bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2020.00804

Elizabethkingia anophelis: Physiologic and Transcriptomic Responses to Iron Stress
Cited by: 13
Author(s): Shicheng Chen, Benjamin K. Johnson, Ting Yu, Brooke N. Nelson, Edward D. Walker
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2018.00124

Worlds Apart – Transcriptome Profiles of Key Oral Microbes in the Periodontal Pocket Compared to Single Laboratory Culture Reflect Synergistic Interactions
Cited by: 41
Author(s): Zhi-Luo Deng, Helena Sztajer, Michael Jarek, Sabin Bhuju, Irene Wagner‐Döbler
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2020.601037

Taxonomic Diversity of Pico-/Nanoeukaryotes Is Related to Dissolved Oxygen and Productivity, but Functional Composition Is Shaped by Limiting Nutrients in Eutrophic Coastal Oceans
Cited by: 10
Author(s): Yaping Wang, Guihao Li, Fei Shi, Jun Dong, Eleni Gentekaki, Songbao Zou, Ping Zhu, Xiaoli Zhang, Jun Gong
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2021.643087

Antibiotrophy: Key Function for Antibiotic-Resistant Bacteria to Colonize Soils—Case of Sulfamethazine-Degrading Microbacterium sp. C448
Cited by: 6
Author(s): Loren Billet, Stéphane Pesce, Nadine Rouard, Aymé Spor, Laurianne Paris, Martin Leremboure, Arnaud Mounier, Pascale Besse-Hoggan, Fabrice Martin-Laurent, Marion Devers‐Lamrani
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2014.00402

Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification
Cited by: 36
Author(s): David H. Keating, Yaoping Zhang, Irene M. Ong, Sean J. McIlwain, Eduardo Morales, Jeffrey A. Grass, Mary Tremaine, William Bothfeld, Alan Higbee, Arne Ulbrich, Allison J. Balloon, Michael S. Westphall, Josh Aldrich, Mary Lipton, Joonhoon Kim, Oleg V. Moskvin, Yury V. Bukhman, Joshua J. Coon, Patricia J. Kiley, Donna M. Bates, Robert Landick
Software Mentions: 2
Published: about 12 years ago

10.3389/fmicb.2016.01731

Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula
Cited by: 41
Author(s): Catherine M. Luria, Linda Amaral‐Zettler, Hugh W. Ducklow, Jeremy J. Rich
Software Mentions: 2
Published: almost 10 years ago

10.3389/fmicb.2018.00268

The Small RNA RyhB Is a Regulator of Cytochrome Expression in Shewanella oneidensis
Cited by: 9
Author(s): Karin L. Meibom, Elena M. Cabello, Rizlan Bernier‐Latmani
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2017.02676

Transcriptional Modulation of Penicillin-Binding Protein 1b, Outer Membrane Protein P2 and Efflux Pump (AcrAB-TolC) during Heat Stress Is Correlated to Enhanced Bactericidal Action of Imipenem on Non-typeable Haemophilus influenzae
Cited by: 3
Author(s): Abdessalam Cherkaoui, Seydina M. Diène, Adrien Fischer, Stefano Leo, Patrice François, Jacques Schrenzel
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2020.01024

Characterization of Bacterial and Fungal Assemblages From Historically Contaminated Metalliferous Soils Using Metagenomics Coupled With Diffusion Chambers and Microbial Traps
Cited by: 14
Author(s): Ashish Pathak, Rajneesh Jaswal, Xiaoyu Xu, John R. White, Bobby Edwards, Jaden Hunt, Scott C. Brooks, Rajesh Rathore, Meenakshi Agarwal, Ashvini Chauhan
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2020.01134

Phenotypic Variation and Carbapenem Resistance Potential in OXA-499-Producing Acinetobacter pittii
Cited by: 5
Author(s): Linyue Zhang, Ying Fu, Xinhong Han, Qingye Xu, Shanshan Weng, Biyong Yan, Lilin Liu, Xiaoting Hua, Yan Chen, Yunsong Yu
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2020.601864

Episodic Decrease in Temperature Increases mcy Gene Transcription and Cellular Microcystin in Continuous Cultures of Microcystis aeruginosa PCC 7806
Cited by: 20
Author(s): Robbie M. Martin, Mohammad Moniruzzaman, Gwendolyn F. Stark, Eric R. Gann, Dominique S. Derminio, Bofan Wei, Ferdi L. Hellweger, Ameet J. Pinto, Gregory L. Boyer, Steven W. Wilhelm
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2017.02321

Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities
Cited by: 23
Author(s): Theodore M. Flynn, Jason C. Koval, Stephanie M. Greenwald, Sarah M. Owens, Kenneth M. Kemner, Dionysios A. Antonopoulos
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2017.02453

Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism
Cited by: 27
Author(s): Elias Broman, Varvara Sachpazidou, Jarone Pinhassi, Mark Dopson
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2018.00698

Interactions Among Host–Parasite MicroRNAs During Nosema ceranae Proliferation in Apis mellifera
Cited by: 13
Author(s): Jay D. Evans, Qiang Huang
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2017.01672

Complete Circular Genome Sequence and Temperature Independent Adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698
Cited by: 0
Author(s): Elena Ferrari, Mathias C. Walter, Christopher Huptas, Siegfried Scherer, Stefanie Müller-Herbst
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2021.626443

Specialization of the Reiterated Copies of the Heterodimeric Integration Host Factor Genes in Geobacter sulfurreducens
Cited by: 5
Author(s): Ángel Andrade, Alberto Hernández-Eligio, Ana Lilia Tirado, Leticia Vega‐Alvarado, Maricela Olvera, Enrique Morett, Katy Juárez
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2018.03190

Specific Effect of Trace Metals on Marine Heterotrophic Microbial Activity and Diversity: Key Role of Iron and Zinc and Hydrocarbon-Degrading Bacteria
Cited by: 13
Author(s): Federico Baltar, Andres Gutiérrez‐Rodríguez, Moana Meyer, Isadora Skudelny, Sylvia G. Sander, Blair Thomson, Scott D. Nodder, Rob Middag, Sergio E. Morales
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2019.00590

Metatranscriptomic Signatures Associated With Phytoplankton Regime Shift From Diatom Dominance to a Dinoflagellate Bloom
Cited by: 48
Author(s): Yaqun Zhang, Xin Lin, Xinguo Shi, Lingxiao Lin, Hao Luo, Ling Li, Senjie Lin
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2021.724345

Blood Meals With Active and Heat-Inactivated Serum Modifies the Gene Expression and Microbiome of Aedes albopictus
Cited by: 2
Author(s): Arley Calle-Tobón, Andrés F. Holguin-Rocha, C Mark Moore, Meagan Rippee-Brooks, Paula Rozo-López, Jania Harrod, Soheila Fatehi, Guillermo Rúa‐Uribe, Yoonseong Park, Berlin Londoño-Rentería
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2018.02413

Transcriptomics Study on Staphylococcus aureus Biofilm Under Low Concentration of Ampicillin
Cited by: 40
Author(s): Junyan Liu, Ling Yang, Yuchao Hou, Thanapop Soteyome, Bingbing Zeng, Jianyu Su, Lin Li, Bing Li, Dingqiang Chen, Yanyan Li, Aiwu Wu, Mark E. Shirtliff, Janette M. Harro, Zhenbo Xu, Brian M. Peters
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2018.01416

Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli
Cited by: 6
Author(s): Christina Gabrielsen, Finn Drabløs, Kjersti Haugum, Jan Egil Afset
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2019.01659

MicroRNA Expression Profiling in Newcastle Disease Virus-Infected DF-1 Cells by Deep Sequencing
Cited by: 13
Author(s): Yu Chen, Wen Liu, Haixu Xu, Jingjing Liu, Yifan Deng, Hao Cheng, Shanshan Zhu, Yuru Pei, Jiao Hu, Zenglei Hu, Xiaowen Liu, Xiaoquan Wang, Minghong Gu, Shunlin Hu
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2020.600463

Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens
Cited by: 23
Author(s): Hunter Dulay, Marcela Tabares, Kazem Kashefi, Gemma Reguera
Software Mentions: 2
Published: almost 6 years ago

10.3389/fpls.2019.01076

Alternative Splicing Regulation During Light-Induced Germination of Arabidopsis thaliana Seeds
Cited by: 27
Author(s): Rocío Soledad Tognacca, Lucas Servi, Carlos Esteban Hernando, Maite Saura-Sánchez, Marcelo J. Yanovsky, Ezequiel Petrillo, Javier Francisco Botto
Software Mentions: 2
Published: almost 7 years ago

10.3389/fpls.2017.01653

Assembly and Annotation of Transcriptome Provided Evidence of miRNA Mobility between Wheat and Wheat Stem Sawfly
Cited by: 18
Author(s): H Busra Cagirici, Sezgi Biyiklioglu, Hikmet Budak
Software Mentions: 2
Published: almost 9 years ago

10.3389/fpls.2017.00873

Small RNA-Sequencing Links Physiological Changes and RdDM Process to Vegetative-to-Floral Transition in Apple
Cited by: 24
Author(s): Xinwei Guo, Zeyang Ma, Zhonghui Zhang, Lailiang Cheng, Xiuren Zhang, Tianhong Li
Software Mentions: 2
Published: over 9 years ago

