bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1186/s12862-021-01818-5

Adaptive evolution of Moniliophthora PR-1 proteins towards its pathogenic lifestyle
Cited by: 1
Author(s): Adrielle Ayumi de Vasconcelos, Juliana José, Paulo M. Tokimatu, Antônio Pedro Camargo, Paulo José Pereira Lima Teixeira, Daniela P. T. Thomazella, Paula Favoretti Vital do Prado, Gabriel Lorencini Fiorin, Juliana Leles Costa, Antônio Figueira, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Renata Moro Baroni
Software Mentions: 1
Published: over 5 years ago

10.1186/s12861-020-00219-z

Identification of vital candidate microRNA/mRNA pairs regulating ovule development using high-throughput sequencing in hazel
Cited by: 11
Author(s): Jianfeng Liu, Qizheng Luo, Xingzheng Zhang, Qiang Zhang, Yufei Cheng
Software Mentions: 1
Published: over 6 years ago

10.1186/s12861-021-00240-w

Changes in the expression levels of elastic fibres in yak lungs at different growth stages
Cited by: 2
Author(s): Jingyi Li, Xiangqiong Meng, Lihan Wang, Hanry Yu, Honggang Yu, Qing Wei
Software Mentions: 1
Published: over 5 years ago

10.1186/s12906-019-2558-9

Antimicrobial characteristics of Berberine against prosthetic joint infection-related Staphylococcus aureus of different multi-locus sequence types
Cited by: 27
Author(s): Jiaqi Tan, Jin Wang, Chuang Yang, Chongzun Zhu, Geyong Guo, Jin Tang, Hao Shen
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1009491

Widespread imprinting of transposable elements and variable genes in the maize endosperm
Cited by: 5
Author(s): Sarah N. Anderson, Peng Zhou, Kaitlin Higgins, Yaniv Brandvain, Nathan M. Springer
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1007578

The roles of SMYD4 in epigenetic regulation of cardiac development in zebrafish
Cited by: 17
Author(s): Deyong Xiao, Huijun Wang, Lili Hao, Xiao Guo, Xiaojing Ma, Yanyan Qian, Hongbo Chen, Jing Ma, Jin Zhang, Wei Sheng, Weinian Shou, Guoying Huang, Ding Ma
Software Mentions: 1
Published: over 8 years ago

10.1002/advs.201900840

Sublethal Levels of Antibiotics Promote Bacterial Persistence in Epithelial Cells
Cited by: 33
Author(s): Xiaoye Liu, Fei Liu, Shuangyang Ding, Jianzhong Shen, Kui Zhu
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1009785

Mediator complex proximal Tail subunit MED30 is critical for Mediator core stability and cardiomyocyte transcriptional network
Cited by: 3
Author(s): Changming Tan, Siting Zhu, Zee Chen, Canzhao Liu, Yang E. Li, Mason Zhu, Zhiyuan Zhang, Zhiwei Zhang, Lunfeng Zhang, Yusu Gu, Zhengyu Liang, Thomas G. Boyer, Kunfu Ouyang, Sylvia M. Evans, Xi Fang
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22031390

Novel Identified Circular Transcript of RCAN2, circ-RCAN2, Shows Deviated Expression Pattern in Pig Reperfused Infarcted Myocardium and Hypoxic Porcine Cardiac Progenitor Cells In Vitro
Cited by: 4
Author(s): Julia Mester-Tonczar, Patrick Einzinger, Johannes Winkler, Nina Kastner, Andreas Spannbauer, Katrin Zlabinger, Denise Traxler, Dominika Lukovic, Ena Hašimbegović, Georg Goliasch, Noémi Pávó, Mariann Gyöngyösi
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12885-018-4621-1

Comprehensive transcriptomic analysis of heat shock proteins in the molecular subtypes of human breast cancer
Cited by: 36
Author(s): Felipe Carlos Martín Zoppino, Martin E. Guerrero-Gimenez, Gisela N. Castro, Daniel R. Ciocca
Software Mentions: 1
Published: over 8 years ago

10.1186/s12885-021-08176-x

Immunological effect of irreversible electroporation on hepatocellular carcinoma
Cited by: 12
Author(s): Xiaoxia Guo, Fukuan Du, Qin Liu, Yan Guo, Qingbing Wang, Wei Huang, Zhongmin Wang, Xiaoyi Ding, Zhiyuan Wu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12885-019-5571-y

The presence of bacteria varies between colorectal adenocarcinomas, precursor lesions and non-malignant tissue
Cited by: 53
Author(s): Caspar Bundgaard‐Nielsen, Ulrik Baandrup, Lars Peter Nielsen, Susanne Sørensen
Software Mentions: 1
Published: over 7 years ago

