bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1172/jci.insight.139965

Stem cell transplantation uncovers TDO-AHR regulation of lung dendritic cells in herpesvirus-induced pathology
Cited by: 5
Author(s): Stephen J. Gurczynski, Nicolas L Pereira, Steven Hrycaj, Carol A. Wilke, Rachel L. Zemans, Bethany B. Moore
Software Mentions: 1
Published: over 5 years ago

10.1042/BSR20194041

RNA-sequencing and bioinformatics analysis of long noncoding RNAs and mRNAs in the asthenozoospermia
Cited by: 14
Author(s): Hui Lü, Dongchuan Xu, Ping Wang, Wenye Sun, Xinhuai Xue, Yuxin Hu, Chunli Xie, Yanlin Ma
Software Mentions: 1
Published: about 6 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: about 7 years ago

10.1186/s13045-019-0765-y

Nuclear factor of activated T-cells, NFATC1, governs FLT3ITD-driven hematopoietic stem cell transformation and a poor prognosis in AML
Cited by: 10
Author(s): Maria Solovey, Ying Wang, Christian Michel, Klaus H. Metzeler, Tobias Herold, Joachim R Göthert, Volker Ellenrieder, Stefan Gattenlöhner, Andreas Neubauer, Dinko Pavlinic, Vladimı́r Beneš, Oliver Rupp, Andreas Burchert
Software Mentions: 1
Published: about 7 years ago

10.1172/jci.insight.144799

Myofibroblast dedifferentiation proceeds via distinct transcriptomic and phenotypic transitions
Cited by: 36
Author(s): S.M. Fortier, L.R.K. Penke, Dana King, Tho X. Pham, Giovanni Ligresti, Marc Peters‐Golden
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms17081324

Genes Expressed Differentially in Hessian Fly Larvae Feeding in Resistant and Susceptible Plants
Cited by: 7
Author(s): Ming‐Shun Chen, Sanzhen Liu, Haiyan Wang, Xiaoyan Cheng, Mustapha El Bouhssini, R. Jeff Whitworth
Software Mentions: 1
Published: about 10 years ago

10.1186/s13058-020-01315-5

Identification and targeting of selective vulnerability rendered by tamoxifen resistance
Cited by: 10
Author(s): Madhurendra Singh, Xiaolei Zhou, Xinsong Chen, Gema Sanz, Sylvain Peuget, Qing Cheng, Ali Rihani, Elias S.J. Arnér, Johan Hartman, Galina Selivanova
Software Mentions: 1
Published: about 6 years ago

10.1172/jci.insight.142205

Selective inhibition of JAK3 signaling is sufficient to reverse alopecia areata
Cited by: 32
Author(s): Zhijun Dai, James Chen, Yi‐Lu Chang, Angela M. Christiano
Software Mentions: 1
Published: over 5 years ago

10.1186/s13058-016-0673-9

p53 deficiency linked to B cell translocation gene 2 (BTG2) loss enhances metastatic potential by promoting tumor growth in primary and metastatic sites in patient-derived xenograft (PDX) models of triple-negative breast cancer
Cited by: 40
Author(s): Emily Powell, Jin Shao, Yuan Yuan, Hsiang Chun Chen, Shirong Cai, Gloria V. Echeverria, Nipun A. Mistry, Keith F. Decker, Christopher Schlosberg, Kim Anh, John Edwards, Han Liang, David Piwnica‐Worms, Helen Piwnica‐Worms
Software Mentions: 1
Published: over 10 years ago

10.1186/s13058-018-1041-8

Key regulators of lipid metabolism drive endocrine resistance in invasive lobular breast cancer
Cited by: 62
Author(s): Tian Du, Matthew J. Sikora, Kevin M. Levine, Nilgun Tasdemir, Rebecca B. Riggins, Stacy G. Wendell, Bennett Van Houten, Steffi Oesterreich
Software Mentions: 1
Published: about 8 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: over 10 years ago

10.1172/jci.insight.144351

Acyl-CoA synthetase 6 is required for brain docosahexaenoic acid retention and neuroprotection during aging
Cited by: 14
Author(s): Regina F. Fernandez, Andrea M. Pereyra, Victoria D Diaz, Emily S Wilson, Karen Litwa, Jonatan Martínez‐Gardeazabal, Shelley N. Jackson, J. Thomas Brenna, Brian P. Hermann, Jeffrey B. Eells, Jessica M. Ellis
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0234837

A tale of two fish: Comparative transcriptomics of resistant and susceptible steelhead following exposure to Ceratonova shasta highlights differences in parasite recognition
Cited by: 15
Author(s): Damien Barrett, Jerri L. Bartholomew
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.3408