10.3389/fpls.2018.01206

The Digestive System of the Two-Spotted Spider Mite, Tetranychus urticae Koch, in the Context of the Mite-Plant Interaction
Cited by: 37
Author(s): Nicolas Bensoussan, Vladimir Zhurov, Sota Yamakawa, Caroline O’Neil, Takeshi Suzuki, Miodrag Grbić, Vojislava Grbić
Software Mentions: 2
Published: almost 8 years ago

10.3389/fpls.2016.01653

Insights from the Cold Transcriptome and Metabolome of Dendrobium officinale: Global Reprogramming of Metabolic and Gene Regulation Networks during Cold Acclimation
Cited by: 64
Author(s): Zhigang Wu, Jiang Wu, Songlin Chen, Nitin Mantri, Zheng-Ming Tao, Chengxi Jiang
Software Mentions: 2
Published: almost 10 years ago

10.3389/fpls.2019.01669

Small RNA Bidirectional Crosstalk During the Interaction Between Wheat and Zymoseptoria tritici
Cited by: 23
Author(s): Xin Ma, Jasmin Wiedmer, Javier Palma‐Guerrero
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2017.00647

Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace
Cited by: 46
Author(s): Carlos Pérez Cantalapiedra, María Jesús García-Pereira, María Pilar Rivero Gracia, Ernesto Igartua, Ana M. Casas, Bruno Contreras‐Moreira
Software Mentions: 2
Published: over 9 years ago

10.3389/fpls.2021.680151

Transcriptomic Analysis of Resistant and Susceptible Responses in a New Model Root-Knot Nematode Infection System Using Solanum torvum and Meloidogyne arenaria
Cited by: 12
Author(s): Kenzo Sato, Taketo Uehara, Julia Holbein, Yuko Sasaki-Sekimoto, Pamela Gan, Takahiro Bino, Katsushi Yamaguchi, Yasunori Ichihashi, Noriko Maki, Shuji Shigenobu, Hiroyuki Ohta, Rochus Franke, Shahid Siddique, Florian M. W. Grundler, Takamasa Suzuki, Yasuhiro Kadota, Ken Shirasu
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2016.01517

Morphological Characterization and Gene Expression Profiling during Bud Development in a Tropical Perennial, Litchi chinensis Sonn.
Cited by: 10
Author(s): Huifen Zhang, Hua Li, Bo Lai, Haoqiang Xia, Huicong Wang, Xu-Ming Huang
Software Mentions: 2
Published: almost 10 years ago

10.3389/fpls.2021.625520

De novo Transcriptome Assembly and Comparative Analysis Highlight the Primary Mechanism Regulating the Response to Selenium Stimuli in Oats (Avena sativa L.)
Cited by: 2
Author(s): Tao Liu, Xiaoting Liu, Rangrang Zhou, Hong Chen, Huaigang Zhang, Bo Zhang
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2014.00658

Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling
Cited by: 50
Author(s): Piyada Juntawong, Anchalee Sirikhachornkit, Rachaneeporn Pimjan, Chutima Sonthirod, Duangjai Sangsrakru, Thippawan Yoocha, Sithichoke Tangphatsornruang, Peerasak Srinives
Software Mentions: 2
Published: over 11 years ago

10.3389/fpls.2014.00277

Transcriptomic landscape of prophase I sunflower male meiocytes
Cited by: 12
Author(s): Nathalia Flórez-Zapata, M. H. Reyes-Valdés, Fernando Hernández-Godínez, Octavio Martínez
Software Mentions: 2
Published: about 12 years ago

10.3389/fpls.2021.719549

High-Throughput Sequencing Reveals the Regulatory Networks of Transcriptome and Small RNAs During the Defense Against Marssonina brunnea in Poplar
Cited by: 4
Author(s): Yangwenke Liao, Qingyue Zhang, Rongrong Cui, Xin Xu, Feng Zhu, Qiang Cheng, Yong Li
Software Mentions: 2
Published: almost 5 years ago

10.3389/fpls.2018.01908

Heliaphen, an Outdoor High-Throughput Phenotyping Platform for Genetic Studies and Crop Modeling
Cited by: 28
Author(s): Florie Gosseau, Nicolas Blanchet, Didier Varès, Philippe Burger, Didier Campergue, Céline Colombet, Louise Gody, Jean-François Liévin, Brigitte Mangin, Gilles Tison, Patrick Vincourt, Pierre Casadebaig, Nicolas B. Langlade
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2017.00958

Discovery of Putative Herbicide Resistance Genes and Its Regulatory Network in Chickpea Using Transcriptome Sequencing
Cited by: 19
Author(s): Mir Asif Iquebal, Khela Ram Soren, Priyanka Gangwar, P. S. Shanmugavadivel, K. Aravind, Deepak Singla, Sarika Jaiswal, Rahul Singh Jasrotia, Sushil K. Chaturvedi, Narendra Pratap Singh, Rajeev K. Varshney, Anil Rai, Dinesh Kumar
Software Mentions: 2
Published: about 9 years ago

