bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3390/genes8030090

Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics
Cited by: 17
Author(s): Joachim von Wulffen, Andreas Ulmer, Günter Jäger, Oliver Sawodny, Ronny Feuer
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-018-5146-3

Cell-type specific RNA-Seq reveals novel roles and regulatory programs for terminally differentiated Dictyostelium cells
Cited by: 18
Author(s): Koryu Kin, Gillian Forbes, Andrew Cassidy, Pauline Schaap
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2015.00065

Computational prediction of molecular pathogen-host interactions based on dual transcriptome data
Cited by: 48
Author(s): Sylvie Schulze, Sebastian Henkel, Dominik Driesch, Reinhard Guthke, JÃ¶rg Linde
Software Mentions: 4
Published: over 11 years ago

10.1534/g3.119.400998

A Collection of Pre-mRNA Splicing Mutants in Arabidopsis thaliana
Cited by: 20
Author(s): Tohru Kanno, Peter Venhuizen, Ming‐Tsung Wu, Phebe Chiou, Chia-Liang Chang, Maria Kalyna, A. J. M. Matzke, Marjori Matzke
Software Mentions: 4
Published: about 6 years ago

10.1098/rsob.160224

Interplay between RNA interference and heat shock response systems in Drosophila melanogaster
Cited by: 9
Author(s): S. Yu. Funikov, Sergei Ryazansky, Alexander Kanapin, Maria D. Logacheva, Aleksey A. Penin, А. В. Снежкина, Victoria Shilova, Д. Г. Гарбуз, Michael B. Evgen’ev, Olga G. Zatsepina
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12864-016-2397-8

Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii)
Cited by: 38
Author(s): Ido Bar, Scott F. Cummins, Abigail Elizur
Software Mentions: 4
Published: over 10 years ago

10.3389/fmicb.2017.01561

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing
Cited by: 211
Author(s): Luisa W. Hugerth, Anders F. Andersson
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2164-14-266

Characterization of differential transcript abundance through time during Nematostella vectensis development
Cited by: 73
Author(s): Rebecca R. Helm, Stefan Siebert, Sarah Tulin, Joel Smith, Casey W. Dunn
Software Mentions: 4
Published: over 13 years ago

10.1534/g3.120.401166

DAF-16 and SMK-1 Contribute to Innate Immunity During Adulthood inCaenorhabditis elegans
Cited by: 14
Author(s): Daniel R. McHugh, Elena Koumis, Paul Jacob, Jennifer Goldfarb, Michelle Schlaubitz-Garcia, Safae Bennani, Paul Regan, Prem Patel, Matthew J. Youngman
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2020.597944

Wine Terroir and the Soil Bacteria: An Amplicon Sequencing–Based Assessment of the Barossa Valley and Its Sub-Regions
Cited by: 8
Author(s): Jia Zhou, Timothy R. Cavagnaro, Roberta De Bei, Tiffanie M. Nelson, J. Stephen, Andrew Metcalfe, Matthew Gilliham, James Breen, Cassandra Collins, Carlos M. Rodríguez López
Software Mentions: 4
Published: over 5 years ago

10.1534/g3.119.400413

The Genome Sequence of the Eastern Woodchuck (Marmota monax) – A Preclinical Animal Model for Chronic Hepatitis B
Cited by: 13
Author(s): Tyler Alioto, Fernando Cruz, Jèssica Gómez-Garrido, Miriam Triyatni, Marta Gut, Leonor Frías, Anna Esteve‐Codina, Stephan Menne, Anna Kiialainen, Nadine Kumpesa, Fabian Birzele, Roland Schmucki, Ivo Gut, Olivia Spleiss
Software Mentions: 4
Published: over 6 years ago

10.1534/g3.119.400757

Machine Learning Enables High-Throughput Phenotyping for Analyses of the Genetic Architecture of Bulliform Cell Patterning in Maize
Cited by: 9
Author(s): Pengfei Qiao, Lin Meng, Miguel Vasquez, Susanne Matschi, James Chamness, Matheus Baseggio, Laurie G. Smith, Mert R. Sabuncu, Michael A. Gore, Michael J. Scanlon
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2020.00410

Transcriptional Responses of Dictyostelium discoideum Exposed to Different Classes of Bacteria
Cited by: 9
Author(s): Otmane Lamrabet, Astrid Melotti, Frédéric Burdet, Nabil Hanna, Jackie Perrin, Jahn Nitschke, Marco Pagni, Hubert Hilbi, Thierry Soldati, Pierre Cosson
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2020.00133

Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun
Cited by: 15
Author(s): Vandana R. Prabhu, . Wasimuddin, Ranganathan Kamalakkannan, Moolamkudy Suresh Arjun, Muniyandi Nagarajan
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-14-S8-S2

Evaluation of read count based RNAseq analysis methods
Cited by: 50
Author(s): Yan Guo, Chung I. Li, Fei Ye, Yu Shyr
Software Mentions: 4
Published: over 13 years ago

10.3389/fmicb.2019.01975

Functional Genomic Analyses of Exopolysaccharide-Producing Streptococcus thermophilus ASCC 1275 in Response to Milk Fermentation Conditions
Cited by: 8
Author(s): Qinglong Wu, Hung Chu, Aparna Padmanabhan, Nagendra P. Shah
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2021.605095

Improvement of Free Fatty Acid Secretory Productivity in Aspergillus oryzae by Comprehensive Analysis on Time-Series Gene Expression
Cited by: 4
Author(s): Pui Shan Wong, Koichi Tamano, Sachiyo Aburatani
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2019.02195

Different Pathways Mediate Amphotericin-Lactoferrin Drug Synergy in Cryptococcus and Saccharomyces
Cited by: 5
Author(s): Yu-Wen Lai, Chi Nam Ignatius Pang, Leona T. Campbell, Wen Chen, Marc R. Wilkins, Dee Carter
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2019.03044

Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti
Cited by: 34
Author(s): Víctor M. Flores‐Núñez, Citlali Fonseca-García, Damaris Desgarennes, Emiley A. Eloe‐Fadrosh, Tanja Woyke, Laila P. Partida‐Martínez
Software Mentions: 4
Published: over 6 years ago

10.1534/g3.118.200880

Activation of the Bile Acid Pathway and No Observed Antimicrobial Peptide Sequences in the Skin of a Poison Frog
Cited by: 1
Author(s): Megan L. Civitello, Robert D. Denton, Michael Zasloff, John H. Malone
Software Mentions: 4
Published: over 7 years ago

10.1534/g3.118.200810

Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression
Cited by: 13
Author(s): Stephen J. Bush, Mary E. B. McCulloch, Charity Muriuki, Mazdak Salavati, Gemma M. Davis, Iseabail L. Farquhar, Zofia M. Lisowski, Alan Archibald, David Hume, Emily L. Clark
Software Mentions: 4
Published: over 7 years ago

10.1534/g3.118.200516

Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
Cited by: 6
Author(s): Cathy Boscarino, Thomas Nalpathamkalam, Giovanna Pellecchia, Weili Li, Bhooma Thiruvahindrapuram, Daniele Merico
Software Mentions: 4
Published: over 7 years ago

10.3389/fmolb.2021.608369

Identification of a DNA Repair Gene Signature and Establishment of a Prognostic Nomogram Predicting Biochemical-Recurrence-Free Survival of Prostate Cancer
Cited by: 9
Author(s): Gongwei Long, Wei Ouyang, Yucong Zhang, Guoliang Sun, Jiahua Gan, Zhiquan Hu, Heng Li
Software Mentions: 4
Published: over 5 years ago

10.1534/g3.118.200677

Genotype-by-Environment-by-Environment Interactions in the Saccharomyces cerevisiae Transcriptomic Response to Alcohols and Anaerobiosis
Cited by: 5
Author(s): Maria Sardi, Molly Krause, Justin Heilberger, Audrey P. Gasch
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-12-364

Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing
Cited by: 82
Author(s): Peter L. Chang, Joseph P. Dunham, Sergey V. Nuzhdin, Michelle N. Arbeitman
Software Mentions: 4
Published: about 15 years ago

10.3389/fnmol.2018.00178

Stable STIM1 Knockdown in Self-Renewing Human Neural Precursors Promotes Premature Neural Differentiation
Cited by: 21
Author(s): Renjitha Gopurappilly, Bipan Kumar Deb, Pragnya Chakraborty, Gaiti Hasan
Software Mentions: 4
Published: about 8 years ago

10.3389/fnmol.2018.00288

Dysregulation of MicroRNAs and Target Genes Networks in Peripheral Blood of Patients With Sporadic Amyotrophic Lateral Sclerosis
Cited by: 84
Author(s): Maria Liguori, Nicoletta Nuzziello, Alessandro Introna, Arianna Consiglio, Flavio Licciulli, Eustachio D’Errico, Antonio Scarafino, Eugenio Distaso, Isabella Laura Simone
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-018-5089-8