Comparative transcriptome analysis of isonuclear-alloplasmic lines unmask key transcription factor genes and metabolic pathways involved in sterility of maize CMS-C
Cited by: 13
Author(s): Chuan Li, Zhigang Zhao, Yongming Liu, Bing Liu, Shuxian Guan, Hai Long, Jing Wang, Yanli Lu, Mengji Cao
Software Mentions: 1
Published: over 9 years ago

10.1186/s12284-021-00512-w

Characterization and Evaluation of Transgenic Rice Pyramided with the Pi Genes Pib, Pi25 and Pi54
Cited by: 8
Author(s): Peng Ma, Lin X, Xingjia Xiang, Haiyan Ren, Xiaoqin Fan, Kegui Chen
Software Mentions: 1
Published: about 5 years ago

10.3390/biom11020281

Serum Acylcarnitines Associated with High Short-Term Mortality in Patients with Alcoholic Hepatitis
Cited by: 6
Author(s): Bei Gao, Josepmaría Argemi, R. Bataller, Bernd Schnabl
Software Mentions: 1
Published: over 5 years ago

10.1016/j.xpro.2021.100447

Application of high-throughput 5′P sequencing for the study of co-translational mRNA decay
Cited by: 4
Author(s): Yujie Zhang, Vicent Pelechano
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2018.01795

Genomic and Functional Characterization of Environmental Strains of SDS-Degrading Pseudomonas spp., Providing a Source of New Sulfatases
Cited by: 14
Author(s): Ewa M. Furmanczyk, Leszek Lipiński, Andrzej Dziembowski, Adam Sobczak
Software Mentions: 1
Published: about 8 years ago

10.1016/j.xpro.2021.100716

Protocol to generate and characterize biofouling transformants of a model marine diatom
Cited by: 0
Author(s): Weiqi Fu, Bushra Dohai, Diana Charles El Assal, Sarah Daakour, Amnah Alzahmi, David R. Nelson, Ashish Jaiswal, Alexandra Mystikou, Mehar Sultana, James Weston, Kourosh Salehi‐Ashtiani
Software Mentions: 1
Published: about 5 years ago

10.3390/biom11050764

Lack of Conserved miRNA Deregulation in HPV-Induced Squamous Cell Carcinomas
Cited by: 5
Author(s): Jaroslav Nunvář, Lucie Pagáčová, Zuzana Vojtěchová, Nayara Azevedo, Jana Šmahelová, Martina Saláková, Ruth Tachezy
Software Mentions: 1
Published: over 5 years ago

10.1093/schbul/sby017.541

F10. DIFFERENTIAL EXPRESSION OF MICRORNAS IN CEREBROSPINAL FLUID AND PLASMA SAMPLES IN SCHIZOPHRENIA
Cited by: 5
Author(s): Juan Gallego, Eric Alsop, Todd Lencz, Kendall Van Keuren‐Jensen, Anil K. Malhotra
Software Mentions: 1
Published: over 8 years ago

10.1126/sciadv.aau7314

Improving the metabolic fidelity of cancer models with a physiological cell culture medium
Cited by: 226
Author(s): Johan Vande Voorde, Tobias Ackermann, Nadja Pfetzer, David Sumpton, Gillian Mackay, Gabriela Kalna, Colin Nixon, Karen Blyth, Eyal Gottlieb, Saverio Tardito
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2020.02022

Amphotericin B Specifically Induces the Two-Component System LnrJK: Development of a Novel Whole-Cell Biosensor for the Detection of Amphotericin-Like Polyenes
Cited by: 11
Author(s): Ainhoa Revilla-Guarinos, Franziska Dürr, Philipp F. Popp, Michaela Döring, Thorsten Mascher
Software Mentions: 1
Published: about 6 years ago

10.1186/s13071-018-2932-3

Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus
Cited by: 24
Author(s): N. Pierre Charrier, Marjorie Couton, Maarten J. Voordouw, Olivier Rais, Axelle Durand-Hermouet, Caroline Hervet, Olivier Plantard, Claude Rispe
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2020.536865

Quorum Sensing System Affects the Plant Growth Promotion Traits of Serratia fonticola GS2
Cited by: 14
Author(s): Byung Kwon Jung, Jerald Conrad Ibal, Huy Quang Pham, Min‐Chul Kim, Gun-Seok Park, Sung-Jun Hong, Hyung Woo Jo, Chang Eon Park, Seung-Dae Choi, Young Hun Jung, Setu Bazie Tagele, Jae‐Ho Shin
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13071-018-2754-3

Transcriptome analysis of pig intestinal cell monolayers infected with Cryptosporidium parvum asexual stages
Cited by: 24
Author(s): Marzieh Ezzaty Mirhashemi, Farzad Noubary, Susan Chapman-Bonofiglio, Saul Tzipori, Gordon S. Huggins, Giovanni Widmer
Software Mentions: 1
Published: over 8 years ago

