bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/1755-8794-7-32

Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers
Cited by: 45
Author(s): Zhifu Sun, Liang Wang, Bruce W. Eckloff, Bo Deng, Yi Wang, Jason A. Wampfler, Jiseon Jang, Eric D. Wieben, Jin Jen, Ming You, Ping Yang
Software Mentions: 4
Published: about 12 years ago

10.15252/msb.20209593

DOMINO: a network‐based active module identification algorithm with reduced rate of false calls
Cited by: 35
Author(s): Hagai Levi, Ran Elkon, Ron Shamir
Software Mentions: 4
Published: over 5 years ago

10.1038/tp.2016.67

Candidate gene networks and blood biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report
Cited by: 26
Author(s): Michael S. Breen, Anne Uhlmann, Christiane M. Nday, Stephen J. Glatt, Mario Mitt, A. Metsalpu, Dan J. Stein, Nicola Illing
Software Mentions: 4
Published: over 10 years ago

10.15252/msb.20209569

Exploring the virulence gene interactome with <scp>CRISPR</scp> / <scp>dC</scp> as9 in the human malaria parasite
Cited by: 30
Author(s): Jessica M. Bryant, Sebastian Baumgarten, Florent Dingli, Damarys Loew, Ameya Sinha, Aurélie Claës, Peter R. Preiser, Peter C. Dedon, Artur Scherf
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms21124453

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA
Cited by: 7
Author(s): Andreas Kloetgen, Sujitha Duggimpudi, Konstantin Schuschel, Kebria Hezaveh, Daniel Picard, Heiner Schaal, Marc Remke, Jan‐Henning Klusmann, Arndt Borkhardt, Alice C. McHardy, Jessica I. Hoell
Software Mentions: 4
Published: about 6 years ago

10.1038/s41398-017-0050-1

Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study
Cited by: 56
Author(s): Pei‐Fen Kuan, Monika A. Waszczuk, Roman Kotov, Sean Clouston, Xiaohua Yang, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 4
Published: over 8 years ago

10.1186/s12870-020-02757-x

Differential gene expression reveals mechanisms related to habitat divergence between hybridizing orchids from the Neotropical coastal plains
Cited by: 5
Author(s): Bárbara Simões Santos Leal, Marcelo Mendes Brandão, Clarisse Palma‐Silva, Fábio Pinheiro
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms20143480

Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize
Cited by: 34
Author(s): Ziwen Li, Xianghai An, Taotao Zhu, Tingwei Yan, Wu Shu, Youhui Tian, Jinping Li, Xiangyuan Wan
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms20143583

Ureaplasma Species Modulate Cytokine and Chemokine Responses in Human Brain Microvascular Endothelial Cells
Cited by: 6
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Nicolas Schlegel, Kirsten Glaser
Software Mentions: 4
Published: about 7 years ago

10.1038/s41398-019-0472-z

DLPFC transcriptome defines two molecular subtypes of schizophrenia
Cited by: 26
Author(s): Elijah F. W. Bowen, Jack L. Burgess, Richard Granger, Joel E. Kleinman, C. Harker Rhodes
Software Mentions: 4
Published: over 7 years ago

10.1186/s12870-015-0661-8

A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit
Cited by: 51
Author(s): Noam Chayut, Hui Yuan, Shachar Ohali, Ayala Meir, Yelena Yeselson, Vitaly Portnoy, Yi Zheng, Zhangjun Fei, Efraim Lewinsohn, Nurit Katzir, Arthur A. Schaffer, Shimon Gepstein, Joseph Burger, L i Li, Yaakov Tadmor
Software Mentions: 4
Published: almost 11 years ago

10.3390/ijms20123101

Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation
Cited by: 29
Author(s): Saurabh Gupta, Yanni Dong, Paul P. Dijkwel, Bernd Mueller‐Roeber, Tsanko Gechev
Software Mentions: 4
Published: about 7 years ago

10.3390/nu12123858

Effects of Daily Raspberry Consumption on Immune-Metabolic Health in Subjects at Risk of Metabolic Syndrome: A Randomized Controlled Trial
Cited by: 18
Author(s): Maximilien Franck, Juan de Toro‐Martín, Véronique Garneau, Valérie Guay, Michèle Kearney, Geneviève Pilon, Denis Roy, Patrick Couture, Charles Couillard, André Marette, Marie‐Claude Vohl
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-017-05724-z

Comprehensive transcriptomics and proteomics analyses of pollinated and parthenocarpic litchi (Litchi chinensis Sonn.) fruits during early development
Cited by: 14
Author(s): Wei Liu, Maoshan Chen, Lijun Bai, Zhenhua Zhuang, Chao Fan, Jiang Nong-hui, Junsheng Zhao, Shuaipeng Ma, Xiang Xu
Software Mentions: 4
Published: about 9 years ago

