bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.3389/fimmu.2021.743030

NOX2-Deficient Neutrophils Facilitate Joint Inflammation Through Higher Pro-Inflammatory and Weakened Immune Checkpoint Activities
Cited by: 7
Author(s): Yi‐Chu Liao, Szu‐Yu Wu, Ya‐Fang Huang, Pei‐Chi Lo, Tzu‐Yi Chan, Chih-An Chen, Chun-Hsin Wu, Che-Chia Hsu, Chia Liang Yen, Peng Chen, Chi‐Chang Shieh
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2021.667450

Multi-Omic Analyses Reveal Habitat Adaptation of Marine Cyanobacterium Synechocystis sp. PCC 7338
Cited by: 4
Author(s): Yu‐Jin Jeong, Seong-Joo Hong, Sang-Hyeok Cho, Seongwon Yoon, Hookeun Lee, Hyung‐Kyoon Choi, Dong‐Myung Kim, Choul-Gyun Lee, Suhyung Cho, Byung-Kwan Cho
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2019.03103

Salmon Gravlax Biopreservation With Lactic Acid Bacteria: A Polyphasic Approach to Assessing the Impact on Organoleptic Properties, Microbial Ecosystem and Volatilome Composition
Cited by: 32
Author(s): Norman Wiernasz, Françoise Leroi, Frédérique Chevalier, Josiane Cornet, Mireille Cardinal, Jens Rohloff, Delphine Passerini, Sigurlaug Skírnisdóttir, Marie-France Pilet
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2018.01781

MADS-Box Transcription Factor MadsA Regulates Dimorphic Transition, Conidiation, and Germination of Talaromyces marneffei
Cited by: 8
Author(s): Qiangyi Wang, Minghao Du, Shuai Wang, Linxia Liu, Liming Xiao, Linqi Wang, Tong Li, Hui Zhang, Ence Yang
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2017.02654

Additive Effects of Quorum Sensing Anti-Activators on Pseudomonas aeruginosa Virulence Traits and Transcriptome
Cited by: 34
Author(s): Kyle L. Asfahl, Martín Schuster
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2021.646273

Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings
Cited by: 5
Author(s): Tyler Dang, Irene Lavagi-Craddock, Sohrab Bodaghi, Georgios Vidalakis
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2019.02512

Sex, Age, and Bacteria: How the Intestinal Microbiota Is Modulated in a Protandrous Hermaphrodite Fish
Cited by: 41
Author(s): M. Carla Piazzon, Fernando Naya-Català, Paula Simó‐Mirabet, Amparo Picard‐Sánchez, Francisco J. Roig, Josep Àlvar Calduch-Giner, Ariadna Sitjà‐Bobadilla, Jaume Pérez‐Sánchez
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2017.00835

Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression Targets to Increase Spiramycin Production in Streptomyces ambofaciens
Cited by: 13
Author(s): Marco Fondi, Eva Pinatel, Adelfia Talà, Fabrizio Damiano, Clarissa Consolandi, Benedetta Mattorre, Daniela Fico, Mariangela Testini, Giuseppe E. De Benedetto, Luisa Siculella, Gianluca De Bellis, Pietro Alifano, Clelia Peano
Software Mentions: 2
Published: over 9 years ago

10.3389/fmicb.2017.00738

Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
Cited by: 184
Author(s): Linda Wampach, Anna Heintz‐Buschart, Angela Hogan, Emilie Muller, Shaman Narayanasamy, Cédric Christian Laczny, Luisa W. Hugerth, Lutz Bindl, Jean Bottu, Anders F. Andersson, Carine de Beaufort, Paul Wilmes
Software Mentions: 2
Published: over 9 years ago

10.3389/fmicb.2019.00967

Salmonella Establishment in Agricultural Soil and Colonization of Crop Plants Depend on Soil Type and Plant Species
Cited by: 84
Author(s): Sven Jechalke, Jasper Schierstaedt, Marlies Becker, Burkhardt Flemer, Rita Grosch, Kornelia Smalla, Adam Schikora
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2019.02180

An Overview of Genes From Cyberlindnera americana, a Symbiont Yeast Isolated From the Gut of the Bark Beetle Dendroctonus rhizophagus (Curculionidae: Scolytinae), Involved in the Detoxification Process Using Genome and Transcriptome Data
Cited by: 8
Author(s): L. Viridiana Soto-Robles, Verónica Torres-Banda, Flor N. Rivera-Orduña, Everardo Curiel-Quesada, María Eugenia Hidalgo-Lara, Gerardo Zúñiga
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2020.584174

Transcriptome Profiles Reveal the Growth-Promoting Mechanisms of Paenibacillus polymyxa YC0136 on Tobacco (Nicotiana tabacum L.)
Cited by: 29
Author(s): Hu Liu, Jun Wang, Huimin Sun, Xiaobin Han, Yuan Peng, Jing Liu, Kai Li, Yuqiang Ding, Chengqiang Wang, Binghai Du
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2018.02815

Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study
Cited by: 19
Author(s): Sean Storey, Mardiana Mohd Ashaari, Nicholas Clipson, Evelyn Doyle, Alexandre B. de Menezes
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2019.02497

Blue Light Sensing in Listeria monocytogenes Is Temperature-Dependent and the Transcriptional Response to It Is Predominantly SigB-Dependent
Cited by: 12
Author(s): Amber Dorey, Bo-Hyung Lee, Björn Rotter, Conor O’Byrne
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2021.652468

Pseudomonas Strains Induce Transcriptional and Morphological Changes and Reduce Root Colonization of Verticillium spp.
Cited by: 6
Author(s): Rebekka Harting, Angela Nagel, Kai Nesemann, Annalena Höfer, Emmanouil Bastakis, Harald Kusch, Claire E. Stanley, Martina Stöckli, Alexander Kaever, Katharina J. Hoff, Mario Stanke, Andrew J. deMello, Markus Künzler, Cara H. Haney, Susanna A. Braus‐Stromeyer, Gerhard H. Braus
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2021.587745

Impact of 6-Month Exposure to Aerosols From Potential Modified Risk Tobacco Products Relative to Cigarette Smoke on the Rodent Gastrointestinal Tract
Cited by: 3
Author(s): James N. D. Battey, Justyna Szostak, Blaine Phillips, Charles Teng, Ching Keong Tung, Wei Ting Lim, Ying Shan Yeo, Sonia Ouadi, Karine Baumer, JH Thomas, Jacopo Martinis, Nicolas Sierro, Nikolai V. Ivanov, Patrick Vanscheeuwijck, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2020.01008

Impact of Acute and Chronic Amyloid-β Peptide Exposure on Gut Microbial Commensals in the Mouse
Cited by: 17
Author(s): Malena dos Santos Guilherme, Hristo Todorov, Carina Osterhof, Anton Möllerke, Kristina Cub, Thomas Hankeln, Susanne Gerber, Kristina Endres
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2021.627099

De novo Sequencing and Comparative Transcriptome Analyses Provide First Insights Into Polysaccharide Biosynthesis During Fruiting Body Development of Lentinula edodes
Cited by: 2
Author(s): Qiaozhen Li, Jing Chen, Jianyu Liu, Hailong Yu, Lujun Zhang, Chunyan Song, Li Yu, Ning Jiang, Qian Tan, Xiaodong Shang, Yunfu Gu
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2021.621336

Transcriptomic Analysis of Wheat Seedling Responses to the Systemic Acquired Resistance Inducer N-Hydroxypipecolic Acid
Cited by: 6
Author(s): Eric T Zhang, Hao Zhang, Weihua Tang
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2021.610196

The Transcriptomic and Bioinformatic Characterizations of Iron Acquisition and Heme Utilization in Avibacterium paragallinarum in Response to Iron-Starvation
Cited by: 2
Author(s): Caiyun Huo, Xianying Zeng, Fanxing Xu, Fangbing Li, Donghai Li, Guiping Li, Zhenguo Hu, Yanxin Hu, Jun Lin, Hsin‐Yun Sun
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2015.01373

Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and β-Lactamase Expression
Cited by: 18
Author(s): Ebrahim M. Abda, Dagmar Krysciak, Ines Krohn-Molt, Uwe Mamat, Christel Schmeisser, Konrad U. Förstner, Ulrich E. Schaible, Thomas A. Kohl, Stefan Nieman, Wolfgang R. Streit
Software Mentions: 2
Published: almost 11 years ago

10.3389/fmicb.2018.00141

Secretome Analysis from the Ectomycorrhizal Ascomycete Cenococcum geophilum
Cited by: 19
Author(s): Maíra de Freitas Pereira, Claire Veneault‐Fourrey, Patrice Vion, Frédéric Guinet, Emmanuelle Morin, Kerrie Barry, Anna Lipzen, Vasanth Singan, Stephanie Pfister, Hyunsoo Na, Megan Kennedy, Simon Egli, Igor V. Grigoriev, Francis Martin, Annegret Kohler, Martina Peter
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2018.00737

Circadian Disruption Changes Gut Microbiome Taxa and Functional Gene Composition
Cited by: 134
Author(s): Jessica A. Deaver, Sung Yong Eum, Michał Toborek
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2017.00153

High Prevalence of Gammaproteobacteria in the Sediments of Admiralty Bay and North Bransfield Basin, Northwestern Antarctic Peninsula
Cited by: 29
Author(s): Diego Castillo Franco, Camila Negrão Signori, Rubens Tadeu Delgado Duarte, Cristina Rossi Nakayama, Lúcia S. Campos, Vivian H. Pellizari
Software Mentions: 2
Published: almost 10 years ago