Impact of energy restriction during late gestation on the muscle and blood transcriptome of beef calves after preconditioning
Cited by: 19
Author(s): Letícia P Sanglard, Moysés Nascimento, Philipe Moriel, Jeffrey R. Sommer, M.S. Ashwell, M. H. Poore, Márcio de Souza Duarte, Nick V. L. Serão
Software Mentions: 4
Published: almost 8 years ago

10.1534/g3.117.300245

Genome-Wide Screen forSaccharomyces cerevisiaeGenes Contributing to Opportunistic Pathogenicity in an Invertebrate Model Host
Cited by: 7
Author(s): Sujal Phadke, Calum J. Maclean, Serena Zhao, Emmi A. Mueller, Lucas A. Michelotti, Kaitlyn L. Norman, Anuj Kumar, Timothy Y. James
Software Mentions: 4
Published: over 8 years ago

10.3389/fnins.2020.00774

Lasting and Sex-Dependent Impact of Maternal Immune Activation on Molecular Pathways of the Amygdala
Cited by: 19
Author(s): Marissa R Keever, Pan Zhang, Courtni R. Bolt, Adrienne M. Antonson, Haley E Rymut, Megan P. Caputo, Alexandra K Houser, Álvaro Gonzalez Hernández, Bruce R. Southey, Laurie A. Rund, Rodney W. Johnson, Sandra L. Rodriguez-Zas
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2020.556497

Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma
Cited by: 19
Author(s): Xing Niu, Jun Xu, Jinwen Liu, Lijie Chen, Xue Qin, Ming Zhong
Software Mentions: 4
Published: almost 6 years ago

10.3389/fonc.2019.00606

Inactivation of Prostaglandin E2 as a Mechanism for UGT2B17-Mediated Adverse Effects in Chronic Lymphocytic Leukemia
Cited by: 10
Author(s): Éric P. Allain, Michèle Rouleau, Trang Le, Katrina Vanura, Lyne Villeneuve, Patrick Caron, Véronique Turcotte, Éric Lévesque, Chantal Guillemette
Software Mentions: 4
Published: about 7 years ago

10.3389/fonc.2019.01181

Circular RNA-Associated Competing Endogenous RNA Network and Prognostic Nomogram for Patients With Colorectal Cancer
Cited by: 42
Author(s): Wei Song, Tao Fu
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms22105066

The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa
Cited by: 10
Author(s): Karolina Kotecka, Adam Kawałek, Kamil Kobyłecki, Aneta Agnieszka Bartosik
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2021.614497

Molecular and Clinical Characterization of CCT2 Expression and Prognosis via Large-Scale Transcriptome Profile of Breast Cancer
Cited by: 6
Author(s): Qiang Liu, Yihang Qi, Xiangyi Kong, Xiangyu Wang, Wenxiang Zhang, Jie Zhai, Yazhe Yang, Yi Fang, Jing Wang
Software Mentions: 4
Published: over 5 years ago

10.1111/rssc.12213

A Bayesian Model Selection Approach for Identifying Differentially Expressed Transcripts from RNA Sequencing Data
Cited by: 5
Author(s): Panagiotis Papastamoulis, Magnus Rattray
Software Mentions: 4
Published: over 9 years ago

10.3389/fonc.2021.650828

Integrative Analysis of a Novel Eleven-Small Nucleolar RNA Prognostic Signature in Patients With Lower Grade Glioma
Cited by: 6
Author(s): Teng Deng, Yizhen Gong, Xiwen Liao, Xiangkun Wang, Xin Zhou, Guangzhi Zhu, Ligen Mo
Software Mentions: 4
Published: about 5 years ago

10.3389/fonc.2020.609601

Identify and Validate the Transcriptomic, Functional Network, and Predictive Validity of FBXL19-AS1 in Hepatocellular Carcinoma
Cited by: 4
Author(s): Dingdong He, Xiaokang Zhang, Xinyu Zhu, Narayani Maharjan, Yingchao Wang, Ping Luo, Chunzi Liang, Jiancheng Tu
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.613333

Construction of Bone Metastasis-Specific Regulation Network Based on Prognostic Stemness-Related Signatures in Breast Invasive Carcinoma
Cited by: 2
Author(s): Runzhi Huang, Zhenyu Li, Jiayao Zhang, Zhiwei Zeng, Jiaqi Zhang, Mingxiao Li, Siqao Wang, Shuyuan Xian, Yuna Xue, Xi Chen, Jie Li, Wing Yan Elizabeth Cheng, Bin Wang, Penghui Yan, Daoke Yang, Zongqiang Huang
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2019.00712