10.1530/ERC-19-0448

Effects of epigenetic pathway inhibitors on corticotroph tumour AtT20 cells
Cited by: 5
Author(s): Kate E Lines, P. Filippakopoulos, Mark Stevenson, Susanne Müller, Helen Lockstone, Benjamin Wright, Stefan Knapp, David Buck, C. Bountra, R V Thakker
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-01943-6

Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1
Cited by: 16
Author(s): Tim-Michael Decker, Michael Kluge, Stefan Krebs, Nilay Shah, Helmut Blum, Caroline C. Friedel, Dirk Eick
Software Mentions: 4
Published: over 9 years ago

10.3390/cancers12051143

Differential B-Cell Receptor Signaling Requirement for Adhesion of Mantle Cell Lymphoma Cells to Stromal Cells
Cited by: 8
Author(s): Laia Sadeghi, Gustav Arvidsson, Magali Merrien, Agata M. Wasik, André Görgens, C. I. Edvard Smith, Birgitta Sander, Anthony P. H. Wright
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-01032-8

Transcriptomic analysis reveals a previously unknown role for CD8+ T-cells in rVSV-EBOV mediated protection
Cited by: 28
Author(s): Andrea Menicucci, Suhas Sureshchandra, Andrea Marzi, Heinz Feldmann, Ilhem Messaoudi
Software Mentions: 4
Published: over 9 years ago

10.1038/srep45125

Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis
Cited by: 42
Author(s): Matthew D. MacManes, Suzanne H. Austin, Andrew S. Lang, April M. Booth, Victoria S. Farrar, Rebecca M. Calisi
Software Mentions: 4
Published: over 9 years ago

10.1080/21505594.2017.1342910

Pseudogymnoascus destructans transcriptome changes during white-nose syndrome infections
Cited by: 22
Author(s): Sophia Reeder, Jonathan M. Palmer, Jenni M. Prokkola, Thomas M. Lilley, DeeAnn M. Reeder, Kenneth A. Field
Software Mentions: 4
Published: about 9 years ago

10.3390/jcm10132973

Meteorin Is a Novel Therapeutic Target for Wet Age-Related Macular Degeneration
Cited by: 4
Author(s): Kimberley Delaunay, Alexandre Sellam, Virginie Dinet, Alexandre Moulin, Min Zhao, Emmanuelle Gélizé, Jérémie Canonica, Marie‐Christine Naud, Patricia Crisanti-Lassiaz, Francine Behar‐Cohen
Software Mentions: 4
Published: about 5 years ago

10.1080/21505594.2020.1768018

Transcriptional host–pathogen responses of Pseudogymnoascus destructans and three species of bats with white-nose syndrome
Cited by: 19
Author(s): Christina M. Davy, Michael E. Donaldson, Hana Banďouchová, Ana M. Breit, Nicole Dorville, Yvonne A. Dzal, Veronika Kováčová, Emma L. Kunkel, Natália Martínková, Kaleigh J. O. Norquay, James E. Paterson, Jan Zukal, Jiří Pikula, Craig K. R. Willis, Christopher J. Kyle
Software Mentions: 4
Published: about 6 years ago

10.3390/jcm8060849

MicroRNA Profile of HCV Spontaneous Clarified Individuals, Denotes Previous HCV Infection
Cited by: 10
Author(s): Óscar Brochado-Kith, Alicia Gómez Sanz, Luis Miguel Real, Javier Crespo, Pablo Ryan, Juan Macı́as, Joaquín Cabezas, Jesús Troya, Juan A Pineda, María Teresa Arias-Loste, Victorino Díez Viñas, María Ángeles Jiménez-Sousa, Luz María Medrano, Isabel Cuesta de la Plaza, Sara Monzón, Salvador Resino, Amanda Fernández‐Rodríguez
Software Mentions: 4
Published: about 7 years ago

10.1111/jcmm.16133

Identification of Smad3‐related transcriptomes in type‐2 diabetic nephropathy by whole transcriptome RNA sequencing
Cited by: 3
Author(s): Qin Zhou, Hong-Hong Guo, Chaolun Yu, Xiao‐Ru Huang, Lijun Liang, Puhua Zhang, Jia-Kuo Yu, Jizhou Zhang, Ting‐Fung Chan, Rong Ma, Hui‐Yao Lan
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.729359

Construction of Interferon-Gamma-Related Gene Signature to Characterize the Immune-Inflamed Phenotype of Glioblastoma and Predict Prognosis, Efficacy of Immunotherapy and Radiotherapy
Cited by: 9
Author(s): Hang Ji, Yixu Ba, Shuai Ma, Kezuo Hou, Shan Mi, Xin Gào, Jiaqi Jin, Qingguo Gong, Ting Liu, Fang Wang, Zhihui Liu, Shupeng Li, Jianyang Du, Shaoshan Hu
Software Mentions: 4
Published: almost 5 years ago

