bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1093/eep/dvv006

Bisphenol A-associated alterations in genome-wide DNA methylation and gene expression patterns reveal sequence-dependent and non-monotonic effects in human fetal liver
Cited by: 56
Author(s): Christopher Faulk, Jung Ho Kim, Tamara R. Jones, Richard C. McEachin, Muna S. Nahar, Dana C. Dolinoy, Maureen A. Sartor
Software Mentions: 2
Published: almost 12 years ago

10.1186/s40793-020-00368-5

The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania
Cited by: 8
Author(s): Dipti Pitta, Nagaraju Indugu, John D. Toth, Joseph S. Bender, Linda D. Baker, Meagan L. Hennessy, Bonnie Vecchiarelli, Helen Aceto, Zhengxia Dou
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40793-021-00378-x

Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils
Cited by: 2
Author(s): Marian Morales, Vladimir Sentchilo, Noushin Hadadi, Jan Roelof van der Meer
Software Mentions: 2
Published: over 5 years ago

10.1021/acs.est.0c07262

Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon
Cited by: 14
Author(s): Elena Cerro‐Gálvez, Jordi Dachs, Daniel Lundin, María-Carmen Fernández-Pinos, Marta Sebastián, Maria Vila‐Costa
Software Mentions: 2
Published: over 5 years ago

10.1186/1756-8935-6-7

Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development
Cited by: 81
Author(s): Kelly Bush, Benjamin Yuen, Bonnie L. Barrilleaux, John W. Riggs, Henriette O’Geen, Rebecca Cotterman, Paul S. Knoepfler
Software Mentions: 2
Published: over 13 years ago

10.1186/s13072-019-0266-9

Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing
Cited by: 7
Author(s): Jiji T. Kurup, Ion J. Campeanu, Benjamin L. Kidder
Software Mentions: 2
Published: over 7 years ago

10.1155/2017/1676808

Antidepressant Mechanism Research of Acupuncture: Insights from a Genome-Wide Transcriptome Analysis of Frontal Cortex in Rats with Chronic Restraint Stress
Cited by: 19
Author(s): Yu Wang, Huili Jiang, Hong Meng, Jing Rong Li, Xiaojian Yang, Bingcong Zhao, Yang Sun, Ting Bao
Software Mentions: 2
Published: about 9 years ago

10.1155/2020/3561235

Transcriptome Analysis Reveals the Effects of Troxerutin and Cerebroprotein Hydrolysate Injection on Injured Spinal Cords in Rats
Cited by: 0
Author(s): Linbang Wang, Hucheng Wang, Ke Tang, Weiyang Zhong, Zhiyu Chen, Zhengxue Quan
Software Mentions: 2
Published: about 6 years ago

10.1155/2021/8861394

The Pharmacological Activity of the Wenjing Decoction in Recurrent Spontaneous Abortion
Cited by: 6
Author(s): Lixue Cao, Hui Chen, Yanxia Huang, Liudan Chen, Mengru Kang, Jing Liang
Software Mentions: 2
Published: over 5 years ago

10.1111/eva.13054

Transcriptomic divergence between upland and lowland ecotypes contributes to rice adaptation to a drought‐prone agroecosystem
Cited by: 9
Author(s): Zhi Luo, Jie Xiong, Hui Xia, Xiaoyan Ma, Min Gao, Lei Wang, Guolan Liu, Yu Xing, Lijun Luo
Software Mentions: 2
Published: over 6 years ago

10.1111/eva.13166

Incipient resistance to an effective pesticide results from genetic adaptation and the canalization of gene expression
Cited by: 12
Author(s): Xiaoshen Yin, Alexander S. Martinez, Abigail Perkins, Morgan Sparks, Avril M. Harder, Janna R. Willoughby, Marı́a S. Sepúlveda, Mark R. Christie
Software Mentions: 2
Published: almost 6 years ago

10.1002/evl3.220

Experimental evolution supports signatures of sexual selection in genomic divergence
Cited by: 11
Author(s): R. Axel W. Wiberg, Paris Veltsos, Rhonda R. Snook, Michael G. Ritchie
Software Mentions: 2
Published: over 5 years ago