10.1186/s12885-020-6600-6

Integrative analysis of breast cancer profiles in TCGA by TNBC subgrouping reveals novel microRNA-specific clusters, including miR-17-92a, distinguishing basal-like 1 and basal-like 2 TNBC subtypes
Cited by: 15
Author(s): Karel Kalecky, Rebecca Modisette, Samantha Pena, Young-Rae Cho, Joseph H. Taube
Software Mentions: 1
Published: over 6 years ago

10.1186/s12885-020-07343-w

ANGPTL4 overexpression inhibits tumor cell adhesion and migration and predicts favorable prognosis of triple-negative breast cancer
Cited by: 18
Author(s): Yuchen Cai, Hang Yang, Kefeng Wang, Tan-Huan Chen, Wenqi Jiang, Yanxia Shi
Software Mentions: 1
Published: about 6 years ago

10.1186/s12885-018-4440-4

Chronophin regulates active vitamin B6 levels and transcriptomic features of glioblastoma cell lines cultured under non-adherent, serum-free conditions
Cited by: 7
Author(s): Markus Schulze, Maria Hutterer, Anja Sabo, S Hoja, Julia Lorenz, Tanja Rothhammer-Hampl, Christel Herold‐Mende, Lucia Floßbach, Camelia Monoranu, Markus J. Riemenschneider
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1009521

Dynamic post-transcriptional regulation by Mrn1 links cell wall homeostasis to mitochondrial structure and function
Cited by: 7
Author(s): Kendra Reynaud, Molly Brothers, Michael Ly, Nicholas T. Ingolia
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1006341

Anchoring of Heterochromatin to the Nuclear Lamina Reinforces Dosage Compensation-Mediated Gene Repression
Cited by: 37
Author(s): Martha J. Snyder, Alyssa C. Lau, Elizabeth A. Brouhard, Mary Ellen Davis, Jiali Jiang, Margarita Sifuentes, Györgyi Csankovszki
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pgen.1007802

A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability
Cited by: 111
Author(s): Mahdieh Jadaliha, Omid Gholamalamdari, Wei Tang, Yang Zhang, Ana Petracovici, Qinyu Hao, Aamira Tariq, Tae Gyoon Kim, Sarah E. Holton, Deepak Kumar Singh, Xiao Ling Li, Susan M. Freier, Stefan Ambs, Rohit Bhargava, Ashish Lal, Supriya G. Prasanth, Jian Ma, Kannanganattu V. Prasanth
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1006134

Next-Generation “-omics” Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa
Cited by: 88
Author(s): Anne Chevallereau, Bob Blasdel, Jeroen De Smet, Marc Monot, Michael Zimmermann, Maria Kogadeeva, Uwe Sauer, Peter Jorth, Marvin Whiteley, Laurent Debarbieux, Rob Lavigne
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1007124

An Arabidopsis Nucleoporin NUP85 modulates plant responses to ABA and salt stress
Cited by: 62
Author(s): Yingfang Zhu, Bangshing Wang, Kai Tang, Chuan‐Chih Hsu, Shaojun Xie, Hongwu Du, Yuting Yang, W. Andy Tao, Jian‐Kang Zhu
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1008425

NusG prevents transcriptional invasion of H-NS-silenced genes
Cited by: 14
Author(s): Lionello Bossi, Mathilde Ratel, Camille Laurent, Patricia Kerboriou, Andrew Camilli, É. Éveno, Marc Boudvillain, Nara Figueroa‐Bossi
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pgen.1005691

Transcriptome Analysis of Targeted Mouse Mutations Reveals the Topography of Local Changes in Gene Expression
Cited by: 24
Author(s): David B. West, Eric K. Engelhard, Michael Adkisson, Alessia Nava, Julia V. Kirov, Andreanna Cipollone, Brandon Willis, Jared Rapp, Pieter J. de Jong, Kevin C K Lloyd
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12885-017-3233-5

Aberrant expression of ALK and EZH2 in Merkel cell carcinoma
Cited by: 20
Author(s): Tuukka Veija, Virve Koljonen, Tom Böhling, Mia Kero, Sakari Knuutila, Virinder Sarhadi
Software Mentions: 1
Published: over 9 years ago

10.1002/advs.202002228

ICAM‐1 Activates Platelets and Promotes Endothelial Permeability through VE‐Cadherin after Insufficient Radiofrequency Ablation
Cited by: 21
Author(s): Jian Kong, Changyu Yao, Shuying Dong, Shilun Wu, Yangkai Xu, Ké Li, Liang Ji, Qiang Shen, Qi Zhang, Rui Zhan, Hongtu Cui, Changping Zhou, Hai-Gang Niu, Guoming Li, Wenbing Sun, Lemin Zheng
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms22041670