10.1128/mBio.02504-18

The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium
Cited by: 73
Author(s): Alexander J. Westermann, Elisa Venturini, Mikael E. Sellin, Konrad U. Förstner, Wolf‐Dietrich Hardt, Jörg Vogel
Software Mentions: 4
Published: over 7 years ago

10.1111/jcmm.15271

Systematic prediction of key genes for ovarian cancer by co‐expression network analysis
Cited by: 12
Author(s): Mingyuan Wang, Jinjin Wang, Jinglan Liu, Lili Zhu, Heng Ma, Jian Zou, Wei Wu, Kangkai Wang
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms19113687

Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities
Cited by: 5
Author(s): Wolfgang Kaisers, Holger Schwender, Heiner Schaal
Software Mentions: 4
Published: almost 8 years ago

10.3390/cancers12123789

Neural Networks Recapitulation by Cancer Cells Promotes Disease Progression: A Novel Role of p73 Isoforms in Cancer-Neuronal Crosstalk
Cited by: 16
Author(s): Stella Logotheti, Stephan Marquardt, Christin Richter, Renée Sophie Hain, Nico Murr, Işıl Takan, Athanasia Pavlopoulou, Brigitte M. Pützer
Software Mentions: 4
Published: over 5 years ago

10.1096/fj.201600675R

New function of the myostatin/activin type I receptor (ALK4) as a mediator of muscle atrophy and muscle regeneration
Cited by: 22
Author(s): Svitlana Pasteuning-Vuhman, Johanna W Boertje-van der Meulen, Maaike van Putten, Maurice Overzier, Peter ten Dijke, Szymon M. Kiełbasa, Wibowo Arindrarto, Ron Wolterbeek, Ksenia Lezhnina, Ivan V. Ozerov, Aleksandr M Aliper, Willem M.H. Hoogaars, Annemieke Aartsma‐Rus, Cindy J.M. Loomans
Software Mentions: 4
Published: almost 10 years ago

10.1111/jcmm.14779

Four transcription profile–based models identify novel prognostic signatures in oesophageal cancer
Cited by: 9
Author(s): Tongyan Liu, Panqi Fang, Chencheng Han, Zhongliang Ma, Weizhang Xu, Wenjia Xia, Jingwen Hu, Yongming Xu, Lin Xu, Rong Yin, Siwei Wang, Qin Zhang
Software Mentions: 4
Published: almost 7 years ago

10.3390/cancers13061421

Efficacy of Targeted Radionuclide Therapy Using [131I]ICF01012 in 3D Pigmented BRAF- and NRAS-Mutant Melanoma Models and In Vivo NRAS-Mutant Melanoma
Cited by: 5
Author(s): Hussein Akil, Mercédès Quintana, J. Raymond, Tommy Billoux, Valentin Benboubker, Sophie Besse, Philippe Auzeloux, Véronique Delmas, Valérie Petit, Lionel Larue, M. D’Incan, Françoise Degoul, Jacques Rouanet
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms19010271

Integrated Analyses Reveal Overexpressed Notch1 Promoting Porcine Satellite Cells’ Proliferation through Regulating the Cell Cycle
Cited by: 21
Author(s): Yiren Jiao, Bo Huang, Yu Chen, Guang-liang Hong, Jian Xu, Chen Hu, Chong Wang
Software Mentions: 4
Published: over 8 years ago

10.3390/v13040593

Probing into the Effects of Grapevine Leafroll-Associated Viruses on the Physiology, Fruit Quality and Gene Expression of Grapes
Cited by: 23
Author(s): Yashu Song, Robert Hanner, Bin Meng
Software Mentions: 4
Published: over 5 years ago

10.7150/jca.57260

Construction of a ceRNA Network and a Prognostic lncRNA Signature associated with Vascular Invasion in Hepatocellular Carcinoma based on Weighted Gene Co-Expression Network Analysis
Cited by: 10
Author(s): Haisu Tao, Li Jiang, Junjie Liu, Tong Yuan, Erlei Zhang, Huifang Liang, Zhiyong Huang
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers12092397

Combined Targeting of Estrogen Receptor Alpha and Exportin 1 in Metastatic Breast Cancers
Cited by: 9
Author(s): Eylem Kulkoyluoglu-Cotul, Qianying Zuo, Ashlie Santaliz-Casiano, Ozan Berk Imir, Ayca Nazli Mogol, Elif Tunç, Kevin Duong, Jenna Kathryn Lee, Rithva Ramesh, Elijah Odukoya, Mrinali P. Kesavadas, Monika Ziogaite, Brandi Patrice Smith, Chengjian Mao, David J. Shapiro, Ben Ho Park, Benita S. Katzenellenbogen, Drew Daly, Evelyn Aranda, John D. O’Neill, Christopher J. Walker, Yosef Landesman, Zeynep Madak-Erdoğan
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1003997

Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia
Cited by: 110
Author(s): Zeynep Kalender Atak, Valentina Gianfelici, Gert Hulselmans, Kim De Keersmaecker, Arun George Devasia, Ellen Geerdens, Nele Mentens, Sabina Chiaretti, Kaat Durinck, Anne Uyttebroeck, Peter Vandenberghe, Iwona Włodarska, Jacqueline Cloos, Robin Foà, Franki Speleman, Jan Cools, Stein Aerts
Software Mentions: 4
Published: over 12 years ago

10.7150/jca.49557

Construction of novel mRNA-miRNA-lncRNA regulatory networks associated with prognosis of ovarian cancer
Cited by: 18
Author(s): Lingling Gao, Xiao Li, Xin Nie, Qin Guo, Qing Liu, Yue Qi, Juanjuan Liu, Bei Lin
Software Mentions: 4
Published: over 6 years ago

10.1002/2211-5463.13062

Chondroitin polymerizing factor promotes breast carcinoma cell proliferation, invasion and migration and affects expression of epithelial‐mesenchymal transition‐related markers
Cited by: 6
Author(s): Li Yang, Hui Gong, Lei Feng, Dan Mao, Yujie Xiao, Yunqi Wang, Huang Li-zhong
Software Mentions: 4
Published: over 5 years ago

10.1111/1462-2920.15554

Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi
Cited by: 7
Author(s): Baojun Wu, Murray P. Cox
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2021.667257

Microbiome Structure of the Aphid Myzus persicae (Sulzer) Is Shaped by Different Solanaceae Plant Diets
Cited by: 12
Author(s): Bin He, Xiaoyulong Chen, Hong Yang, Tomislav Cernava
Software Mentions: 4
Published: about 5 years ago

10.7150/jca.44413

Comprehensive Analysis of the Tumor Microenvironment in Cutaneous Melanoma associated with Immune Infiltration
Cited by: 17
Author(s): Pan Wang, Xinyu Zhang, Nan Sun, Zhihong Zhao, Jie He
Software Mentions: 4
Published: over 6 years ago

10.1074/jbc.RA120.015896

YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation
Cited by: 21
Author(s): Fabiana Passaro, Ilaria De Martino, Federico Zambelli, Giorgia Di Benedetto, Matteo Barbato, Anna Maria D’Erchia, Caterina Manzari, Graziano Pesole, Margherita Mutarelli, Davide Cacchiarelli, Dario Antonini, Silvia Parisi, Tommaso Russo
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers12051325

Tumor Cell Associated Hyaluronan-CD44 Signaling Promotes Pro-Tumor Inflammation in Breast Cancer
Cited by: 18
Author(s): Patrice M Witschen, Thomas S. Chaffee, Nicholas J. Brady, Danielle N. Huggins, Todd P. Knutson, Rebecca S. LaRue, Sarah A. Munro, Lyubov Tiegs, James B. McCarthy, Andrew C. Nelson, Kathryn L. Schwertfeger
Software Mentions: 4
Published: over 6 years ago

10.1186/2049-1891-3-8

Current status and future perspectives for sequencing livestock genomes
Cited by: 40
Author(s): Yongsheng Bai, Maureen A. Sartor, James D. Cavalcoli
Software Mentions: 4
Published: over 14 years ago

10.1128/mSystems.00284-18

Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis : Implications for Isoprenoid Production
Cited by: 22
Author(s): Julia Martien, Alexander S. Hebert, David Stevenson, Matthew Regner, Daven B. Khana, Joshua J. Coon, Daniel Amador‐Noguez
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1005474

Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana
Cited by: 16
Author(s): Christian Kappel, Gerda Trost, Hjördis Czesnick, Anna Ramming, Benjamin Kolbe, Son Lang, Cláudia Bispo, Jörg Becker, Cornelia H. de Moor, Michael Lenhard
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pgen.1008797

UVR8-mediated inhibition of shade avoidance involves HFR1 stabilization in Arabidopsis
Cited by: 23
Author(s): Eleni Tavridou, Emanuel Schmid‐Siegert, Christian Fankhauser, Roman Ulm
Software Mentions: 4
Published: over 6 years ago

10.1200/CCI.19.00118

Statistical Assessment of Depth Normalization for Small RNA Sequencing
Cited by: 7
Author(s): Li‐Xuan Qin, Jian Zou, Jiejun Shi, Ann Lee, Aleksandra Mihailović, Thalia A. Farazi, Thomas Tuschl, Samuel Singer
Software Mentions: 4
Published: almost 6 years ago

10.1172/jci.insight.142980

Treating ICB-resistant glioma with anti-CD40 and mitotic spindle checkpoint controller BAL101553 (lisavanbulin)
Cited by: 5
Author(s): Vassilis Genoud, Felipe I Espinoza, Eliana Marinari, Viviane Rochemont, Pierre‐Yves Dietrich, Paul M.J. McSheehy, Felix Bachmann, Heidi A. Lane, Paul R Walker
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1006295

Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster
Cited by: 35
Author(s): Hangnoh Lee, Dong-Yeon Cho, Cale Whitworth, Robert C. Eisman, Melissa A. S. Phelps, John Roote, Thomas C. Kaufman, Kevin R. Cook, Steven Russell, Teresa M. Przytycka, Brian Oliver
Software Mentions: 4
Published: almost 10 years ago

10.1002/ece3.6946

Genomic analysis of Asian honeybee populations in China reveals evolutionary relationships and adaptation to abiotic stress
Cited by: 6
Author(s): Peng Shi, Jun Zhou, Huali Song, Yujuan Wu, Lan Lan, Xiangyou Tang, Zhengang Ma, Charles R. Vossbrinck, Bettina Vossbrinck, Zeyang Zhou, Jianlong Xu
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12870-017-1108-1

Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription
Cited by: 17
Author(s): Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino, Serena Varotto
Software Mentions: 4
Published: almost 9 years ago

10.3390/insects11050323

Transcriptome Analysis of the Oriental Fruit Fly Bactrocera dorsalis Early Embryos
Cited by: 2
Author(s): Wei Peng, Shu-Ning Yu, Alfred M. Handler, H. Zhang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1004824

Microevolution of Candida albicans in Macrophages Restores Filamentation in a Nonfilamentous Mutant
Cited by: 64
Author(s): Anja Wartenberg, Jörg Linde, Ronny Martin, Maria Schreiner, Fabian Horn, Ilse D. Jacobsen, Sabrina Jenull, Thomas Wolf, Karl Kuchler, Reinhard Guthke, Oliver Kurzai, Anja Forche, Christophe d’Enfert, Sascha Brunke, Bernhard Hube
Software Mentions: 4
Published: over 11 years ago

10.1186/s12987-021-00269-w

Characterization of the blood–brain barrier in genetically diverse laboratory mouse strains
Cited by: 16
Author(s): Johanna Schaffenrath, Sheng‐Fu Huang, Tania Wyss, Mauro Delorenzi, Annika Keller
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1002789

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection
Cited by: 125
Author(s): Yoichiro Shibata, Nathan C. Sheffield, Olivier Fédrigo, Courtney C. Babbitt, Matthew Wortham, Alok K. Tewari, Darin London, Lingyun Song, Bum Kyu Lee, Vishwanath R. Iyer, Stephen C. J. Parker, Elliott H. Margulies, Gregory A. Wray, Terrence S. Furey, Gregory E. Crawford
Software Mentions: 4
Published: about 14 years ago

10.3390/insects11010004

Comparative Transcriptome Analysis of Thitarodes Armoricanus in Response to the Entomopathogenic Fungi Paecilomyces Hepiali and Ophiocordyceps Sinensis
Cited by: 7
Author(s): Zhongchen Rao, Li Cao, Hua Wu, Xuehong Qiu, Guiqing Liu, Richou Han
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms19010031

Transcriptome Analysis of Tomato Leaf Spot Pathogen Fusarium proliferatum: De novo Assembly, Expression Profiling, and Identification of Candidate Effectors
Cited by: 15
Author(s): Meiling Gao, Siyu Yao, Yang Liu, Haining Yu, Pao Xu, Wenhui Sun, Zhongji Pu, Hongman Hou, Yongming Bao
Software Mentions: 4
Published: over 8 years ago

10.1097/MIB.0000000000001131

Azathioprine with Allopurinol
Cited by: 7
Author(s): Sally A. Coulthard, Phil Berry, Sarah McGarrity, Simon D. McLaughlin, Azhar Ansari, Christopher P.F. Redfern
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pgen.1005755

Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer
Cited by: 12
Author(s): Najeeb Halabi, Alejandra Martinez, Halema Al-Farsi, Eliane Mery-Lamarche, Laurence Puydenus, Pascal Pujol, Hanif Khalak, Cameron Mclurcan, Gwénaël Ferron, Denis Querleu, Iman K. Al-Azwani, Eman K. Al-Dous, Yasmin Ali Mohamoud, Joel A. Malek, Arash Rafii
Software Mentions: 4
Published: over 10 years ago

10.3390/ijms18030627

Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens
Cited by: 14
Author(s): Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert T. Greenlee, Deborah Multerer, Stacey Honda, Yihe G. Daida, Heather Spencer Feigelson, Andrew G. Glass, Fergus J. Couch, Thomas E. Rohan, Iddo Z. Ben‐Dov
Software Mentions: 4
Published: over 9 years ago

10.1016/j.immuni.2021.05.016

A PGE2-MEF2A axis enables context-dependent control of inflammatory gene expression
Cited by: 22
Author(s): Francesco Cilenti, Giulia Barbiera, Nicoletta Caronni, Dario Iodice, Elisa Montaldo, Simona Barresi, Eleonora Lusito, Vincenzo Cuzzola, Francesco Maria Vittoria, Luca Mezzanzanica, Paolo Miotto, Pietro Di Lucia, Dejan Lazarevic, Daniela María Cirillo, Matteo Iannacone, Marco Genua, Renato Ostuni
Software Mentions: 4
Published: about 5 years ago