10.1016/j.exphem.2016.11.003

MLL-AF4 binds directly to a BCL-2 specific enhancer and modulates H3K27 acetylation
Cited by: 24
Author(s): Laura Godfrey, Jon Kerry, Ross Thorne, Emmanouela Repapi, James O. J. Davies, Marta Tapia, Erica Ballabio, Jim R. Hughes, Huimin Geng, Marina Konopleva, Thomas A. Milne
Software Mentions: 2
Published: over 9 years ago

10.1186/s40164-021-00226-1

Pan-cancer analysis reveals tumor-associated macrophage communication in the tumor microenvironment
Cited by: 21
Author(s): Linbang Wang, Tao He, Jingkun Liu, Jiaojiao Tai, Bing Wang, Zhiyu Chen, Zhengxue Quan
Software Mentions: 2
Published: over 5 years ago

10.1038/s12276-019-0328-x

Silencing of long noncoding RNA HOXA11-AS inhibits the Wnt signaling pathway via the upregulation of HOXA11 and thereby inhibits the proliferation, invasion, and self-renewal of hepatocellular carcinoma stem cells
Cited by: 33
Author(s): Juncheng Guo, Yijun Yang, Jinfang Zheng, Jianquan Zhang, Min Guo, Yang Xiang, Xiong-Fei Jiang, Xiang Li, You Li, Ping Huang, Lang Zhuo
Software Mentions: 2
Published: almost 7 years ago

10.12688/f1000research.6402.2

The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs
Cited by: 11
Author(s): Jóhannes Guðbrandsson, Ehsan Pashay Ahi, Sigríður Rut Franzdóttir, Kalina H. Kapralova, Bjarni K. Kristjánsson, S. Sophie Steinhaeuser, Valerie H. Maier, Isak M. Johannesson, Sigurður S. Snorrason, Zophonı́as O. Jónsson, Arnar Pálsson
Software Mentions: 2
Published: over 10 years ago

10.1002/2211-5463.12709

Profiling and functional analysis of differentially expressed circular RNAs in high glucose‐induced human umbilical vein endothelial cells
Cited by: 26
Author(s): Guoxi Jin, Qiong Wang, Xiaolei Hu, Xiaoli Li, Xiuying Pei, Erdi Xu, Minglong Li
Software Mentions: 2
Published: about 7 years ago

10.1093/femsle/fnz081

In silico prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus Verticillium dahliae
Cited by: 14
Author(s): Xiaoqian Shi-Kunne, Roger de Pedro Jové, Jasper R L Depotter, Malaika K. Ebert, Michael Seidl, Bart P.H.J. Thomma
Software Mentions: 2
Published: over 7 years ago

10.3389/fimmu.2018.02403

Acute Toxoplasma Gondii Infection in Cats Induced Tissue-Specific Transcriptional Response Dominated by Immune Signatures
Cited by: 11
Author(s): Wei Cong, Tania Dottorini, Faraz Khan, Richard D. Emes, Fu-Kai Zhang, Chun-Xue Zhou, Jun-Jun He, Xiaoxuan Zhang, Hany M. Elsheikha, Xingquan Zhu
Software Mentions: 2
Published: about 8 years ago

10.3389/fimmu.2019.00612

Bovine Derived in vitro Cultures Generate Heterogeneous Populations of Antigen Presenting Cells
Cited by: 10
Author(s): Efrain Guzman, Myriam Pujol, Paolo Ribeca, María Montoya
Software Mentions: 2
Published: over 7 years ago

10.3389/fimmu.2019.00984

Dual RNA-Seq Unveils Pseudomonas plecoglossicida htpG Gene Functions During Host-Pathogen Interactions With Epinephelus coioides
Cited by: 22
Author(s): Lixing Huang, Lingmin Zhao, Wenjia Liu, Xiaojin Xu, Yongquan Su, Yingxue Qin, Qingpi Yan
Software Mentions: 2
Published: over 7 years ago

10.3389/fimmu.2017.00704

Involvement of MicroRNAs in Probiotics-Induced Reduction of the Cecal Inflammation by Salmonella Typhimurium
Cited by: 36
Author(s): Qiaoling Chen, Chao Tong, Shaoyang Ma, Lifeng Zhou, Lili Zhao, Xin Zhao
Software Mentions: 2
Published: over 9 years ago

