bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/srep32366

Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians
Cited by: 73
Author(s): Iliona Wolfowicz, Sebastian Baumgarten, Philipp A. Voss, Elizabeth A. Hambleton, Christian R. Voolstra, Masayuki Hatta, Annika Guse
Software Mentions: 1
Published: about 10 years ago

10.7150/ijms.49997

Research on the circadian clock gene HNF4a in different malignant tumors
Cited by: 0
Author(s): Mengjun Qiu, Li Zhang, Xiefan Fang, Qiuting Li, Lisheng Zhu, Bin Zhang, Shengli Yang, Zhifan Xiong
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-020-07080-1

Transcriptome characterization of BPG axis and expression profiles of ovarian steroidogenesis-related genes in the Japanese sardine
Cited by: 6
Author(s): Mitsuo Nyuji, Yuki Hongo, Michio Yoneda, Masahiro Nakamura
Software Mentions: 1
Published: about 6 years ago

10.1038/srep32731

Tissue-specific Co-expression of Long Non-coding and Coding RNAs Associated with Breast Cancer
Cited by: 24
Author(s): Wenting Wu, Erin K. Wagner, Yangyang Hao, Xi Rao, Hong Dai, Jiali Han, Jinhui Chen, Anna Maria Storniolo, Yunlong Liu, Chunyan He
Software Mentions: 1
Published: about 10 years ago

10.3390/pathogens6040068

Prebiotic Oligosaccharides Potentiate Host Protective Responses against L. Monocytogenes Infection
Cited by: 20
Author(s): Poyin Chen, Taylor Reiter, Bihua C. Huang, Nguyet Kong, Bart C. Weimer
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-015-2359-6

IL-10 and integrin signaling pathways are associated with head and neck cancer progression
Cited by: 36
Author(s): Sophia Bornstein, Mark Schmidt, Gabrielle Choonoo, Trevor G. Levin, Joe W. Gray, Charles R. Thomas, Melissa Wong, Shannon K. McWeeney
Software Mentions: 1
Published: almost 11 years ago

10.3389/fmicb.2021.651744

Growth on Formic Acid Is Dependent on Intracellular pH Homeostasis for the Thermoacidophilic Methanotroph Methylacidiphilum sp. RTK17.1
Cited by: 11
Author(s): Carlo R. Carere, Kiel Hards, Kathryn Wigley, Luke Carman, Karen M. Houghton, Gregory M. Cook, Matthew B. Stott
Software Mentions: 1
Published: over 5 years ago

10.1002/cbin.11454

ERO1L promotes NSCLC development by modulating cell cycle‐related molecules
Cited by: 6
Author(s): Xiujuan Shi, Jiawen Wu, Yi Liu, Yuxiong Jiang, Changjiang Zhi, Jue Li
Software Mentions: 1
Published: about 6 years ago

10.1038/s41368-019-0070-1

Transcriptome analysis of ankylosed primary molars with infraocclusion
Cited by: 3
Author(s): Annie Tong, Yuh-Lit Chow, Katie Xu, Rita Hardiman, Paul M. Schneider, Seong‐Seng Tan
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-14-634

Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki
Cited by: 43
Author(s): Kevin T. Bilyk, C.‐H. Christina Cheng
Software Mentions: 1
Published: almost 14 years ago

10.3389/fmicb.2016.00078

Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae
Cited by: 31
Author(s): Xiao-Yan Yang, Kui He, Gaofei Du, Xiaohui Wu, Guangchuang Yu, Yunlong Pan, Gong Zhang, Xia Sun, Qing‐Yu He
Software Mentions: 1
Published: over 10 years ago

10.3390/v13071325

Virus-Targeted Transcriptomic Analyses Implicate Ranaviral Interaction with Host Interferon Response in Frog Virus 3-Infected Frog Tissues
Cited by: 1
Author(s): Yun Tian, Francisco De Jesús Andino, Collins N. Khwatenge, Jiuyi Li, Jacques Robert, Yongming Sang
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2016.01545

New Genes Involved in Osmotic Stress Tolerance in Saccharomyces cerevisiae
Cited by: 18
Author(s): Ramón González, Pilar Morales, Jordi Tronchoni, Gustavo Cordero-Bueso, Enrico Vaudano, Manuel Quirós, Maïté Novo, Rafael Torres‐Pérez, Eva Valero
Software Mentions: 1
Published: about 10 years ago