10.3390/nu12051464

Maternal Protein Restriction in Rats Alters the Expression of Genes Involved in Mitochondrial Metabolism and Epitranscriptomics in Fetal Hypothalamus
Cited by: 7
Author(s): Morgane Frapin, Simon Guignard, Dimitri Meistermann, Isabelle Grit, Valentine S. Moullé, Vincent Paillé, Patricia Parnet, Valérie Amarger
Software Mentions: 1
Published: over 6 years ago

10.1126/sciadv.abb3713

GADL1 is a multifunctional decarboxylase with tissue-specific roles in β-alanine and carnosine production
Cited by: 23
Author(s): Elaheh Mahootchi, Selina Cannon Homaei, Rune Kleppe, Ingeborg Winge, Tor‐Arne Hegvik, Ricardo Pérez, Christian Totland, Floriana Mogavero, Anne Baumann, Jeffrey Glennon, Hrvoje Miletić, Petri Kursula, Jan Haavik
Software Mentions: 1
Published: about 6 years ago

10.1126/sciadv.aba0353

Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community
Cited by: 23
Author(s): Tahmineh Khazaei, Rory L. Williams, Said R. Bogatyrev, John C. Doyle, Christopher S. Henry, Rustem F. Ismagilov
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2018.00366

The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial
Cited by: 68
Author(s): Shumeng Kou, Gilles Vincent, Emmanuel González, Frédéric E. Pitre, Michel Labrecque, Nicholas J. B. Brereton
Software Mentions: 1
Published: over 8 years ago

10.3390/biom11040525

Sphingosine Promotes Embryo Biomass in Upland Cotton: A Biochemical and Transcriptomic Analysis
Cited by: 3
Author(s): Li Wang, Xiaodong Suo, Yujie Liu, Chen Liu, Ming Luo
Software Mentions: 1
Published: over 5 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

10.3389/fmicb.2021.664598

Genomic and Transcriptomic Investigation of the Physiological Response of the Methylotroph Bacillus methanolicus to 5-Aminovalerate
Cited by: 3
Author(s): Carsten Haupka, Luciana Fernandes de Brito, Tobias Busche, Daniel Wibberg, Volker F. Wendisch
Software Mentions: 1
Published: over 5 years ago

10.1038/s41419-020-03060-1

Metabolic defects in splenic B cell compartments from patients with liver cirrhosis
Cited by: 2
Author(s): Man Huang, Xiaoju Liu, Haocheng Ye, Xinyang Zhao, Juanjuan Zhao, Yang Liu, Xiaomeng He, Mengmeng Qu, Jing Pan, Baidong Hou, Yue Cheng, Zhenwen Liu, Zhiwei Li, Lei Liu, Jian Sun, Shuye Zhang, Zheng Zhang
Software Mentions: 1
Published: almost 6 years ago

10.3390/biom10091296

Autophagy Inhibits Grass Carp Reovirus (GCRV) Replication and Protects Ctenopharyngodon idella Kidney (CIK) Cells from Excessive Inflammatory Responses after GCRV Infection
Cited by: 18
Author(s): Pengfei Chu, Libo He, Rong Huang, Lanjie Liao, Yongming Li, Zhu Zhang, Wei Hu, Yaping Wang
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0212031

Extraction-free whole transcriptome gene expression analysis of FFPE sections and histology-directed subareas of tissue
Cited by: 25
Author(s): Christy L. Trejo, Miloš Babić, Elliot Imler, Migdalia Gonzalez, Sergei I. Bibikov, Peter J. Shepard, Harper VanSteenhouse, Joanne M. Yeakley, Bruce Seligmann
Software Mentions: 1
Published: over 7 years ago

10.1186/s13071-020-04498-0

The Phlebotomus papatasi systemic transcriptional response to trypanosomatid-contaminated blood does not differ from the non-infected blood meal
Cited by: 6
Author(s): Megan A. Sloan, Jovana Sádlová, Tereza Leštinová, Mandy Sanders, James A. Cotton, Petr Volf, Petros Ligoxygakis
Software Mentions: 1
Published: over 5 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: about 8 years ago

10.1126/sciadv.abg5283

Human tumor microenvironment chip evaluates the consequences of platelet extravasation and combinatorial antitumor-antiplatelet therapy in ovarian cancer
Cited by: 35
Author(s): Biswajit Saha, Tanmay Mathur, James J. Tronolone, Mithil Chokshi, Giriraj Lokhande, Amirali Selahi, Akhilesh K. Gaharwar, Vahid Afshar-Kharghan, Anil K. Sood, Gang Bao, Abhishek Jain
Software Mentions: 1
Published: about 5 years ago

10.1128/JVI.02106-18

Investigating the Biological Relevance of <i>In Vitro</i> -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

10.3389/fmicb.2019.02074

The Transcription Unit Architecture of Streptomyces lividans TK24
Cited by: 23
Author(s): Yong Jae Lee, Namil Lee, Yu‐Jin Jeong, Soonkyu Hwang, Woori Kim, Suhyung Cho, Bernhard Ø. Palsson, Byung-Kwan Cho
Software Mentions: 1
Published: about 7 years ago