10.3389/fmed.2021.637803

Development and Multi-Data Set Verification of an RNA Binding Protein Signature for Prognosis Prediction in Glioma
Cited by: 2
Author(s): Chunpeng Sheng, Zhihua Chen, Jianwei Lei, Jianming Zhu, Shuxin Song
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2021.692313

Endophytic Bacillus altitudinis Strain Uses Different Novelty Molecular Pathways to Enhance Plant Growth
Cited by: 17
Author(s): Dening Zhang, Hongmin Xu, Jingyao Gao, Roxana Portieles, Lihua Du, Xiangyou Gao, Carlos Borroto Nordelo, Orlando Borrás‐Hidalgo
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2019.00330

Transcriptional and Proteomic Choreography Under Phosphorus Deficiency and Re-supply in the N2 Fixing Cyanobacterium Trichodesmium erythraeum
Cited by: 11
Author(s): Kyle R. Frischkorn, Sheean T. Haley, Sonya T. Dyhrman
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2019.00247

The Active Sulfate-Reducing Microbial Community in Littoral Sediment of Oligotrophic Lake Constance
Cited by: 16
Author(s): Susanne Wörner, Michael Pester
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2021.632095

Integrated Proteomic and Transcriptomic Analyses Reveal the Roles of Brucella Homolog of BAX Inhibitor 1 in Cell Division and Membrane Homeostasis of Brucella suis S2
Cited by: 2
Author(s): Guangdong Zhang, Fangli Zhong, Lei Chen, Peipei Qin, Junmei Li, Feijie Zhi, Lulu Tian, Dong Zhou, Peng Lin, Huatao Chen, Kai-Fu Tang, Wei Liu, Yaping Jin, Aihua Wang
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2021.724676

A Global Analysis of Photoreceptor-Mediated Transcriptional Changes Reveals the Intricate Relationship Between Central Metabolism and DNA Repair in the Filamentous Fungus Trichoderma atroviride
Cited by: 7
Author(s): Enrique Pola-Sánchez, José Manuel Villalobos-Escobedo, Nohemí Carreras-Villaseñor, Pedro Martı́nez-Hernández, Emma Beatriz Beltrán-Hernández, Edgardo Ulises Esquivel-Naranjo, Alfredo Herrera‐Estrella
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2017.00949

Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond
Cited by: 53
Author(s): Zarraz M.-P. Lee, Amisha T. Poret-Peterson, Janet L. Siefert, Drishti Kaul, Ahmed Moustafa, Andrew E. Allen, Chris L. Dupont, Luis E. Eguiarte, Valeria Souza, James J. Elser
Software Mentions: 2
Published: over 9 years ago

10.3389/fmicb.2016.00794

Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets
Cited by: 8
Author(s): Punita Manga, Dawn M. Klingeman, Tse-Yuan S. Lu, Tonia L. Mehlhorn, Dale A. Pelletier, Loren Hauser, Charlotte M. Wilson, Steven D. Brown
Software Mentions: 2
Published: over 10 years ago

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: almost 6 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: almost 9 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: over 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: over 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: almost 6 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: almost 9 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: about 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: almost 8 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: about 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: about 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: over 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: over 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

10.1534/g3.116.037069

Genome-Wide Analysis of lncRNA and mRNA Expression During Differentiation of Abdominal Preadipocytes in the Chicken
Cited by: 47
Author(s): Tao Zhang, Xiangqian Zhang, Kai Han, Genxi Zhang, Jinyu Wang, Kaizhou Xie, Qingwu Xue
Software Mentions: 2
Published: over 9 years ago

10.1534/g3.117.300493

Uncovering Genomic Regions Associated withTrypanosomaInfections in Wild Populations of the Tsetse FlyGlossina fuscipes
Cited by: 7
Author(s): Andrea Gloria‐Soria, William A. Dunn, Xiaoqing Yu, Aurélien Vigneron, Kuang‐Yao Lee, Mo Li, Brian L. Weiss, Hongyu Zhao, Serap Aksoy, Adalgisa Caccone
Software Mentions: 2
Published: over 8 years ago

10.1534/g3.118.200208

Differential Expression Profiling of Microspores During the Early Stages of Isolated Microspore Culture Using the Responsive Barley Cultivar Gobernadora
Cited by: 19
Author(s): Sébastien Bélanger, Suzanne Marchand, Pierre-Étienne Jacques, Blake C. Meyers, François Belzile
Software Mentions: 2
Published: over 8 years ago