10.3389/fmicb.2020.594838

Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea
Cited by: 10
Author(s): Thandi S. Schwarz, Sarah J. Berkemer, Stephan H. Bernhart, Matthias Weiß, Sébastien Ferreira-Cerca, Peter F. Stadler, Anita Marchfelder
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2020.01580

Comparative Transcriptomic Analysis of Rhinovirus and Influenza Virus Infection
Cited by: 12
Author(s): Thrimendra Kaushika Dissanayake, Sascha Schäuble, Mohammad H. Mirhakkak, Wai-Lan Wu, Anthony Chin-Ki Ng, Cyril C. Y. Yip, Albert García López, Thomas Wolf, M.R. Yeung, Kwok‐Hung Chan, Kwok‐Yung Yuen, Gianni Panagiotou, Kelvin Kai‐Wang To
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2020.00576

Integrated Transcriptomic and Proteomic Analyses of the Interaction Between Chicken Synovial Fibroblasts and Mycoplasma synoviae
Cited by: 5
Author(s): Rui Li, Bin Xu, Shuang Yu, Jingfeng Zhang, Huawei Sun, Chuanmin Liu, Fengying Lu, Qunxing Pan, Xiaofei Zhang
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2020.01204

Differential Gene Expression and Allele Frequency Changes Favour Adaptation of a Heterogeneous Yeast Population to Nitrogen-Limited Fermentations
Cited by: 3
Author(s): Eduardo I. Kessi-Pérez, Belén Ponce, Jing Li, Jennifer Molinet, Camila Baeza, David J. Figueroa, Camila Bastías, Marco Gaete, Gianni Liti, Álvaro Díaz-Barrera, F. Salinas, Claudio Martı́nez
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2018.00863

Regulation Mechanism Mediated by Trans-Encoded sRNA Nc117 in Short Chain Alcohols Tolerance in Synechocystis sp. PCC 6803
Cited by: 7
Author(s): Yanqi Bi, Guangsheng Pei, Tao Sun, Zixi Chen, Lei Chen, Weiwen Zhang
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2019.00329

How Does Fusarium oxysporum Sense and Respond to Nicotinaldehyde, an Inhibitor of the NAD+ Salvage Biosynthesis Pathway?
Cited by: 6
Author(s): Gautam Anand, Daniel Waiger, Nuria Yulia Vital, Jacob Maman, Jun Li, Shay Covo
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2019.02694

The Impact of Soil-Applied Biochars From Different Vegetal Feedstocks on Durum Wheat Plant Performance and Rhizospheric Bacterial Microbiota in Low Metal-Contaminated Soil
Cited by: 20
Author(s): Arianna Latini, Giovanni Bacci, Manuel Teodoro, Daniele Mirabile Gattia, Annamaria Bevivino, Lukáš Trakal
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2018.02735

Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum 20ZR
Cited by: 27
Author(s): Ilya R. Akberdin, Dave Collins, Richard Hamilton, Dmitry Oshchepkov, Anil Shukla, Carrie Nicora, Ernesto Nakayasu, Joshua N. Adkins, Marina G. Kalyuzhnaya
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2020.606482

Effects of Peptide Thanatin on the Growth and Transcriptome of Penicillium digitatum
Cited by: 8
Author(s): Guo-Gang Feng, Xindan Li, Wenjun Wang, Lili Deng, Kaifang Zeng
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2020.00252

Dominance of Mating Type A1 and Indication of Epigenetic Effects During Early Stages of Mating in Phytophthora infestans
Cited by: 6
Author(s): Georgios Tzelepis, Kristian Persson Hodén, Johan Fogelqvist, Anna K. M. Åsman, Ramesh R. Vetukuri, Christina Dixelius
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2019.01747

Evidence of Spatial Homogeneity in an Electromethanogenic Cathodic Microbial Community
Cited by: 19
Author(s): Ala’a Ragab, Krishna P. Katuri, Muhammad Ali, Pascal E. Saikaly
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2021.671453

A Single Nucleotide Polymorphism in lptG Increases Tolerance to Bile Salts, Acid, and Staining of Calcofluor-Binding Polysaccharides in Salmonella enterica Serovar Typhimurium E40
Cited by: 1
Author(s): Taylor A. Wahlig, Eliot Stanton, Jared J. Godfrey, Andrew J. Stasic, Amy C. Lee Wong, Charles W. Kaspar
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2020.01716

Differential Regulation of miRNA Profiles of Human Cells Experimentally Infected by Leishmania donovani Isolated From Indian Visceral Leishmaniasis and Post-Kala-Azar Dermal Leishmaniasis
Cited by: 7
Author(s): Ashish Kumar, Saravanan Vijaykumar, Manas Ranjan Dikhit, Kumar Abhishek, Rimi Mukherjee, Abhik Sen, Pradeep Das, Sushmita Das
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2021.715767