Prognostic lncRNAs, miRNAs, and mRNAs Form a Competing Endogenous RNA Network in Colon Cancer
Cited by: 33
Author(s): Qianrong Huang, Xin-Bin Pan
Software Mentions: 4
Published: about 7 years ago

10.3389/fonc.2021.546455

Identification of an Individualized Immune-Related Prognostic Risk Score in Lung Squamous Cell Cancer
Cited by: 9
Author(s): Yuan Zhuang, Sihan Li, Chang Liu, Guang Li
Software Mentions: 4
Published: over 5 years ago

10.3390/jpm9020018

Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research
Cited by: 12
Author(s): Isaac Raplee, Alexei V. Evsikov, Caralina Marín de Evsikova
Software Mentions: 4
Published: over 7 years ago

10.1111/acel.12352

Eicosapentaenoic acid but not docosahexaenoic acid restores skeletal muscle mitochondrial oxidative capacity in old mice
Cited by: 50
Author(s): Matthew L. Johnson, Antigoni Z. Lalia, Surendra Dasari, Maximilian Pallauf, Mark Fitch, Marc K. Hellerstein, Ian R. Lanza
Software Mentions: 4
Published: about 11 years ago

10.1111/acel.13195

Growth differentiation factor 15 protects against the aging‐mediated systemic inflammatory response in humans and mice
Cited by: 59
Author(s): Ji Sun Moon, Ludger Goeminne, Jung Tae Kim, Jing Tian, Seok Hwan Kim, Ha Thi Nga, Sun Hyung Kang, Baeki E. Kang, Jin Seok Byun, Young‐Sun Lee, Jae‐Han Jeon, Minho Shong, Johan Auwerx, Dongryeol Ryu, Hyon‐Seung Yi
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms22073674

Can miRNA Indicate Risk of Illness after Continuous Exposure to M. tuberculosis?
Cited by: 3
Author(s): Cleonardo Augusto Silva, André M. Ribeiro-dos-Santos, Wanderson Gonçalves e Gonçalves, Pablo Diego do Carmo Pinto, Rafael Pompeu Pantoja, Tatiana Vinasco-Sandoval, André M. Ribeiro-dos-Santos, Mara H. Hutz, Amanda Ferreira Vidal, Gilderlanio Santana de Araújo, Sidney Emanuel Batista dos Santos
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22063125

A Transcriptomic Approach to Understanding the Combined Impacts of Supra-Optimal Temperatures and CO2 Revealed Different Responses in the Polyploid Coffea arabica and Its Diploid Progenitor C. canephora
Cited by: 12
Author(s): Isabel Marques, Isabel Fernandes, Octávio S. Paulo, Fernando C. Lidon, Fábio M. DaMatta, José C. Ramalho, Ana I. Ribeiro‐Barros
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22052481

Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species
Cited by: 5
Author(s): Jodi B Callwood, Kalpalatha Melmaiee, Krishnanand P. Kulkarni, Amaranatha R. Vennapusa, Diarra Aicha, Michael J. Moore, Nicholi Vorsa, Purushothaman Natarajan, Umesh K. Reddy, Sathya Elavarthi
Software Mentions: 4
Published: over 5 years ago

10.1186/s13568-021-01225-5

Manipulating the soil microbiomes during a community recovery process with plant beneficial species for the suppression of Fusarium wilt of watermelon
Cited by: 14
Author(s): Xu Zhang, Cong Xue, D. C. Fang, Xiangming He, Mengyu Wei, Chenjin Zhuo, Junyao Jin, Biao Shen, Rong Li, Ning Ling, Qirong Shen
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-016-2646-x

A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species
Cited by: 25
Author(s): Montserrat Torres-Oliva, Isabel Almudí, Alistair P. McGregor, Nico Posnien
Software Mentions: 4
Published: over 10 years ago

10.1111/acel.13178

The inherited methylome landscape is directly altered with paternal aging and associated with offspring neurodevelopmental disorders
Cited by: 27
Author(s): Michelle M. Denomme, Mary E. Haywood, Jason C. Parks, William B. Schoolcraft, Mandy G. Katz‐Jaffe
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms21249560

Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses
Cited by: 2
Author(s): Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-021-07729-5

