropic receptors provides insight into their evolution in Heliconius butterflies
Cited by: 33
Author(s): Bas van Schooten, Chris D. Jiggins, Adriana D. Briscoe, Riccardo Papa
Software Mentions: 3
Published: over 10 years ago

10.3389/fonc.2021.684396

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

10.3389/fonc.2021.644612

The Diagnostic and Immunotherapeutic Value of CD248 in Renal Cell Carcinoma
Cited by: 10
Author(s): Keying Zhang, Chao Xu, Shaojie Li, Yao Jiang, Xiaolong Zhao, Shanjin Ma, Yu Liu, Yang Fa, Yan Wang, Ping Meng, Changhong Shi, Donghui Han, Weihong Wen, Weijun Qin
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2019.00649

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

10.3389/fonc.2020.571167

Identification of CHRNB4 as a Diagnostic/Prognostic Indicator and Therapeutic Target in Human Esophageal Squamous Cell Carcinoma
Cited by: 3
Author(s): Nan Li, Kaisheng Liu, Shaowei Dong, Ling Ou, Jieling Li, Minshan Lai, Yue Wang, Yifan Bao, Huidong Shi, Wang Xiao, Shaoxiang Wang
Software Mentions: 3
Published: almost 6 years ago

10.1002/advs.201902040

Deubiquitylase OTUD6B Governs pVHL Stability in an Enzyme‐Independent Manner and Suppresses Hepatocellular Carcinoma Metastasis
Cited by: 27
Author(s): Xinxin Liu, Xiaoli Zhang, Zhiqiang Peng, Chunnan Li, Ze Wang, Chanjuan Wang, Zhikang Deng, Bo Wu, Yu Cui, Zhanxin Wang, Chun-Ping Chu, Ming‐Hua Zheng, Lingqiang Zhang
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2021.679262

RNA Sequence Profiling Reveals Unique Immune and Metabolic Features of Breast Cancer Brain Metastases
Cited by: 4
Author(s): Liuling Xiao, Jie Zhou, Hongyi Liu, Yuanyuan Zhou, Weibin Chen, Wugeng Cui, Yilin Zhao
Software Mentions: 3
Published: about 5 years ago

10.3389/fonc.2019.00632

Understanding the Mechanistic Contribution of Herbal Extracts in Compound Kushen Injection With Transcriptome Analysis
Cited by: 21
Author(s): Hao Shen, Zhibo Qu, Yuka Harata-Lee, Thazin Nwe Aung, Jingang Cui, Wei Wang, R. Daniel Kortschak, David L. Adelson
Software Mentions: 3
Published: over 7 years ago

10.3389/fphar.2020.00544

Identification of Prognostic miRNA Signature and Lymph Node Metastasis-Related Key Genes in Cervical Cancer
Cited by: 27
Author(s): Shuoling Chen, Chang Gao, Yangyuan Wu, Zunnan Huang
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-16-S12-S7

A novel analysis strategy for integrating methylation and expression data reveals core pathways for thyroid cancer aetiology
Cited by: 3
Author(s): Buğra Özer, Uğur Sezerman
Software Mentions: 3
Published: almost 11 years ago

10.3389/fphar.2021.596535

The Widely Used Antihelmintic Drug Albendazole is a Potent Inducer of Loss of Heterozygosity
Cited by: 3
Author(s): Luiza Sheyla Evenni Porfírio Will Castro, Wietske Pieters, Mir Farshid Alemdehy, Muhammad Aslam, Olimpia Alessandra Buoninfante, Jonne A. Raaijmakers, Bas Pilzecker, Paul C.M. van den Berk, Hein te Riele, René H. Medema, Rozangela Curi Pedrosa, Heinz Jacobs
Software Mentions: 3
Published: over 5 years ago

10.3389/fphar.2020.622658

Involvement of Circulating Exosomal MicroRNAs in Jian-Pi-Yi-Shen Formula Protection Against Adenine-Induced Chronic Kidney Disease
Cited by: 5
Author(s): Xinhui Liu, Siqi Liu, Denggui Luo, Shiying Huang, Fochang Wang, Bing Zhang, Yulian Chen, Lin Zheng, Jiandong Lu, Shunmin Li
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-017-4016-8