10.1038/srep33210

The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome
Cited by: 12
Author(s): Swaraj Basu, Yavor Hadzhiev, Giuseppe Petrosino, Chirag Nepal, Jochen Gehrig, Olivier Armant, Marco Ferg, Uwe Strähle, Remo Sanges, Ferenc Müller
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2017.00180

Critical Issues in Mycobiota Analysis
Cited by: 63
Author(s): Bettina Halwachs, Nandhitha Madhusudhan, Robert Krause, R. Henrik Nilsson, Christine Moissl-Eichinger, Christoph Högenauer, Gerhard G. Thallinger, Gregor Gorkiewicz
Software Mentions: 1
Published: over 9 years ago

10.1038/srep33398

An integrative and comparative study of pan-cancer transcriptomes reveals distinct cancer common and specific signatures
Cited by: 21
Author(s): Zhen Cao, Shihua Zhang
Software Mentions: 1
Published: about 10 years ago

10.1186/s13071-020-3914-9

Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis
Cited by: 6
Author(s): Lucas Gentil Azevedo, Artur T. L. Queiroz, Aldina Barral, Luciane Amorim Santos, Pablo Ivan Pereira Ramos
Software Mentions: 1
Published: over 6 years ago

10.1186/s12862-019-1362-y

Effects of adult temperature on gene expression in a butterfly: identifying pathways associated with thermal acclimation
Cited by: 6
Author(s): Kristin Franke, Isabell Karl, Tonatiuh Peña Centeno, Barbara Feldmeyer, Christian Lassek, Vicencio Oostra, Katharina Riedel, Mario Stanke, Christopher W. Wheat, Klaus Fischer
Software Mentions: 1
Published: almost 8 years ago

10.3389/fmicb.2018.00356

Comparative Genomics of the Baltic Sea Toxic Cyanobacteria Nodularia spumigena UHCC 0039 and Its Response to Varying Salinity
Cited by: 12
Author(s): Jonna Teikari, Songjun Hou, Matti Wahlsten, Wolfgang R. Hess, Kaarina Sivonen
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2148-13-165

Horizontally transferred genes in the genome of Pacific white shrimp, Litopenaeus vannamei
Cited by: 14
Author(s): Jianbo Yuan, Xiaojun Zhang, Cheng-Zhang Liu, Jiankai Wei, Fuhua Li, Jianhai Xiang
Software Mentions: 1
Published: about 13 years ago

10.3389/fmicb.2021.615893

Transcriptome Profiling Reveals a Novel Mechanism of Antiviral Immunity Upon Sacbrood Virus Infection in Honey Bee Larvae (Apis cerana)
Cited by: 10
Author(s): Yanjun Guo, Zhengyi Zhang, Mingsheng Zhuang, Liuhao Wang, Kai Li, Jun Yao, Huipeng Yang, Jiaxing Huang, Ya Hao, Ying Fan, Hira Mannan, Jie Wu, Yanping Chen, Jilian Li
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2019.00150

Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach
Cited by: 35
Author(s): Murugesan Sivaranjani, Katarzyna Leskinen, Chairmandurai Aravindraja, Päivi Saavalainen, Shunmugiah Karutha Pandian, Mikael Skurnik, Arumugam Veera Ravi
Software Mentions: 1
Published: over 7 years ago

10.1186/s12862-015-0322-4

Genetic variation of transgenerational plasticity of offspring germination in response to salinity stress and the seed transcriptome of Medicago truncatula
Cited by: 52
Author(s): Wendy Vu, Peter L. Chang, Ken S. Moriuchi, Maren Friesen
Software Mentions: 1
Published: over 11 years ago

10.1038/srep36254

Understanding the immune system architecture and transcriptome responses to southern rice black-streaked dwarf virus in Sogatella furcifera
Cited by: 22
Author(s): Lin Wang, Nan Tang, Xinlei Gao, Dongyang Guo, Zhaoxia Chang, Yating Fu, Ibukun A. Akinyemi, Qingfa Wu
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep36388

Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data
Cited by: 7
Author(s): Hongyang Wang, Rui Li, Xiang Zhou, Liyao Xue, Xuewen Xu, Bang Liu
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pgen.1005536

Fungal Infection Induces Sex-Specific Transcriptional Changes and Alters Sexual Dimorphism in the Dioecious Plant Silene latifolia
Cited by: 24
Author(s): Niklaus Zemp, Raquel Tavares, Alex Widmer
Software Mentions: 1
Published: about 11 years ago

