bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3390/biom10050698

Exomes of Ductal Luminal Breast Cancer Patients from Southwest Colombia: Gene Mutational Profile and Related Expression Alterations
Cited by: 3
Author(s): Carolina Cortes-Urrea, Fernando Bueno-Gutiérrez, Melissa Solarte, Miguel Guevara-Burbano, Fabián Tobar-Tosse, Patricia E. Vélez-Varela, Juan Carlos Leiva, Guillermo Barreto, Jaime Velasco-Medina, Pedro Moreno, Javier De Las Rivas
Software Mentions: 2
Published: over 6 years ago

10.1038/s41388-020-01593-5

C-terminal truncated HBx initiates hepatocarcinogenesis by downregulating TXNIP and reprogramming glucose metabolism
Cited by: 45
Author(s): Yu Zhang, Qian Yan, Lanqi Gong, Hang Xu, Beilei Liu, Xiaona Fang, Dandan Yu, Lei Li, Ting Wei, Ying Wang, Ching Ngar Wong, Zhaojie Lyu, Ying Tang, Pak C. Sham, Xin‐Yuan Guan
Software Mentions: 2
Published: almost 6 years ago

10.1038/oncsis.2017.30

Epigenetic pathway inhibitors represent potential drugs for treating pancreatic and bronchial neuroendocrine tumors
Cited by: 33
Author(s): Kate E Lines, Mark Stevenson, P. Filippakopoulos, Susanne Müller, Helen Lockstone, Benjamin Wright, Simona Grozinsky‐Glasberg, Ashley Grossman, S. Knapp, David Buck, C. Bountra, R V Thakker
Software Mentions: 2
Published: over 9 years ago

10.18632/oncotarget.11455

Activation of HERV-K Env protein is essential for tumorigenesis and metastasis of breast cancer cells
Cited by: 89
Author(s): Fuling Zhou, Ming Li, Yongchang Wei, Kevin Lin, Yue Lu, Jianjun Shen, Gary L. Johanning, Feng Wang-Johanning
Software Mentions: 2
Published: about 10 years ago

10.3389/fonc.2021.608433

A Survival-Related Competitive Endogenous RNA Network of Prognostic lncRNAs, miRNAs, and mRNAs in Wilms Tumor
Cited by: 7
Author(s): Hengchen Liu, Mingzhao Zhang, Manyu Shi, Tingting Zhang, Zenan Zhang, QingBo Cui, Shaoyu Yang, ZhaoZhu Li
Software Mentions: 2
Published: over 5 years ago

10.1111/jcmm.16850

Knockdown of CENPK inhibits cell growth and facilitates apoptosis via PTEN‐PI3K‐AKT signalling pathway in gastric cancer
Cited by: 8
Author(s): Shusheng Wu, Lulu Cao, Lihong Ke, Ying Yan, Huiqin Luo, Xiucai Hu, Jingping Niu, Huimin Li, Huijun Xu, Wenju Chen, Yueyin Pan, Yong He
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0138162

Transcriptome Analysis of Poplar during Leaf Spot Infection with Sphaerulina spp.
Cited by: 29
Author(s): Adam Foster, G. Pelletier, Philippe Tanguay, Armand Séguin
Software Mentions: 2
Published: about 11 years ago

10.7717/peerj.11875

Importance of experimental information (metadata) for archived sequence data: case of specific gene bias due to lag time between sample harvest and RNA protection in RNA sequencing
Cited by: 1
Author(s): Tomoko Matsuda
Software Mentions: 2
Published: about 5 years ago

10.3389/fendo.2020.00510

Identification of a Prognostic 3-Gene Risk Prediction Model for Thyroid Cancer
Cited by: 8
Author(s): Haiping Zhao, Shiwei Zhang, Shijie Shao, Haixing Fang
Software Mentions: 2
Published: about 6 years ago

10.1242/jcs.167148

Dgcr8 and Dicer are essential for sex chromosome integrity during meiosis in males
Cited by: 39
Author(s): A Modzelewski, Stephanie Hilz, Elizabeth A. Crate, Caterina T. H. Schweidenback, Elizabeth A. Fogarty, Jennifer K. Grenier, Raimundo Freire, Paula E. Cohen, Andrew Grimson
Software Mentions: 2
Published: over 11 years ago

10.1007/s10911-017-9385-8

Menin Modulates Mammary Epithelial Cell Numbers in Bovine Mammary Glands Through Cyclin D1
Cited by: 6
Author(s): Kerong Shi, Xue Li, Honghui Li, Xueyan Lin, Zhiying Yan, Qiaoqiao Cao, Meng Zhao, Zhongjin Xu, Zhonghua Wang
Software Mentions: 2
Published: almost 9 years ago

10.7717/peerj.7946

High expression of HSP90 is associated with poor prognosis in patients with colorectal cancer
Cited by: 22
Author(s): Shuming Zhang, Shichao Guo, Zhangfu Li, Dan Li, Qimin Zhan
Software Mentions: 2
Published: about 7 years ago

10.7717/peerj.7360

A 3-mRNA-based prognostic signature of survival in oral squamous cell carcinoma
Cited by: 22
Author(s): Ruoyan Cao, Qiqi Wu, Qiulan Li, Meiling Yao, Hongbo Zhou
Software Mentions: 2
Published: over 7 years ago

10.1007/s00239-020-09951-3

Spatial Patterns of Gene Expression in Bacterial Genomes
Cited by: 13
Author(s): Daniella F. Lato, G. Brian Golding
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2017.02021