10.1534/g3.115.021550

Joint Transcriptomic and Metabolomic Analyses Reveal Changes in the Primary Metabolism and Imbalances in the Subgenome Orchestration in the Bread Wheat Molecular Response toFusarium graminearum
Cited by: 33
Author(s): Thomas Nußbaumer, Benedikt Warth, Sapna Sharma, Christian Ametz, Christoph Bueschl, Alexandra Parich, Matthias Pfeifer, Gerald Siegwart, Barbara Steiner, Marc Lemmens, Rainer Schuhmacher, Hermann Buerstmayr, Klaus Mayer, Karl G. Kugler, Wolfgang Schweiger
Software Mentions: 4
Published: over 10 years ago

10.1186/s12870-021-02997-5

Low nitrogen availability inhibits the phosphorus starvation response in maize (Zea mays ssp. mays L.)
Cited by: 10
Author(s): J. Vladimir Torres-Rodríguez, M. Nancy Salazar-Vidal, Ricardo A. Chávez Montes, Julio A. Massange‐Sánchez, C. Stewart Gillmor, Ruairidh J. H. Sawers
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms160921310

Gene Expression Variations of Red—White Skin Coloration in Common Carp (Cyprinus carpio)
Cited by: 19
Author(s): Xiaomin Li, Yijun Song, Gao Xiao, Bai-Han Zhu, Gui-Cai Xu, Mingyuan Sun, Jun Xiao, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Jiong-Tang Li
Software Mentions: 4
Published: almost 11 years ago

10.1534/g3.115.020016

Transcriptomic Features of Bovine Blastocysts Derived by Somatic Cell Nuclear Transfer
Cited by: 20
Author(s): Byungkuk Min, Sunwha Cho, Jung Sun Park, Yun-Gyeong Lee, Namshin Kim, Yong‐Kook Kang
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pgen.1008280

PAX5 is part of a functional transcription factor network targeted in lymphoid leukemia
Cited by: 30
Author(s): Kazuki Okuyama, Tobias Strid, Jacob Kuruvilla, Rajesh Somasundaram, Susana Cristóbal, Emma Smith, Mahadesh A. J. Prasad, Thoas Fioretos, Henrik Lilljebjörn, Shamit Soneji, Stefan Lang, Jonas Ungerbäck, Mikael Sigvardsson
Software Mentions: 4
Published: about 7 years ago

10.1534/g3.114.016238

A Survey of Imprinted Gene Expression in Mouse Trophoblast Stem Cells
Cited by: 27
Author(s): J. Mauro Calabrese, Joshua Starmer, Megan D. Schertzer, Della Yee, Terry Magnuson
Software Mentions: 4
Published: over 11 years ago

10.1534/g3.114.013508

De Novo Assembly and Annotation of the Transcriptome of the Agricultural Weed Ipomoea purpurea Uncovers Gene Expression Changes Associated with Herbicide Resistance
Cited by: 41
Author(s): Trent A Leslie, Regina S. Baucom
Software Mentions: 4
Published: almost 12 years ago

10.3389/fmicb.2019.03007

Core and Differentially Abundant Bacterial Taxa in the Rhizosphere of Field Grown Brassica napus Genotypes: Implications for Canola Breeding
Cited by: 37
Author(s): Zelalem M. Taye, Bobbi L. Helgason, Jennifer K. Bell, Charlotte E. Norris, Sally Vail, Stephen J. Robinson, Isobel A. P. Parkin, Melissa M. Arcand, Steven D. Mamet, Matthew G. Links, Tanner Dowhy, Steven D. Siciliano, Eric G. Lamb
Software Mentions: 4
Published: over 6 years ago

10.1186/s13072-018-0246-5

Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus
Cited by: 54
Author(s): Adam J. Bewick, Zachary Sanchez, Elizabeth C. McKinney, Allen J. Moore, Patricia J. Moore, Robert J. Schmitz
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1009097

Diversified regulation of circadian clock gene expression following whole genome duplication
Cited by: 9
Author(s): Alexander C. West, Marianne Iversen, Even H. Jørgensen, Simen Rød Sandve, David G. Hazlerigg, Shona H. Wood
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13072-019-0319-0

Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells
Cited by: 29
Author(s): Ryuichiro Nakato, Youichiro Wada, Ryo Nakaki, Genta Nagae, Yuki Katou, Sadami Tsutsumi, N. Nakajima, Hiroshi Fukuhara, Atsushi Iguchi, Takahide Kohro, Yasuharu Kanki, Yutaka Saitô, Mika Kobayashi, Akashi Izumi-Taguchi, Naoki Osato, Kenji Tatsuno, Asuka Kamio, Yoko Hayashi‐Takanaka, Hiromi Wada, Shinzo Ohta, Masamichi Aikawa, Hiroyuki Nakajima, Masaki Nakamura, Rebecca C. McGee, Kyle W. Heppner, Tatsuo Kawakatsu, Michiru Genno, Hiroshi Yanase, Haruki Kume, Takaaki Senbonmatsu, Yukio Homma, Shigeyuki Nishimura, Toutai Mitsuyama, Hiroyuki Aburatani, Hiroshi Kimurâ, Katsuhiko Shirahige
Software Mentions: 4
Published: over 6 years ago

