bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s13287-019-1335-5

High temperature suppressed SSC self-renewal through S phase cell cycle arrest but not apoptosis
Cited by: 12
Author(s): Jia Wang, Wei-Jun Gao, Shoulong Deng, Lei Xiang, Jia Hua, Wenzhi Ma
Software Mentions: 3
Published: over 5 years ago

10.1186/s12860-020-00331-9

Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages
Cited by: 18
Author(s): Sabin Bhandari, Ruomei Li, Jaione Simón-Santamaría, Peter McCourt, Steinar Johansen, Bård Smedsrød, Iñigo Martínez-Zubiaurre, Karen Kristine Sørensen
Software Mentions: 3
Published: about 4 years ago

10.1186/s13018-020-01994-y

Differential gene expression in skin RNA of horses affected with degenerative suspensory ligament desmitis
Cited by: 7
Author(s): Abigail Haythorn, M.F. Young, James B. Stanton, Jian Zhang, P. O. E. Mueller, Jaroslava Halper
Software Mentions: 3
Published: about 4 years ago

10.3390/cancers11040479

Combined Targeting of Estrogen Receptor Alpha and XPO1 Prevent Akt Activation, Remodel Metabolic Pathways and Induce Autophagy to Overcome Tamoxifen Resistance
Cited by: 13
Author(s): Eylem Kulkoyluoglu-Cotul, Brandi Patrice Smith, Kinga Wrobel, Yijia Zhao, Karen Lee Ann Chen, Kadriye Hieronymi, Ozan Berk Imir, Kevin Duong, Caitlin O’Callaghan, Aditi Mehta, Sunati Sahoo, Barbara Haley, Hua Chang, Yosef Landesman, Zeynep Madak-Erdoğan
Software Mentions: 3
Published: over 5 years ago

10.1186/s13287-019-1191-3

In vitro expansion affects the response of human bone marrow stromal cells to irradiation
Cited by: 8
Author(s): Yang Xiang, Chun Wu, Jiang Wu, Weili Quan, Chao Cheng, Jian Zhou, Li Chen, Lan Xiang, Fengjie Li, Kebin Zhang, Qian Ran, Yi Zhang, Zhongjun Li
Software Mentions: 3
Published: almost 6 years ago

10.1534/g3.117.300318

Pas de deux: An Intricate Dance of Anther Smut and Its Host
Cited by: 5
Author(s): Su San Toh, Zehua Chen, Eric C. Rouchka, David J. Schultz, Christina A. Cuomo, Michael H. Perlin
Software Mentions: 3
Published: almost 7 years ago

10.3389/fonc.2020.00215

A Novel Long Non-coding RNA, MSTRG.51053.2 Regulates Cisplatin Resistance by Sponging the miR-432-5p in Non-small Cell Lung Cancer Cells
Cited by: 24
Author(s): Jie Zhang, Chuanqin Xu, Y Gao, Yi Wang, Zongli Ding, Yueming Zhang, Wenyi Shen, Yulong Zheng, Yufeng Wan
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13018-021-02604-1

Identification and comparison of novel circular RNAs with associated co-expression and competing endogenous RNA networks in postmenopausal osteoporosis
Cited by: 4
Author(s): Weiyi Diao, Yongguang Wang, Jun Zhang, Haiyu Shao, Yanlei Huang, Mengran Jin
Software Mentions: 3
Published: over 3 years ago

10.1186/s13287-018-1104-x

Comparative analysis of mesenchymal stem cells derived from amniotic membrane, umbilical cord, and chorionic plate under serum-free condition
Cited by: 62
Author(s): Jiao Ma, Jun Wu, Han Liu, Xiangxiang Jiang, Yan Long, Jie Hao, Hongmei Wang
Software Mentions: 3
Published: almost 6 years ago

10.3390/md19080429

RKC-B1 Blocks Activation of NF-κB and NLRP3 Signaling Pathways to Suppress Neuroinflammation in LPS-Stimulated Mice
Cited by: 3
Author(s): Man Liu, Yinglin Yang, Shanshan Zhang, Dong-Ni Liu, Lian-Hua Fang, Guanhua Du, Yue-Hua Wang
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-32579-9