C1q/TNF-Related Protein 3 (CTRP-3) Deficiency of Adipocytes Affects White Adipose Tissue Mass but Not Systemic CTRP-3 Concentrations
Cited by: 5
Author(s): Andreas Schmid, M Roderfeld, Jonas Gehl, Elke Roeb, Andrea Nist, Ho‐Ryun Chung, Thorsten Stiewe, Thomas Karrasch, Andréas Schäffler
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12885-021-07905-6

EML4-ALK induces cellular senescence in mortal normal human cells and promotes anchorage-independent growth in hTERT-transduced normal human cells
Cited by: 3
Author(s): Akihiko Miyanaga, Masaru Matsumoto, Jessica Beck, Izumi Horikawa, Takahiro Oike, Hirokazu Okayama, Hiromi Tanaka, Sandra Burkett, Ana I. Robles, Mohammed A. Khan, Delphine Lissa, Masahiro Seike, Akihiko Gemma, Hiroyuki Mano, Curtis C. Harris
Software Mentions: 1
Published: over 5 years ago

10.1002/advs.202004507

Hypermethylation of Hepatic Mitochondrial ND6 Provokes Systemic Insulin Resistance
Cited by: 19
Author(s): Ke Cao, Weiqiang Lv, Xueqiang Wang, Shanshan Dong, Xuyun Liu, Tie‐Lin Yang, Jie Xu, Mengqi Zeng, Xuan Zou, Daina Zhao, Qingqing Ma, Ming Tsan Lin, Long Jiang, Weijin Zang, Feng Gao, Zhihui Feng, Jiankang Liu
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22042181

Altered Expression of OsAAP3 Influences Rice Lesion Mimic and Leaf Senescence by Regulating Arginine Transport and Nitric Oxide Pathway
Cited by: 12
Author(s): Qilang Wei, Zhenwei Yan, Yifan Xiong, Zhongming Fang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1007571

Naturally-occurring canine invasive urothelial carcinoma harbors luminal and basal transcriptional subtypes found in human muscle invasive bladder cancer
Cited by: 28
Author(s): Deepika Dhawan, Noah M. Hahn, José A. Ramos‐Vara, Deborah W. Knapp
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1005295

Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm
Cited by: 83
Author(s): Carolin A. Rebernig, Clément Lafon‐Placette, Marcelinus Rocky Hatorangan, Tanja Slotte, Claudia Köhler
Software Mentions: 1
Published: over 11 years ago

10.3390/nu11102310

Loss of Diurnal Oscillatory Rhythms in Gut Microbiota Correlates with Changes in Circulating Metabolites in Type 2 Diabetic db/db Mice
Cited by: 35
Author(s): Eleni Beli, Samantha Prabakaran, Preethi Krishnan, Carmella Evans‐Molina, Maria B. Grant
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms22052399

Combined Transcriptomic and Metabolomic Analysis Reveals the Role of Phenylpropanoid Biosynthesis Pathway in the Salt Tolerance Process of Sophora alopecuroides
Cited by: 32
Author(s): Youcheng Zhu, Qingyu Wang, Ying Wang, Yang Xu, Jingwen Li, Suoqi Zhao, Doudou Wang, Zuwei Ma, Yanting Fan, Yajing Liu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12915-020-00925-x

Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats
Cited by: 29
Author(s): Octavio M. Palacios-Gimenez, Julia Koelman, Marc Palmada-Flores, Tessa M. Bradford, Karl K. Jones, Steven J. Cooper, Takeshi Kawakami, Alexander Suh
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms22052518

Selenite Inhibits Notch Signaling in Cells and Mice
Cited by: 5
Author(s): Michael R. Powers, Liu Liu, Dane Deemer, Selina Chen, Aaron Scholl, Masafumi Yoshinaga, Zijuan Liu
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1008678

Light affects tissue patterning of the hypocotyl in the shade-avoidance response
Cited by: 12
Author(s): Esther Botterweg-Paredes, Anko Blaakmeer, Suk‐Yoon Hong, Bin Sun, Lorenzo Mineri, Valdeko Kruusvee, Yakun Xie, Daniel Straub, Delphine Ménard, Edouard Pesquet, Stephan Wenkel
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1009483

Androgens regulate ovarian gene expression by balancing Ezh2-Jmjd3 mediated H3K27me3 dynamics
Cited by: 10
Author(s): Subhransu Roy, Binbin Huang, Niharika Sinha, Jianrong Wang, Aritro Sen
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1007510

Genetic basis and evolution of rapid cycling in railway populations of tetraploid Arabidopsis arenosa
Cited by: 34
Author(s): Pierre Baduel, Ben Hunter, Sarang Yeola, Kirsten Bomblies
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1009640