Cold-Triggered Induction of ROS- and Raffinose Metabolism in Freezing-Sensitive Taproot Tissue of Sugar Beet
Cited by: 11
Author(s): Isabel Keller, Christina Müdsam, Cristina Martins Rodrigues, Dominik Kischka, Wolfgang Zierer, Uwe Sonnewald, Karsten Harms, Olaf Czarnecki, Karin Fiedler‐Wiechers, Wolfgang Koch, H. Ekkehard Neuhaus, Frank Ludewig, Benjamin Pommerrenig
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2016.00800

Low Temperature Affects Stem Cell Maintenance in Brassica oleracea Seedlings
Cited by: 8
Author(s): J. de Jonge, Jan Kodde, Edouard Severing, Guusje Bonnema, Gerco C. Angenent, Richard G. H. Immink, Steven P. C. Groot
Software Mentions: 2
Published: over 10 years ago

10.3389/fpls.2021.738261

Multi-Omics Analyses Reveal the Regulatory Network and the Function of ZmUGTs in Maize Defense Response
Cited by: 5
Author(s): Chunxia Ge, Yi-Ge Wang, Shouping Lu, Xiang Zhao, Bing-Kai Hou, Peter Balint‐Kurti, Guan‐Feng Wang
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2019.01659

Cultivar-Dependent Variation of the Cotton Rhizosphere and Endosphere Microbiome Under Field Conditions
Cited by: 40
Author(s): Feng Wei, Lihong Zhao, Xiangming Xu, Hongjie Feng, Yùzhēn Shí, Greg Deakin, Zili Feng, Heqin Zhu
Software Mentions: 2
Published: almost 7 years ago

10.3389/fpls.2021.670306

Characterization of a Plant Nuclear Matrix Constituent Protein in Liverwort
Cited by: 11
Author(s): Nan Wang, Ezgi Süheyla Karaaslan, Natalie Faiß, Kenneth W. Berendzen, Chang Liu
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.637956

A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes
Cited by: 7
Author(s): Cerys Jones, Jose De Vega, Margaret Worthington, Ann Thomas, Dagmara Gasior, John A. Harper, John Doonan, Yuan Fu, Marina Bosch, Fiona Corke, Jacobo Arango, Juan Andrés Cardoso, Juan de la Cruz Jiménez, Ian Armstead, Narcís Fernández-Fuentes
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2017.02029

Inference of Transcription Regulatory Network in Low Phytic Acid Soybean Seeds
Cited by: 15
Author(s): Neelam Redekar, Guillaume Pilot, Victor Raboy, Song Li, M. A. Saghai Maroof
Software Mentions: 2
Published: almost 9 years ago

10.3389/fpls.2018.00434

Novel Fungal Pathogenicity and Leaf Defense Strategies Are Revealed by Simultaneous Transcriptome Analysis of Colletotrichum fructicola and Strawberry Infected by This Fungus
Cited by: 36
Author(s): Liqing Zhang, Xin Huang, Chengyong He, Qingyu Zhang, Xiaohua Zou, Danxia Ke, Qing‐Hua Gao
Software Mentions: 2
Published: over 8 years ago

10.3389/fpls.2021.681283

Overexpression of the Peach Transcription Factor Early Bud-Break 1 Leads to More Branches in Poplar
Cited by: 5
Author(s): Xuehui Zhao, Binbin Wen, Chen Li, Qiuping Tan, Li Liu, Xiude Chen, Ling Li, Xiling Fu
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2020.579529

Classification of Grain Amaranths Using Chromosome-Level Genome Assembly of Ramdana, A. hypochondriacus
Cited by: 5
Author(s): Saptarathi Deb, Suvratha Jayaprasad, Samathmika Ravi, Kanchan Rao, Saurabh Whadgar, Nivedita Hariharan, Swati Dixit, Meeta Sunil, Bibha Choudhary, Piergiorgio Stevanato, Eswarayya Ramireddy, Subhashini Srinivasan
Software Mentions: 2
Published: about 6 years ago

10.3389/fpls.2021.666266

Flower Development in Cassava Is Feminized by Cytokinin, While Proliferation Is Stimulated by Anti-Ethylene and Pruning: Transcriptome Responses
Cited by: 7
Author(s): Deborah N. Oluwasanya, Olayemisi C Esan, Peter Hyde, Peter Kulakow, Tim L. Setter
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.694859

Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid
Cited by: 9
Author(s): Jhon Henry Trujillo-Montenegro, María Juliana Rodríguez Cubillos, Cristian D Loaiza, Manuel Quintero, Hector F. Espitia-Navarro, Fredy Antonio Salazar Villareal, Carlos Arturo Viveros Valens, Andrés Fernando González Barrios, Jose J De Vega, Jorge Duitama, John J. Riascos
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2020.617020