Characterization of mechanisms underlying degradation of sclerotia of Sclerotinia sclerotiorum by Aspergillus aculeatus Asp-4 using a combined qRT-PCR and proteomic approach
Cited by: 15
Author(s): Xiaojia Hu, Lü Qin, Daniel P. Roberts, Dilip K. Lakshman, Yiqin Gong, Jude E. Maul, Lin Xie, Chang Yeon Yu, Yinshui Li, Lei Hu, Liao Xiang-sheng, Lixin Xing
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-020-06870-x

Shedding light on cashmere goat hair follicle biology: from morphology analyses to transcriptomic landascape
Cited by: 8
Author(s): Cristina Nocelli, Katia Cappelli, Stefano Capomaccio, Luisa Pascucci, Francesca Mercati, Irene Pazzaglia, Samanta Mecocci, Marco Antonini, Carlo Renieri
Software Mentions: 3
Published: over 6 years ago

10.18632/aging.102566

Development and validation of a nomogram with an autophagy-related gene signature for predicting survival in patients with glioblastoma
Cited by: 63
Author(s): Zihao Wang, Lu Gao, Xiaopeng Guo, Cheng Feng, Wei Lian, Kan Deng, Bing Xing
Software Mentions: 3
Published: almost 7 years ago

10.3389/fphys.2017.00188

Molecular and Cellular Mechanisms of Apoptosis during Dissociated Spermatogenesis
Cited by: 28
Author(s): Tengfei Liu, Lingling Wang, Hong Chen, Yufei Huang, Ping Yang, Nisar Ahmed, Taozhi Wang, Yi Liu, Qiusheng Chen
Software Mentions: 3
Published: over 9 years ago

10.3389/fphys.2019.00101

Characterization of Endothelial and Smooth Muscle Cells From Different Canine Vessels
Cited by: 19
Author(s): Loes A. Oosterhoff, Hedwig S. Kruitwagen, Monique E. van Wolferen, Bas W. M. van Balkom, Michal Mokrý, Nico Lansu, Noortje A.M. van den Dungen, Louis C. Penning, Talitha C.F. Spanjersberg, Johannes W. de Graaf, Tomas Veenendaal, Flin Zomerdijk, Joost O. Fledderus, Bart Spee, Frank G. van Steenbeek
Software Mentions: 3
Published: over 7 years ago

10.3389/fphys.2021.658518

Mechanisms of Impaired Lung Development and Ciliation in Mannosidase-1-Alpha-2 (Man1a2) Mutants
Cited by: 2
Author(s): Mylarappa Ningappa, Morayooluwa Adenuga, Kim A. Ngo, Nada Mohamed, Tejaswini Narayanan, Krishna Prasadan, Chethan Ashokkumar, Jishnu Das, Lori Schmitt, Hannah Hartman, Anuradha Sehrawat, Cláudia Salgado, Miguel Reyes‐Múgica, George K. Gittes, Cecilia Lo, Shankar Subramaniam, Rakesh Sindhi
Software Mentions: 3
Published: over 5 years ago

10.3389/fphys.2020.587358

Transcriptional Programs Driving Shear Stress-Induced Differentiation of Kidney Proximal Tubule Cells in Culture
Cited by: 18
Author(s): Hyun Jung Park, Zhenjiang Fan, Yinge Bai, Qidong Ren, Youssef Rbaibi, Kimberly R. Long, Megan L. Gliozzi, Natalie Rittenhouse, Joseph Locker, Amanda C. Poholek, Ora A. Weisz
Software Mentions: 3
Published: about 6 years ago

10.3389/fphys.2019.00214

Understanding Molecular Mechanisms of the Brain Through Transcriptomics
Cited by: 14
Author(s): Wei Wang, Guang-Zhong Wang
Software Mentions: 3
Published: over 7 years ago

10.3389/fphys.2020.588450

Transcriptome Analysis and Knockdown of the Juvenile Hormone Esterase Gene Reveal Abnormal Feeding Behavior in the Sugarcane Giant Borer
Cited by: 5
Author(s): Daniel D. Noriega, Fabrício Barbosa Monteiro Arraes, José Dijair Antonino, Leonardo Lima Pepino Macedo, Fernando Fonseca, Roberto Coiti Togawa, Priscila Grynberg, Maria C. M. Silva, A. S. Negrisoli, Maria Fátima Grossi-de-Sá
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2164-15-905