10.1038/srep36463

RNA-seq based transcriptomic analysis uncovers α-linolenic acid and jasmonic acid biosynthesis pathways respond to cold acclimation in Camellia japonica
Cited by: 55
Author(s): Qingyuan Li, Sheng Lei, Kun Du, Lizhi Liu, Xufeng Pang, Zhanchang Wang, Ming Wei, Shao Ping Fu, Limin Hu, Lin Xu
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13071-020-3910-0

Expanded complement of Niemann-Pick type C2-like protein genes in Clonorchis sinensis suggests functions beyond sterol binding and transport
Cited by: 3
Author(s): Marziyeh Anari, Andreas J. Stroehlein, Ross S. Hall, Bill C.H. Chang, Robin B. Gasser, Neil D. Young
Software Mentions: 1
Published: almost 7 years ago

10.1038/srep37082

Doxycycline, metronidazole and isotretinoin: Do they modify microRNA/mRNA expression profiles and function in murine T-cells?
Cited by: 19
Author(s): Eugenia Becker, Susan Bengs, Sirisha Aluri, Lennart Opitz, Kirstin Atrott, Claudia Stanzel, Pedro A. Ruiz-Castro, Gerhard Rogler, Isabelle Frey-Wagner
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pgen.1005093

Male-Biased Aganglionic Megacolon in the TashT Mouse Line Due to Perturbation of Silencer Elements in a Large Gene Desert of Chromosome 10
Cited by: 32
Author(s): Karl-F. Bergeron, Tatiana Cardinal, Aboubacrine M. Touré, Mélanie Béland, Diana L. Raiwet, David W. Silversides, Nicolas Pilon
Software Mentions: 1
Published: over 11 years ago

10.3390/ijms22094910

Extracellular Vesicles in Synovial Fluid from Rheumatoid Arthritis Patients Contain miRNAs with Capacity to Modulate Inflammation
Cited by: 15
Author(s): Andrew D Foers, Alexandra L. Garnham, Simon Chatfield, Gordon K. Smyth, Lesley Cheng, Andrew F. Hill, Ian P. Wicks, Ken C Pang
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2018.01643

Long-Term Land Use Affects Phosphorus Speciation and the Composition of Phosphorus Cycling Genes in Agricultural Soils
Cited by: 54
Author(s): Liu Jin, Barbara J. Cade-Menun, Jianjun Yang, Yongfeng Hu, Corey W. Liu, Julien Tremblay, Kerry LaForge, Michael P. Schellenberg, Chantal Hamel, Luke D. Bainard
Software Mentions: 1
Published: over 8 years ago

10.1038/srep37158

Identification of aberrant tRNA-halves expression patterns in clear cell renal cell carcinoma
Cited by: 57
Author(s): Malin Nientiedt, Mario C. Deng, Doris Schmidt, Sven Perner, Stefan Müller, Jörg Ellinger
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep37821

Long intergenic non-coding RNA expression signature in human breast cancer
Cited by: 25
Author(s): Yan Feng Zhang, Erin K. Wagner, Xingyi Guo, Isaac May, Qiuyin Cai, Zheng Wang, Chunyan He, Jirong Long
Software Mentions: 1
Published: almost 10 years ago

10.1016/j.ijpddr.2016.09.005

Profiling the macrofilaricidal effects of flubendazole on adult female Brugia malayi using RNAseq
Cited by: 13
Author(s): Maeghan O’Neill, Cristina Ballesteros, Lucienne Tritten, Erica Burkman, Weam I. Zaky, Jianguo Xia, Andrew R. Moorhead, Steven A. Williams, Timothy G. Geary
Software Mentions: 1
Published: almost 10 years ago

10.3389/fmicb.2018.00859

Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8
Cited by: 62
Author(s): Helen L. Hayden, Keith W. Savin, Jenny Wadeson, Vadakattu V. S. R. Gupta, Pauline M. Mele
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1008451

The comprehensive role of E-cadherin in maintaining prostatic epithelial integrity during oncogenic transformation and tumor progression
Cited by: 19
Author(s): Adam Olson, Vien Le, Joseph Aldahl, Eui-Young Yu, Erika Hooker, Yongfeng He, Dong-Hoon Lee, Won Kyung Kim, Robert D. Cardiff, Joseph Geradts, Zijie Sun
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2018.01765

Comparative Transcriptomic Analysis of Streptococcus thermophilus TH1436 and TH1477 Showing Different Capability in the Use of Galactose
Cited by: 18
Author(s): Sabrina Giaretta, Laura Treu, Veronica Vendramin, Vinícius da Silva Duarte, Armin Tarrah, Stefano Campanaro, Viviana Corich
Software Mentions: 1
Published: about 8 years ago