Differentiation of Tracheary Elements in Sugarcane Suspension Cells Involves Changes in Secondary Wall Deposition and Extensive Transcriptional Reprogramming
Cited by: 7
Author(s): Marcella Siqueira Simões, Sávio Siqueira Ferreira, Adriana Grandis, Jorge Rencoret, Staffan Persson, Eny Iochevet Segal Floh, André Ferraz, José C. del Rı́o, Marcos Silveira Buckeridge, Igor Cesarino
Software Mentions: 2
Published: almost 6 years ago

10.3389/fpls.2021.685136

Unraveling the Regulatory Mechanism of Color Diversity in Camellia japonica Petals by Integrative Transcriptome and Metabolome Analysis
Cited by: 44
Author(s): Mingyue Fu, Yongsheng Xu, Jiarui Zheng, Ling Wang, Xiaoyan Yang, Yi Fang Tu, Jiabao Ye, Weiwei Zhang, Yongling Liao, Shuiyuan Cheng, Feng Xu
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2016.01184

Genome-Wide Analysis of MicroRNA Responses to the Phytohormone Abscisic Acid in Populus euphratica
Cited by: 27
Author(s): Hui Duan, Xiaoxuan Lu, Conglong Lian, Yi An, Xinli Xia, Weilun Yin
Software Mentions: 2
Published: about 10 years ago

10.3389/fpls.2018.00110

Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association of rp1 with Resistance to Goss's Wilt of Maize
Cited by: 21
Author(s): Ying Hu, Jie Ren, Zhao Peng, Arnoldo A. Umana, Ha Le, Tatiana Danilova, Junjie Fu, Haiyan Wang, Alison E. Robertson, Scot H. Hulbert, Frank F. White, Sanzhen Liu
Software Mentions: 2
Published: almost 9 years ago

10.3389/fpls.2019.00333

Salt-Enhanced Reproductive Development of Suaeda salsa L. Coincided With Ion Transporter Gene Upregulation in Flowers and Increased Pollen K+ Content
Cited by: 28
Author(s): Jianrong Guo, Xiao-Qiao Dong, Guoliang Han, Baoshan Wang
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2018.01676

Modification of Barley Plant Productivity Through Regulation of Cytokinin Content by Reverse-Genetics Approaches
Cited by: 52
Author(s): Katarína Holubová, Goetz Hensel, Petr Vojta, Petr Tarkowski, Véronique Bergougnoux, Petr Galuszka
Software Mentions: 2
Published: almost 8 years ago

10.3389/fpls.2021.604810

Toward Systematic Understanding of Flower Bud Induction in Apple: A Multi-Omics Approach
Cited by: 10
Author(s): Anton Milyaev, Julian Kofler, Iris Klaiber, Stefan Czemmel, Jens Pfannstiel, Henryk Flachowsky, D. Stefanelli, Magda‐Viola Hanke, J. Wünsche
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.652570

Molecular Analysis of the E2F/DP Gene Family of Daucus carota and Involvement of the DcE2F1 Factor in Cell Proliferation
Cited by: 2
Author(s): Lara Perrotta, Roberta Giordo, Dennis Francis, Hilary J. Rogers, Diego Albani
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.658787

Abscisic Acid Mediates Drought-Enhanced Rhizosheath Formation in Tomato
Cited by: 11
Author(s): Joseph K. Karanja, Mehtab Muhammad Aslam, Qian Zhang, Richard Yankey, Ian C. Dodd, Weifeng Xu
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.650252

Transcriptome and Coexpression Network Analyses Reveal Hub Genes in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) During Different Stages of Plasmodiophora brassicae Infection
Cited by: 16
Author(s): Yuxiang Yuan, Liu-yue QIN, Henan Su, Yang Shu, Xiaochun Wei, Zhiyong Wang, Yanyan Zhao, Lin Li, Honglei Liu, Bin Tian, Xiaowei Zhang
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2019.00268

Identification and Expression Analysis of GRAS Transcription Factor Genes Involved in the Control of Arbuscular Mycorrhizal Development in Tomato
Cited by: 32
Author(s): Tania Ho‐Plágaro, Nuria Molinero-Rosales, David Fariña Flores, Miriam Villena Díaz, José Manuel García‐Garrido
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2018.00345

Long-Term Irrigation Affects the Dynamics and Activity of the Wheat Rhizosphere Microbiome
Cited by: 62
Author(s): Dmitri V. Mavrodi, Olga V. Mavrodi, Liam D. H. Elbourne, Sasha G. Tetu, Robert F. Bonsall, James A. Parejko, Mingming Yang, Ian T. Paulsen, David M. Weller, Linda S. Thomashow
Software Mentions: 2
Published: over 8 years ago

10.3389/fpls.2021.635714

Complex-Type N-Glycans Influence the Root Hair Landscape of Arabidopsis Seedlings by Altering the Auxin Output
Cited by: 7
Author(s): Manuel Frank, Heidi Kaulfürst-Soboll, Kerstin Fischer, Antje von Schaewen
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.694229