The holobiont transcriptome of teneral tsetse fly species of varying vector competence
Cited by: 3
Author(s): Miguel Medina Munoz, Caitlyn Brenner, Dylan Richmond, Noah Spencer, Rita V. M. Rio
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-021-07592-4

RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish
Cited by: 8
Author(s): Matt J. Thorstensen, Melinda R. Baerwald, Ken M. Jeffries
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.24570

EED orchestration of heart maturation through interaction with HDACs is H3K27me3-independent
Cited by: 36
Author(s): Shanshan Ai, Yong Peng, Chen Li, Fei Gu, Xianhong Yu, Yanzhu Yue, Qing Ma, Jinghai Chen, Zhiqiang Lin, Pingzhu Zhou, Huafeng Xie, Terence Prendiville, Wen Zheng, Yuli Liu, Stuart H. Orkin, Dazhi Wang, Jia Yu, William T. Pu, Aibin He
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-016-2952-3

Global transcriptional analysis suggests Lasiodiplodia theobromae pathogenicity factors involved in modulation of grapevine defensive response
Cited by: 46
Author(s): Marcos Paolinelli, José Manuel Villalobos-Escobedo, Philippe E. Rolshausen, Alfredo Herrera-Estrella, Clara E. Galindo-Sánchez, José Fabricio López-Hernández, Rufina Hernández-Martínez
Software Mentions: 4
Published: about 10 years ago

10.7554/eLife.53237

Rapid sex-specific adaptation to high temperature in Drosophila
Cited by: 20
Author(s): Sheng‐Kai Hsu, Ana Marija Jakšić, Viola Nolte, Manolis Lirakis, Robert Kofler, Neda Barghi, Elisabetta Versace, Christian Schlötterer
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-016-3070-y

The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets
Cited by: 27
Author(s): Pablo Ivan Pereira Ramos, Márlon Grégori Flores Custódio, Guadalupe del Rosario Quispe Saji, Thiago Bérgamo Cardoso, Gisele Lucchetti da Silva, Graziela Braun, Willames M. B. S. Martins, Raquel Girardello, Ana Tereza Ribeiro de Vasconcelos, Elmer Fernández, Ana Cristina Gales, Marisa Fabiana Nicolás
Software Mentions: 4
Published: almost 10 years ago

10.1186/1471-2164-14-S1-S9

Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information
Cited by: 2
Author(s): Ellis Patrick, Michael Buckley, David M. Lin, Jean Yee Hwa Yang
Software Mentions: 4
Published: over 13 years ago

10.18632/oncotarget.27488

MAGE-A inhibit apoptosis and promote proliferation in multiple myeloma through regulation of BIM and p21Cip1
Cited by: 10
Author(s): Anna Mei, Kaity Tung, Jessie Han, Deepak Perumal, Alessandro Laganà, Jonathan J. Keats, Daniel Auclair, Ajai Chari, Sundar Jagannath, Samir Parekh, Hearn Jay Cho
Software Mentions: 4
Published: over 6 years ago

10.1186/1748-7188-7-5

A normalization strategy for comparing tag count data
Cited by: 72
Author(s): Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu
Software Mentions: 4
Published: over 14 years ago

10.1186/s12864-019-5530-7

Gene expression of Hanwoo satellite cell differentiation in longissimus dorsi and semimembranosus
Cited by: 17
Author(s): Sara de las Heras‐Saldana, Ki Yong Chung, Seung Hwan Lee, Cedric Gondro
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-015-2114-z

Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis
Cited by: 9
Author(s): Gareth D. Weedall, Helen Irving, Margaret Hughes, Charles S. Wondji
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12864-016-2403-1

RNA sequencing-based analysis of the spleen transcriptome following infectious bronchitis virus infection of chickens selected for different mannose-binding lectin serum concentrations
Cited by: 20
Author(s): Edin Hamzić, Rikke Brødsgaard Kjærup, Núria Mach, Guilietta Minozzi, Francesco Strozzi, V. Gualdi, J. L. Williams, Jun Chen, Eva Wattrang, Bart Buitenhuis, Helle R. Juul‐Madsen, Tina Sørensen Dalgaard
Software Mentions: 4
Published: over 10 years ago

10.18632/aging.102820

Development and validation of a prognostic classifier based on HIF-1 signaling for hepatocellular carcinoma
Cited by: 22
Author(s): Feiwen Deng, Chen Dong, Xiaoli Wei, Shilin Lu, Xuan Luo, Jincan He, Junting Liu, Tiebao Meng, Anli Yang, Huanwei Chen
Software Mentions: 4
Published: over 6 years ago