Transcript Profiling Identifies Gene Cohorts Controlled by Each Signal Regulating Trans-Differentiation of Epidermal Cells of Vicia faba Cotyledons to a Transfer Cell Phenotype
Cited by: 5
Author(s): Huiming Zhang, Simon Wheeler, Xue Xia, Kim Colyvas, Christina E. Offler, John W. Patrick
Software Mentions: 2
Published: almost 9 years ago

10.3390/cancers11081179

Papillary Thyroid Carcinoma Variants are Characterized by Co-dysregulation of Immune and Cancer Associated Genes
Cited by: 14
Author(s): Jaideep Chakladar, Wei Tse Li, Michael Bouvet, Eric Y. Chang, Jessica Wang‐Rodriguez, Weg M. Ongkeko
Software Mentions: 2
Published: about 7 years ago

10.1007/s00109-020-02020-8

3D culture conditions support Kaposi’s sarcoma herpesvirus (KSHV) maintenance and viral spread in endothelial cells
Cited by: 10
Author(s): Tatyana Dubich, Anne Dittrich, Kristine Bousset, Robert Geffers, Guntram Büsche, Mario Köster, Hansjörg Hauser, Thomas F. Schulz, Dagmar Wirth
Software Mentions: 2
Published: almost 6 years ago

10.1172/JCI144195

A therapeutic cancer vaccine delivers antigens and adjuvants to lymphoid tissues using genetically modified T cells
Cited by: 11
Author(s): Joshua R. Veatch, Naina Singhi, Shivani Srivastava, Julia Szeto, Brenda L. Jesernig, Sylvia M. Stull, Matthew Fitzgibbon, Megha Sarvothama, Sushma Yechan-Gunja, Scott James, Stanley R. Riddell
Software Mentions: 2
Published: about 5 years ago

10.3390/cancers13061433

Epigenetic Mechanisms Are Involved in the Oncogenic Properties of ZNF518B in Colorectal Cancer
Cited by: 3
Author(s): Francisco Gimeno-Valiente, Ángela L. Riffo‐Campos, Luís Torres, Noelia Tarazona, Gerardo López-Rodas, Luís Franco, Josefa Castillo
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers12113169

Id1 and PD-1 Combined Blockade Impairs Tumor Growth and Survival of KRAS-mutant Lung Cancer by Stimulating PD-L1 Expression and Tumor Infiltrating CD8+ T Cells
Cited by: 8
Author(s): Iosune Baraibar, Marta Cimavilla Román, María Rodríguez‐Remírez, Inés López, Anna Vilalta, Elizabeth Guruceaga, Margarita Ecay, María Collantes, Teresa Lozano, Diego Alignani, A. Puyalto, Carolina Oliver, Sergio Ortiz‐Espinosa, Haritz Moreno, María Dolores Torregrosa, Christian Rolfo, Christian Caglevic, David García-Ros, María Villalba-Esparza, Carlos de Andrea, Silvestre Vicent, Rubén Pı́o, Juan José Lasarte, Alfonso Calvo, Daniel Ajona, Ignacio Gil‐Bazo
Software Mentions: 2
Published: about 6 years ago

10.3390/cancers11050673

SIRT2 Contributes to the Resistance of Melanoma Cells to the Multikinase Inhibitor Dasatinib
Cited by: 19
Author(s): Iwona Karwaciak, Anna Sałkowska, Kaja Karaś, Marta Sobalska‐Kwapis, Aurelia Walczak‐Drzewiecka, Łukasz Pułaski, Dominik Strapagiel, Jarosław Dastych, Marcin Ratajewski
Software Mentions: 2
Published: over 7 years ago

10.3390/cancers13050957

Bifidobacterium Strain-Specific Enhances the Efficacy of Cancer Therapeutics in Tumor-Bearing Mice
Cited by: 23
Author(s): Young‐In Yoon, Gihyeon Kim, Bu‐Nam Jeon, Sungsoon Fang, Hansoo Park
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers13092009

Distinct mRNAs in Cancer Extracellular Vesicles Activate Angiogenesis and Alter Transcriptome of Vascular Endothelial Cells
Cited by: 5
Author(s): Pan Zhang, Su Bin Lim, Kuan Jiang, Ti Weng Chew, Boon Chuan Low, Chwee Teck Lim
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers12092674

Direct Antiviral Treatments for Hepatitis C Virus Have Off-Target Effects of Oncologic Relevance in Hepatocellular Carcinoma
Cited by: 11
Author(s): Catia Giovannini, Francesca Fornari, Valentina Indio, Davide Treré, Matteo Renzulli, Francesco Vasuri, Matteo Cescon, Matteo Ravaioli, Alessia Perrucci, Annalisa Astolfi, Fabio Piscaglia, Laura Gramantieri
Software Mentions: 2
Published: about 6 years ago

10.3390/cancers10110403

Simultaneous Inhibition of MEK and Hh Signaling Reduces Pancreatic Cancer Metastasis
Cited by: 13
Author(s): Dongsheng Gu, Hai Lin, Xiaoli Zhang, Qipeng Fan, Shaoxiong Chen, Safi Shahda, Yunlong Liu, Jie Sun, Jingwu Xie
Software Mentions: 2
Published: about 8 years ago