Transcriptomic, Metabolomic, and Physiological Analyses Reveal That the Culture Temperatures Modulate the Cryotolerance and Embryogenicity of Developing Somatic Embryos in Picea glauca
Cited by: 5
Author(s): Ying Cui, Ying Gao, Ruirui Zhao, Jian Zhao, Yixuan Li, Shuaizheng Qi, Jinfeng Zhang, Lisheng Kong
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2021.630155

Tomato Cultivars Resistant or Susceptible to Spider Mites Differ in Their Biosynthesis and Metabolic Profile of the Monoterpenoid Pathway
Cited by: 11
Author(s): Nati Weinblum, Alon Cna’ani, Beery Yaakov, Adi Sadeh, Lior Avraham, Itai Opatovsky, Vered Tzin
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2020.622748

RNA-Seq Highlights Molecular Events Associated With Impaired Pollen-Pistil Interactions Following Short-Term Heat Stress in Brassica napus
Cited by: 12
Author(s): Neeta Lohani, Mohan B. Singh, Prem L. Bhalla
Software Mentions: 2
Published: almost 6 years ago

10.3389/fpls.2021.733846

Gene Body Methylation Confers Transcription Robustness in Mangroves During Long-Term Stress Adaptation
Cited by: 3
Author(s): Yushuai Wang, Aimei Dai, Yiping Chen, Tian Tang
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2021.711838

Plasmodiophora brassicae-Triggered Cell Enlargement and Loss of Cellular Integrity in Root Systems Are Mediated by Pectin Demethylation
Cited by: 8
Author(s): Karolina Stefanowicz, Monika Szymańska-Chargot, William Truman, Piotr Walerowski, Marcin Olszak, Adam Augustyniak, Arkadiusz Kosmala, Artur Zdunek, Robert Malinowski
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.714907

Knockdown of miR393 Promotes the Growth and Biomass Production in Poplar
Cited by: 11
Author(s): Liwei Chu, Xuejiao He, Wenbo Shu, Limin Wang, Fang Tang
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.690124

Predicting Protein–Protein Interactions Between Rice and Blast Fungus Using Structure-Based Approaches
Cited by: 8
Author(s): Cunjian Zheng, Yuan Liu, Fangnan Sun, Lingxia Zhao, Lida Zhang
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.643579

An SNP Mutation of Gene RsPP Converts Petal Color From Purple to White in Radish (Raphanus sativus L.)
Cited by: 1
Author(s): Dongming Liu, Xiaochun Wei, Dongling Sun, Yang Shu, Henan Su, Zhiyong Wang, Yanyan Zhao, Lin Li, Jinfang Liang, Luming Yang, Xiaowei Zhang, Yuxiang Yuan
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2019.01705

Defensive Responses of Tea Plants (Camellia sinensis) Against Tea Green Leafhopper Attack: A Multi-Omics Study
Cited by: 50
Author(s): Xiujuan Zhao, Si Chen, Shanshan Wang, Wenna Shan, Xiaoxia Wang, Yunting Lin, Feng Su, Zhenbiao Yang, Xiaomin Yu
Software Mentions: 2
Published: almost 7 years ago

10.3389/fpls.2019.01101

Ethylene Signaling Is Required for Fully Functional Tension Wood in Hybrid Aspen
Cited by: 13
Author(s): Carolin Seyfferth, Bernard A. Wessels, András Gorzsás, Jonathan Love, Markus Rüggeberg, Nicolas Delhomme, Thomas Vain, Kamil Antos, Hannele Tuominen, Björn Sundberg, Judith Felten
Software Mentions: 2
Published: about 7 years ago

10.3389/fpls.2019.00971

Cellular and Transcriptional Responses of Resistant and Susceptible Cultivars of Alfalfa to the Root Lesion Nematode, Pratylenchus penetrans
Cited by: 15
Author(s): Paulo Vieira, Joseph Mowery, J. D. Eisenback, Jonathan Shao, Lev G. Nemchinov
Software Mentions: 2
Published: over 7 years ago

10.1093/genetics/iyaa036

The regulatory network for petal anthocyanin pigmentation is shaped by the MYB5a/NEGAN transcription factor in <i>Mimulus</i>
Cited by: 12
Author(s): Xingyu Zheng, Kuenzang Om, Kimmy A Stanton, Daniel Thomas, Philip A Cheng, Allison Eggert, Emily Simmons, Yao‐Wu Yuan, Gregory D. Smith, Joshua R. Puzey, Arielle M. Cooley
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13059-015-0679-0

quantro: a data-driven approach to guide the choice of an appropriate normalization method
Cited by: 70
Author(s): Stephanie C. Hicks, Rafael A. Irizarry
Software Mentions: 2
Published: over 11 years ago