ADIPOR1 is essential for vision and its RPE expression is lost in the Mfrprd6 mouse
Cited by: 32
Author(s): Valentin M. Sluch, Angela Banks, Hui Li, Maura Crowley, Vanessa Davis, Chuanxi Xiang, Junzheng Yang, John Demirs, Joanna Vrouvlianis, Barrett Leehy, Shawn Hanks, Alexandra M. Hyman, Jorge Aranda, Bo Chang, Chad E. Bigelow, Dennis S. Rice
Software Mentions: 3
Published: about 6 years ago

10.18632/oncotarget.11309

Proteolysis-a characteristic of tumor-initiating cells in murine metastatic breast cancer
Cited by: 8
Author(s): Larissa E. Hillebrand, Fee Bengsch, Jochen Hochrein, Jan Hülsdünker, Julia Lynne Glade Bender, Marie Follo, Hauke Busch, Melanie Boerries, Thomas Reinheckel
Software Mentions: 3
Published: over 8 years ago

10.1186/s12920-019-0580-x

A comprehensive genome-wide profiling comparison between HBV and HCV infected hepatocellular carcinoma
Cited by: 21
Author(s): Suofeng Sun, Yuan Li, Sun‐Young Han, Huiying Jia, Xiuling Li, Xiaofang Li
Software Mentions: 3
Published: about 5 years ago

10.18632/oncotarget.15829

Re-expression of miR-200c suppresses proliferation, colony formation and<i>in vivo</i>tumor growth of murine claudin-low mammary tumor cells
Cited by: 18
Author(s): Robert A. Jones, Katrina L. Watson, Anthony Bruce, Sarah Nersesian, Jenna Kitz, Roger A. Moorehead
Software Mentions: 3
Published: almost 8 years ago

10.7717/peerj.12091

Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation
Cited by: 0
Author(s): Wenyan Kang, Liqing Du, Qianyu Liang, Rui Zhang, Chunxu Lv, Shaohua Ge
Software Mentions: 3
Published: over 3 years ago

10.3390/jpm11020062

Modified Significance Analysis of Microarrays in Heterogeneous Diseases
Cited by: 2
Author(s): I‐Shiang Tzeng
Software Mentions: 3
Published: almost 4 years ago

10.1534/g3.117.042440

Transcriptional Profiling of Biofilm Regulators Identified by an Overexpression Screen in <i>Saccharomyces cerevisiae</i>
Cited by: 14
Author(s): Gareth A. Cromie, Zhihao Tan, Michelle Hays, Amy Sirr, Eric Jeffery, Andrew T. Dudley
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-33478-9

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues
Cited by: 54
Author(s): Bryan J. Pavlovic, Lauren E. Blake, Julien Roux, Claudia Chavarria, Yoav Gilad
Software Mentions: 3
Published: about 6 years ago

10.3390/pathogens9020131

Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy
Cited by: 9
Author(s): Julia Bespyatykh, Egor Shitikov, Dmitry Bespiatykh, Andrei Guliaev, Ksenia M. Klimina, Vladimir A. Veselovsky, Georgij Arapidi, Marine Dogonadze, Viacheslav Zhuravlev, Elena Ilina, Vadim M. Govorun
Software Mentions: 3
Published: almost 5 years ago

10.3390/cancers13092161

Low Plasma Citrate Levels and Specific Transcriptional Signatures Associated with Quiescence of CD34+ Progenitors Predict Azacitidine Therapy Failure in MDS/AML Patients
Cited by: 1
Author(s): Pavla Kořalková, Monika Beličková, David Kundrát, Michaela Dostálová Merkerová, Zdeněk Krejčík, Katarína Szikszai, Monika Kaisrlikova, Jitka Veselá, Pavla Vyhlidalova, Jan Stetka, Alžběta Hlaváčková, Jiřı́ Suttnar, Patrik Flodr, J Stříteský, Anna Jonášová, Jaroslav Čermák, Vladimír Divoký
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.47990