Limited sex-biased neural gene expression patterns across strains in Zebrafish (Danio rerio)
Cited by: 54
Author(s): Ryan Y. Wong, Melissa M McLeod, John Godwin
Software Mentions: 3
Published: almost 13 years ago

10.18632/aging.101985

Prediction of competing endogenous RNA coexpression network as prognostic markers in AML
Cited by: 38
Author(s): Jun Dan Wang, Hongsheng Zhou, Xi Xiang Tu, Yi He, Qi Fa Liu, Quentin Liu, Zi Long
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2016.01934

De novo Sequencing and Comparative Transcriptomics of Floral Development of the Distylous Species Lithospermum multiflorum
Cited by: 14
Author(s): James I. Cohen
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-019-5795-x

Transcriptional analysis of renal dopamine-mediated Na+ homeostasis response to environmental salinity stress in Scatophagus argus
Cited by: 10
Author(s): Maoliang Su, Jia Zhou, Zhengyu Duan, Junbin Zhang
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2016.01255

Photosynthate Regulation of the Root System Architecture Mediated by the Heterotrimeric G Protein Complex in Arabidopsis
Cited by: 28
Author(s): Yashwanti Mudgil, Abhijit Karve, Paulo José Pereira Lima Teixeira, Kun Jiang, Meral Tunc‐Ozdemir, Alan M. Jones
Software Mentions: 3
Published: about 10 years ago

10.3389/fpls.2019.01772

Coexpression of PalbHLH1 and PalMYB90 Genes From Populus alba Enhances Pathogen Resistance in Poplar by Increasing the Flavonoid Content
Cited by: 33
Author(s): Qiuxian Bai, Bingbing Duan, Jianchao Ma, Yannan Fen, Shujiao Sun, Qiming Long, Jiaojiao Lv, Dongshi Wan
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2016.00682

Transcriptomic Analysis Identifies Differentially Expressed Genes (DEGs) Associated with Bolting and Flowering in Radish (Raphanus sativus L.)
Cited by: 17
Author(s): Shaoping Nie, Chao Li, Yan Wang, Liang Xu, Everlyne M. Muleke, Mingjia Tang, Xiaochuan Sun, Liwang Liu
Software Mentions: 3
Published: over 10 years ago

10.3389/fpls.2016.01943

Comparative Temporal Transcriptome Profiling of Wheat near Isogenic Line Carrying Lr57 under Compatible and Incompatible Interactions
Cited by: 30
Author(s): Inderjit Singh Yadav, Amandeep Sharma, Satinder Kaur, Natasha Nahar, Subhash Bhardwaj, Tilak Raj Sharma, Parveen Chhuneja
Software Mentions: 3
Published: almost 10 years ago

10.3389/fpls.2020.554520

Characterization of the DREBA4-Type Transcription Factor (SlDREBA4), Which Contributes to Heat Tolerance in Tomatoes
Cited by: 14
Author(s): Lianzhen Mao, Minghua Deng, Shurui Jiang, Haishan Zhu, Yang Zhou, Yanling Yue, Kai Zhao
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-017-4374-2

A survey on cellular RNA editing activity in response to Candida albicans infections
Cited by: 3
Author(s): Yao‐Wei Huang, Yingying Cao, Jiarui Li, Yuanhua Liu, Zhong Wu, Xuan Li, Chen Chen, Pei Hao
Software Mentions: 3
Published: almost 9 years ago

10.3389/fpls.2021.729261

Genome-Wide Characterization of the MLO Gene Family in Cannabis sativa Reveals Two Genes as Strong Candidates for Powdery Mildew Susceptibility
Cited by: 9
Author(s): Noémi Pépin, François Hébert, David L. Joly
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2021.691790

Epigenomic Regulators Elongator Complex Subunit 2 and Methyltransferase 1 Differentially Condition the Spaceflight Response in Arabidopsis
Cited by: 7
Author(s): Anna‐Lisa Paul, Natasha J. Haveman, Brandon Califar, Robert J. Ferl
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-018-4679-9

Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles
Cited by: 39
Author(s): Andrea Grilli, Rossella Bengalli, Eleonora Longhin, Laura Capasso, Maria Carla Proverbio, Mattia Forcato, Silvio Bicciato, Maurizio Gualtieri, Cristina Battaglia, Marina Camatini
Software Mentions: 3
Published: over 8 years ago