10.1186/s13059-016-0980-6

MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses
Cited by: 196
Author(s): Vanni Bucci, Belinda Tzen, Ning Li, Matt Simmons, Takeshi Tanoue, Elijah Bogart, Luxue Deng, Vladimir Yeliseyev, Mary L. Delaney, Qing Liu, Bernat Olle, Richard R. Stein, Kenya Honda, Lynn Bry, Georg K. Gerber
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-016-0990-4

Functional genomics analyses of RNA-binding proteins reveal the splicing regulator SNRPB as an oncogenic candidate in glioblastoma
Cited by: 78
Author(s): Bruna Corrêa, Patrícia Rosa de Araújo, Mu Qiao, Suzanne Perea Burns, Chen Chen, Richard Schlegel, Seema Agarwal, Pedro A. F. Galante, Luiz O. F. Penalva
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-016-1054-5

Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection
Cited by: 94
Author(s): Rieza Aprianto, Jelle Slager, Siger Holsappel, Jan‐Willem Veening
Software Mentions: 2
Published: about 10 years ago

10.1186/s13059-016-1096-8

TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells
Cited by: 78
Author(s): Lorenzo de la Rica, Özgen Deniz, Kevin Cheng, Christopher D. Todd, Cristina Cruz, Jonathan Houseley, Miguel R. Branco
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13059-016-1139-1

Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain
Cited by: 245
Author(s): Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xiaoteng Jia, Ronald Micura, Alexandra Lusser
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13059-017-1206-2

Proximal methylation features associated with nonrandom changes in gene body methylation
Cited by: 29
Author(s): Colette L. Picard, Mary Gehring
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-018-1478-1

DNA Topoisomerase I differentially modulates R-loops across the human genome
Cited by: 103
Author(s): Stefano Giustino Manzo, Stella R. Hartono, Lionel A. Sanz, Jessica Marinello, Sara De Biasi, Andrea Cossarizza, Giovanni Capranico, Frédéric Chédin
Software Mentions: 2
Published: over 8 years ago

10.1186/s13059-018-1497-y

Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries
Cited by: 73
Author(s): Seung-Hoon Baek, Kyung Choi, Goon-Bo Kim, Hee‐Ju Yu, Ara Cho, Hoyeol Jang, Changkyun Kim, Hyuk-Jin Kim, Kyung‐Il Chang, Joohwan Kim, Jeong‐Hwan Mun
Software Mentions: 2
Published: about 8 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: about 8 years ago

10.1186/s13059-019-1651-1

Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells
Cited by: 49
Author(s): Shraddha Sharma, Jianmin Wang, Emad Alqassim, Scott Portwood, Eduardo Cortes Gomez, Orla Maguire, Per H. Basse, Eunice S. Wang, Brahm H. Segal, Bora E. Baysal
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-019-1749-5

Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene
Cited by: 25
Author(s): Simon Lalonde, Valérie-Anne Codina-Fauteux, Sébastian Méric de Bellefon, F. Leblanc, Mélissa Beaudoin, Simon Maguire, Rola Dali, Tony Kwan, Ken Sin Lo, Tomi Pastinen, Guillaume Lettre
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-019-1787-z

MPRAnalyze: statistical framework for massively parallel reporter assays
Cited by: 54
Author(s): Tal Ashuach, David Fischer, Anat Kreimer, Nadav Ahituv, Fabian J. Theis, Nir Yosef
Software Mentions: 2
Published: about 7 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: almost 7 years ago

10.1186/s13059-020-01966-9

Decode-seq: a practical approach to improve differential gene expression analysis
Cited by: 11
Author(s): Yingshu Li, Hang Yang, Zhang HuJun, Yongjie Liu, Hanqiao Shang, Herong Zhao, Ting Zhang, Qiang Tu
Software Mentions: 2
Published: over 6 years ago

10.1186/s13059-020-02166-1

Clonal tracing reveals diverse patterns of response to immune checkpoint blockade
Cited by: 12
Author(s): Shengqing Stan Gu, Xiaoqing Wang, Xihao Hu, Peng Jiang, Ziyi Li, Nicole Traugh, Xia Bu, Qin Tang, Chenfei Wang, Zexian Zeng, Jingxin Fu, Cliff A. Meyer, Yi Zhang, Paloma Cejas, Klothilda Lim, Jin Wang, Wubing Zhang, Collin Tokheim, Avinash Sahu, Xiaofang Xing, Benjamin Kroger, Zhangyi Ouyang, Henry W. Long, Gordon J. Freeman, Myles Brown, X. Shirley Liu
Software Mentions: 2
Published: about 6 years ago

10.1172/jci.insight.149137

Gene expression atlas of energy balance brain regions
Cited by: 5
Author(s): Maria Caterina De Rosa, Hannah J Glover, George Stratigopoulos, Charles A. LeDuc, Qi Su, Yufeng Shen, Mark W. Sleeman, Wendy K. Chung, Rudolph L. Leibel, Judith Y. Altarejos, Claudia A. Doege
Software Mentions: 2
Published: about 5 years ago