10.4049/jimmunol.1400943

Themis2 Is Not Required for B Cell Development, Activation, and Antibody Responses
Cited by: 12
Author(s): Harald Hartweger, Edina Schweighoffer, Sophia Davidson, Matthew J. Peirce, Andreas Wack, Victor L. J. Tybulewicz
Software Mentions: 1
Published: over 12 years ago

10.1186/s40478-019-0750-2

Restoration of histone acetylation ameliorates disease and metabolic abnormalities in a FUS mouse model
Cited by: 53
Author(s): Elisabeth Rossaert, Eveliina Pollari, Tom Jaspers, Lawrence Van Helleputte, Matthew Jarpe, Philip Van Damme, Katrien De Bock, Matthieu Moisse, Ludo Van Den Bosch
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2014.00430

Wolbachia is not all about sex: male-feminizing Wolbachia alters the leafhopper Zyginidia pullula transcriptome in a mainly sex-independent manner
Cited by: 12
Author(s): Hosseinali Asgharian, Peter L. Chang, Peter John Mazzoglio, Ilaria Negri
Software Mentions: 1
Published: about 12 years ago

10.1007/s00192-016-3033-5

Urinary proteomic pattern in female stress urinary incontinence: a pilot study
Cited by: 13
Author(s): Marianne Koch, Goran Mitulović, Engelbert Hanzal, Wolfgang Umek, Sonja Seyfert, Thomas Mohr, Heinz Koelbl, Rosa Maria Laterza
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1008045

Discovery and characterization of variance QTLs in human induced pluripotent stem cells
Cited by: 55
Author(s): Abhishek Sarkar, Po-Yuan Tung, John Blischak, Jonathan E. Burnett, Yang Li, Matthew Stephens, Yoav Gilad
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2019.01873

Hydrogen Oxidation Influences Glycogen Accumulation in a Verrucomicrobial Methanotroph
Cited by: 12
Author(s): Carlo R. Carere, Ben McDonald, Hanna Peach, Chris Greening, Daniel J. Gapes, Christophe Collet, Matthew B. Stott
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2020.01264

Yeast Assimilable Nitrogen Concentrations Influence Yeast Gene Expression and Hydrogen Sulfide Production During Cider Fermentation
Cited by: 10
Author(s): Yangbo Song, Patrick A. Gibney, Lailiang Cheng, Shuwen Liu, Gregory M. Peck
Software Mentions: 1
Published: over 6 years ago

10.1038/srep39109

Identification of Development-Related Genes in the Ovaries of Adult Harmonia axyridis (Pallas) Lady Beetles Using a Time- Series Analysis by RNA-seq
Cited by: 10
Author(s): Wei Du, Fanrong Zeng
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-018-4638-5

Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine
Cited by: 24
Author(s): Darren Chern Jan Wong, Li Zhang, Isabelle Merlin, Simone D. Castellarin, Grégory A. Gambetta
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2020.00460

Investigating the Role of FlhF Identifies Novel Interactions With Genes Involved in Flagellar Synthesis in Campylobacter jejuni
Cited by: 11
Author(s): Xiaofei Li, Fangzhe Ren, Guoqiang Cai, Pingyu Huang, Qinwen Chai, Ozan Gundogdu, Xinan Jiao, Jinlin Huang
Software Mentions: 1
Published: over 6 years ago

10.3390/cancers11121919

The Landscape of Long Non-Coding RNA Dysregulation and Clinical Relevance in Muscle Invasive Bladder Urothelial Carcinoma
Cited by: 4
Author(s): Haotian Shen, Lauren Wong, Wei Tse Li, Megan Chu, Rachel High, Eric Y. Chang, Jessica Wang‐Rodriguez, Weg M. Ongkeko
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2020.563139

tpo3 and dur3, Aspergillus fumigatus Plasma Membrane Regulators of Polyamines, Regulate Polyamine Homeostasis and Susceptibility to Itraconazole
Cited by: 6
Author(s): Mingcong Chen, Guowei Zhong, Sha Wang, Jun Zhu, Lei Tang, Lei Li
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-015-2219-4

Gonadal transcriptomic analysis and differentially expressed genes in the testis and ovary of the Pacific white shrimp (Litopenaeus vannamei)
Cited by: 59
Author(s): J. Peng, Pinyuan Wei, Bin Zhang, Yang Zhao, Dingyuan Zeng, Xiuli Chen, Ming Li, Xiaohan Chen
Software Mentions: 1
Published: almost 11 years ago