10.1186/s40303-016-0017-9

αT-catenin in restricted brain cell types and its potential connection to autism
Cited by: 20
Author(s): Stephen Sai Folmsbee, Douglas R. Wilcox, Koen Tyberghein, Pieter De Bleser, Warren G. Tourtellotte, Jolanda van Hengel, Frans van Roy, Cara J. Gottardi
Software Mentions: 4
Published: about 10 years ago

10.1186/s12864-017-3809-0

Gene dispersion is the key determinant of the read count bias in differential expression analysis of RNA-seq data
Cited by: 20
Author(s): Susan A. Yoon, Dougu Nam
Software Mentions: 4
Published: about 9 years ago

10.1186/s12864-016-2973-y

Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch)
Cited by: 15
Author(s): Kanjana Worarad, Tomohiro Suzuki, Kazuo Ishii, Toshinori Kozaki, Masayuki Iigo, Kenji Yamane
Software Mentions: 4
Published: about 10 years ago

10.1186/s12864-018-4457-8

Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon
Cited by: 10
Author(s): Li Liu, Shuchao Ren, Junqiang Guo, Qingyi Wang, Xiaotuo Zhang, Peiran Liao, Shipeng Li, Ramanjulu Sunkar, Yun Zheng
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2164-15-133

Virus-independent and common transcriptome responses of leafhopper vectors feeding on maize infected with semi-persistently and persistent propagatively transmitted viruses
Cited by: 33
Author(s): Bryan J. Cassone, Saranga Wijeratne, Andrew P. Michel, Lucy R. Stewart, Yuting Chen, Pearlly S. Yan, Margaret G. Redinbaugh
Software Mentions: 4
Published: over 12 years ago

10.1186/s12864-018-5184-x

Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification
Cited by: 7
Author(s): Yung-Chih Lai, Ya-Chen Liang, Ting‐Xin Jiang, Randall B. Widelitz, Ping Wu, Cheng‐Ming Chuong
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-018-5160-5

Analysis and correction of compositional bias in sparse sequencing count data
Cited by: 62
Author(s): M. S. Binoj Kumar, Eric V. Slud, Kwame Okrah, Stephanie Hicks, Sridhar Hannenhalli, Héctor Corrada Bravo
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-019-5767-1

Transcriptomic responses to diet quality and viral infection in Apis mellifera
Cited by: 23
Author(s): Lindsay Rutter, Jimena Carrillo-Tripp, Bryony C. Bonning, Dianne Cook, Amy L. Toth, Adam Doležal
Software Mentions: 4
Published: over 7 years ago

10.3390/ijerph18157975

Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data
Cited by: 6
Author(s): Yongjun Piao, Wanxue Xu, Kwang Ho Park, Keun Ho Ryu, Rong Xiang
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-020-07091-y

Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning
Cited by: 10
Author(s): Fernando Henrique Correr, Guilherme Kenichi Hosaka, Fernando Barreto, Isabella Barros Valadão, Thiago Willian Almeida Balsalobre, Agnelo Furtado, Robert J. Henry, Monalisa Sampaio Carneiro, Gabriel Rodrigues Alves Margarido
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijerph17207386

Environmental Epigenetics of Diesel Particulate Matter Toxicogenomics
Cited by: 0
Author(s): Stephanie M. Bilinovich, Kristy Lewis, Barbara L. Thompson, Jeremy W. Prokop, Daniel B. Campbell
Software Mentions: 4
Published: almost 6 years ago

10.3390/ani11082241

Transcriptomic Response under Heat Stress in Chickens Revealed the Regulation of Genes and Alteration of Metabolism to Maintain Homeostasis
Cited by: 8
Author(s): Hana Kim, Hye‐Ran Kim, Pil‐Nam Seong, D. K. Arora, Donghyun Shin, Woncheoul Park, Jong-Eun Park
Software Mentions: 4
Published: about 5 years ago

10.18632/oncotarget.25382

Aberration hubs in protein interaction networks highlight actionable targets in cancer
Cited by: 4
Author(s): Mehran Karimzadeh, Pouria Jandaghi, Andreas I. Papadakis, Sebastian Trainor, Johan Rung, Mar Gonzàlez-Porta, Ghislaine Scélo, Naveen S. Vasudev, Alvis Brāzma, Sidong Huang, Rosamonde E. Banks, Mark Lathrop, Hamed S. Najafabadi, Yasser Riazalhosseini
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-015-1660-8