10.3389/fpls.2021.655565

PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses
Cited by: 2
Author(s): Huiyuan Wang, Sheng Liu, Xiufang Dai, Yongkang Yang, Yunjun Luo, Yanfeng Gao, Xuqing Liu, Wentao Wei, Huihui Wang, Xi Xu, Anireddy S. N. Reddy, Pankaj Jaiswal, Wei Li, Bo Liu, Lianfeng Gu
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2017.01985

Transcriptomic Profiling and Physiological Responses of Halophyte Kochia sieversiana Provide Insights into Salt Tolerance
Cited by: 17
Author(s): Lijie Zhao, Zongze Yang, Qiaobing Guo, Shun Mao, Shaoqiang Li, Fasheng Sun, Huan Wang, Chunwu Yang
Software Mentions: 2
Published: almost 9 years ago

10.3389/fpls.2015.01148

RNA Sequencing Analysis of the msl2msl3, crl, and ggps1 Mutants Indicates that Diverse Sources of Plastid Dysfunction Do Not Alter Leaf Morphology Through a Common Signaling Pathway
Cited by: 4
Author(s): Darron R. Luesse, Margaret E. Wilson, Elizabeth S. Haswell
Software Mentions: 2
Published: over 10 years ago

10.3389/fpls.2021.701969

Transcriptome Alterations of an in vitro-Selected, Moderately Resistant, Two-Row Malting Barley in Response to 3ADON, 15ADON, and NIV Chemotypes of Fusarium graminearum
Cited by: 5
Author(s): James R. Tucker, W. G. Legge, Sujit Maiti, Colin W. Hiebert, Şenay Şimşek, Zhen Yao, Wayne Xu, Ana Badea, W. G. Dilantha Fernando
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2019.00192

Transcriptome Profiling and Genome-Wide Association Studies Reveal GSTs and Other Defense Genes Involved in Multiple Signaling Pathways Induced by Herbicide Safener in Grain Sorghum
Cited by: 23
Author(s): You Soon Baek, Loren V. Goodrich, Patrick J. Brown, Brandon T. James, Stephen P. Moose, Kris N. Lambert, Dean E. Riechers
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2019.00892

sRNA Profiling Combined With Gene Function Analysis Reveals a Lack of Evidence for Cross-Kingdom RNAi in the Wheat – Zymoseptoria tritici Pathosystem
Cited by: 37
Author(s): Graeme J. Kettles, Bernhard J. Hofinger, Patrick J. Hu, Carlos Bayón, J. J. Rudd, Dirk Balmer, Mikaël Courbot, K. E. Hammond‐Kosack, Gabriel Scalliet, K. Kanyuka
Software Mentions: 2
Published: about 7 years ago

10.3389/fpls.2021.637595

The RsmA RNA-Binding Proteins in Pseudomonas syringae Exhibit Distinct and Overlapping Roles in Modulating Virulence and Survival Under Different Nutritional Conditions
Cited by: 9
Author(s): Jun Li, Menghao Yu, Yixin Ge, Yuee Tian, Baishi Hu, Youfu Zhao
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2018.01160

Global Transcriptome Analyses Reveal Differentially Expressed Genes of Six Organs and Putative Genes Involved in (Iso)flavonoid Biosynthesis in Belamcanda chinensis
Cited by: 8
Author(s): Mei Tian, Xiang Zhang, Zhu Yu, Xie GuangHui, Min-Jian Qin
Software Mentions: 2
Published: about 8 years ago

10.3389/fpls.2016.00925

A De Novo-Assembly Based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies
Cited by: 7
Author(s): Li Guo, Kelly S. Allen, Greg Deiulio, Yong Zhang, Angela M. Madeiras, Robert L. Wick, Lijun Ma
Software Mentions: 2
Published: about 10 years ago

10.3389/fpls.2019.01019

A Role for Pre-mRNA-PROCESSING PROTEIN 40C in the Control of Growth, Development, and Stress Tolerance in Arabidopsis thaliana
Cited by: 12
Author(s): Carlos Esteban Hernando, Mariano García Hourquet, María José de Leone, Daniel Alejandro Careno, Javier Alonso Iserte, Santiago Mora Garcia, Marcelo J. Yanovsky
Software Mentions: 2
Published: about 7 years ago