10.3390/cells10061543

Profiling of Extracellular Small RNAs Highlights a Strong Bias towards Non-Vesicular Secretion
Cited by: 8
Author(s): Helena Sork, Mariana Conceição, Giulia Corso, Joel Z. Nordin, Yi Xin Fiona Lee, Kaarel Krjutškov, Jakub Orzechowski Westholm, Pieter Vader, Marie J. Pauwels, Roosmarijn E. Vandenbroucke, Matthew J. Wood, Samir El Andaloussi, Imre Mäger
Software Mentions: 1
Published: over 5 years ago

10.1038/s41419-021-03606-x

TFAP2A potentiates lung adenocarcinoma metastasis by a novel miR-16 family/TFAP2A/PSG9/TGF-β signaling pathway
Cited by: 28
Author(s): Yanlu Xiong, Yangbo Feng, Jinbo Zhao, Jie Lei, Tianyun Qiao, Yongsheng Zhou, Qiang Lü, Tao Jiang, Lintao Jia, Han Ye
Software Mentions: 1
Published: over 5 years ago

10.1126/sciadv.abc8145

NSG-Pro mouse model for uncovering resistance mechanisms and unique vulnerabilities in human luminal breast cancers
Cited by: 9
Author(s): Yunguang Sun, Ning Yang, Fransiscus E. Utama, Sameer S. Udhane, Junling Zhang, Amy R. Peck, Alicia F Yanac, Katherine E. Duffey, John F. Langenheim, Vindhya Udhane, Guanjun Xia, Jess F. Peterson, Julie M. Jorns, Marja T. Nevalainen, Romain Rouet, Peter Schofield, Daniel Christ, Christopher J. Ormandy, Anne Rosenberg, Inna Chervoneva, Shirng‐Wern Tsaih, Michael J. Flister, Serge Y. Fuchs, Kay Uwe Wagner, Hallgeir Rui
Software Mentions: 1
Published: about 5 years ago

10.3390/biom11010021

Transcriptomic Analysis of Naïve Human Embryonic Stem Cells Cultured in Three-Dimensional PEG Scaffolds
Cited by: 4
Author(s): Christina McKee, Christina Brown, Shreeya Bakshi, Keegan Walker, Chhabi K. Govind, G. Rasul Chaudhry
Software Mentions: 1
Published: over 5 years ago

10.3390/biom11050677

Unravelling the Molecular Mechanisms Underlying the Protective Effect of Lactate on the High-Pressure Resistance of Listeria monocytogenes
Cited by: 5
Author(s): Cristina Serra-Castelló, Ilario Ferrocino, Anna Jofré, Luca Simone Cocolin, Sara Bover‐Cid, Kalliopi Rantsiou
Software Mentions: 1
Published: over 5 years ago

10.3390/biom11091395

A Set of 17 microRNAs Common for Brain and Cerebrospinal Fluid Differentiates Primary Central Nervous System Lymphoma from Non-Malignant Brain Tumors
Cited by: 3
Author(s): Maria Sromek, Grzegorz Rymkiewicz, Agnieszka Paziewska, Lukasz Szafron, Maria Kulecka, Michalina Zajdel, Mariusz Kulińczak, Michalina Dąbrowska, Aneta Bałabas, Zbigniew Bystydzieński, Magdalena Chechlińska, Jan Konrad Siwicki
Software Mentions: 1
Published: almost 5 years ago

10.1038/sdata.2016.101

ROCK signalling induced gene expression changes in mouse pancreatic ductal adenocarcinoma cells
Cited by: 7
Author(s): Nicola Rath, Gabriela Kalna, William Clark, Michael F. Olson
Software Mentions: 1
Published: almost 10 years ago

10.3390/ijms20246114

Deciphering Genetic Architecture of Adventitious Root and Related Shoot Traits in Populus Using QTL Mapping and RNA-Seq Data
Cited by: 24
Author(s): Peng Sun, Huixia Jia, Yahong Zhang, Jianbo Li, Mengzhu Lu, Jianjun Hu
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2020.00744

Genomic and Transcriptomic Study for Screening Genes Involved in the Limonene Biotransformation of Penicillium digitatum DSM 62840
Cited by: 10
Author(s): Lulu Zhang, Wen Huang, Yingying Zhang, Gang Fan, Jin He, Jianmin Ren, Zhi Li, Xiao Li, Siyi Pan
Software Mentions: 1
Published: over 6 years ago

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

10.3390/ijms20246206

Assessment of the Effects of Bisphenol A on Dopamine Synthesis and Blood Vessels in the Goldfish Brain
Cited by: 9
Author(s): Qing Wang, Fangmei Lin, Qi He, Xiaochun Liu, Shiqiang Xiao, Li Zheng, Huirong Yang, Haifeng Zhao
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41419-018-0453-9