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus
Cited by: 59
Author(s): Michael H. Perlin, Joëlle Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, Jonathan M. Goldberg, Sébastien Duplessis, Bernard Henrissat, Sarah Young, Qiandong Zeng, Gabriela Aguileta, Elsa Petit, Hélène Badouin, Jared Andrews, Dominique Razeeq, Toni Gabaldón, Hadi Quesneville, Tatiana Giraud, Michael E. Hood, David J. Schultz, Christina A. Cuomo
Software Mentions: 4
Published: about 11 years ago

10.7150/ijms.51297

Heat shock factor 5 correlated with immune infiltration serves as a prognostic biomarker in lung adenocarcinoma
Cited by: 5
Author(s): Aizemaiti Rusidanmu, Zhigang Wu, Jie Tang, Haimeng Yan, Xiaoshu Lv
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-6564-6

Transcriptome analysis of fungicide-responsive gene expression profiles in two Penicillium italicum strains with different response to the sterol demethylation inhibitor (DMI) fungicide prochloraz
Cited by: 15
Author(s): Tingfu Zhang, Qing Cao, Na Li, De Li Liu, Yongze Yuan
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.24898

Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets
Cited by: 17
Author(s): Rosemarie Weikard, Frieder Hadlich, H.M. Hammon, D. Frieten, C. Gerbert, Christian Koch, G. Dusel, Christa Kühn
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-017-3840-1

Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent, Peromyscus eremicus
Cited by: 9
Author(s): Lauren Kordonowy, Matthew D. MacManes
Software Mentions: 4
Published: about 9 years ago

10.1186/s12967-019-1851-1

Reduced protocadherin17 expression in leukemia stem cells: the clinical and biological effect in acute myeloid leukemia
Cited by: 17
Author(s): Zi‐jun Xu, Ji‐chun Ma, Jing‐Dong Zhou, Xiang‐mei Wen, Dong‐ming Yao, Wei Zhang, Runbi Ji, Dehong Wu, Li‐Juan Tang, Zhaoqun Deng, Jun Qian, Lin Jiang
Software Mentions: 4
Published: over 7 years ago

10.18632/oncotarget.23638

YAP-associated chromosomal instability and cholangiocarcinoma in mice
Cited by: 41
Author(s): Sumera Rizvi, Samantha R. Fischbach, Steven F. Bronk, Petra Hirsova, Anuradha Krishnan, Renumathy Dhanasekaran, James B. Smadbeck, Rory L. Smoot, George Vasmatzis, Gregory J. Gores
Software Mentions: 4
Published: over 8 years ago

10.1186/1479-5876-12-159

An eight-miRNA signature as a potential biomarker for predicting survival in lung adenocarcinoma
Cited by: 95
Author(s): Xuelian Li, Yunrui Shi, Zhihua Yin, Xiaoxia Xue, Baosen Zhou
Software Mentions: 4
Published: about 12 years ago

10.3390/ani11082165

Comprehensive Transcriptomic Comparison between Porcine CD8− and CD8+ Gamma Delta T Cells Revealed Distinct Immune Phenotype
Cited by: 7
Author(s): Sang–Wook Kim, Bee-Oh Lim, Sameer-ul-Salam Mattoo, Eunyoung Oh, Chang-Gi Jeong, Won-Il Kim, Kyung-Tai Lee, Sang-Myeong Lee, Junmo Kim
Software Mentions: 4
Published: about 5 years ago

10.3390/ani11092705

Ruminal and Fecal Bacteriome of Dairy Calves Fed Different Levels and Sources of NDF
Cited by: 2
Author(s): Gercino Ferreira Virgínio Júnior, Ana Paula da Silva, Ariany Faria de Toledo, Milaine Poczynek, Amanda Moelemberg Cezar, Horácio Montenegro, Luiz Lehmann Coutinho, Carla Maris Machado Bittar
Software Mentions: 4
Published: almost 5 years ago

10.18632/aging.103454

Weighted correlation gene network analysis reveals a new stemness index-related survival model for prognostic prediction in hepatocellular carcinoma
Cited by: 14
Author(s): Qiujing Zhang, Jia Wang, Menghan Liu, Qingqing Zhu, Qiang Li, Chao Xie, Congcong Han, Yali Wang, Min Gao, Jie Liu
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-021-07889-4