10.3389/fpls.2018.01345

Co-expression and Transcriptome Analysis of Marchantia polymorpha Transcription Factors Supports Class C ARFs as Independent Actors of an Ancient Auxin Regulatory Module
Cited by: 37
Author(s): Eduardo Flores-Sandoval, Facundo Romani, John L. Bowman
Software Mentions: 3
Published: about 8 years ago

10.18632/aging.104088

An eleven metabolic gene signature-based prognostic model for clear cell renal cell carcinoma
Cited by: 11
Author(s): Yue Wu, Wa Xian, Huan Feng, Bintao Hu, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Shaogang Wang, Jihong Liu, Tao Wang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-5502-y

Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes
Cited by: 2
Author(s): Hao Cai, Xiangyu Li, Jun He, Wenbin Zhou, Kai Song, You Guo, Huaping Liu, Qingzhou Guan, Haidan Yan, Xianlong Wang, Zheng Guo
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2019.01301

Differential Expression of Candidate Salivary Effector Genes in Pea Aphid Biotypes With Distinct Host Plant Specificity
Cited by: 25
Author(s): Hélène Boulain, Fabrice Legeai, Julie Jaquiéry, Endrick Guy, Stéphanie Morlière, Jean‐Christophe Simon, Akiko Sugio
Software Mentions: 3
Published: about 7 years ago

10.3389/fpls.2016.01920

Glutathione S-transferases and UDP-glycosyltransferases Are Involved in Response to Aluminum Stress in Flax
Cited by: 45
Author(s): Alexey A. Dmitriev, George S. Krasnov, Tatiana A. Rozhmina, Natalya V. Kishlyan, Alexander V. Zyablitsin, А. Ф. Садритдинова, Anastasiya V. Snezhkina, Maria Fedorova, Olga Yu. Yurkevich, Olga V. Muravenko, Nadezhda L. Bolsheva, Anna V. Kudryavtseva, Nataliya V. Melnikova
Software Mentions: 3
Published: almost 10 years ago

10.3389/fpls.2019.00152

Phytochrome A Regulates Carbon Flux in Dark Grown Tomato Seedlings
Cited by: 10
Author(s): Keisha D. Carlson, Sneha Bhogale, Drew Anderson, Lars Tomanek, Andreas Madlung
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-337

Transcriptome differences between two sister desert poplar species under salt stress
Cited by: 36
Author(s): Jian Zhang, Jiexiong Feng, Jing Lü, Yongzhi Yang, Xu Zhang, Dongshi Wan, Jianquan Liu
Software Mentions: 3
Published: over 12 years ago

10.3389/fpls.2020.01124

Novel Role of JAC1 in Influencing Photosynthesis, Stomatal Conductance, and Photooxidative Stress Signalling Pathway in Arabidopsis thaliana
Cited by: 5
Author(s): Weronika Czarnocka, Anna Rusaczonek, Patrick J. Willems, Marzena Sujkowska‐Rybkowska, Frank Van Breusegem, Stanisław Karpiński
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2017.01260

Tissue-Specific Floral Transcriptome Analysis of the Sexually Deceptive Orchid Chiloglottis trapeziformis Provides Insights into the Biosynthesis and Regulation of Its Unique UV-B Dependent Floral Volatile, Chiloglottone 1
Cited by: 16
Author(s): D. Wong, Ranamalie Amarasinghe, Claudia Rodriguez‐Delgado, Rodney Eyles, Eran Pichersky, Rod Peakall
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2017.01545

De novo Assembly of the Camellia nitidissima Transcriptome Reveals Key Genes of Flower Pigment Biosynthesis
Cited by: 41
Author(s): Xingyi Zhou, Jiyuan Li, Yong‐Guan Zhu, Ni Sui, Jinling Chen, Xiaojuan Feng, Yunfeng Zhang, Shuangquan Li, Hongxiang Zhu, Wen Yu
Software Mentions: 3
Published: about 9 years ago

10.3389/fpls.2020.01208

Fruit Development in Ficus carica L.: Morphological and Genetic Approaches to Fig Buds for an Evolution From Monoecy Toward Dioecy
Cited by: 15
Author(s): Ilaria Marcotuli, Andrea Mazzeo, Pasqualina Colasuonno, Roberto Terzano, Domenica Nigro, Carlo Porfido, Annalisa Tarantino, Riccardo Aiese Cigliano, Walter Sanseverino, Ágata Gadaleta, Giuseppe Ferrara
Software Mentions: 3
Published: about 6 years ago