10.1186/s12983-020-00366-w

Gut transcriptomic changes during hibernation in the greater horseshoe bat (Rhinolophus ferrumequinum)
Cited by: 4
Author(s): Haijian Sun, Jiaying Wang, Yanfeng Xing, Yi-Hsuan Pan, Xiuguang Mao
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1004595

The Groucho Co-repressor Is Primarily Recruited to Local Target Sites in Active Chromatin to Attenuate Transcription
Cited by: 26
Author(s): Aamna K Kaul, Eugene F. Schuster, Barbara Jennings
Software Mentions: 4
Published: almost 12 years ago

10.3389/fsurg.2021.717084

Identification of a Novel Signature Predicting Overall Survival in Head and Neck Squamous Cell Carcinoma
Cited by: 4
Author(s): Haige Zheng, Huixian Liu, Yumin Lu, Li Hengguo
Software Mentions: 4
Published: almost 5 years ago

10.1128/mSphereDirect.00120-18

Zika Virus Infection Preferentially Counterbalances Human Peripheral Monocyte and/or NK Cell Activity
Cited by: 26
Author(s): Fok‐Moon Lum, David Lee, Tze-Kwang Chua, Jeslin J. L. Tan, Cheryl Yi‐Pin Lee, Xuan Li, Yongxiang Fang, Bernett Lee, Wearn‐Xin Yee, Natasha Y. Rickett, Po Ying Chia, Vanessa Lim, Yee‐Sin Leo, David A. Matthews, Julian A. Hiscox, Lisa F. P. Ng
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pgen.1004953

Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling
Cited by: 73
Author(s): Kazunari Nozue, An V. Tat, Upendra Kumar Devisetty, Matthew C. Robinson, Maxwell R. Mumbach, Yasunori Ichihashi, Saradadevi Lekkala, Julin N. Maloof
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pgen.1005211

Early Lineage Priming by Trisomy of Erg Leads to Myeloproliferation in a Down Syndrome Model
Cited by: 12
Author(s): Ashley P Ng, Yifang Hu, Donald Metcalf, Craig D. Hyland, Helen Ierino, Belinda Phipson, Di Wu, Tracey M. Baldwin, Maria Kauppi, Hiu Kiu, Ladina Di Rago, Douglas J. Hilton, Gordon K. Smyth, Warren S. Alexander
Software Mentions: 4
Published: over 11 years ago

10.3389/fpls.2017.01939

De novo Transcriptome Assembly and Comparison of C3, C3-C4, and C4 Species of Tribe Salsoleae (Chenopodiaceae)
Cited by: 19
Author(s): Maximilian Lauterbach, Hanno Schmidt, Kumari Billakurthi, Thomas Hankeln, Peter Westhoff, Udo Gowik, Gudrun Kadereit
Software Mentions: 4
Published: almost 9 years ago

10.15252/embr.201846557

Tamoxifen mechanically reprograms the tumor microenvironment via <scp>HIF</scp> ‐1A and reduces cancer cell survival
Cited by: 55
Author(s): Ernesto Cortés, Dariusz Lachowski, Benjamin Robinson, Müge Sarper, Jaakko Teppo, Stephen D. Thorpe, Tyler J Lieberthal, Kenji Iwamoto, David A. Lee, Mariko Okada‐Hatakeyama, Markku Varjosalo, Armando E. del Río Hernández
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2021.632033

The Genomic Impact of Mycoheterotrophy in Orchids
Cited by: 8
Author(s): Marcin Jąkalski, Julita Minasiewicz, José Caïus, Michał May, Marc‐André Selosse, Étienne Delannoy
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-018-2261-8

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
Cited by: 43
Author(s): Thomas P. Quinn, Tamsyn M. Crowley, Mark F. Richardson
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0069401

TCW: Transcriptome Computational Workbench
Cited by: 16
Author(s): Carol Soderlund, William M. Nelson, Mark R. Willer, David R. Gang
Software Mentions: 4
Published: about 13 years ago

10.1371/journal.pone.0216679

Seasonal adaptations of the hypothalamo-neurohypophyseal system of the dromedary camel
Cited by: 8
Author(s): Fatma Zohra Djazouli Alim, Elena V. Romanova, Yea Ling Tay, Ahmad Yamin bin Abdul Rahman, Kok‐Gan Chan, Kar‐Wai Hong, Mark F. Rogers, Bruce R. Southey, Michael Greenwood, André Souza Mecawi, Mohammad Rais Mustafa, Nicole Mahy, Colin Campbell, José Antunes‐Rodrigues, Jonathan V. Sweedler, David Murphy, Charles C.T. Hindmarch
Software Mentions: 4
Published: about 7 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