Multi-omics analysis of glucose-mediated signaling by a moonlighting Gβ protein Asc1/RACK1
Cited by: 13
Author(s): Shuang Li, Yuanyuan Li, Blake R. Rushing, Sarah E. Harris, Susan McRitchie, Janice C. Jones, Daniel Domínguez, Susan Sumner, Henrik G. Dohlman
Software Mentions: 1
Published: over 5 years ago

10.1186/s12915-020-0764-z

DDX39B interacts with the pattern recognition receptor pathway to inhibit NF-κB and sensitize to alkylating chemotherapy
Cited by: 14
Author(s): Szymon J. Szymura, Giovanna M. Bernal, Longtao Wu, Zhongqin Zhang, Clayton D. Crawley, David J. Voce, Paige-Ashley Campbell, Diana E. Ranoa, Ralph R. Weichselbaum, Bakhtiar Yamini
Software Mentions: 1
Published: over 6 years ago

10.1186/s12915-019-0634-8

Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida
Cited by: 9
Author(s): Courtney W. Stairs, Anna Kokla, Ásgeir Ástvaldsson, Jon Jerlström-Hultqvist, Staffan G. Svärd, Thijs J. G. Ettema
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22062803

Overexpression of Salicylic Acid Carboxyl Methyltransferase (CsSAMT1) Enhances Tolerance to Huanglongbing Disease in Wanjincheng Orange (Citrus sinensis (L.) Osbeck)
Cited by: 13
Author(s): Xin Zou, Ke Zhao, Yunuo Liu, Meirong Du, Lin Zheng, Shuai Wang, Le Xu, Aihong Peng, Yongrui He, Long Qin, Shanchun Chen
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1006338

Widespread Shortening of 3’ Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection
Cited by: 80
Author(s): Athma A. Pai, Golshid Baharian, Ariane Pagé Sabourin, Jessica F. Brinkworth, Yohann Nédélec, Joseph W. Foley, Jean Grenier, Katherine J. Siddle, Anne Dumaine, Vania Yotova, Zachary P. Johnson, Robert E. Lanford, Christopher B. Burge, Luis B. Barreiro
Software Mentions: 1
Published: about 10 years ago

10.1186/s12915-020-00777-5

Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae
Cited by: 7
Author(s): Alfonso Soler-Bistué, Sebastián Aguilar-Pierlé, Marc García-Garcerá, Marie-Eve Val, Odile Sismeiro, Hugo Varet, Rodrigo Sieira, Evelyne Krin, Ove Skovgaard, Diego J. Comerci, Eduardo P. C. Rocha, Didier Mazel
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pntd.0006368

Discovery of genomic intervals that underlie nematode responses to benzimidazoles
Cited by: 59
Author(s): Mostafa Zamanian, Daniel E. Cook, Stefan Zdraljevic, Shannon C. Brady, Daehan Lee, Jun-Ho Lee, Erik C. Andersen
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pntd.0006152

Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut
Cited by: 37
Author(s): Vincent Raquin, Sarah H. Merkling, Valérie Gausson, Isabelle Moltini-Conclois, Lionel Frangeul, Hugo Varet, Marie‐Agnès Dillies, Maria‐Carla Saleh, Louis Lambrechts
Software Mentions: 1
Published: almost 9 years ago

10.1099/acmi.0.000121

Transcriptome profiling of Variovorax paradoxus EPS under different growth conditions reveals regulatory and structural novelty in biofilm formation
Cited by: 2
Author(s): Richard J. Fredendall, Jenny L. Stone, Michael J. Pehl, Paul M. Orwin
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pntd.0007949

Transcriptional analysis of THP-1 cells infected with Leishmania infantum indicates no activation of the inflammasome platform
Cited by: 19
Author(s): Mariana Gatto, Patrícia Aparecida Borim, Ivan Rodrigo Wolf, Taís Fukuta da Cruz, Gustavo Augusto Ferreira Mota, Aline Márcia Marques Braz, Bárbara Casella Amorim, Guilherme Targino Valente, Márjorie de Assis Golim, James Venturini, João Pessoa Araújo, Alessandra Pontillo, Alexandrina Sartori
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pntd.0008014

Distinct gene expression patterns in vector-residing Leishmania infantum identify parasite stage-enriched markers
Cited by: 15
Author(s): Iliano V. Coutinho-Abreu, Tiago D. Serafim, Claudio Meneses, Shaden Kamhawi, Fabiano Oliveira, Jesús G. Valenzuela
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pntd.0009738

In vitro culture of freshly isolated Trypanosoma brucei brucei bloodstream forms results in gene copy-number changes
Cited by: 6
Author(s): Julius Mulindwa, Geofrey Ssentamu, Enock Matovu, Kevin Kamanyi Marucha, Francisco Aresta‐Branco, Claudia Helbig, Christine Clayton
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pntd.0008387