10.1016/j.cell.2017.11.042

Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner
Cited by: 497
Author(s): Morgane Sonia Thion, Donovan Low, Aymeric Silvin, Jinmiao Chen, Pauline Grisel, Jonas Schulte-Schrepping, Ronnie Blecher‐Gonen, Thomas Ulas, Paola Squarzoni, Guillaume Hoeffel, Fanny Coulpier, Eleni Siopi, Friederike S. David, Claus‐Jürgen Scholz, Shihui Foo, Josephine Lum, Arlaine Anne Amoyo, Anis Larbi, Michael Poidinger, Anne Buttgereit, Pierre-Marie Lledo, Melanie Greter, Jerry Kok Yen Chan, Ido Amit, Marc Beyer, Joachim L. Schultze, Andreas Schlitzer, Sven Pettersson, Florent Ginhoux, Sonia Garel
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.12828

Which statistical significance test best detects oncomiRNAs in cancer tissues? An exploratory analysis
Cited by: 34
Author(s): Wei Tang, Zhijun Liao, Quan Zou
Software Mentions: 2
Published: about 10 years ago

10.1007/s10565-020-09516-6

Estrogen receptor alpha (ERα)–mediated coregulator binding and gene expression discriminates the toxic ERα agonist diethylstilbestrol (DES) from the endogenous ERα agonist 17β-estradiol (E2)
Cited by: 10
Author(s): Aziza Hussein Bakheit Adam, L.H.J. de Haan, Ignacio Miro Estruch, Guido Hooiveld, Jochem Louisse, Ivonne M.C.M. Rietjens
Software Mentions: 2
Published: over 6 years ago

10.3390/biomedicines9081021

Utilizing Patient-Derived Epithelial Ovarian Cancer Tumor Organoids to Predict Carboplatin Resistance
Cited by: 11
Author(s): J Górski, Zhuwei Zhang, Joseph R. McCorkle, Jodi M. DeJohn, Chi Wang, Rachel W. Miller, Holly H. Gallion, Charles S. Dietrich, Frederick R. Ueland
Software Mentions: 2
Published: about 5 years ago

10.3390/cancers13092012

Inhibition of the Myocardin-Related Transcription Factor Pathway Increases Efficacy of Trametinib in NRAS-Mutant Melanoma Cell Lines
Cited by: 5
Author(s): Kathryn M. Appleton, Charuta C. Palsuledesai, Sean A. Misek, Maja K. Blake, Joseph Zagorski, Kathleen A. Gallo, Thomas S. Dexheimer, Richard R. Neubig
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0108200

Comparative Transcriptome Analysis Reveals the Genetic Basis of Skin Color Variation in Common Carp
Cited by: 72
Author(s): Yanliang Jiang, Songhao Zhang, Jian Xu, Jianxin Feng, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Peng Xu
Software Mentions: 2
Published: about 12 years ago

10.3390/jcm8111772

A CTC-Cluster-Specific Signature Derived from OMICS Analysis of Patient-Derived Xenograft Tumors Predicts Outcomes in Basal-Like Breast Cancer
Cited by: 35
Author(s): Hariprasad Thangavel, Carmine De Angelis, Suhas Vasaikar, Raksha Bhat, Mohit Kumar Jolly, Chandandeep Nagi, Chad J. Creighton, Ken Chen, Lacey E. Dobrolecki, Jason T. George, Tanya Kumar, Noor Mazin Abdulkareem, Sufeng Mao, Agostina Nardone, Mothaffar F. Rimawi, C. Kent Osborne, Michael T. Lewis, Herbert Levine, Bing Zhang, Rachel Schiff, Mario Giuliano, Meghana V. Trivedi
Software Mentions: 2
Published: about 7 years ago

10.18632/oncotarget.22405

RNA-sequencing reveals genome-wide long non-coding RNAs profiling associated with early development of diabetic nephropathy
Cited by: 12
Author(s): Wanxin Tang, Dongmei Zhang, Xiaoke Ma
Software Mentions: 2
Published: almost 9 years ago

10.7717/peerj.6991

Functional analysis of lncRNAs based on competitive endogenous RNA in tongue squamous cell carcinoma
Cited by: 18
Author(s): Yidan Song, Yihua Pan, Jun Li
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pntd.0005826

The microbiome in urogenital schistosomiasis and induced bladder pathologies
Cited by: 36
Author(s): Adewale Adebayo, Mangesh V. Suryavanshi, Shrikant Bhute, Atinuke M Agunloye, Raphael D. Isokpehi, Chiaka I. Anumudu, Yogesh S. Shouche
Software Mentions: 2
Published: about 9 years ago

10.1038/s41418-020-0541-0

Targeting triple-negative breast cancers with the Smac-mimetic birinapant
Cited by: 27
Author(s): Najoua Lalaoui, Delphine Mérino, Göknur Giner, François Vaillant, Diep Chau, Lin Liu, Tobias Kratina, Bhupinder Pal, James R. Whittle, Nima Etemadi, Jean Berthelet, Julius Gräsel, Cathrine Hall, Matthew E. Ritchie, Matthias Ernst, Gordon K. Smyth, David Vaux, Jane E. Visvader, Geoffrey J. Lindeman, John Silke
Software Mentions: 2
Published: over 6 years ago

10.3389/fonc.2020.00316

Promoter-Level Transcriptome Identifies Stemness Associated With Relatively High Proliferation in Pancreatic Cancer Cells
Cited by: 0
Author(s): Ru Chen, Aiko Sugiyama, Naoyuki Kataoka, Masahiro Sugimoto, Shoko Yokoyama, Akira Fukuda, Shigeo Takaishi, Hiroshi Seno
Software Mentions: 2
Published: over 6 years ago