10.3389/fpls.2016.01039

Comparative Transcriptome Reconstruction of Four Hypericum Species Focused on Hypericin Biosynthesis
Cited by: 17
Author(s): Miroslav Soták, Odeta Czeranková, Daniel Klein, Zuzana Jurčacková, Ling Li, Eva Čellárová
Software Mentions: 3
Published: over 10 years ago

10.3389/fpls.2016.01083

De novo Assembly and Characterization of the Transcriptome of Broomcorn Millet (Panicum miliaceum L.) for Gene Discovery and Marker Development
Cited by: 21
Author(s): Hong Yue, Le Wang, Hui Liu, Wenjie Yue, Xianghong Du, Weining Song, Xiaojun Nie
Software Mentions: 3
Published: over 10 years ago

10.3389/fpls.2015.01246

A De novo Transcriptomic Approach to Identify Flavonoids and Anthocyanins “Switch-Off” in Olive (Olea europaea L.) Drupes at Different Stages of Maturation
Cited by: 30
Author(s): Domenico Iaria, Adriana Chiappetta, Innocenzo Muzzalupo
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-020-6570-8

MicroRNA expression profile analysis in sperm reveals hsa-mir-191 as an auspicious omen of in vitro fertilization
Cited by: 37
Author(s): Hua Xu, Xin Wang, Zhikai Wang, Jianhui Li, Zhiming Xu, Maohua Miao, Guowu Chen, Xiang-Dong Lei, Jun Wu, Huijuan Shi, Ke Wang, Tiancheng Zhang, Xiaoxi Sun
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-4521-4

Lineage-specific duplications of NBS-LRR genes occurring before the divergence of six Fragaria species
Cited by: 20
Author(s): Yan Zhong, Xiaohui Zhang, Zong‐Ming Cheng
Software Mentions: 3
Published: over 8 years ago

10.18632/aging.202493

Identification of hub genes associated with adult acute myeloid leukemia progression through weighted gene co-expression network analysis
Cited by: 4
Author(s): Ruiqi Zhu, Wenyi Lin, Liang Tang, Yu Hu
Software Mentions: 3
Published: over 5 years ago

10.3389/fpls.2017.01866

Transcriptomic and Hormonal Analyses Reveal that YUC-Mediated Auxin Biogenesis Is Involved in Shoot Regeneration from Rhizome in Cymbidium
Cited by: 11
Author(s): Yang Liu, Hai-Liang Zhang, He-Rong Guo, Li Xie, Ruizhen Zeng, Xiangqian Zhang, Zhisheng Zhang
Software Mentions: 3
Published: about 9 years ago

10.3389/fpls.2017.00468

Transcriptomic Response of Chinese Yew (Taxus chinensis) to Cold Stress
Cited by: 29
Author(s): Delong Meng, YU Xiang-hua, Liyuan Ma, Jin Hu, Yili Liang, Xueduan Liu, Huaqun Yin, Hongwei Liu, Xiaojia He, Diqiang Li
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2018.01163

Gene Co-expression Network Analysis Suggests the Existence of Transcriptional Modules Containing a High Proportion of Transcriptionally Differentiated Homoeologs in Hexaploid Wheat
Cited by: 15
Author(s): Kotaro Takahagi, Komaki Inoue, Keiichi Mochida
Software Mentions: 3
Published: about 8 years ago

10.3389/fvets.2015.00068

Cystoisospora suis – A Model of Mammalian Cystoisosporosis
Cited by: 22
Author(s): Aruna Shrestha, Ahmed Abdelfattah, Barbara Freudenschuss, Barbara Hinney, Nicola Palmieri, Bärbel Ruttkowski, Anja Joachim
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12983-017-0245-6

Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics
Cited by: 17
Author(s): Yalin Cheng, Bin Gao, Haitao Wang, Ning Han, Shimiao Shao, Shaoyuan Wu, Gang Song, Yong E. Zhang, Zhu Xihua, Xin Lü, Yanhua Qu, Fumin Lei
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-016-2704-4

Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
Cited by: 30
Author(s): Nikol Voutsina, Adrienne Payne, Robert D. Hancock, Graham J. J. Clarkson, Steve D. Rothwell, Mark A. Chapman, Gail Taylor
Software Mentions: 3
Published: over 10 years ago