Growth velocity in children with Environmental Enteric Dysfunction is associated with specific bacterial and viral taxa of the gastrointestinal tract in Malawian children
Cited by: 19
Author(s): Chandni Desai, Scott A. Handley, Rachel Rodgers, Cynthia Rodríguez, M. Isabel Ordiz, Mark Manary, Lori R. Holtz
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-018-2216-0

MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization
Cited by: 6
Author(s): Lingtao Su, Guixia Liu, Tian Bai, Xiangyu Meng, Qingshan Ma
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pntd.0009320

Distinct transcriptional profiles of Leptospira borgpetersenii serovar Hardjo strains JB197 and HB203 cultured at different temperatures
Cited by: 8
Author(s): Ellie J. Putz, Sathesh K Sivasankaran, Luis G. V. Fernandes, Brian W. Brunelle, John D. Lippolis, David P. Alt, Darrell O. Bayles, Richard L. Hornsby, Jarlath E. Nally
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pntd.0008709

Mycolactone induces cell death by SETD1B-dependent degradation of glutathione
Cited by: 11
Author(s): Birgit Förster, Caroline Demangel, Thorsten Thye
Software Mentions: 1
Published: about 6 years ago

10.1186/s12859-019-2709-5

A likelihood ratio test for changes in homeolog expression bias
Cited by: 8
Author(s): Ronald D. Smith, Taliesin J Kinser, Gregory D. Smith, Joshua R. Puzey
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-018-2434-5

Feature related multi-view nonnegative matrix factorization for identifying conserved functional modules in multiple biological networks
Cited by: 13
Author(s): Peizhuo Wang, Lin Gao, Yuxuan Hu, Feng Li
Software Mentions: 1
Published: about 8 years ago

10.3390/nu12103221

A High Protein Calorie Restriction Diet Alters the Gut Microbiome in Obesity
Cited by: 32
Author(s): Tien S. Dong, Kayti Luu, Venu Lagishetty, Farzaneh Sedighian, Sung Oh Woo, Benjamin W. Dreskin, William Katzka, Candace Chang, Yi Zhou, Nerea Arias-Jayo, Julianne C. Yang, Aaron I. Ahdoot, Zhaoping Li, Joseph R. Pisegna, Jonathan P. Jacobs
Software Mentions: 1
Published: about 6 years ago

10.3390/jpm11090923

αβ-T Cells Engineered to Express γδ-T Cell Receptors Can Kill Neuroblastoma Organoids Independent of MHC-I Expression
Cited by: 4
Author(s): Josephine G M Strijker, Ronja Pscheid, Esther Drent, Jessica J. F. van der Hoek, Bianca Koopmans, Kimberley Ober, Sander R. van Hooff, Waleed M. Kholosy, Annelisa M. Cornel, Chris Coomans, Andrea Bisso, Marleen M. van Loenen, Jan J. Molenaar, Judith Wienke
Software Mentions: 1
Published: about 5 years ago

10.3390/jpm11090827

PTGDR2 Expression in Peripheral Blood as a Potential Biomarker in Adult Patients with Asthma
Cited by: 5
Author(s): Asunción Garcı́a-Sánchez, Miguel Estravís, Marı́a Jesús Martı́n, Jacqueline Pérez‐Pazos, Cristina Martín‐García, María Gil-Melcón, Jacinto Ramos‐González, Ibon Eguíluz-Gracia, Juan Carlos Triviño, María Isidoro‐García, Ignacio Dávila, Catalina Sanz
Software Mentions: 1
Published: about 5 years ago

10.1080/21623945.2020.1859789

Mouse Embryonic Fibroblast Adipogenic Potential: A Comprehensive Transcriptome Analysis
Cited by: 6
Author(s): Mohamed Al-Sayegh, Hamad Ali, Mohammad H. Jamal, Mei ElGindi, Tina Chanyong, Khulood Al-Awadi, Mohamed Abu‐Farha
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12859-020-3346-8

Ensemble disease gene prediction by clinical sample-based networks
Cited by: 5
Author(s): Ping Luo, Li Tian, Bolin Chen, Qianghua Xiao, Fang‐Xiang Wu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-019-2641-8

Shambhala: a platform-agnostic data harmonizer for gene expression data
Cited by: 30
Author(s): Nicolas Borisov, Irina Shabalina, Victor Tkachev, Maxim Sorokin, Andrew Garazha, А А Пулин, И И Еремин, Anton Buzdin
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pntd.0006835

Stress susceptibility in Trypanosoma brucei lacking the RNA-binding protein ZC3H30
Cited by: 9
Author(s): Chaitali Chakraborty, Christine Clayton
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pntd.0007052