10.1038/s41418-020-00653-3

HDAC inhibition ameliorates cone survival in retinitis pigmentosa mice
Cited by: 21
Author(s): Marijana Samardzija, Andrea Corna, Raquel Gómez‐Sintes, Mohamed Ali Jarboui, Angela Armento, Jérôme E. Roger, Eleni Petridou, Wadood Haq, François Paquet-Durand, Eberhart Zrenner, Pedro de la Villa, Günther Zeck, Christian Grimm, Patricia Boya, Marius Ueffing, Dragana Trifunović
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0223554

An integrated epigenome and transcriptome analysis identifies PAX2 as a master regulator of drug resistance in high grade pancreatic ductal adenocarcinoma
Cited by: 7
Author(s): Imlimaong Aier, Rahul Semwal, Aiindrila Dhara, Nirmalya Sen, Pritish Kumar Varadwaj
Software Mentions: 2
Published: about 7 years ago

10.1038/s41419-020-2435-y

CCL5 derived from tumor-associated macrophages promotes prostate cancer stem cells and metastasis via activating β-catenin/STAT3 signaling
Cited by: 131
Author(s): Renlun Huang, Shengqi Wang, Neng Wang, Yifeng Zheng, Jianfu Zhou, Bowen Yang, Xuan Wang, Juping Zhang, Lang Guo, Shusheng Wang, Zhiqiang Chen, Zhiyu Wang, Shulin Xiang
Software Mentions: 2
Published: over 6 years ago

10.3390/jcm10184095

Biological Mechanism(s) Underpinning the Association between Antipsychotic Drugs and Weight Gain
Cited by: 8
Author(s): Bruna Panizzutti, Chiara C. Bortolasci, Briana Spolding, Srisaiyini Kidnapillai, Timothy Connor, Mark F. Richardson, Trang T. T. Truong, Zoe Liu, Laura J. Gray, Jee Hyun Kim, Olivia Dean, Michael Berk, Ken Walder
Software Mentions: 2
Published: about 5 years ago

10.1038/s41419-021-04005-y

ETV7 regulates breast cancer stem-like cell features by repressing IFN-response genes
Cited by: 11
Author(s): Laura Pezzè, Erna Marija Meškytė, Mattia Forcato, Stefano Pontalti, Kalina Aleksandra Badowska, Dario Rizzotto, Ira Skvortsova, Silvio Bicciato, Yari Ciribilli
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers12020353

Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of Cancer
Cited by: 22
Author(s): Martin Metzenmacher, Renáta Váraljai, Balázs Hegedűs, Igor Cima, Jan Förster, Alexander Schramm, Björn Scheffler, Peter A. Horn, Christoph A. Klein, Tibor Szarvas, Henning Reis, Nicola Bielefeld, Alexander Roesch, Clemens Aigner, Volker Kunzmann, Marcel Wiesweg, Jens T. Siveke, Martin Schüler, Smiths Lueong
Software Mentions: 2
Published: over 6 years ago

10.18632/oncotarget.22732

Survival prediction of kidney renal papillary cell carcinoma by comprehensive LncRNA characterization
Cited by: 19
Author(s): Huihua Lan, Jiang‐Hui Zeng, Gang Chen, Huayi Huang
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41419-021-04076-x

Toll-like receptor 4 is a master regulator for colorectal cancer growth under high-fat diet by programming cancer metabolism
Cited by: 6
Author(s): Xianjing Hu, Sarwat Fatima, Minting Chen, Keyang Xu, Chunhua Huang, Rui Gong, Tao Su, Hoi Leong Xavier Wong, Zhaoxiang Bian, Hiu Yee Kwan
Software Mentions: 2
Published: about 5 years ago

10.1038/s41419-019-1938-x

TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP
Cited by: 22
Author(s): Janin Knop, Lisanne M. Spilgies, Stefanie Rufli, Ramona Reinhart, Lazaros Vasilikos, Monica Yabal, Erika Owsley, Philipp J. Jost, Rebecca Marsh, Harald Wajant, Mark D. Robinson, Thomas Kaufmann, Wendy Wei-Lynn Wong
Software Mentions: 2
Published: about 7 years ago

10.3389/fpls.2021.700479

Biochar-Enhanced Resistance to Botrytis cinerea in Strawberry Fruits (But Not Leaves) Is Associated With Changes in the Rhizosphere Microbiome
Cited by: 8
Author(s): Caroline De Tender, Bart Vandecasteele, Bruno Verstraeten, Sarah Ommeslag, Tina Kyndt, Jane Debode
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pntd.0008341

Expansions of chemosensory gene orthologs among selected tsetse fly species and their expressions in Glossina morsitans morsitans tsetse fly
Cited by: 8
Author(s): Joy M. Kabaka, Benson M. Wachira, Clarence M. Mang’era, Martin K. Rono, Ahmed Hassanali, Sylvance Okoth, Vincent O. Oduol, Rosaline W. Macharia, Grace Murilla, Paul O. Mireji
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2021.738261

Multi-Omics Analyses Reveal the Regulatory Network and the Function of ZmUGTs in Maize Defense Response
Cited by: 5
Author(s): Chunxia Ge, Yi-Ge Wang, Shouping Lu, Xiang Zhao, Bing-Kai Hou, Peter Balint‐Kurti, Guan‐Feng Wang
Software Mentions: 2
Published: about 5 years ago