10.1534/g3.114.013417

Population- and Sex-Biased Gene Expression in the Excretion Organs of Drosophila melanogaster
Cited by: 34
Author(s): Ann Kathrin Huylmans, John Parsch
Software Mentions: 3
Published: almost 12 years ago

10.1534/g3.115.020982

An Examination of Dynamic Gene Expression Changes in the Mouse Brain During Pregnancy and the Postpartum Period
Cited by: 42
Author(s): Surjyendu Ray, Ruei-Ying Tzeng, Lisa M. DiCarlo, Joseph L. Bundy, Cynthia Vied, Gary Tyson, Richard S. Nowakowski, Michelle N. Arbeitman
Software Mentions: 3
Published: almost 11 years ago

10.1534/g3.116.034595

Obp56hModulates Mating Behavior inDrosophila melanogaster
Cited by: 21
Author(s): John R. Shorter, Lauren M. Dembeck, Logan J. Everett, Tatiana V. Morozova, Gunjan H. Arya, Lavanya Turlapati, Genevieve E. St. Armour, Coby Schal, Trudy F. C. Mackay, Robert R. H. Anholt
Software Mentions: 3
Published: about 10 years ago

10.1534/g3.116.032839

Transcriptome Analysis Reveals that Vitamin A Metabolism in the Liver Affects Feed Efficiency in Pigs
Cited by: 31
Author(s): Yi‐Fang Zhao, Ye Hou, Fei Liu, An Liu, Jing Lü, Changzhi Zhao, Yu Luan, Yuanxin Miao, Shuhong Zhao, Xinyun Li
Software Mentions: 3
Published: about 10 years ago

10.1038/sdata.2017.20

Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells
Cited by: 11
Author(s): Stephen J. Pettitt, Dragomir B. Krastev, Helen Pemberton, Yari Fontebasso, Jessica Frankum, Farah L. Rehman, Rachel Brough, Feifei Song, Ilirjana Bajrami, Rumana Rafiq, Fredrik Wållberg, Iwanka Kozarewa, Kerry Fenwick, Javier Armisen-Garrido, Amanda Swain, Aditi Gulati, James Campbell, Alan Ashworth, Christopher J. Lord
Software Mentions: 3
Published: over 9 years ago

10.1038/sdata.2017.118

A gene expression atlas of adult Schistosoma mansoni and their gonads
Cited by: 44
Author(s): Zhigang Lu, Florian Sessler, Nancy Holroyd, Steffen Hahnel, Thomas Quack, Matthew Berriman, Christoph G. Grevelding
Software Mentions: 3
Published: about 9 years ago

10.1038/sdata.2017.163

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system
Cited by: 4
Author(s): Margherita Francescatto, Marina Lizio, Ingrid H.C.H.M. Philippens, Luba M. Pardo, Ronald E. Bontrop, Mizuho Sakai, Shoko Watanabe, Masayoshi Itoh, Akira Hasegawa, Timo Lassmann, Jessica Severin, Jayson Harshbarger, Imad Abugessaisa, Takeya Kasukawa, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Hideya Kawaji, Patrizia Rizzu, Peter Heutink
Software Mentions: 3
Published: about 9 years ago

10.1038/s41597-019-0117-3

Metagenomics and transcriptomics data from human colorectal cancer
Cited by: 5
Author(s): Tina Visnovska, Patrick J. Biggs, Frank Frizelle, Rachel Purcell
Software Mentions: 3
Published: over 7 years ago

10.1038/s41597-020-00628-6

Consensus transcriptional regulatory networks of coronavirus-infected human cells
Cited by: 23
Author(s): Scott A. Ochsner, Rudolf T. Pillich, Neil J. McKenna
Software Mentions: 3
Published: about 6 years ago

10.1111/acel.13420

Circulating microRNA profile in humans and mice with congenital GH deficiency
Cited by: 6
Author(s): Tatiana D. Saccon, Augusto Schneider, Cindi G. Marinho, Allancer D C Nunes, Sarah Noureddine, Joseph M. Dhahbi, Yury O. Nunez Lopez, Gage LeMunyan, Roberto Salvatori, Carla R. P. Oliveira, Alécia A Oliveira-Santos, Nicolas Musi, Andrzej Bartke, Manuel H. Aguiar‐Oliveira, Michał M. Masternak
Software Mentions: 3
Published: over 5 years ago