10.1172/jci.insight.147280

Endothelial SOCS3 maintains homeostasis and promotes survival in endotoxemic mice
Cited by: 18
Author(s): Nina Martino, Ramon Bossardi Ramos, Shuhan Lu, Kara Leyden, Lindsay Tomaszek, Sudeshna Sadhu, Gabrielle Fredman, Ariel Jaitovich, Peter Vincent, Alejandro P. Adam
Software Mentions: 2
Published: over 5 years ago

10.1172/jci.insight.149149

Endothelium-protective, histone-neutralizing properties of the polyanionic agent defibrotide
Cited by: 20
Author(s): Hui Shi, Alex A. Gandhi, Stephanie A. Smith, Qiuyu Wang, Diane Chiang, Srilakshmi Yalavarthi, Ramadan A. Ali, Chao Liu, Gautam Sule, Pei‐Suen Tsou, Yu Zuo, Yogendra Kanthi, Evan A. Farkash, Jiandie D. Lin, James H. Morrissey, Jason S. Knight
Software Mentions: 2
Published: about 5 years ago

10.1172/jci.insight.147692

Anterograde regulation of mitochondrial genes and FGF21 signaling by hepatic LSD1
Cited by: 6
Author(s): Yang Cao, Lingyi Tang, Kang Du, Kitt D. Paraiso, Qiong Sun, Zhengxia Liu, Xiaolong Ye, Yuan Fang, Yuan Fang, Hank Chen, Yumay Chen, Xiaorong Wang, Clinton Yu, Ira L. Blitz, Ping H. Wang, Lan Huang, Haibo Cheng, Xiang Lü, Ken W.Y. Cho, Marcus M. Seldin, Zheng Fang, Qin Yang
Software Mentions: 2
Published: about 5 years ago

10.1161/JAHA.120.017091

Unique Transcriptome Signature Distinguishes Patients With Heart Failure With Myopathy
Cited by: 10
Author(s): Talia Caspi, Sam Straw, Chew Weng Cheng, Jack Garnham, Jason L. Scragg, Jessica Smith, Aaron Koshy, Eylem Levelt, Piruthivi Sukumar, John Gierula, David J. Beech, Mark T. Kearney, Richard M Cubbon, Stephen Wheatcroft, Klaus K. Witte, Lee D. Roberts, T. Scott Bowen
Software Mentions: 2
Published: about 6 years ago

10.1186/s40104-020-00436-3

High rumen degradable starch decreased goat milk fat via trans-10, cis-12 conjugated linoleic acid-mediated downregulation of lipogenesis genes, particularly, INSIG1
Cited by: 10
Author(s): Zheng Li, Shengru Wu, Jing Shen, Xiaoying Han, Chunjia Jin, Xiao Chen, Shengguo Zhao, Yangchun Cao, Junhu Yao
Software Mentions: 2
Published: over 6 years ago

10.1038/ja.2017.78

Insight into synergetic mechanisms of tetracycline and the selective serotonin reuptake inhibitor, sertraline, in a tetracycline-resistant strain of Escherichia coli
Cited by: 24
Author(s): Lili Li, Sofie Kromann, John Elmerdahl Olsen, Søren Wedel Svenningsen, Rikke Heidemann Olsen
Software Mentions: 2
Published: over 9 years ago

10.1007/s10815-021-02191-4

Single-center thorough evaluation and targeted treatment of globozoospermic men
Cited by: 9
Author(s): Stephanie Cheung, Alessandra Parrella, Danielle Rebecca Tavares, Derek Keating, Philip Xie, Zev Rosenwaks, Gianpiero D. Palermo
Software Mentions: 2
Published: over 5 years ago

10.1016/j.jaut.2017.03.004

B cells expressing the IgA receptor FcRL4 participate in the autoimmune response in patients with rheumatoid arthritis
Cited by: 49
Author(s): Khaled Amara, Elizabeth Clay, Lorraine Yeo, Daniel Ramsköld, Julia Spengler, Natalie Sippl, J. A. Cameron, Lena Israelsson, Philip J. Titcombe, Caroline Grönwall, Ilfita Sahbudin, Andrew Filer, Karim Raza, Vivianne Malmström, Dagmar Scheel‐Toellner
Software Mentions: 2
Published: over 9 years ago

10.1128/JB.00780-18

Refining the Pneumococcal Competence Regulon by RNA Sequencing
Cited by: 33
Author(s): Jelle Slager, Rieza Aprianto, Jan‐Willem Veening
Software Mentions: 2
Published: over 7 years ago

Projects: bioconductor: DESeq2

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Science Score: 100/100

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Papers Mentioning DESeq2 9,583