10.1186/s12862-014-0260-6

At the brink of eusociality: transcriptomic correlates of worker behaviour in a small carpenter bee
Cited by: 59
Author(s): Sandra M. Rehan, Ali J. Berens, Amy L. Toth
Software Mentions: 4
Published: over 11 years ago

10.1186/s12862-018-1288-9

Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers
Cited by: 16
Author(s): Bette Hecox-Lea, David B. Mark Welch
Software Mentions: 4
Published: over 7 years ago

10.1186/s12862-017-1103-z

De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus
Cited by: 11
Author(s): Alexey Moskalev, Anna V. Kudryavtseva, Alexander S. Graphodatsky, Violetta R. Beklemisheva, Natalia A. Serdyukova, Konstantin V. Krutovsky, Vadim V. Sharov, Ivan V. Kulakovskiy, Andrey S. Lando, Artem S. Kasianov, Dmitry A. Kuzmin, Yuliya A. Putintseva, Sergey Feranchuk, Mikhail Shaposhnikov, Vadim E. Fraifeld, Dmitri Toren, А. В. Снежкина, Vasily Sitnik
Software Mentions: 4
Published: over 8 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

10.1371/journal.pone.0137782

Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization
Cited by: 23
Author(s): Zhilong Jia, Xiang Zhang, Naiyang Guan, Xiaochen Bo, Michael R. Barnes, Zhigang Luo
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0233543

A transcriptome-based approach to identify functional modules within and across primary human immune cells
Cited by: 10
Author(s): Saraï Mola, Sylvain Foisy, Gabrielle Boucher, François Major, Claudine Beauchamp, Mohamad Karaky, Philippe Goyette, Sylvie Lesage, John D. Rioux
Software Mentions: 4
Published: about 6 years ago

10.18632/aging.202950

Multiomics integrative analysis identifies APOE allele-specific blood biomarkers associated to Alzheimer’s disease etiopathogenesis
Cited by: 13
Author(s): Laura Madrid, Sonia Moreno‐Grau, Shahzad Ahmad, Antonio González‐Pérez, Itziar de Rojas, Rui Xia, Pamela Victoria Martino Adami, Pablo García‐González, Luca Kleineidam, Qiong Yang, Vincent Damotte, Joshua C. Bis, Fuensanta Noguera-Perea, Céline Bellenguez, Xueqiu Jian, Juan Marín-Muñoz, Benjamin Grenier‐Boley, Adela Orellana, M. Arfan Ikram, Philippe Amouyel, Claudia L. Satizábal, Alzheimer’s Disease Neuroimaging Initiative, Luis Miguel Real, Carmen Antúnez-Almagro, Anita L. DeStefano, Alfredo Cabrera-Socorro, Rebecca Sims, Cornelia M. van Duijn, Eric Boerwinkle, Alfredo Ramı́rez, Myriam Fornage, Jean‐Charles Lambert, Julie Williams, Sudha Seshadri, Janina S. Ried, Agustín Ruiz, María Eugenia Sáez
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

10.1371/journal.pone.0207952

RNA-sequencing analysis of umbilical cord plasma microRNAs from healthy newborns
Cited by: 8
Author(s): Gary P. Brennan, Dimitrios Vitsios, Sophie Casey, Ann-Marie Looney, Boubou Hallberg, David C. Henshall, Geraldine B. Boylan, Deirdre M. Murray, Catherine Mooney
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0247378

Stool metabolome-microbiota evaluation among children and adolescents with obesity, overweight, and normal-weight using 1H NMR and 16S rRNA gene profiling
Cited by: 11
Author(s): José Diógenes Jaimes, Andrea Slavíčková, Jakub Hurych, Ondřej Cinek, Ben Nichols, Lucie Vodolánová, K. Černý, Jaroslav Havlík
Software Mentions: 4
Published: over 5 years ago

10.1186/s12863-019-0790-4

Transcriptome, physiological and biochemical analysis of Triarrhena sacchariflora in response to flooding stress
Cited by: 17
Author(s): Jia Wang, Hao Sun, Jiajin Sheng, Surong Jin, Fangjian Zhou, Zhongli Hu, Youxiang Diao
Software Mentions: 4
Published: over 6 years ago

10.1186/s12863-018-0608-9

RNA-seq analysis of lncRNA-controlled developmental gene expression during puberty in goat & rat
Cited by: 21
Author(s): Xiaoxiao Gao, Jing Ye, Chen Yang, Lei Luo, Ya Liu, Jianping Ding, Yunhai Zhang, Yinghui Ling, Weiping Huang, Xiaorong Zhang, Kaifa Zhang, Xiumei Li, Jie Zhou, Fugui Fang, Zubing Cao
Software Mentions: 4
Published: over 8 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568