Genomic instability at the locus of sterol C24-methyltransferase promotes amphotericin B resistance in Leishmania parasites
Cited by: 38
Author(s): Andrew W. Pountain, Stefan Weidt, Clément Regnault, Paul A. Bates, Anne M. Donachie, Nicholas J. Dickens, Michael P. Barrett
Software Mentions: 1
Published: almost 8 years ago

10.1186/s40478-020-00946-1

Epigenomics and transcriptomics analyses of multiple system atrophy brain tissue supports a role for inflammatory processes in disease pathogenesis
Cited by: 4
Author(s): Conceição Bettencourt, Ignazio S. Piras, Sandrine C. Foti, Joshua S. Talboom, Yasuo Miki, Tammaryn Lashley, R. Balázs, Emmanuelle Viré, Thomas T. Warner, Matt Huentelman, Janice L. Holton
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0199083

Role of the tomato TAGL1 gene in regulating fruit metabolites elucidated using RNA sequence and metabolomics analyses
Cited by: 13
Author(s): Xiaodan Zhao, Xinyu Yuan, Sha Chen, Lanhuan Meng, Daqi Fu
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0230266

Comparison of transcriptomes from two chemosensory organs in four decapod crustaceans reveals hundreds of candidate chemoreceptor proteins
Cited by: 35
Author(s): Mihika T. Kozma, Hanh Ngo-Vu, YW Wong, Neal S. Shukla, Shrikant Pawar, Adriano Senatore, Manfred Schmidt, Charles D. Derby
Software Mentions: 1
Published: over 6 years ago

10.3390/nu12123701

Understanding the Heterogeneity of Obesity and the Relationship to the Brain-Gut Axis
Cited by: 6
Author(s): Tony Hung, Tien S. Dong, Zixi Chen, David Elashoff, Janet S. Sinsheimer, Jonathan P. Jacobs, Venu Lagishetty, Priten Vora, Jean Stains, Emeran A. Mayer, Abha R. Gupta
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0143161

Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide
Cited by: 25
Author(s): Amanda E. Hargrove, Thomas F. Martínez, Alissa A. Hare, Alexis A. Kurmis, John W. Phillips, Sudha Sud, Kenneth J. Pienta, Peter B. Dervan
Software Mentions: 1
Published: almost 11 years ago

10.1098/rsob.160012

Acute stress is detrimental to heart regeneration in zebrafish
Cited by: 46
Author(s): Pauline Sallin, Anna Jaźwińska
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0220365

Transcriptomic differences noted in Glaesserella parasuis between growth in broth and on agar
Cited by: 2
Author(s): Samantha J. Hau, Kathy T. Mou, Darrell O. Bayles, Susan L. Brockmeier
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0238380

Transcriptional and immunohistological assessment of immune infiltration in pancreatic cancer
Cited by: 8
Author(s): Brady Bernard, Venkatesh Rajamanickam, Christopher Dubay, Brian D. Piening, Emilio Alonso, Zeljka Jutric, Ephraim Tang, Pippa Newell, Paul Hansen, Terry R. Medler, Andrew Gunderson, Kristina H. Young, Carlo Bifulco, Joanna Pucliowska, Marka R. Crittenden, Michael Gough
Software Mentions: 1
Published: about 6 years ago

10.1098/rsob.160293

Peripheral self-reactivity regulates antigen-specific CD8 T-cell responses and cell division under physiological conditions
Cited by: 6
Author(s): Lee Kim Swee, Zhen Tan, Anna Smerdel-Ramoya, Norimasa Yoshida, Harshil Patel, Gijsbert M. Grotenbreg, Eva‐Maria Frickel, Hidde L. Ploegh
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0152792

Identifying Cancer Subtypes from miRNA-TF-mRNA Regulatory Networks and Expression Data
Cited by: 57
Author(s): Taosheng Xu, Thuc Duy Le, Lin Liu, Rujing Wang, Bingyu Sun, Jiuyong Li
Software Mentions: 1
Published: over 10 years ago

10.1002/art.40545

Functional Characterization of the Osteoarthritis Genetic Risk Residing at ALDH1A2 Identifies rs12915901 as a Key Target Variant
Cited by: 41
Author(s): Colin Shepherd, Dongxing Zhu, Andrew Skelton, Jennifer Combe, Harrison Threadgold, Longji Zhu, Tonia L. Vincent, Paul Stuart, Louise N. Reynard, John Loughlin
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0146555

The Effect of Root Exudate 7,4′-Dihydroxyflavone and Naringenin on Soil Bacterial Community Structure
Cited by: 51
Author(s): Márton Szoboszlay, A.C. White-Monsant, Luke A. Moe
Software Mentions: 1
Published: almost 11 years ago