10.1534/g3.118.200292

Sex Determination in Ceratopteris richardii Is Accompanied by Transcriptome Changes That Drive Epigenetic Reprogramming of the Young Gametophyte
Cited by: 19
Author(s): Nadia M. Atallah, Olga Vitek, Federico Gaiti, Miloš Tanurdžić, Jo Ann Banks
Software Mentions: 2
Published: over 8 years ago

10.1534/g3.118.200647

Domestication and Temperature Modulate Gene Expression Signatures and Growth in the Australasian Snapper Chrysophrys auratus
Cited by: 20
Author(s): Maren Wellenreuther, Jérémy Le Luyer, Denham G. Cook, Peter A. Ritchie, Louis Bernatchez
Software Mentions: 2
Published: almost 8 years ago

10.1534/g3.118.200920

Transcriptional Basis of Copper-Induced Olfactory Impairment in the Sea Lamprey, a Primitive Invasive Fish
Cited by: 7
Author(s): Jenna Jones, Kyle Wellband, Barbara S. Zielinski, Daniel D. Heath
Software Mentions: 2
Published: over 7 years ago

10.1534/g3.119.400723

A Mouse Mutation That Dysregulates Neighboring Galnt17 and Auts2 Genes Is Associated with Phenotypes Related to the Human AUTS2 Syndrome
Cited by: 5
Author(s): Patricia A. Weisner, Chih‐Ying Chen, Younguk Sun, Jennifer Yoo, Wei-Chun Kao, Huimin Zhang, Emily T Baltz, Joseph M. Troy, Lisa Stubbs
Software Mentions: 2
Published: almost 7 years ago

10.1534/g3.119.400469

Investigating the Influence of Glycerol on the Utilization of Glucose in Yarrowia lipolytica Using RNA-Seq-Based Transcriptomics
Cited by: 11
Author(s): Patrice Lubuta, Mhairi Workman, Eduard J. Kerkhoven, Christopher Workman
Software Mentions: 2
Published: almost 7 years ago

10.1534/g3.119.400993

Epigenetic Regulation of ABA-Induced Transcriptional Responses in Maize
Cited by: 16
Author(s): Stefania Vendramin, Ji Huang, Peter A. Crisp, Thelma F. Madzima, Karen M. McGinnis
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.119.400947

Forebrain Transcriptional Response to Transient Changes in Circulating Androgens in a Cichlid Fish
Cited by: 2
Author(s): Ana S. Félix, Sara D. Cardoso, António Roleira, Rui Filipe Oliveira
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.120.401487

Identification of Hypoxia-Specific Biomarkers in Salmonids Using RNA-Sequencing and Validation Using High-Throughput qPCR
Cited by: 13
Author(s): Arash Akbarzadeh, Aimee Lee S. Houde, Ben J. G. Sutherland, Oliver P. Günther, Kristina M. Miller
Software Mentions: 2
Published: about 6 years ago

10.1534/g3.120.401769

Adapting Drosophila melanogaster Cell Lines to Serum-Free Culture Conditions
Cited by: 3
Author(s): Arthur Luhur, Daniel Mariappa, Kristin M. Klueg, Kasun Buddika, Jason M. Tennessen, Andrew C. Zelhof
Software Mentions: 2
Published: almost 6 years ago

10.1093/g3journal/jkab162

Genome-wide analysis of the soybean root transcriptome reveals the impact of nitrate on alternative splicing
Cited by: 2
Author(s): Binhui Guo, Yi Dai, Lin Chen, Zhenzhi Pan, Li Song
Software Mentions: 2
Published: over 5 years ago

10.1093/g3journal/jkab113

Interacting impact of maternal inflammatory response and stress on the amygdala transcriptome of pigs
Cited by: 11
Author(s): Marissa R. Keever-Keigher, Pan Zhang, Courtni R. Bolt, Haley E Rymut, Adrienne M. Antonson, Megan P Corbett, Alexandra K Houser, Álvaro Gonzalez Hernández, Bruce R. Southey, Laurie A. Rund, Rodney W. Johnson, Sandra L. Rodriguez-Zas
Software Mentions: 2
Published: over 5 years ago