10.18632/oncotarget.21918

Integrated analysis of mRNA and miRNA expression profiles in livers of Yimeng black pigs with extreme phenotypes for backfat thickness
Cited by: 8
Author(s): Wentong Li, Yalan Yang, Ying Liu, Shuai Liu, Xiuxiu Li, Ying‐Ping Wang, Yanmin Zhang, Hui Tang, Rong Zhou, Kui Li
Software Mentions: 2
Published: about 9 years ago

10.1042/BSR20190996

Integrated analysis of a competing endogenous RNA network in renal cell carcinoma using bioinformatics tools
Cited by: 14
Author(s): Weidong Jiang, Zhihua Ye
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.12114

Expression and prognosis of CDC45 in cervical cancer based on the GEO database
Cited by: 7
Author(s): Zikang He, Xiaojin Wang, Zhiming Yang, Ying Jiang, Luhui Li, Zheyao Song, Jiahui Wan, Jiangbo Shu, Naiwen Zhang, Rongjun Cui
Software Mentions: 2
Published: about 5 years ago

10.1186/s12967-019-02151-8

Two precision medicine predictive tools for six malignant solid tumors: from gene-based research to clinical application
Cited by: 19
Author(s): Zhiqiao Zhang, Tingshan He, Liwen Huang, Yanling Ouyang, Jing Li, Yiyan Huang, Peng Wang, Jianqiang Ding
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.34114

Transcriptomic analyses reveal rhythmic and CLOCK-driven pathways in human skeletal muscle
Cited by: 81
Author(s): Laurent Perrin, Ursula Loizides‐Mangold, Stéphanie Chanon, Cédric Gobet, Nicolas Hulo, Laura Isenegger, Benjamin D. Weger, Eugenia Migliavacca, Aline Charpagne, James A. Betts, Jean–Philippe Walhin, Iain Templeman, Keith Stokes, Dylan Thompson, Kostas Tsintzas, M. Robert, Cédric Howald, Howard Riezman, Jérôme N. Feige, Leonidas G. Karagounis, Jeanne D. Johnston, Emmanouil T. Dermitzakis, Frédéric Gachon, Étienne Lefai, Charna Dibner
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-25605-3

Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle
Cited by: 45
Author(s): Robert Mukiibi, Michael Vinsky, Kate Keogh, Carolyn Fitzsimmons, Paul Stothard, Sinéad M. Waters, Changxi Li
Software Mentions: 2
Published: over 8 years ago

10.3389/fonc.2021.625271

Establishment of a Novel Risk Score System of Immune Genes Associated With Prognosis in Esophageal Carcinoma
Cited by: 9
Author(s): Zhenghua Fei, Rongrong Xie, Zhi Chen, Junhui Xie, Yuyang Gu, Yue Zhou, Tongpeng Xu
Software Mentions: 2
Published: over 5 years ago

10.3389/fncel.2019.00310

Comprehensive Evaluation of White Matter Damage and Neuron Death and Whole-Transcriptome Analysis of Rats With Chronic Cerebral Hypoperfusion
Cited by: 9
Author(s): Wenxian Li, Di Wei, Jianye Liang, Xiaomei Xie, Kangping Song
Software Mentions: 2
Published: over 7 years ago

10.1038/s41419-019-1696-9

FGF1ΔHBS ameliorates chronic kidney disease via PI3K/AKT mediated suppression of oxidative stress and inflammation
Cited by: 48
Author(s): Dezhong Wang, Mengyun Jin, Xinyu Zhao, Tianyang Zhao, Wei Lin, Zhengle He, Miaojuan Fan, Wei Jin, Jie Zhou, Lingwei Jin, Chao Zheng, Hui Jin, Yushuo Zhao, Xiaokun Li, Ying Lei, Yang Wang, Guo‐Qing Zhu, Zhifeng Huang
Software Mentions: 2
Published: over 7 years ago

10.3389/fonc.2020.575737

Combination of T-Cell Bispecific Antibodies With PD-L1 Checkpoint Inhibition Elicits Superior Anti-Tumor Activity
Cited by: 25
Author(s): Johannes Sam, Sara Colombetti, Tanja Fauti, Andreas Roller, Marlene Biehl, Linda Fahrni, Valeria Nicolini, Mario Perro, Tapan K. Nayak, Esther Bommer, Anne Schoenle, Μaria Karagianni, Marine Le Clech, Nathalie Steinhoff, Christian Klein, Pablo Umaña, Marina Bacac
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41419-020-2589-7

BCL-xL/BCL2L1 is a critical anti-apoptotic protein that promotes the survival of differentiating pancreatic cells from human pluripotent stem cells
Cited by: 19
Author(s): Larry Sai Weng Loo, Andreas Alvin Purnomo Soetedjo, Hwee Hui Lau, Natasha Hui Jin Ng, Soumita Ghosh, Linh Nguyen, Vidhya G. Krishnan, Hyungwon Choi, Xavier Roca, Shawn Hoon, Adrian Kee Keong Teo
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.52063

The genetic basis of aneuploidy tolerance in wild yeast
Cited by: 59
Author(s): James Hose, Leah E. Escalante, Katie J. Clowers, H Auguste Dutcher, DeElegant Robinson, Venera Bouriakov, Joshua J. Coon, Evgenia Shishkova, Audrey P. Gasch
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.59795