10.3389/fpls.2015.01086

De novo Transcriptome Assembly of a Chinese Locoweed (Oxytropis ochrocephala) Species Provides Insights into Genes Associated with Drought, Salinity, and Cold Tolerance
Cited by: 18
Author(s): Wei He, Zhuang Hu, Yànpíng Fù, Linwei Guo, Bin Guo, Lizhu Guo, Xiuhong Zhang, Yahui Wei
Software Mentions: 2
Published: over 10 years ago

10.3389/fpls.2021.664311

Comparative Transcriptomics and Proteomics Analyses of Leaves Reveals a Freezing Stress-Responsive Molecular Network in Winter Rapeseed (Brassica rapa L.)
Cited by: 7
Author(s): Wei Ji, Guoqiang Zheng, Xingwang Yu, Sushuang Liu, Xiaoyun Dong, Xiaodong Cao, Xinling Fang, Hui Li, Jiaojiao Jin, Wenbo Mi, Liu Zigang
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2020.572193

Functional Analysis of the teosinte branched 1 Gene in the Tetraploid Switchgrass (Panicum virgatum L.) by CRISPR/Cas9-Directed Mutagenesis
Cited by: 10
Author(s): Yang Liu, Weiling Wang, Bing Yang, Christopher J. Currey, Shui‐zhang Fei
Software Mentions: 2
Published: almost 6 years ago

10.3389/fnsys.2018.00063

Gene Network Dysregulation in the Trigeminal Ganglia and Nucleus Accumbens of a Model of Chronic Migraine-Associated Hyperalgesia
Cited by: 19
Author(s): Hyeonsoo Jeong, Laura S. Moye, Bruce R. Southey, Álvaro Gonzalez Hernández, Isaac Dripps, Elena V. Romanova, Stanislav S. Rubakhin, Jonathan V. Sweedler, Amynah Pradhan, Sandra L. Rodriguez-Zas
Software Mentions: 2
Published: over 7 years ago

10.3389/fnsys.2020.571011

Prolonged Targeted Cardiovascular Epidural Stimulation Improves Immunological Molecular Profile: A Case Report in Chronic Severe Spinal Cord Injury
Cited by: 7
Author(s): Ona Bloom, Jill M. Wecht, Bonnie Legg Ditterline, Siqi Wang, Alexander V. Ovechkin, Cláudia A. Angeli, Anthony A. Arcese, Susan J. Harkema
Software Mentions: 2
Published: almost 6 years ago

10.3389/fvets.2021.587659

Next-Generation Intestinal Toxicity Model of Human Embryonic Stem Cell-Derived Enterocyte-Like Cells
Cited by: 2
Author(s): Bokyeong Ryu, Mi‐Young Son, Kwang Bo Jung, Ukjin Kim, Jin Kim, Ohman Kwon, Ye Seul Son, Cho‐Rok Jung, Jae‐Hak Park, C‐Yoon Kim
Software Mentions: 2
Published: almost 5 years ago

10.3389/fvets.2021.662002

RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course
Cited by: 5
Author(s): Kirsten E. McLoughlin, Carolina N. Correia, John A. Browne, David A. Magee, Nicolas C. Nalpas, Kévin Rue-Albrecht, Adam O. Whelan, Bernardo Villarreal‐Ramos, H. M. Vordermeier, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 2
Published: over 5 years ago

10.3389/fvets.2021.625609

Deep Insight Into Long Non-coding RNA and mRNA Transcriptome Profiling in HepG2 Cells Expressing Genotype IV Swine Hepatitis E Virus ORF3
Cited by: 1
Author(s): Jiao Hu, Xuehong Shuai, Yichen Luo, Zhixiong Zhou, Yu Zhao, Bowen Li, Guojing Gu, Wenjie Li, Mengjuan Li, Hui Zeng, Xi Guo, Yinlong Xiao, Zhenhui Song, Ling Gan, Qingzhou Huang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12983-020-00355-z

Full-length transcriptome sequencing and comparative transcriptomic analysis to uncover genes involved in early gametogenesis in the gonads of Amur sturgeon (Acipenser schrenckii)
Cited by: 17
Author(s): Xiujuan Zhang, Jiabin Zhou, Linmiao Li, Wumeng Huang, Hafiz Ishfaq Ahmad, Huiming Li, Haiying Jiang, Jinping Chen
Software Mentions: 2
Published: over 6 years ago

10.1007/s10142-019-00709-9

Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean
Cited by: 18
Author(s): Jamie A. O’Rourke, Chantal E. McCabe, Michelle A. Graham
Software Mentions: 2
Published: almost 7 years ago

10.4155/fsoa-2018-0046

Profiling and bioinformatics analyses of differential circular RNA expression in prostate cancer cells
Cited by: 21
Author(s): Chunlei Zhang, Jun Xiong, Qi Yang, Ye Wang, Haoqing Shi, Quan Tian, Hai Huang, De-Pei Kong, Jian-Min Lv, Dan Liŭ, Xu Gao, Xiaoyuan Zi, Yinghao Sun
Software Mentions: 2
Published: almost 8 years ago