10.1053/j.gastro.2018.05.050

Selection and Application of Tissue microRNAs for Nonendoscopic Diagnosis of Barrett’s Esophagus
Cited by: 35
Author(s): Xiaodun Li, Sam O. Kleeman, Sally B Coburn, Carlo Fumagalli, Juliane Perner, Sriganesh Jammula, Ruth M. Pfeiffer, Linda D. Orzolek, Haiping Hao, Philip R. Taylor, Ahmad Miremadi, Núria Galeano-Dalmau, Pierre Lao-Sirieix, Maria Tennyson, Shona MacRae, Michael B. Cook, Rebecca C. Fitzgerald
Software Mentions: 2
Published: about 8 years ago

10.3390/genes2040689

RNA-Seq for Plant Pathogenic Bacteria
Cited by: 8
Author(s): Jeffrey A. Kimbrel, Yanming Di, Jason S. Cumbie, Jeff H. Chang
Software Mentions: 2
Published: about 15 years ago

10.3390/genes8010014

mRNA Expression and DNA Methylation Analysis of Serotonin Receptor 2A (HTR2A) in the Human Schizophrenic Brain
Cited by: 29
Author(s): Sern-Yih Cheah, Bruce R. Lawford, Ross McD. Young, Charles P. Morris, Joanne Voisey
Software Mentions: 2
Published: almost 10 years ago

10.3390/genes8090234

Circulating microRNAs and Bioinformatics Tools to Discover Novel Diagnostic Biomarkers of Pediatric Diseases
Cited by: 27
Author(s): Antonella Baldassarre, Cristina Felli, Giorgio Prantera, Andrea Masotti
Software Mentions: 2
Published: about 9 years ago

10.3390/genes9030170

Long Non-Coding RNAs Responsive to Salt and Boron Stress in the Hyper-Arid Lluteño Maize from Atacama Desert
Cited by: 47
Author(s): Wilson Huanca‐Mamani, Raúl Arias‐Carrasco, Steffany Cárdenas-Ninasivincha, Marcelo Rojas-Herrera, Gonzalo Sepúlveda-Hermosilla, José Carlos Caris-Maldonado, Elizabeth Bastías, Vinicius Maracaja‐Coutinho
Software Mentions: 2
Published: over 8 years ago

10.3390/genes10070494

Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi
Cited by: 16
Author(s): Maria Immacolata Ferrante, Laura Entrambasaguas, Mathias Johansson, Mats Töpel, Anke Kremp, Marina Montresor, Anna Godhe
Software Mentions: 2
Published: over 7 years ago

10.3390/genes10090704

Genetic Characteristic and RNA-Seq Analysis in Transparent Mutant of Carp–Goldfish Nucleocytoplasmic Hybrid
Cited by: 4
Author(s): Lingling Zhou, Hongwei Liang, Xin Zhou, Jingyi Jia, Ya Cheng, Qiongyao Hu, Shaohua Xu, Ying Yu, Guiwei Zou, Guangfu Hu
Software Mentions: 2
Published: about 7 years ago

10.3390/genes10100804

Transcriptional Analysis of Masson Pine (Pinus massoniana) under High CO2 Stress
Cited by: 17
Author(s): Fan Wu, Xiaobo Sun, Bingzhang Zou, Peihuang Zhu, Nengqing Lin, Jingquan Lin, Kongshu Ji
Software Mentions: 2
Published: about 7 years ago

10.3390/genes10100747

Common Nevus and Skin Cutaneous Melanoma: Prognostic Genes Identified by Gene Co-Expression Network Analysis
Cited by: 16
Author(s): Lingge Yang, Yu Xu, Yan Yan, Peng Luo, Shiqi Chen, Biqiang Zheng, Wangjun Yan, Yong Chen, Chunmeng Wang
Software Mentions: 2
Published: about 7 years ago

10.3390/genes10100733

Transcriptomic Signatures of Experimental Alkaloid Consumption in a Poison Frog
Cited by: 10
Author(s): Eugenia Sanchez, Ariel Rodríguez, José Horacio Grau, Stefan Lötters, Sven Künzel, Ralph A. Saporito, Eva Ringler, Stefan Schulz, Katharina C. Wollenberg Valero, Miguel Vences
Software Mentions: 2
Published: about 7 years ago