10.1111/acel.13357

Age‐related telomere attrition causes aberrant gene expression in sub‐telomeric regions
Cited by: 8
Author(s): Xiao Dong, Shixiang Sun, Lei Zhang, Seung-Soo Kim, Zhidong Tu, Cristina Montagna, Alexander Y. Maslov, Yousin Suh, Tao Wang, Judith Campisi, Jan Vijg
Software Mentions: 3
Published: over 5 years ago

10.1038/srep02898

Soft truncation thresholding for gene set analysis of RNA-seq data: Application to a vaccine study
Cited by: 15
Author(s): Brooke L. Fridley, Gregory D. Jenkins, Diane E. Grill, Richard B. Kennedy, Gregory A. Poland, Ann L. Oberg
Software Mentions: 3
Published: about 13 years ago

10.1111/acel.13232

Autophagy‐Sirt3 axis decelerates hematopoietic aging
Cited by: 21
Author(s): Yixuan Fang, Ni An, Lingjiang Zhu, Yue Gu, Jiawei Qian, Gaoyue Jiang, Ruijin Zhao, Wei Wen, Li Xu, Gaochuan Zhang, Xingyun Yao, Na Yuan, Suping Zhang, Yun Zhao, Jianrong Wang
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-019-5556-x

Linear models enable powerful differential activity analysis in massively parallel reporter assays
Cited by: 272
Author(s): Leslie Myint, Dimitrios Avramopoulos, Loyal A. Goff, Kasper D. Hansen
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-020-07151-3

Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and the transcription factor ZGPAT co-regulate milk production
Cited by: 3
Author(s): Jinwei Xin, Zhixin Chai, Chengfu Zhang, Qiang Zhang, Yong Zhu, Hanwen Cao, Yangji Cidan, Xiaoying Chen, Hui Jiang, Jincheng Zhong, Qiumei Ji
Software Mentions: 3
Published: about 6 years ago

10.1038/srep13456

TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability
Cited by: 15
Author(s): Lamiaa Bahnassawy, Thanneer M. Perumal, Laura González-Cano, Anna-Lena Hillje, Leila Taher, Wojciech Makałowski, Yutaka Suzuki, Georg Fuellen, Antonio del Sol, Jens Christian Schwamborn
Software Mentions: 3
Published: about 11 years ago

10.1186/s12864-019-5574-8

YPR2 is a regulator of light modulated carbon and secondary metabolism in Trichoderma reesei
Cited by: 28
Author(s): Eva Hitzenhammer, Christoph Büschl, Michael Sulyok, Rainer Schuhmacher, Bernhard Kluger, Elisabeth Wischnitzki, Monika Schmoll
Software Mentions: 3
Published: over 7 years ago

10.1038/srep18399

Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing
Cited by: 56
Author(s): Aroa Suárez-Vega, Christophe Klopp, Christèle Robert-Granié, Gwenola Tosser‐Klopp, Juan José Arranz
Software Mentions: 3
Published: almost 11 years ago

10.1038/srep20837

Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model
Cited by: 15
Author(s): Els Willems, Carlos Guerrero-Bosagna, Eddy Decuypere, Steven Janssens, Johan Buyse, Nadine Buys, Per Jensen, Nadia Everaert
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-016-2720-4

Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus
Cited by: 27
Author(s): Jamie M. Wilkinson, Hua Bao, Andrea Ladinig, Linjun Hong, Paul Stothard, Joan K. Lunney, Graham Plastow, John C. S. Harding
Software Mentions: 3
Published: over 10 years ago

10.1038/srep24061

Empirical insights into the stochasticity of small RNA sequencing
Cited by: 5
Author(s): Li‐Xuan Qin, Thomas Tuschl, Samuel Singer
Software Mentions: 3
Published: over 10 years ago

10.1038/srep24964

Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection
Cited by: 34
Author(s): Guanxiang Liang, Nilusha Malmuthuge, Yongjuan Guan, Yan Ren, Philip Griebel, Le Luo Guan
Software Mentions: 3
Published: over 10 years ago

10.1038/srep25474

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells
Cited by: 41
Author(s): Pamela Milani, Renan Escalante-Chong, Brandon Shelley, Natasha L. Patel-Murray, Xin X, Miriam Adam, Berhan Mandefro, Dhruv Sareen, Clive N. Svendsen, Ernest Fraenkel
Software Mentions: 3
Published: over 10 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568