Amino acid synthesis loss in parasitoid wasps and other hymenopterans
Cited by: 0
Author(s): Xinhai Ye, Shijiao Xiong, Ziwen Teng, Yi Yang, Jiale Wang, Kaili Yu, Huizi Wu, Mei Yang, Zhichao Yan, Sammy Cheng, Chuanlin Yin, Fang Wang, Hongwei Yao, Qi Fang, Qisheng Song, John H. Werren, Gōngyín Yè, Fēi Li
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.10204

Transcriptome analysis of diploid and triploid Populus tomentosa
Cited by: 3
Author(s): Bin Wen, Xiaozhen Liu, Zhiming Zhang, Hanyao Zhang
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-018-25845-3

De novo characterization of Phenacoccus solenopsis transcriptome and analysis of gene expression profiling during development and hormone biosynthesis
Cited by: 13
Author(s): Shashi Arya, Yogeshwar Vikram Dhar, Santosh Kumar Upadhyay, Mehar Hasan Asif, Praveen Chandra Verma
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-26035-x

Computational identification and validation of alternative splicing in ZSF1 rat RNA-seq data, a preclinical model for type 2 diabetic nephropathy
Cited by: 10
Author(s): Chi Zhang, Ken Dower, Baohong Zhang, Robert V. Martinez, Lih-Ling Lin, Shanrong Zhao
Software Mentions: 2
Published: over 8 years ago

10.1038/s41419-020-2704-9

Reduced replication origin licensing selectively kills KRAS-mutant colorectal cancer cells via mitotic catastrophe
Cited by: 4
Author(s): Bastian Gastl, Kathleen Klotz-Noack, Bertram Klinger, Sylvia Ispasanie, Krenoula Hani Fouad Salib, Johannes Zuber, Soulafa Mamlouk, Natalie Bublitz, Nils Blüthgen, David Horst, Markus Morkel, Reinhold Schäfer, Christine Sers
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2021.666660

Comparative Transcriptome Analysis of Salt Stress-Induced Leaf Senescence in Medicago truncatula
Cited by: 15
Author(s): Shihao Dong, Lijun Sang, Hong Xie, Maofeng Chai, Zeng‐Yu Wang
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.8684

Comprehensive phenotyping and transcriptome profiling to study nanotoxicity inC. elegans
Cited by: 10
Author(s): Charles Viau, Orçun Haçarız, Farial Karimian, Jianguo Xia
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.9704

miR-224, miR-147b and miR-31 associated with lymph node metastasis and prognosis for lung adenocarcinoma by regulating PRPF4B, WDR82 or NR3C2
Cited by: 12
Author(s): Yan Wang, Shengtao Shang, Kun Yu, Hongbin Sun, Wenrui Ma, Wei Zhao
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41419-018-1296-0

Transcriptome profiling of caspase-2 deficient EμMyc and Th-MYCN mouse tumors identifies distinct putative roles for caspase-2 in neuronal differentiation and immune signaling
Cited by: 4
Author(s): Loretta Dorstyn, Emily Hackett-Jones, Andrej Nikolic, Murray D. Norris, Yoon Pin Lim, John Toubia, Michelle Haber, Sharad Kumar
Software Mentions: 2
Published: almost 8 years ago

10.7717/peerj.3696

RNA expression and disease tolerance are associated with a “keystone mutation” in the ochre sea star Pisaster ochraceus
Cited by: 4
Author(s): V. Katelyn Chandler, John P. Wares
Software Mentions: 2
Published: about 9 years ago

10.3389/fgene.2020.562937

Transcriptomic Analysis Reveals Important Roles of Lignin and Flavonoid Biosynthetic Pathways in Rice Thermotolerance During Reproductive Stage
Cited by: 19
Author(s): Zhenzhen Cai, Fengyu He, Xin Feng, Tom Liang, Hongwei Wang, Shuangcheng Ding, Xiaohai Tian
Software Mentions: 2
Published: about 6 years ago

10.1038/s41419-018-0869-2

LncRNA MIR100HG promotes cell proliferation in triple-negative breast cancer through triplex formation with p27 loci
Cited by: 105
Author(s): Shaowei Wang, Ke Hao, Honglei Zhang, Yujie Ma, Lei Ao, Li Zou, Qin Yang, Huiping Zhu, Jianyun Nie, Chen Wu, Baowei Jiao
Software Mentions: 2
Published: over 8 years ago

10.1038/s41419-020-2372-9

Myofibroblast induces hepatocyte-to-ductal metaplasia via laminin–ɑvβ6 integrin in liver fibrosis
Cited by: 15
Author(s): Ting Xu, Zhijie Lu, Zhuanglong Xiao, Fang Liu, Yuhua Chen, Zhijun Wang, Shenghua Zhu, Yufang Song
Software Mentions: 2
Published: over 6 years ago

10.3390/cancers12040786

A Novel Role for the Tumor Suppressor Gene ITF2 in Tumorigenesis and Chemotherapy Response
Cited by: 9
Author(s): Olga Pernía, Ana Sastre-Perona, Carlos Rodriguez-Antolín, Álvaro García-Guede, María Palomares‐Bralo, Rocío Rosas, Darío Sánchez-Cabrero, Patricia Cruz, Carmen Rodrı́guez, MDolores Diestro, Rubén Martín‐Arenas, Verónica Pulido, Pilar Santisteban, Javier de Castro, Olga Vera, Inmaculada Ibáñez de Cáceres
Software Mentions: 2
Published: over 6 years ago