10.3390/genes10120970

Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak
Cited by: 12
Author(s): Xiaoming Ma, Jia Chen, Min Chen, Donghai Fu, Qinhui Lei, Xuezhi Ding, Xiaoyun Wu, Xian Guo, Jie Pei, Pengjia Bao, Ping Yan, Chunnian Liang
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes11040349

Analysis of Long Noncoding RNA and mRNA Expression Profiles of Testes with High and Low Sperm Motility in Domestic Pigeons (Columba livia)
Cited by: 9
Author(s): Xiuli Xu, Yuge Tan, Haoyu Mao, Honghua Liu, Xin Dong, Zhan Yin
Software Mentions: 2
Published: over 6 years ago

10.3390/genes11060631

Gill Transcriptome Sequencing and De Novo Annotation of Acanthogobius ommaturus in Response to Salinity Stress
Cited by: 14
Author(s): Zhicheng Sun, Fangrui Lou, Yuan Zhang, Na Song
Software Mentions: 2
Published: over 6 years ago

10.3390/genes11091016

The Acidic Stress Response of the Intracellular Pathogen Brucella melitensis: New Insights from a Comparative, Genome-Wide Transcriptome Analysis
Cited by: 0
Author(s): Jonathan D. Kornspan, Tamar Zahavi, Mali Salmon‐Divon
Software Mentions: 2
Published: about 6 years ago

10.3390/genes11091002

Prediction and Analysis of SARS-CoV-2-Targeting MicroRNA in Human Lung Epithelium
Cited by: 74
Author(s): Jonathan Tak-Sum Chow, Leonardo Salmena
Software Mentions: 2
Published: about 6 years ago

10.3390/genes11091003

Transcriptome Analysis Reveals Inhibitory Effects of Lentogenic Newcastle Disease Virus on Cell Survival and Immune Function in Spleen of Commercial Layer Chicks
Cited by: 2
Author(s): J. Zhang, Michael G. Kaiser, Rodrigo A. Gallardo, T. Ross Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 2
Published: about 6 years ago

10.1186/s13059-020-01999-0

The preceding root system drives the composition and function of the rhizosphere microbiome
Cited by: 42
Author(s): Yi Zhou, David Coventry, Vadakattu V. S. R. Gupta, David Fuentes, Andrew Merchant, Brent N. Kaiser, Jishun Li, Yanli Wei, Huan Liu, Yayu Wang, Shuheng Gan, Matthew D. Denton
Software Mentions: 2
Published: over 6 years ago

10.1186/s13059-020-02069-1

Mapping regulatory variants controlling gene expression in drought response and tolerance in maize
Cited by: 67
Author(s): Shengxue Liu, Cuiping Li, Hongwei Wang, Shuhui Wang, Shiping Yang, Xiaohu Liu, Jianbing Yan, Bailin Li, Mary Beatty, Gina Zastrow-Hayes, Shuhui Song, Feng Qin
Software Mentions: 2
Published: over 6 years ago

10.1186/s13059-020-02097-x

Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution
Cited by: 69
Author(s): Catherine L. Peichel, Shaugnessy R. McCann, Joseph A. Ross, Alice F.S. Naftaly, James R. Urton, Jennifer N. Cech, Jane Grimwood, Jeremy Schmutz, R Myers, David M. Kingsley, Michael A. White
Software Mentions: 2
Published: over 6 years ago

10.1093/gbe/evu266

Constraint and Adaptation in newt Toll-Like Receptor Genes
Cited by: 34
Author(s): Wiesław Babik, Katarzyna Dudek, Anna Fijarczyk, Maciej Pabijan, Michał Stuglik, Rafał Szkotak, Piotr Zieliński
Software Mentions: 2
Published: almost 12 years ago

10.1093/gbe/evx230

Copy Number Variation and Expression Analysis Reveals a Nonorthologous Pinta Gene Family Member Involved in Butterfly Vision
Cited by: 2
Author(s): Aide Macias-Muñoz, Kyle J. McCulloch, Adriana D. Briscoe
Software Mentions: 2
Published: almost 9 years ago