10.3389/fmicb.2018.00877

Genome-Wide Comparative Functional Analyses Reveal Adaptations of Salmonella sv. Newport to a Plant Colonization Lifestyle
Cited by: 16
Author(s): Marcos H. de Moraes, Emanuel Becerra Soto, Isaí Salas González, Prerak Desai, Chu Wu, Steffen Porwollik, Michael McClelland, Max Teplitski
Software Mentions: 1
Published: over 8 years ago

10.1038/srep39395

Localisation and origin of the bacteriochlorophyll-derived photosensitizer in the retina of the deep-sea dragon fish Malacosteus niger
Cited by: 10
Author(s): R. H. Douglas, Martin J. Genner, Alan G. Hudson, Julian C. Partridge, H Wagner
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-019-5554-z

Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana
Cited by: 37
Author(s): Mingqi Zhou, Natasha Sng, Collin LeFrois, Anna‐Lisa Paul, Robert J. Ferl
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2018.02418

Transcriptome Analysis of a Spray Drying-Resistant Subpopulation Reveals a Zinc-Dependent Mechanism for Robustness in L. lactis SK11
Cited by: 7
Author(s): Annereinou Dijkstra, Marjo Starrenburg, Tilman Todt, Sacha A. F. T. van Hijum, Jeroen Hugenholtz, Peter A. Bron
Software Mentions: 1
Published: about 8 years ago

10.1186/s13071-020-04457-9

RNA sequencing analysis of altered expression of long noncoding RNAs associated with Schistosoma japonicum infection in the murine liver and spleen
Cited by: 9
Author(s): Tianqi Xia, Bikash Ranjan Giri, Jingyi Liu, Pengfei Du, Xue Li, Xuxin Li, Shun Li, Guofeng Cheng
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijerph16081374

Transcriptional Analysis of Chlorella Pyrenoidosa Exposed to Bisphenol A
Cited by: 23
Author(s): Leyi Duan, Qi Chen, Shunshan Duan
Software Mentions: 1
Published: over 7 years ago

10.3390/ijerph16234718

The State-of-the Art of Environmental Toxicogenomics: Challenges and Perspectives of “Omics” Approaches Directed to Toxicant Mixtures
Cited by: 33
Author(s): Charles Ferreira Martins, Kristian Dreij, Pedro M. Costa
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0245613

A transcriptomic analysis of sugarcane response to Leifsonia xyli subsp. xyli infection
Cited by: 7
Author(s): Kai Zhu, Li‐Tao Yang, Chengxi Li, Prakash Lakshmanan, Yong‐Xiu Xing, Yang–Rui Li
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1006772

Pheromone independent unisexual development in Cryptococcus neoformans
Cited by: 27
Author(s): Rachana Gyawali, Youbao Zhao, Jianfeng Lin, Yumeng Fan, Xinping Xu, Srijana Upadhyay, Xiaorong Lin
Software Mentions: 1
Published: over 9 years ago

10.3389/fmicb.2018.01565

Comparative Transcriptomics of Cold Growth and Adaptive Features of a Eury- and Steno-Psychrophile
Cited by: 31
Author(s): Isabelle Raymond-Bouchard, Julien Tremblay, Ianina Altshuler, Charles W. Greer, Lyle G. Whyte
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0169177

Transcriptome Analysis of Taxillusi chinensis (DC.) Danser Seeds in Response to Water Loss
Cited by: 27
Author(s): Shugen Wei, Xiaojun Ma, Limei Pan, Miao Jin, Jine Fu, Longhua Bai, Zhonglian Zhang, Yanjun Guan, Changming Mo, Hao Huang, Maoshan Chen
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-017-4151-2

Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization
Cited by: 39
Author(s): Audrey M. V. Ah‐Fong, Jolly Shrivastava, Howard S. Judelson
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1004845

Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize
Cited by: 172
Author(s): Jason G. Wallace, Peter J. Bradbury, Nengyi Zhang, Yves Gibon, Mark Stitt, Edward S. Buckler
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-015-1707-x

Analysis of the TGFβ-induced program in primary airway epithelial cells shows essential role of NF-κB/RelA signaling network in type II epithelial mesenchymal transition
Cited by: 74
Author(s): Bing Tian, Xueling Li, Mridul Kalita, Steven G. Widen, Jun Yang, Suresh K. Bhavnani, Bryant Dang, Andrzej Kudlicki, Mala Sinha, Fanlei Kong, Thomas G. Wood, Bruce A. Luxon, Allan R. Brasier
Software Mentions: 1
Published: over 11 years ago