10.1534/g3.111.001115

Correlation of Global MicroRNA Expression With Basal Cell Carcinoma Subtype
Cited by: 35
Author(s): Christopher Heffelfinger, Zhengqing Ouyang, Anna Engberg, David J. Leffell, Allison Hanlon, Patricia B. Gordon, Wei Zheng, Hongyu Zhao, M Snyder, Allen E. Bale
Software Mentions: 2
Published: over 14 years ago

10.1534/g3.113.008565

Design and Analysis of Bar-seq Experiments
Cited by: 79
Author(s): David G. Robinson, Wei Chen, John D. Storey, David Gresham
Software Mentions: 2
Published: over 12 years ago

10.1534/g3.113.009241

Comparative Genomic and Transcriptomic Analysis of Wangiella dermatitidis, A Major Cause of Phaeohyphomycosis and a Model Black Yeast Human Pathogen
Cited by: 53
Author(s): Zehua Chen, Diego Martínez, Sharvari Gujja, Sean M. Sykes, Qiandong Zeng, Paul J. Szaniszlo, Zheng Wang, Christina A. Cuomo
Software Mentions: 2
Published: over 12 years ago

10.1534/g3.115.019620

Comparative Transcriptome Analysis of the Cosmopolitan Marine Fungus Corollospora maritima Under Two Physiological Conditions
Cited by: 16
Author(s): Patricia Vélez, Naholi D. Alejandri-Ramírez, Martha Letícia Gaeta González, Karel Estrada, Alejandro Sánchez-Flores, Tzvetanka D. Dinkova
Software Mentions: 2
Published: almost 11 years ago

10.1534/g3.115.021261

Developmental Transcriptome for a Facultatively Eusocial Bee,Megalopta genalis
Cited by: 17
Author(s): Beryl M. Jones, William T. Wcislo, Gene E. Robinson
Software Mentions: 2
Published: almost 11 years ago

10.1534/g3.116.027300

Staufen Negatively Modulates MicroRNA Activity in Caenorhabditis elegans
Cited by: 13
Author(s): Zhenning Ren, Isana Veksler-Lublinsky, David Morrissey, Victor R. Ambros
Software Mentions: 2
Published: over 10 years ago

10.1534/g3.116.036194

Age and Diet Affect Genetically Separable Secondary Injuries that Cause Acute Mortality Following Traumatic Brain Injury in Drosophila
Cited by: 32
Author(s): Rebeccah J. Katzenberger, Barry Ganetzky, David A. Wassarman
Software Mentions: 2
Published: over 9 years ago

10.1534/g3.116.036160

Dissecting Gene Expression Changes Accompanying a Ploidy-Based Phenotypic Switch
Cited by: 18
Author(s): Gareth A. Cromie, Zhihao Tan, Michelle Hays, Eric Jeffery, Andrew T. Dudley
Software Mentions: 2
Published: almost 10 years ago

10.3390/genes11111301

PURα Promotes the Transcriptional Activation of PCK2 in Oesophageal Squamous Cell Carcinoma Cells
Cited by: 6
Author(s): Yan Sun, Jiajia Gao, Zongpan Jing, Yan Zhao, Yulin Sun, Xiaohang Zhao
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes12010100

Systematic Identification and Analysis of Circular RNAs of Japanese Flounder (Paralichthys olivaceus) in Response to Vibrio anguillarum Infection
Cited by: 5
Author(s): Xianhui Ning, Li Sun
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12020180

Identification of Key Pathways and Genes Related to the Development of Hair Follicle Cycle in Cashmere Goats
Cited by: 19
Author(s): Jianfang Wang, Jie Sui, Chao Mao, Xiaorui Li, Xingyi Chen, Chengcheng Liang, Xiaohui Wang, Si-Hu Wang, Caixia Jia
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12020189

Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions
Cited by: 23
Author(s): Kinga Kęska, Michał Wojciech Szcześniak, Izabela Makałowska, Małgorzata Czernicka
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12050614

Novel lincRNA Discovery and Tissue-Specific Gene Expression across 30 Normal Human Tissues
Cited by: 3
Author(s): Xianfeng Chen, Zhifu Sun
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12050630

Identification of Potential Key lncRNAs in the Context of Mouse Myeloid Differentiation by Systematic Transcriptomics Analysis
Cited by: 0
Author(s): Yongqing Lan, Meng Li, Shuangli Mi
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12050760

Differential mRNA and miRNA Profiles Reveal the Potential Roles of Genes and miRNAs Involved in LPS Infection in Chicken Macrophages
Cited by: 1
Author(s): Qi Zhang, Jie Wang, Jin Zhang, Jie Wen, Guiping Zhao, Qinghe Li
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12060893