Use of the XRCC2 promoter for in vivo cancer diagnosis and therapy
Cited by: 11
Author(s): Yu Chen, Zhen Li, Zhu Xu, Herman Tang, Wenbo Guo, Xian-He Sun, Wenjun Zhang, Jian Zhang, Xiaoping Wan, Ying Jiang, Zhiyong Mao
Software Mentions: 1
Published: over 8 years ago

10.1038/sdata.2017.172

Transcriptomic profiling of human breast and melanoma cells selected by migration through narrow constraints
Cited by: 6
Author(s): Dominika A. Rudzka, William Clark, Ann Hedley, Gabriela Kalna, Michael F. Olson
Software Mentions: 1
Published: almost 9 years ago

10.1167/iovs.62.7.24

Small RNA Sequencing of Aqueous Humor and Plasma in Patients With Primary Open-Angle Glaucoma
Cited by: 12
Author(s): Wouter Hubens, Julian Krauskopf, Henny J. M. Beckers, Jos Kleinjans, Carroll A.B. Webers, Theo G. M. F. Gorgels
Software Mentions: 1
Published: about 5 years ago

10.3390/ijerph17051471

Remediation of Crude Oil-Polluted Soil by the Bacterial Rhizosphere Community of Suaeda Salsa Revealed by 16S rRNA Genes
Cited by: 26
Author(s): Yanhua Yu, Yinghua Zhang, Na Zhao, Jia Guo, W. Wang and X.Q. Xu, Meihu Ma, Xiaoxia Li
Software Mentions: 1
Published: over 6 years ago

10.1038/sdata.2018.123

Transcriptional profiling of stellate ganglia from normotensive and spontaneously hypertensive rat strains
Cited by: 9
Author(s): Harvey Davis, Emma N. Bardsley, David J. Paterson
Software Mentions: 1
Published: about 8 years ago

10.1038/sdata.2018.170

Transcriptomic analyses of murine ventricular cardiomyocytes
Cited by: 14
Author(s): Morgan Yoann Edwin Chevalier, Sarah H. Vermij, Kurt Wyler, Ludovic Gillet, Irene Keller, Hugues Abriel
Software Mentions: 1
Published: about 8 years ago

10.1186/s13058-018-1087-7

Impact of obesity on breast cancer recurrence and minimal residual disease
Cited by: 51
Author(s): Brett L. Ecker, J. Y. Lee, Christopher J. Sterner, Aaron C. Solomon, Dhruv K. Pant, Fei Shen, Javier Peraza, Lauren A. Vaught, S V Mahendra, George K. Belka, Tien Chi Pan, Kathryn H. Schmitz, Lewis A. Chodosh
Software Mentions: 1
Published: over 7 years ago

10.3390/ijerph17155466

The Impact of the Deepwater Horizon Oil Spill upon Lung Health—Mouse Model-Based RNA-Seq Analyses
Cited by: 4
Author(s): Yaozhong Liu, Charles A. Miller, Yan Zhuang, Sudurika Mukhopadhyay, Shigeki Saito, Edward B. Overton, Gilbert F. Morris
Software Mentions: 1
Published: about 6 years ago

10.3390/biom11081206

Sex-Biased Expression of Pharmacogenes across Human Tissues
Cited by: 6
Author(s): Maria Laura Idda, Ilaria Campesi, Giovanni Fiorito, Andrea Vecchietti, Silvana Anna Maria Urru, Giuliana Solinas, Flavia Franconi, Matteo Floris
Software Mentions: 1
Published: about 5 years ago

10.3390/ijerph18042174

Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing
Cited by: 52
Author(s): Martina Rueca, A. Fontana, Barbara Bartolini, Pierluca Piselli, Antonio Mazzarelli, Massimiliano Copetti, Elena Binda, Francesco Perri, Cesare Ernesto Maria Gruber, Emanuele Nicastri, Luisa Marchioni, Giuseppe Ippolito, Maria Rosaria Capobianchi, Antonino Di, Valerio Pazienza
Software Mentions: 1
Published: over 5 years ago

10.3390/biom10010150

Identification of miRNAs Enriched in Extracellular Vesicles Derived from Serum Samples of Breast Cancer Patients
Cited by: 33
Author(s): Patrícia Midori Murobushi Ozawa, Evelyn Vieira, Débora S. Lemos, Ingrid L.M. Souza, Sı́lvio M. Zanata, Vânia C. S. Pankievicz, Thalita Regina Tuleski, Emanuel Maltempi de Souza, Pryscilla Fanini Wowk, Cı́cero de Andrade Urban, Fusakuni Kuroda, Rubens Silveira de Lima, Rodrigo Coutinho de Almeida, Daniela Fiori Gradia, Iglenir João Cavalli, Luciane R. Cavalli, Danielle Malheiros, Enilze M.S.F. Ribeiro
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms20246341