10.3389/fpls.2016.01338

Identification of Candidate Anthocyanin-Related Genes by Transcriptomic Analysis of ‘Furongli’ Plum (Prunus salicina Lindl.) during Fruit Ripening Using RNA-Seq
Cited by: 46
Author(s): Zhi‐Zhen Fang, Dan‐Rong Zhou, Xinfu Ye, Cuicui Jiang, Shao‐Lin Pan
Software Mentions: 1
Published: about 10 years ago

10.1038/srep40472

De novo assembly, annotation, and characterization of the whole brain transcriptome of male and female Syrian hamsters
Cited by: 16
Author(s): Katharine E. McCann, David M. Sinkiewicz, Alisa Norvelle, Kim L. Huhman
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep41661

Differentiation of Club Cells to Alveolar Epithelial Cells In Vitro
Cited by: 36
Author(s): Dahai Zheng, Boon Seng Soh, Yin Lu, Guangan Hu, Yi‐Ping Phoebe Chen, Hyungwon Choi, Jongyoon Han, Vincent T. K. Chow, Jianzhu Chen
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-15-183

Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilissymbionts
Cited by: 57
Author(s): Yuuki Kodama, Haruo Suzuki, Hideo Dohra, Manabu Sugii, Tatsuya Kitazume, Katsushi Yamaguchi, Shuji Shigenobu, Masahiro Fujishima
Software Mentions: 1
Published: over 12 years ago

10.1111/acel.13106

Transplanting cells from old but not young donors causes physical dysfunction in older recipients
Cited by: 43
Author(s): Binsheng Wang, Zukai Liu, Vicky P. Chen, Lichao Wang, Christina L. Inman, Yueying Zhou, Chun Guo, Tamar Tchkonia, David W. Rowe, George A. Kuchel, Paul Robson, James L. Kirkland, Ming Xu
Software Mentions: 1
Published: almost 7 years ago

10.1007/s00253-021-11309-8

Exploring the molecular content of CHO exosomes during bioprocessing
Cited by: 16
Author(s): Christoph Keysberg, Oliver Hertel, Louise Schelletter, Busche Tobias, Chiara Sochart, Jörn Kalinowski, Raimund Hoffrogge, Kerstin Otte, Thomas Noll
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1006994

Ribosomal DNA copy number amplification and loss in human cancers is linked to tumor genetic context, nucleolus activity, and proliferation
Cited by: 92
Author(s): Meng Wang, Bernardo Lemos
Software Mentions: 1
Published: about 9 years ago

10.3390/s21061938

Gated Graph Attention Network for Cancer Prediction
Cited by: 2
Author(s): Linling Qiu, Li Han, Meihong Wang, Xiaoli Wang
Software Mentions: 1
Published: over 5 years ago

10.1038/srep43062

Targeted RP9 ablation and mutagenesis in mouse photoreceptor cells by CRISPR-Cas9
Cited by: 16
Author(s): Ji‐Neng Lv, Gao-Hui Zhou, Xuejiao Chen, Hui Chen, Kun Wu, Lan Xiang, Xin‐Lan Lei, Xiao Zhang, Ronghan Wu, Zi‐Bing Jin
Software Mentions: 1
Published: over 9 years ago

10.3389/fpls.2016.00432

Using Transcriptomics to Identify Differential Gene Expression in Response to Salinity among Australian Phragmites australis Clones
Cited by: 18
Author(s): Gareth D. Holmes, Nathan E. Hall, Anthony R. Gendall, Paul I. Boon, Elizabeth A. James
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-018-4770-2

Differences between fast and slow muscles in scallops revealed through proteomics and transcriptomics
Cited by: 21
Author(s): Xiujun Sun, Zhihong Liu, Biao Wu, Liqing Zhou, Qi Wang, Wei Wu, Aiguo Yang
Software Mentions: 1
Published: over 8 years ago

10.3389/fpls.2018.00252

The Novel Secreted Meloidogyne incognita Effector MiISE6 Targets the Host Nucleus and Facilitates Parasitism in Arabidopsis
Cited by: 27
Author(s): Qianqian Shi, Zhenchuan Mao, Xiaoping Zhang, Jian Ling, Runmao Lin, Xi Zhang, Rui Li, Yunsheng Wang, Youyou Yang, Xinyue Cheng, Bingyan Xie
Software Mentions: 1
Published: over 8 years ago