Differential Transcript Profiles in Cumulus-Oocyte Complexes Originating from Pre-Ovulatory Follicles of Varied Physiological Maturity in Beef Cows
Cited by: 9
Author(s): Sarah E. Moorey, Jenna Marie Monnig, Michael F. Smith, M. Sofía Ortega, Jonathan A. Green, Ky G Pohler, G.A. Bridges, Susanta K. Behura, T. W. Geary
Software Mentions: 2
Published: about 5 years ago

10.1186/s12711-017-0319-0

Exploring the genetic architecture and improving genomic prediction accuracy for mastitis and milk production traits in dairy cattle by mapping variants to hepatic transcriptomic regions responsive to intra-mammary infection
Cited by: 51
Author(s): Lingzhao Fang, Goutam Sahana, Peipei Ma, Guosheng Su, Ying Yu, Shengli Zhang, Mogens Sandø Lund, Peter Sørensen
Software Mentions: 2
Published: over 9 years ago

10.1186/s12711-018-0384-z

Epigenetics and early domestication: differences in hypothalamic DNA methylation between red junglefowl divergently selected for high or low fear of humans
Cited by: 33
Author(s): Johan Bélteky, Beatrix Agnvall, Lejla Bektic, Andrey Höglund, Per Jensen, Carlos Guerrero-Bosagna
Software Mentions: 2
Published: over 8 years ago

10.1186/s12711-020-00532-y

An eQTL in the cystathionine beta synthase gene is linked to osteoporosis in laying hens
Cited by: 12
Author(s): Dirk-Jan de Koning, Nazaret Domínguez-Gasca, Robert Fleming, Andrew C. Gill, Dominic Kurian, Andrew Law, Heather McCormack, David Morrice, Estefanía Sánchez-Rodríguez, Alejandro B. Rodrı́guez-Navarro, Rudolf Preisinger, M. Schmutz, Veronika Šmídová, Frances Turner, Peter W.F. Wilson, Rongyan Zhou, Ian C. Dunn
Software Mentions: 2
Published: over 6 years ago

10.1186/gb-2011-12-1-r7

Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi
Cited by: 182
Author(s): Anke Burmester, Ekaterina Shelest, Gernot Glöckner, Christoph Heddergott, Susann Schindler, Peter Staib, Andrew J. Heidel, Marius Felder, A. Petzold, Karol Szafranski, Marc Feuermann, Ivo Pedruzzi, Stefan Priebe, Marco Groth, Robert Winkler, Wenjun Li, Olaf Kniemeyer, Volker Schroeckh, Christian Hertweck, Bernhard Hube, Theodore C. White, Matthias Platzer, Reinhard Guthke, Joseph Heitman, Johannes Wöstemeyer, Peter F. Zipfel, Michel Monod, Axel A. Brakhage
Software Mentions: 2
Published: over 15 years ago

10.1186/gb-2013-14-1-r6

Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells
Cited by: 112
Author(s): Deborah A. Sanders, Caryn S. Ross-Innes, Dario Beraldi, Jason S. Carroll, Shankar Balasubramanian
Software Mentions: 2
Published: over 13 years ago

10.1186/gb-2013-14-9-r98

The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells
Cited by: 44
Author(s): Gonçalo Castelo‐Branco, Paulo Amaral, Pär G. Engström, Samuel Robson, Sueli Marques, Paul Bertone, Tony Kouzarides
Software Mentions: 2
Published: over 13 years ago

10.1186/gb-2013-14-3-r26

RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome
Cited by: 92
Author(s): Katie Ayers, N. Davidson, Diana Demiyah, Kelly N. Roeszler, Frank Grützner, Andrew H. Sinclair, Alicia Oshlack, Craig A. Smith
Software Mentions: 2
Published: over 13 years ago

10.1186/gb-2014-15-1-r15

Differential protein occupancy profiling of the mRNA transcriptome
Cited by: 69
Author(s): Markus Schueler, Mathias Munschauer, Lea H. Gregersen, Ana Finzel, Alexander Loewer, Weiwei Chen, Markus Landthaler, Christoph Dieterich
Software Mentions: 2
Published: over 12 years ago

10.1186/s13059-015-0706-1

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
Cited by: 316
Author(s): Xiaoying Fan, Xiannian Zhang, Xinglong Wu, Hongshan Guo, Yuqiong Hu, Fuchou Tang, Yanyi Huang
Software Mentions: 2
Published: about 11 years ago