Genetic and Physiological Dissection of Photosynthesis in Barley Exposed to Drought Stress
Cited by: 26
Author(s): Agata Daszkowska‐Golec, Anna Collin, Krzysztof Sitko, Agnieszka Janiak, Hazem M. Kalaji, Iwona Szarejko
Software Mentions: 1
Published: almost 7 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: about 7 years ago

10.1186/s12964-019-0396-5

OMICs approaches-assisted identification of macrophages-derived MIP-1γ as the therapeutic target of botanical products TNTL in diabetic retinopathy
Cited by: 10
Author(s): Ning Wang, Cheng Zhang, Yu Xu, Sha Li, Hor‐Yue Tan, Wen Xia, Yibin Feng
Software Mentions: 1
Published: about 7 years ago

10.1093/jncics/pkz067

DNA Repair Biomarker for Lung Cancer Risk and its Correlation With Airway Cells Gene Expression
Cited by: 10
Author(s): Tamar Paz-Elizur, Yael Leitner‐Dagan, Kerstin B. Meyer, Barak Markus, Federico M. Giorgi, Martin O’Reilly, Hyun‐Jin Kim, Yentl Evgy, Ronen Fluss, Laurence S. Freedman, Robert C. Rintoul, Bruce A.J. Ponder, Zvi Livneh
Software Mentions: 1
Published: about 7 years ago

10.1038/s41597-019-0101-y

Transcriptome profiles of three Muscat table grape cultivars to dissect the mechanism of terpene biosynthesis
Cited by: 5
Author(s): Lina Sun, Baoqing Zhu, Xuanyin Zhang, Guojun Zhang, Ailing Yan, Huiling Wang, Xiaoyue Wang, Huini Xu
Software Mentions: 1
Published: over 7 years ago

10.3390/biom11091265

Attenuation of PITPNM1 Signaling Cascade Can Inhibit Breast Cancer Progression
Cited by: 0
Author(s): Zihao Liu, Yu Shi, Qun Lin, Wenqian Yang, Qing Luo, Yinghuan Cen, Juanmei Li, Xiaolin Fang, Wen Guo Jiang, Chang Gong
Software Mentions: 1
Published: about 5 years ago

10.1186/s13058-018-1034-7

Paternal malnutrition programs breast cancer risk and tumor metabolism in offspring
Cited by: 34
Author(s): Raquel Santana da Cruz, Erin Carney, Johan Clarke, Hong Cao, M. Idalia Cruz, Carlos Benitez, Lü Jin, Yi Fu, Zuolin Cheng, Yue Wang, Sônia de Assis
Software Mentions: 1
Published: about 8 years ago

10.3390/cells10010134

Neuron–Glia Interactions in Tuberous Sclerosis Complex Affect the Synaptic Balance in 2D and Organoid Cultures
Cited by: 13
Author(s): Stephanie Dooves, Arianne J.H. van Velthoven, Linda G Suciati, Vivi M. Heine
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2016.00175

Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis
Cited by: 60
Author(s): Lílian dos Santos Castro, Renato Graciano de Paula, Amanda Cristina Campos Antoniêto, Gabriela Félix Persinoti, Rafael Silva‐Rocha, Roberto do Nascimento Silva
Software Mentions: 1
Published: over 10 years ago

10.1038/s41597-019-0210-7

Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress
Cited by: 13
Author(s): Zhibo Li, Zeng XiaoYan, Jianwei Xu, Ruihai Zhao, Wei Yinong
Software Mentions: 1
Published: almost 7 years ago

10.3390/nu12051395

Dietary Protein, Fiber and Coffee Are Associated with Small Intestine Microbiome Composition and Diversity in Patients with Liver Cirrhosis
Cited by: 10
Author(s): Shehnaz K. Hussain, Tien S. Dong, Vatche G. Agopian, Joseph R. Pisegna, Francisco Durazo, Pedram Enayati, Vinay Sundaram, Jihane N. Benhammou, Mazen Noureddin, Gina Choi, Walid Ayoub, Venu Lagishetty, David Elashoff, Marc T. Goodman, Jonathan P. Jacobs
Software Mentions: 1
Published: over 6 years ago

10.1093/bib/bbz066

A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs
Cited by: 1
Author(s): Meik Kunz, Beat Wolf, Maximilian Fuchs, Jan Christoph, Xiaoyan Ke, Thomas Thum, David Atlan, Hans‐Ulrich Prokosch, Thomas Dandekar
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12863-017-0499-1

Transcriptome profiling of Arabian horse blood during training regimens
Cited by: 21
Author(s): Katarzyna Ropka‐Molik, Monika Stefaniuk‐Szmukier, Kacper Żukowski, Katarzyna Piórkowska, Artur Gurgul, Monika Bugno‐Poniewierska
Software Mentions: 1
Published: over 9 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 <sup>+</sup> 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