10.1093/gbe/evaa181

Between-Generation Phenotypic and Epigenetic Stability in a Clonal Snail
Cited by: 2
Author(s): Mark W. Smithson, Jennifer L. M. Thorson, Ingrid Sadler‐Riggleman, Daniel Beck, Michael K. Skinner, Mark F. Dybdahl
Software Mentions: 2
Published: about 6 years ago

10.1093/gbe/evaa263

The Iron-Responsive Genome of the Chiton Acanthopleura granulata
Cited by: 35
Author(s): Rebecca M. Varney, Daniel I. Speiser, Carmel McDougall, Bernard M. Degnan, Kevin M. Kocot
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13073-015-0183-x

Restoration of mesenchymal retinal pigmented epithelial cells by TGFβ pathway inhibitors: implications for age-related macular degeneration
Cited by: 87
Author(s): Monte J. Radeke, Carolyn M. Radeke, Ying-Hsuan Shih, Jane Hu, Dean Bok, Lincoln V. Johnson, Peter Coffey
Software Mentions: 2
Published: over 11 years ago

10.1186/s13073-016-0381-1

Allele-specific expression in the human heart and its application to postoperative atrial fibrillation and myocardial ischemia
Cited by: 6
Author(s): Martin I. Sigurdsson, Louis A. Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary F. Aranki, Gregory S. Couper, Stanton K. Shernan, J. G. Seidman, Simon C. Body, Jochen D. Muehlschlegel
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13073-017-0407-3

Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance
Cited by: 26
Author(s): David J. Duffy, Aleksandar Krstić, Melinda Halász, Thomas Schwarzl, Anja Konietzny, Kristiina Iljin, Desmond G. Higgins, Walter Kölch
Software Mentions: 2
Published: over 9 years ago

10.1186/s13073-018-0558-x

Disease-specific regulation of gene expression in a comparative analysis of juvenile idiopathic arthritis and inflammatory bowel disease
Cited by: 35
Author(s): Angela Mo, Urko M. Marigorta, Dalia Arafat, Lai Hin Kimi Chan, Lori Ponder, Se Ryeong Jang, Jarod Prince, Subra Kugathasan, Sampath Prahalad, Greg Gibson
Software Mentions: 2
Published: over 8 years ago

10.5808/GI.2019.17.1.e2

Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease
Cited by: 5
Author(s): Seokjin Ham, Yeon‐Mok Oh, Tae-Young Roh
Software Mentions: 2
Published: over 7 years ago

10.1016/j.gpb.2020.06.003

m6A Regulates Liver Metabolic Disorders and Hepatogenous Diabetes
Cited by: 43
Author(s): Yuhuan Li, Qingyang Zhang, Guanshen Cui, Fen Zhao, Xin Tian, Bao‐Fa Sun, Ying Yang, Wei Li
Software Mentions: 2
Published: over 6 years ago

10.1093/gigascience/giy045

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis
Cited by: 10
Author(s): N. Davidson, Alicia Oshlack
Software Mentions: 2
Published: over 8 years ago

10.1080/19490976.2016.1186334

The mucin-degradation strategy ofRuminococcus gnavus: The importance of intramoleculartrans-sialidases
Cited by: 101
Author(s): Emmanuelle H. Crost, Louise E. Tailford, Marie Monestier, David Swarbreck, Bernard Henrissat, Lisa Crossman, Nathalie Juge
Software Mentions: 2
Published: over 10 years ago

10.1038/s41438-021-00542-x

Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome
Cited by: 65
Author(s): Pengjie Wang, Jiaxin Yu, Shan Jin, Shuai Chen, Chuan Yue, Wenling Wang, Shuilian Gao, Hongli Cao, Yuanrun Zheng, Mengya Gu, Xuejin Chen, Yun Sun, Yuqiong Guo, Jing Yang, Xingtan Zhang, Naixing Ye
Software Mentions: 2
Published: over 5 years ago

10.1038/s41438-020-00421-x

Integrated transcriptome and proteome analysis provides insight into chilling-induced dormancy breaking in Chimonanthus praecox
Cited by: 22
Author(s): Zhineng Li, Ning Liu, Wei Zhang, C. F. Wu, Yunbin Jiang, Jing Ma, Mingyang Li, Shunzhao Sui
Software Mentions: 2
Published: almost 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568