10.1186/s13059-015-0717-y

Global SUMOylation on active chromatin is an acute heat stress response restricting transcription
Cited by: 81
Author(s): Einari A. Niskanen, Marjo Malinen, Päivi Sutinen, Sari Toropainen, Ville Paakinaho, Anniina Vihervaara, Jenny Joutsen, Minna U. Kaikkonen, Lea Sistonen, Jorma J. Palvimo
Software Mentions: 2
Published: about 11 years ago

10.1186/s13059-015-0771-5

The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages
Cited by: 52
Author(s): Shruthi S. Vembar, Cameron Ross MacPherson, Odile Sismeiro, Jean‐Yves Coppée, Artur Scherf
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13059-015-0853-4

Meta-analysis of RNA-seq expression data across species, tissues and studies
Cited by: 115
Author(s): Peter H. Sudmant, Maria S. Alexis, Christopher B. Burge
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-016-1136-4

Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation
Cited by: 12
Author(s): Irene Cantone, Gopuraja Dharmalingam, Yi‐Wah Chan, Anne-Céline Kohler, Boris Lenhard, Matthias Merkenschlager, Amanda G. Fisher
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-017-1338-4

Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses
Cited by: 34
Author(s): Joseph L. Costello, Christopher J. Kershaw, Lydia M. Castelli, David Talavera, William Rowe, Paul F. G. Sims, Mark P. Ashe, Chris M. Grant, Simon J. Hubbard, Graham D. Pavitt
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13059-018-1538-6

CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens
Cited by: 34
Author(s): Timothy Daley, Zhixiang Lin, Xueqiu Lin, Yanxia Liu, Wing Hung Wong, Lei Qi
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13059-019-1682-7

DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis
Cited by: 21
Author(s): Bin Xiong, Yiben Yang, Frank R. Fineis, Ji Ping Wang
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-019-1722-3

Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana
Cited by: 25
Author(s): Stefan Grob, Ueli Grossniklaus
Software Mentions: 2
Published: about 7 years ago

10.1186/s13059-019-1786-0

Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes
Cited by: 81
Author(s): Nilusha Malmuthuge, Guanxiang Liang, Le Luo Guan
Software Mentions: 2
Published: about 7 years ago

10.1186/s13059-019-1865-2

Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference
Cited by: 130
Author(s): Yuanhua Huang, Davis J. McCarthy, Oliver Stegle
Software Mentions: 2
Published: over 6 years ago

10.1186/s13059-019-1915-9

RADAR: differential analysis of MeRIP-seq data with a random effect model
Cited by: 37
Author(s): Zijie Zhang, Qi Zhan, Mark A. Eckert, Allen Zhu, Agnieszka Chryplewicz, Dario F. De Jesus, Decheng Ren, Rohit Kulkarni, Ernst Lengyel, Chuan He, Mengjie Chen
Software Mentions: 2
Published: over 6 years ago

10.1111/jeb.12895

Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy
Cited by: 21
Author(s): Luke T. Dunning, Helen Hipperson, William J. Baker, Roger K. Butlin, Céline Devaux, I. Hutton, Javier Igea, Alexander S. T. Papadopulos, Xiangqian Quan, Carole Smadja, Colin Turnbull, Vincent Savolainen
Software Mentions: 2
Published: about 10 years ago

10.1242/jeb.226233

High temperature induces transcriptomic changes in Crassostrea gigas that hinders progress of Ostreid herpesvirus (OsHV-1) and promotes survival
Cited by: 18
Author(s): Lizenn Delisle, Marianna Pauletto, Jérémie Vidal-Dupiol, Bruno Petton, Luca Bargelloni, Caroline Montagnani, Fabrice Pernet, Charlotte Corporeau, Elodie Fleury
Software Mentions: 2
Published: over 6 years ago

10.1093/jxb/erw346

Analysis of high iron rice lines reveals new miRNAs that target iron transporters in roots
Cited by: 25
Author(s): Soumitra Paul, Dipak Gayen, Swapan K. Datta, Karabi Datta
Software Mentions: 2
Published: almost 10 years ago

10.1093/jxb/erw347

Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development
Cited by: 56
Author(s): Jelle Van Leene, Jonas Blomme, Shubhada Rajabhau Kulkarni, Bernard Cannoot, Nancy De Winne, Dominique Eeckhout, Geert Persiau, Eveline Van De Slijke, Leen Vercruysse, Robin Vanden Bossche, Ken S. Heyndrickx, Steffen Vanneste, Alain Goossens, Kris Gevaert, Klaas Vandepoele, Nathalie González, Dirk Inzé, Geert De Jaeger
Software Mentions: 2
Published: almost 10 years ago

10.1093/jxb/erw361

Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways
Cited by: 94
Author(s): Qili Fei, Yang Li, Wanqi Liang, Dabing Zhang, Blake C. Meyers
Software Mentions: 2
Published: almost 10 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568