10.1186/s40425-019-0728-4

Targeting interferon signaling and CTLA-4 enhance the therapeutic efficacy of anti-PD-1 immunotherapy in preclinical model of HPV+ oral cancer
Cited by: 46
Author(s): Stephanie Dorta‐Estremera, Venkatesh L. Hegde, Ravaen Slay, Rachel Sun, Ananta V. Yanamandra, Courtney Nicholas, Sita S. Nookala, Gloria Sierra, Michael A. Curran, K. Jagannadha Sastry
Software Mentions: 1
Published: about 7 years ago

10.3389/fgene.2020.00888

Transcriptome Dynamics of the Inflorescence in Reciprocally Formed Allopolyploid Tragopogon miscellus (Asteraceae)
Cited by: 17
Author(s): Shengchen Shan, J. Lucas Boatwright, Xiaoxian Liu, André S. Chanderbali, Chao‐Nan Fu, Pamela S. Soltis, Douglas E. Soltis
Software Mentions: 1
Published: about 6 years ago

10.1186/s40425-019-0745-3

Domatinostat favors the immunotherapy response by modulating the tumor immune microenvironment (TIME)
Cited by: 44
Author(s): Anne Catherine Bretz, Ulrike Parnitzke, Kerstin Kronthaler, Tobias Dreker, René Bartz, Frank Hermann, Astrid Ammendola, Tanja Wulff, Svetlana Hamm
Software Mentions: 1
Published: almost 7 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

10.7717/peerj.8797

Pan-cancer systematic identification of lncRNAs associated with cancer prognosis
Cited by: 3
Author(s): Matthew Ung, Evelien Schaafsma, Daniel Mattox, George L. Wang, Chao Cheng
Software Mentions: 1
Published: over 6 years ago

10.3390/biom10040501

BET Inhibitors Synergize with Carfilzomib to Induce Cell Death in Cancer Cells via Impairing Nrf1 Transcriptional Activity and Exacerbating the Unfolded Protein Response
Cited by: 18
Author(s): Janakiram R. Vangala, Ajay Potluri, Senthil K. Radhakrishnan
Software Mentions: 1
Published: over 6 years ago

10.3390/cells10092308

Differential Expression Pattern of Goat Uterine Fluids Extracellular Vesicles miRNAs during Peri-Implantation
Cited by: 7
Author(s): Yanshe Xie, Guangbin Liu, Xupeng Zang, Qun Hu, Chunmei Zhou, Yaokun Li, Dewu Liu, Linjun Hong
Software Mentions: 1
Published: about 5 years ago

10.1038/srep11126

Co-existence of intact stemness and priming of neural differentiation programs in mES cells lacking Trim71
Cited by: 38
Author(s): Sibylle Mitschka, Thomas Ulas, Tobias Goller, Karin Schneider, Angela Egert, Jérôme Mertens, Oliver Brüstle, Hubert Schorle, Marc Beyer, Kathrin Klee, Jia Xue, Patrick Günther, Kevin Baßler, Joachim L. Schultze, Waldemar Kolanus
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0257417

Oscillating dietary crude protein concentrations increase N retention of calves by affecting urea-N recycling and nitrogen metabolism of rumen bacteria and epithelium
Cited by: 3
Author(s): Ningning Zhang, Zhanwei Teng, Pengtao Li, Tong Fu, Hongxia Lian, Linfeng Wang, Gao Teng-yun
Software Mentions: 1
Published: about 5 years ago

10.3389/fgene.2020.00491

Patterns of Sequence and Expression Diversification Associate Members of the PADRE Gene Family With Response to Fungal Pathogens
Cited by: 7
Author(s): Marie Didelon, Mehdi Khafif, Laurence Godiard, Adelin Barbacci, Sylvain Raffaele
Software Mentions: 1
Published: over 6 years ago

10.1038/srep13443

CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data
Cited by: 7
Author(s): Praveen Kumar, Thanh Hoang, Michael L. Robinson, Panagiotis A. Tsonis, Chun Liang
Software Mentions: 1
Published: about 11 years ago

10.1038/s41419-021-04078-9

Alcohol-abuse drug disulfiram targets pediatric glioma via MLL degradation
Cited by: 10
Author(s): Stefanie Meier, Sandra Cantilena, Maria Victoria Niklison Chirou, John Anderson, Darren Hargrave, Paolo Salomoni, Jasper de Boer, David Michod
Software Mentions: 1
Published: about 5 years ago

10.1186/s40425-019-0643-8

Tumor regression mediated by oncogene withdrawal or erlotinib stimulates infiltration of inflammatory immune cells in EGFR mutant lung tumors
Cited by: 20
Author(s): Deborah Ayeni, Braden Miller, Alexandra Kuhlmann, Ping‐Chih Ho, Camila Robles-Oteiza, Mmaserame Gaefele, Stellar Levy, Fernando J. de Miguel, Curtis J. Perry, Tianxia Guan, Gerald Krystal, William W. Lockwood, Daniel Zelterman, Robert J. Homer, Zongzhi Liu, Susan M. Kaech, Katerina Politi
Software Mentions: 1
Published: about 7 years ago