10.1098/rsob.200246

Temperature modulates immune gene expression in mosquitoes during arbovirus infection
Cited by: 18
Author(s): B. M. C. Randika Wimalasiri-Yapa, Roberto A. Barrero, Liesel Stassen, Louise M. Hafner, Elizabeth A. McGraw, Alyssa T. Pyke, Cassie C. Jansen, Andreas Suhrbier, Laith Yakob, Wenbiao Hu, Gregor J. Devine, Francesca D. Frentiu
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0212462

Stress response to CO2 deprivation by Arabidopsis thaliana in plant cultures
Cited by: 12
Author(s): Souvik Banerjee, Oskar Siemianowski, Meiling Liu, Kara R. Lind, X. C. Tian, Dan Nettleton, Ludovico Cademartiri
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0224094

Stringent response governs the oxidative stress resistance and virulence of Francisella tularensis
Cited by: 14
Author(s): Zhuo Ma, Kayla C. King, Maha Alqahtani, Madeline Worden, Parthasarathy Muthuraman, Christopher Cioffi, Chandra Shekhar Bakshi, Meenakshi Malik
Software Mentions: 1
Published: about 7 years ago

10.1186/s13075-019-1988-6

Cartilage endoplasmic reticulum stress may influence the onset but not the progression of experimental osteoarthritis
Cited by: 12
Author(s): Louise H. W. Kung, Lorna Mullan, Jamie Soul, Ping Wang, Kazutoshi Mori, John F. Bateman, Michael D. Briggs, Raymond P. Boot-Handford
Software Mentions: 1
Published: about 7 years ago

10.1098/rsob.200182

Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome
Cited by: 4
Author(s): Siriluck Ponsuksili, Michael Oster, Henry Reyer, Frieder Hadlich, Nares Trakooljul, M. Rodehutscord, Amélia Camarinha‐Silva, Jörn Bennewitz, Klaus Wimmers
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0147903

Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids
Cited by: 18
Author(s): Valèria Romero‐Soriano, María del Pilar García Guerreiro
Software Mentions: 1
Published: almost 11 years ago

10.1186/s40478-020-00942-5

Restoration of miR-193a expression is tumor-suppressive in MYC amplified Group 3 medulloblastoma
Cited by: 10
Author(s): Harish Shrikrishna Bharambe, Annada Anil Joshi, Kedar Yogi, Sadaf Kazi, Neelam Shirsat
Software Mentions: 1
Published: over 6 years ago

10.1186/s13075-017-1378-x

Identification of differential co-expressed gene networks in early rheumatoid arthritis achieving sustained drug-free remission after treatment with a tocilizumab-based or methotrexate-based strategy
Cited by: 17
Author(s): Xavier M Teitsma, Johannes W. G. Jacobs, Michal Mokrý, Michelle E A Borm, Attila Pethö‐Schramm, Jacob M van Laar, J. W. J. Bijlsma, Floris P. J. G. Lafeber
Software Mentions: 1
Published: over 9 years ago

10.1128/JVI.02106-18

Investigating the Biological Relevance of In Vitro -Identified Putative Packaging Signals at the 5′ Terminus of Satellite Tobacco Necrosis Virus 1 Genomic RNA
Cited by: 9
Author(s): Ioly Kotta‐Loizou, Hadrien Peyret, Keith Saunders, Robert H.A. Coutts, George P. Lomonossoff
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0167003

Regulation and Maintenance of an Adoptive T-Cell Dependent Memory B Cell Pool
Cited by: 2
Author(s): Marie Anson, Inês F. Amado, Marie-Pierre Mailhé, Emmanuel Donnadieu, Sylvie Garcia, François Huetz, António A. Freitas
Software Mentions: 1
Published: almost 10 years ago

10.1128/JVI.00102-19

RIG-I Activation by a Designer Short RNA Ligand Protects Human Immune Cells against Dengue Virus Infection without Causing Cytotoxicity
Cited by: 9
Author(s): Victor Ho, Hui Yee Yong, Marion Chevrier, Vipin Narang, Josephine Lum, Ying-Xiu Toh, Bernett Lee, Jinmiao Chen, Ern Yu Tan, Dahai Luo, Katja Fink
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0225267

Genome wide analysis of gene expression changes in skin from patients with type 2 diabetes
Cited by: 17
Author(s): Eri Takematsu, Adrianne Spencer, Jeff Auster, Po-Chih Chen, Annette Graham, Patricia Martin, Aaron Baker
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0168075

Two Subclasses of Differentially Expressed TPS1 Genes and Biochemically Active TPS1 Proteins May Contribute to Sugar Signalling in Kiwifruit Actinidia chinensis
Cited by: 3
Author(s): Charlotte Voogd, Lara Brian, Erika Varkonyi‐Gasic
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0179571