10.18632/aging.102797

Obg-like ATPase 1 (OLA1) overexpression predicts poor prognosis and promotes tumor progression by regulating P21/CDK2 in hepatocellular carcinoma
Cited by: 16
Author(s): Shanzhou Huang, Chuanzhao Zhang, Chengjun Sun, Ying Hou, Yixi Zhang, Nga Lei Tam, Zekang Wang, Jia Yu, Bowen Huang, Hongkai Zhuang, Zixuan Zhou, Zuyi Ma, Zhonghai Sun, Xiaoshun He, Qi Zhou, Baohua Hou, Linwei Wu
Software Mentions: 1
Published: over 6 years ago

10.1038/srep43023

Identification of novel cancer therapeutic targets using a designed and pooled shRNA library screen
Cited by: 32
Author(s): David J. Oliver, Hao Jiang, Piaomu Liu, Alexander V. Gasparian, Ellen Gardiner, Samuel Lee, Adrián Zenteno, Lillian O. Perinskaya, Mengqian Chen, Phillip Buckhaults, Eugenia V. Broude, Michael D. Wyatt, Homayoun Valafar, Edsel A. Peña, Michael Shtutman
Software Mentions: 1
Published: over 9 years ago

10.7717/peerj.9021

Identification of exosomal miRNAs associated with the anthracycline-induced liver injury in postoperative breast cancer patients by small RNA sequencing
Cited by: 14
Author(s): Yue Zhang, Di Wang, Di Shen, Yang Luo, Yi‐Qun Che
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0135670

Transcriptomic Profiling of Spleen in Grass-Fed and Grain-Fed Angus Cattle
Cited by: 9
Author(s): Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Jianan Liu, George E. Liu, Zan Liu, Jiuzhou Song
Software Mentions: 1
Published: about 11 years ago

10.1038/srep45295

Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum
Cited by: 41
Author(s): Pradeep Singh, Gagandeep Singh, Abhishek Bhandawat, Gopal Singh, Rajni Parmar, Romit Seth, Ram Kumar Sharma
Software Mentions: 1
Published: over 9 years ago

10.1186/s12861-017-0147-z

Transcriptome profiling reveals expression signatures of cranial neural crest cells arising from different axial levels
Cited by: 23
Author(s): Rachael Lumb, Sam Buckberry, Genevieve A. Secker, David Lawrence, Quenten Schwarz
Software Mentions: 1
Published: over 9 years ago

10.3390/cancers11091273

Etiology-Specific Analysis of Hepatocellular Carcinoma Transcriptome Reveals Genetic Dysregulation in Pathways Implicated in Immunotherapy Efficacy
Cited by: 9
Author(s): Wei Tse Li, Angela E. Zou, Christine O. Honda, Hao Zheng, Xiao Qi Wang, Tatiana Kisseleva, Eric Y. Chang, Weg M. Ongkeko
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms221910696

RNA-Seq and Electrical Penetration Graph Revealed the Role of Grh1-Mediated Activation of Defense Mechanisms towards Green Rice Leafhopper (Nephotettix cincticeps Uhler) Resistance in Rice (Oryza sativa L.)
Cited by: 1
Author(s): Young Ho Kwon, Nkulu Rolly Kabange, Ji-Yoon Lee, Bo Yoon Seo, Dongjin Shin, So-Myeong Lee, Jin-Kyung Cha, Jun-Hyeon Cho, Ju-Won Kang, Dong-Soo Park, Jong-Min Ko, Jonghee Lee
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-018-24509-6

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages
Cited by: 69
Author(s): Sugata Roy, Sebastian Schmeier, Bogumił Kaczkowski, Peter Arner, Tanvir Alam, Mumin Ozturk, Ousman Tamgue, Suraj P. Parihar, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Reto Guler, Vladimir B. Bajic, Frank Brombacher, Harukazu Suzuki
Software Mentions: 1
Published: over 8 years ago

10.18632/aging.102332

Loss of FoxA2 accelerates neoplastic changes in the intrahepatic bile duct partly via the MAPK signaling pathway
Cited by: 5
Author(s): Jian Shen, Yongjie Zhou, Xiaoyun Zhang, Wei Peng, Chihan Peng, Qiang Zhou, Chuan Li, Tianfu Wen, Yujun Shi
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-017-4253-x

Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data
Cited by: 20
Author(s): J. B. Griffiths, Antonio Scialdone, John C. Marioni
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-018-25611-5

Ca2+ imaging and gene expression profiling of Lonicera Confusa in response to calcium-rich environment
Cited by: 10
Author(s): Wenwen Jin, Yan Long, Chunhua Fu, Libin Zhang, Jun Xiang, Baoshan Wang, Maoteng Li
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1006372

Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae
Cited by: 74
Author(s): Trey K. Sato, Mary Tremaine, Lucas S. Parreiras, Alexander S. Hebert, Kevin S. Myers, Alan Higbee, Maria Sardi, Sean J. McIlwain, Irene M. Ong, Rebecca J. Breuer, Ragothaman Avanasi Narasimhan, Mick McGee, Quinn Dickinson, Alex La Reau, Dan Xie, Mingyuan Tian, Jennifer L. Reed, Yaoping Zhang, Joshua J. Coon, Chris Todd Hittinger, Audrey P. Gasch, Robert Landick
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-018-5180-1

Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-Seq
Cited by: 10
Author(s): Qiming Cheng, Shiqie Bai, Gentu Ge, Ping Li, Liying Liu, Chengdong Zhang, Yushan Jia
Software Mentions: 1
Published: almost 8 years ago

10.3389/fpls.2021.625729

A Meta-Analysis Reveals Opposite Effects of Biotic and Abiotic Stresses on Transcript Levels of Arabidopsis Intracellular Immune Receptor Genes
Cited by: 11
Author(s): Leiyun Yang, Zhixue Wang, Jian Hua
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-25103-6

Whole-transcriptome analysis of atrophic ovaries in broody chickens reveals regulatory pathways associated with proliferation and apoptosis
Cited by: 35
Author(s): Lingbin Liu, Qihai Xiao, Elizabeth R. Gilbert, Zhifu Cui, Xiaoling Zhao, Yan Wang, Huadong Yin, Diyan Li, Haihan Zhang, Qing Zhu
Software Mentions: 1
Published: over 8 years ago

10.3389/fpls.2015.00389

Molecular characterization of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family from Citrus and the effect of fruit load on their expression
Cited by: 37
Author(s): Liron Shalom, Lyudmila Shlizerman, Naftali Zur, Adi Doron‐Faigenboim, Eduardo Blumwald, Avi Sadka
Software Mentions: 1
Published: over 11 years ago

10.3389/fpls.2017.00109

Differential Gene Expression Analysis in Polygonum minus Leaf upon 24 h of Methyl Jasmonate Elicitation
Cited by: 24
Author(s): Reyhaneh Rahnamaie-Tajadod, Kok Keong Loke, Hoe-Han Goh, Normah Mohd Noor
Software Mentions: 1
Published: over 9 years ago

10.3389/fpls.2019.01147

Genome-Wide Identification of Calcium-Dependent Protein Kinases in Chlamydomonas reinhardtii and Functional Analyses in Nitrogen Deficiency-Induced Oil Accumulation
Cited by: 9
Author(s): Yajun Li, Xiaowen Fei, Hao‐Fu Dai, Jiangyue Li, Wei Zhu, Xiaodong Deng
Software Mentions: 1
Published: about 7 years ago

10.1136/jitc-2020-001392

Antimetabolite pemetrexed primes a favorable tumor microenvironment for immune checkpoint blockade therapy
Cited by: 24
Author(s): Chia-Sing Lu, Ching-Wen Lin, Ya‐Hsuan Chang, Hsuan‐Yu Chen, Wei-Chia Chung, Wei-Yun Lai, Chao‐Chi Ho, Tong Hong Wang, Chi-Yuan Chen, Chen-Lin Yeh, Sean M. Wu, Shuping Wang, Pan‐Chyr Yang
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-016-3059-6

RNAseq analysis of heart tissue from mice treated with atenolol and isoproterenol reveals a reciprocal transcriptional response
Cited by: 6
Author(s): Andrea Prunotto, Brian J. Stevenson, Corinne Berthonneche, Fanny Schüpfer, Jacques S. Beckmann, Fabienne Maurer, Sven Bergmann
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-018-25516-3

Additional mitochondrial DNA influences the interactions between the nuclear and mitochondrial genomes in a bovine embryo model of nuclear transfer
Cited by: 18
Author(s): Kanokwan Srirattana, Justin C. St. John
Software Mentions: 1
Published: over 8 years ago

10.3389/fpls.2017.00319

Comparative Transcriptome Reveals Benzenoid Biosynthesis Regulation as Inducer of Floral Scent in the Woody Plant Prunus mume
Cited by: 23
Author(s): Kai Zhao, Weiru Yang, Yuzhen Zhou, Jie Zhang, Yushu Li, Sagheer Ahmad, Qixiang Zhang
Software Mentions: 1
Published: over 9 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568