10.1038/srep14976

A high-throughput RNA-seq approach to profile transcriptional responses
Cited by: 23
Author(s): Gregory A Moyerbrailean, Gordon O Davis, Chris T. Harvey, Donovan Watza, Xiaoquan Wen, Roger Piqué-Regi, Francesca Luca
Software Mentions: 1
Published: almost 11 years ago

10.3389/fgene.2018.00230

Small Non-coding RNA Expression and Vertebrate Anoxia Tolerance
Cited by: 27
Author(s): Claire L. Riggs, Amanda Summers, Daniel E. Warren, Göran Nilsson, Sjannie Lefevre, W. Wesley Dowd, Sarah L. Milton, Jason E. Podrabsky
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms20246220

Translational Regulation of Pmt1 and Pmt2 by Bfr1 Affects Unfolded Protein O-Mannosylation
Cited by: 5
Author(s): Joan Castells-Ballester, Natalie Rinis, Ilgin Kotan, Lihi Gal, Daniela Bausewein, Ilia Kats, Ewa Zatorska, Günter Krämer, Bernd Bukau, Maya Schuldiner
Software Mentions: 1
Published: almost 7 years ago

10.1038/srep20316

Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention
Cited by: 21
Author(s): Samantha N. McNulty, Christina Strübe, Bruce A. Rosa, John Martin, Rahul Tyagi, Young Jun Choi, Qi Wang, Kymberlie H. Pepin, Xu Zhang, Philip Ozersky, Richard K. Wilson, Paul W. Sternberg, Robin B. Gasser, Makedonka Mitreva
Software Mentions: 1
Published: over 10 years ago

10.1038/srep21962

Improved lipids, diastolic pressure and kidney function are potential contributors to familial longevity: a study on 60 Chinese centenarian families
Cited by: 13
Author(s): Yonghan He, Shao-Yan Pu, Fu-Hui Xiao, Xiao‐Qiong Chen, Dongjing Yan, Yaowen Liu, Rong Lin, Xiaoping Liao, Qin Yu, Libin Yang, Xiaoxi Yang, Ming-Xia Ge, Ying Liu, Jianjun Jiang, Wei Cai, Qing‐Peng Kong
Software Mentions: 1
Published: over 10 years ago

10.1038/srep22416

RNA sequencing reveals region-specific molecular mechanisms associated with epileptogenesis in a model of classical hippocampal sclerosis
Cited by: 18
Author(s): André Schwambach Vieira, A. H. de Matos, Amanda Morato do Canto, Cristiane S. Rocha, Benilton Carvalho, Vinícius D'Ávila Bitencourt Pascoal, Braxton A. Norwood, Sebastian Bauer, Felix Rosenow, Rovílson Gilioli, Fernando Cendes, Íscia Lopes‐Cendes
Software Mentions: 1
Published: over 10 years ago

10.1038/srep22611

Dispersal of Bacillus subtilis and its effect on strawberry phyllosphere microbiota under open field and protection conditions
Cited by: 53
Author(s): Feng Wei, Xiaoping Hu, Xiangming Xu
Software Mentions: 1
Published: over 10 years ago

10.3390/nu12061586

Effect of a Multispecies Probiotic on Intestinal and Skin Colonization by Multidrug-Resistant Gram-Negative Bacteria in Patients in a Long-Term Care Facility: A Pilot Study
Cited by: 2
Author(s): Ines Zollner‐Schwetz, Monika Scarpatetti, Gerhard Pichler, Christian Pux, Ingeborg Klymiuk, Slave Trajanoski, Robert Krause
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms17101758

Stage-Wise Identification and Analysis of miRNA from Root-Knot Nematode Meloidogyne incognita
Cited by: 12
Author(s): Parthiban Subramanian, Inchan Choi, Vimalraj Mani, Jun Hyung Park, Sathiyamoorthy Subramaniyam, Kang-Hyun Choi, Ji Hyun Sim, Chang-Muk Lee, Jun Mo Koo, Bum-Soo Hahn
Software Mentions: 1
Published: almost 10 years ago

10.3389/fgene.2019.00315

Bovine Embryo-Secreted microRNA-30c Is a Potential Non-invasive Biomarker for Hampered Preimplantation Developmental Competence
Cited by: 25
Author(s): Xiaoyuan Lin, Evy Beckers, Séan Mc Cafferty, Yannick Gansemans, Katarzyna Szymanska, Krishna Chaitanya Pavani, João Portela Catani, Filip Van Nieuwerburgh, Dieter Deforce, Petra De Sutter, Ann Van Soom, Luc Peelman
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