WetA bridges cellular and chemical development in Aspergillus flavus
Cited by: 34
Author(s): Ming-Yueh Wu, Matthew E. Mead, Sun-Chang Kim, Antonis Rokas, Jae-Hyuk Yu
Software Mentions: 1
Published: over 9 years ago

10.1007/s00204-018-2256-2

Comparison of base-line and chemical-induced transcriptomic responses in HepaRG and RPTEC/TERT1 cells using TempO-Seq
Cited by: 36
Author(s): Alice Limonciel, Gamze Ates, Giada Carta, Anja Wilmes, Manfred Watzele, Peter J. Shepard, Harper VanSteenhouse, Bruce Seligmann, Joanne M. Yeakley, Bob van de Water, Mathieu Vinken, Paul Jennings
Software Mentions: 1
Published: over 8 years ago

10.1007/s00204-020-02835-x

Valproic acid promotes mitochondrial dysfunction in primary human hepatocytes in vitro; impact of C/EBPα-controlled gene expression
Cited by: 8
Author(s): Florian Caiment, Jarno E J Wolters, Evelyn Smit, Yannick Schrooders, Jos Kleinjans, Twan van den Beucken
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0254985

Interleukin-22 mitigates acute respiratory distress syndrome (ARDS)
Cited by: 7
Author(s): Sharven Taghavi, Olan Jackson‐Weaver, Sarah Abdullah, Alanna Wanek, Robert Drury, Jacob Packer, Aaron Cotton-Betteridge, Juan Duchesne, Derek Pociask, Jay K. Kolls
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0248996

Reduction of fibrosis and immune suppressive cells in ErbB2-dependent tumorigenesis by an LXR agonist
Cited by: 3
Author(s): Sheng Gao, Hongyan Yuan, Lü Jin, Suman Ranjit, Julia Panov, Xun Lu, Moshe Levi, Robert I. Glazer
Software Mentions: 1
Published: over 5 years ago

10.1186/s40478-021-01231-5

Protein farnesylation is upregulated in Alzheimer’s human brains and neuron-specific suppression of farnesyltransferase mitigates pathogenic processes in Alzheimer’s model mice
Cited by: 11
Author(s): Angela Jeong, Shaowu Cheng, Rui Zhong, David A. Bennett, Martin O. Bergö, Li L
Software Mentions: 1
Published: over 5 years ago

10.1128/JVI.01094-19

Pharmacological Modulation of the Wnt/β-Catenin Pathway Inhibits Proliferation and Promotes Differentiation of Long-Lived Memory CD4 + T Cells in Antiretroviral Therapy-Suppressed Simian Immunodeficiency Virus-Infected Macaques
Cited by: 13
Author(s): Maud Mavigner, Michelle Zanoni, Gregory K. Tharp, Jakob Habib, Cameron Mattingly, Mathias Lichterfeld, Melon T. Nega, Thomas H. Vanderford, Steven E. Bosinger, Ann Chahroudi
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0189608

Microcystin-LR does not induce alterations to transcriptomic or metabolomic profiles of a model heterotrophic bacterium
Cited by: 4
Author(s): Robbie M. Martin, Stephen P. Dearth, Gary R. LeCleir, Shawn R. Campagna, Elizabeth Fozo, Erik R. Zinser, Steven W. Wilhelm
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0213770

Investigation of somatic single nucleotide variations in human endogenous retrovirus elements and their potential association with cancer
Cited by: 7
Author(s): Ting-Chia Chang, Santosh Goud, John Torcivia-Rodriguez, Yu Hu, Qing Pan, Robel Kahsay, Jonas Blomberg, Raja Mazumder
Software Mentions: 1
Published: over 7 years ago

10.1128/AEM.00483-18

Enrichment of Clinically Relevant Organisms in Spontaneous Preterm-Delivered Placentas and Reagent Contamination across All Clinical Groups in a Large Pregnancy Cohort in the United Kingdom
Cited by: 60
Author(s): Lydia J. Leon, Ronan Doyle, Ernest Diez Benavente, Taane G. Clark, Nigel Klein, Philip Stanier, Gudrun E. Moore
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0201969

Cranberry-derived proanthocyanidins induce a differential transcriptomic response within Candida albicans urinary biofilms
Cited by: 3
Author(s): Anitha Sundararajan, Hallie S. Rane, Thiruvarangan Ramaraj, Johnny A. Sena, Amy B. Howell, Stella M. Bernardo, Faye Schilkey, Samuel A. Lee
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0220907

Altered expression of miRNAs and mRNAs reveals the potential regulatory role of miRNAs in the developmental process of early weaned goats
Cited by: 15
Author(s): Rongrong Liao, Yuhua Lv, Lihui Zhu, Yu Lin
Software Mentions: 1
Published: over 7 years ago

Projects: bioconductor: DESeq2

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Science Score: 100/100

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Papers Mentioning DESeq2 9,583