Experimental Babesia rossi infection induces hemolytic, metabolic, and viral response pathways in the canine host
Cited by: 6
Author(s): Rachel Smith, Amelia Goddard, Arun K. Boddapati, Steven Brooks, Johan P. Schoeman, Justin Lack, Andrew L. Leisewitz, Hans Ackerman
Software Mentions: 4
Published: about 5 years ago

10.1080/20013078.2018.1461450

ISEV2018 abstract book
Cited by: 157
Author(s): Clotilde Théry, Kenneth W. Witwer
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-017-3661-2

Detect tissue heterogeneity in gene expression data with BioQC
Cited by: 42
Author(s): Jitao David Zhang, Klas Hatje, Gregor Sturm, Clemens Broger, Martin Ebeling, Martine Burtin, Fabiola Terzi, Silvia Pomposiello, Laura Badi
Software Mentions: 4
Published: over 9 years ago

10.3390/antiox10091380

NRF2 Mediates Therapeutic Resistance to Chemoradiation in Colorectal Cancer through a Metabolic Switch
Cited by: 7
Author(s): Séan M. O’Cathail, Chieh‐Hsi Wu, Russell J. Thomas, M. Hawkins, Tim Maughan, Annabelle Lewis
Software Mentions: 4
Published: almost 5 years ago

10.1084/jem.20200137

PDGFA-associated protein 1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification
Cited by: 6
Author(s): Verónica Delgado-Benito, Maria Berruezo-Llacuna, Robert Altwasser, Wiebke Winkler, Devakumar Sundaravinayagam, Sandhya Balasubramanian, Marieta Caganova, Robin Graf, Ali Rahjouei, Marie-Thérèse Henke, Madlen Driesner, Lisa Keller, Alessandro Prigione, Martin Janz, Altuna Akalin, Michela Di Virgilio
Software Mentions: 4
Published: about 6 years ago

10.1186/s13046-020-01752-2

MiRNA-340-5p mediates the functional and infiltrative promotion of tumor-infiltrating CD8+ T lymphocytes in human diffuse large B cell lymphoma
Cited by: 9
Author(s): Yangyang Xu, Zhenchuan Liu, Lixin Lv, Ping Li, Bing Xu, Wenbin Qian, Aibin Liang
Software Mentions: 4
Published: almost 6 years ago

10.18632/oncotarget.22878

Identification of cancer prognosis-associated functional modules using differential co-expression networks
Cited by: 10
Author(s): Wenshuai Yu, Shengjie Zhao, Yongcui Wang, Brian Nlong Zhao, Weiling Zhao, Xiaobo Zhou
Software Mentions: 4
Published: over 8 years ago

10.1186/s13046-020-1541-0

FKBP9 promotes the malignant behavior of glioblastoma cells and confers resistance to endoplasmic reticulum stress inducers
Cited by: 16
Author(s): Huizhe Xu, Peng Liu, Yumei Yan, Kun Fang, Dapeng Liang, Yangcheng Liu, Xiaohong Zhang, Songyan Wu, Jin Ma, Ruoyu Wang, Tao Li, Haozhe Piao, Meng Shao
Software Mentions: 4
Published: over 6 years ago

10.1186/s13046-019-1254-4

Long noncoding RNA MYOSLID promotes invasion and metastasis by modulating the partial epithelial-mesenchymal transition program in head and neck squamous cell carcinoma
Cited by: 74
Author(s): Hong‐Gang Xiong, Hao Li, Yao Xiao, Qi‐Chao Yang, Leilei Yang, Lei Chen, Lin‐Lin Bu, Wenfeng Zhang, Jiali Zhang, Zhi‐Jun Sun
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-019-5428-4

New insights in the control of antioxidants accumulation in tomato by transcriptomic analyses of genotypes exhibiting contrasting levels of fruit metabolites
Cited by: 20
Author(s): Adriana Sacco, Assunta Raiola, Roberta Calafiore, Amalia Barone, Maria Manuela Rigano
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-019-5572-x

Differential isoform expression and alternative splicing in sex determination in mice
Cited by: 21
Author(s): Benjamín Planells, Isabel Gómez-Redondo, Eva Pericuesta, Patrick Lonergan, Alfonso Gutiérrez‐Adán
Software Mentions: 4
Published: over 7 years ago

10.1099/acmi.0.000082

Transcriptome analysis of Brucella abortus S19∆per immunized mouse spleen revealed activation of MHC-I and MHC-II pathways
Cited by: 2
Author(s): K. S. Solanki, Ravikumar Gandham, Prasad Thomas, Pallab Chaudhuri
Software Mentions: 4
Published: over 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568