10.18632/oncotarget.23716

Novel mutational landscapes and expression signatures of lung squamous cell carcinoma
Cited by: 17
Author(s): Donghai Xiong, Jing Pan, Yuxin Yin, Hui Jiang, Éva Szabó, Ronald A. Lubet, Yian Wang, Ming You
Software Mentions: 2
Published: almost 9 years ago

10.3389/fonc.2020.554138

Identification of Immune-Related Therapeutically Relevant Biomarkers in Breast Cancer and Breast Cancer Stem Cells by Transcriptome-Wide Analysis: A Clinical Prospective Study
Cited by: 5
Author(s): Linbang Wang, Wei Liu, Jingkun Liu, Yuanyuan Wang, Jiaojiao Tai, Xuedong Yin, Jinxiang Tan
Software Mentions: 2
Published: over 5 years ago

10.1038/s41420-020-00295-x

The prognostic value of six survival-related genes in bladder cancer
Cited by: 7
Author(s): Songbai Cheng, Jiang Zhou, Jing Xiao, Huiling Guo, Zhengrong Wang, Yuhui Wang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41420-020-00392-x

Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae
Cited by: 5
Author(s): Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
Software Mentions: 2
Published: almost 6 years ago

10.1128/IAI.00385-17

Variation in the Early Host-Pathogen Interaction of Bovine Macrophages with Divergent Mycobacterium bovis Strains in the United Kingdom
Cited by: 15
Author(s): Kirsty Jensen, Iain J. Gallagher, Nicholas Johnston, Michael Welsh, Robin Skuce, J. L. Williams, Elizabeth Glass
Software Mentions: 2
Published: over 8 years ago

10.1038/s41420-021-00560-7

Identification of a seven-long non-coding RNA signature associated with Jab1/CSN5 in predicting hepatocellular carcinoma
Cited by: 7
Author(s): Weijie Ma, Ye Yao, Gang Xu, Xiaoling Wu, Jinghua Liu, Ganggang Wang, Xi Chen, Kunlei Wang, Yirang Chen, Yonghua Guo, Yongsheng Li, Deli Tan, Hui Guo, Zhisu Liu, Yufeng Yuan, François X. Claret
Software Mentions: 2
Published: over 5 years ago

10.1155/2017/8682057

Identifying the Genes Responsible for Iron-Limited Condition in Riemerella anatipestifer CH-1 through RNA-Seq-Based Analysis
Cited by: 11
Author(s): Mafeng Liu, Huang Mi, Dekang Zhu, Mingshu Wang, Renyong Jia, Shun Chen, Kunfeng Sun, Qiao Yang, Ying Wu, Francis Biville, Anchun Cheng
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-018-27019-7

Immunome differences between porcine ileal and jejunal Peyer’s patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues
Cited by: 12
Author(s): Tatiana Maroilley, Mustapha Berri, Gaëtan Lemonnier, Diane Esquerré, Claire Chevaleyre, Sandrine Melo, François Meurens, Jean‐Luc Coville, Jean Jacques Leplat, Andrea Rau, Bertrand Bed’Hom, Silvia Vincent‐Naulleau, Marie‐José Mercat, Yvon Billon, Patricia Lepage, Claire Rogel–Gaillard, Jordi Estellé
Software Mentions: 2
Published: over 8 years ago

10.1128/IAI.00686-19

Cutaneous Immunoprofiles of Three Spotted Fever Group Rickettsia Cases
Cited by: 5
Author(s): Na Jia, Hongbo Liu, Yuan-Chun Zheng, Wenqiang Shi, Ran Wei, Yan-Li Chu, Nianzhi Ning, Bao-Gui Jiang, Rui-Ruo Jiang, Tao Li, Qiu-Bo Huo, Cai Bian, Xiong Liu, Yi Sun, Lian-Feng Li, Qian Wang, Wei Wei, Yawei Wang, Frans Jongejan, Jia-Fu Jiang, Jie Song, Hui Wang, Wu‐Chun Cao
Software Mentions: 2
Published: over 6 years ago

10.14252/foodsafetyfscj.D-20-00032

Effect of Transgenic Rootstock Grafting on the Omics Profiles in Tomato
Cited by: 9
Author(s): Hiroaki Kodama, Taira Miyahara, Taichi Oguchi, Takashi Tsujimoto, Yoshihiro Ozeki, Toshiki Ogawa, Yube Yamaguchi, Daisaku Ohta
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.11714

Short-term high fat diet alters genes associated with metabolic and vascular dysfunction during adolescence in rats: a pilot study
Cited by: 1
Author(s): Alex E. Mohr, Rebecca A. Reiss, Monique Beaudet, Johnny A. Sena, Jay S. Naik, Benjimen R. Walker, Karen L. Sweazea
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2020.01012

Dual-mTOR Inhibitor Rapalink-1 Reduces Prostate Cancer Patient-Derived Xenograft Growth and Alters Tumor Heterogeneity
Cited by: 19
Author(s): Federico La Manna, Marta De Menna, Nikhil Patel, Sofia Karkampouna, Maria Rosaria De Filippo, Irena Klima, Peter Kloen, Lijkele Beimers, George N. Thalmann, Rob C.M. Pelger, Estela Jacinto, Marianna Kruithof-de Julio
Software Mentions: 2
Published: over 6 years ago

10.3390/foods10050936

Transcriptomic Analysis of Pseudomonas aeruginosa Response to Pine Honey via RNA Sequencing Indicates Multiple Mechanisms of Antibacterial Activity
Cited by: 16
Author(s): Ioannis Kafantaris, Christina Tsadila, Marios Nikolaidis, Eleni Tsavea, Tilemachos G. Dimitriou, Ioannis Iliopoulos, Grigoris D. Amoutzias, Dimitris Mossialos
Software Mentions: 2
Published: over 5 years ago

10.3389/fnagi.2021.645649

Transcriptome Analysis of Microglia Reveals That the TLR2/IRF7 Signaling Axis Mediates Neuroinflammation After Subarachnoid Hemorrhage
Cited by: 5
Author(s): Shenbin Xu, Shuhao Mei, Jianing Lu, Haijian Wu, Xiao Dong, Ligen Shi, Jingyi Zhou, Jianmin Zhang
Software Mentions: 2
Published: over 5 years ago

10.1042/BSR20200487

The transcription factor USF1 promotes glioma cell invasion and migration by activating lncRNA HAS2-AS1
Cited by: 21
Author(s): Juntong Wang, Jingshun Gu, Aiwu You, Jun Li, Yuyan Zhang, Guomin Rao, Xuehua Ge, Kun Zhang, Jianfeng Li, Xiaohui Lu, Qianchao Wang, Tzu Chen Lin, Ling Cheng, Meiying Zhu, Xiaotang Wu, Dongchun Wang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-27646-0

Independent regulation of Plasmodium falciparum rif gene promoters
Cited by: 5
Author(s): Rosana Beatriz Duque Araujo, Tatiane Macedo Silva, Charlotte Kaiser, Gabriela Fernandes Leite, Diego Peres Alonso, Paulo Eduardo Martins Ribolla, Gerd Wunderlich
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.6949

Comprehensive transcriptional profiling of aging porcine liver
Cited by: 6
Author(s): Jianning Chen, Qin Zou, Daojun Lv, Muhammad Ali Raza, Xue Wang, Chen Yan, Xiaoyu Xi, Peilin Li, Anxiang Wen, Li Zhu, Guoqing Tang, Mingzhou Li, Xuewei Li, Yanzhi Jiang
Software Mentions: 2
Published: over 7 years ago

10.1128/IAI.00270-21

A Trifecta of New Insights into Ovine Footrot for Infection Drivers, Immune Response, and Host-Pathogen Interactions
Cited by: 2
Author(s): Adam Blanchard, Ceri Staley, Laurence Shaw, Sean Wattegedera, Christina‐Marie Baumbach, Jule Kristin Michler, Catrin S. Rutland, Charlotte Back, Nerissa Newbold, Gary Entrican, Sabine Tötemeyer
Software Mentions: 2
Published: about 5 years ago

10.3390/cancers11020208

ORAI1 and ORAI3 in Breast Cancer Molecular Subtypes and the Identification of ORAI3 as a Hypoxia Sensitive Gene and a Regulator of Hypoxia Responses
Cited by: 42
Author(s): Iman Azimi, Michael J. G. Milevskiy, Silke B. Chalmers, Kunsala T. D. S. Yapa, Mélanie Robitaille, Christopher Henry, Gregory J. Baillie, Erik W. Thompson, Sarah J. Roberts‐Thomson, Gregory R. Monteith
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.7732

Liver slice culture as a model for lipid metabolism in fish
Cited by: 7
Author(s): Thomas Nelson Harvey, Simen Rød Sandve, Yang Jin, Jon Olav Vik, Jacob Torgersen
Software Mentions: 2
Published: about 7 years ago

10.3390/cancers12092541

Combination Treatment with GSK126 and Pomalidomide Induces B-Cell Differentiation in EZH2 Gain-of-Function Mutant Diffuse Large B-Cell Lymphoma
Cited by: 5
Author(s): Sungryul Park, Seunghyun Jo, Jong-Hwan Kim, Seon‐Young Kim, Jae Du Ha, Jong Yeon Hwang, Myeong Youl Lee, Jong Soon Kang, Tae-Su Han, Sung Goo Park, Sunhong Kim, Byoung Chul Park, Jeong-Hoon Kim
Software Mentions: 2
Published: about 6 years ago

10.3389/fbioe.2018.00019

Phosphoproteome of the Oleaginous Green Alga, Chlorella vulgaris UTEX 395, under Nitrogen-Replete and -Deplete Conditions
Cited by: 1
Author(s): Michael T. Guarnieri, Alida T. Gerritsen, Calvin A. Henard, Eric P. Knoshaug
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-28957-y

Comprehensive analysis of competitive endogenous RNAs network associated with head and neck squamous cell carcinoma
Cited by: 51
Author(s): Xiaonan Fang, Miao Yin, Hua Li, Cheng Liang, Cong Xu, Yang Gao, Huaxiang Zhang
Software Mentions: 2
Published: over 8 years ago

10.3389/fbioe.2021.701039

Identification of Key mRNAs as Prediction Models for Early Metastasis of Pancreatic Cancer Based on LASSO
Cited by: 7
Author(s): Ke Xue, Huilin Zheng, Xiaowen Qian, Zheng Chen, Yangjun Gu, Zhenhua Hu, Lei Zhang, Jian Wan
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2020.587402

Transcriptional Profiling Reveals the Regulatory Role of DNER in Promoting Pancreatic Neuroendocrine Neoplasms
Cited by: 4
Author(s): Rui He, Wunai Zhang, Shuo Chen, Liu Yang, Wen‐Bin Yang, Junhui Li
Software Mentions: 2
Published: almost 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568