Accelerated phosphatidylcholine turnover in macrophages promotes adipose tissue inflammation in obesity
Cited by: 40
Author(s): Kasparas Petkevicius, Samuel Virtue, Guillaume Bidault, Benjamin Jenkins, Cankut Çubuk, Cecilia Morgantini, Myriam Aouadi, Joaquín Dopazo, Mireille J. Serlie, Albert Koulman, António Vidal-Puig
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-39608-1

Field transcriptome revealed a novel relationship between nitrate transport and flowering in Japanese beech
Cited by: 16
Author(s): Akiko Satake, Kazutaka Kawatsu, Kenjiro Teshima, Daisuke Kabeya, Qingmin Han
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-33943-5

Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation
Cited by: 33
Author(s): Erich Hofmann, Rhett M. Rautsaw, Jason L. Strickland, Matthew L. Holding, Michael Hogan, Andrew J. Mason, Darin R. Rokyta, Christopher L. Parkinson
Software Mentions: 3
Published: about 6 years ago

10.3390/pathogens10091127

Delineating the Role of Aedes aegypti ABC Transporter Gene Family during Mosquito Development and Arboviral Infection via Transcriptome Analyses
Cited by: 8
Author(s): Vijoy Kumar, Shilpi Garg, Lalita Gupta, Kuldeep Gupta, Cheikh Tidiane Diagne, Dorothée Missé, Julien Pompon, Sanjeev Kumar, Vishal Saxena
Software Mentions: 3
Published: over 3 years ago

10.3390/pathogens8030132

Whole Transcriptome Analysis of Aedes albopictus Mosquito Head and Thorax Post-Chikungunya Virus Infection
Cited by: 9
Author(s): Ravikiran Vedururu, Matthew J. Neave, Vinod Sundaramoorthy, Diane Green, Jennifer Harper, Paul R Gorry, Jean‐Bernard Duchemin, Prasad N. Paradkar
Software Mentions: 3
Published: over 5 years ago

10.3390/pathogens10020167

Characterization of the Rhipicephalus (Boophilus) microplus Sialotranscriptome Profile in Response to Theileria equi Infection
Cited by: 5
Author(s): Patrícia Gonzaga Paulino, Gabriela Lopes Vivas Vitari, Antônio Mauro Rezende, Joana Couto, Sandra Antunes, Ana Domingos, Maristela Peckle, Carlos Luiz Massard, Flávio Marcos Gomes Araújo, Huarrisson Azevedo Santos
Software Mentions: 3
Published: almost 4 years ago

10.3390/medicines6030071

Effect of Sulforaphane and 5-Aza-2’-Deoxycytidine on Melanoma Cell Growth
Cited by: 5
Author(s): Tung-Chin Chiang, Brian Koss, L. Joseph Su, Charity L. Washam, Stephanie D. Byrum, Aaron J. Storey, Alan J. Tackett
Software Mentions: 3
Published: over 5 years ago

10.1186/1755-8794-6-S2-S1

Analysis of small-sample clinical genomics studies using multi-parameter shrinkage: application to high-throughput RNA interference screening
Cited by: 7
Author(s): Mark A. van de Wiel, Renée X. de Menezes, Ellen Siebring-van Olst, Victor W. van Beusechem
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12920-021-00878-2

Expression and gene regulatory network of SNHG1 in hepatocellular carcinoma
Cited by: 4
Author(s): Chaoran Zheng, Shicheng Yu
Software Mentions: 3
Published: almost 4 years ago

10.3390/cancers13040681

Subcellular Localization of uc.8+ as a Prognostic Biomarker in Bladder Cancer Tissue
Cited by: 12
Author(s): Sara Terreri, Sara Mancinelli, Matteo Ferro, Maria Concetta Vitale, Sisto Perdoná, Luigi Castaldo, Vincenzo Gigantino, Vincenzo Mercadante, Rossella De Cecio, Gabriella Aquino, Marco Montella, Claudia Angelini, Eugenio Del Prete, Marianna Aprile, Angelo Ciaramella, Giovanna L. Liguori, Valerio Costa, George A. Calin, Evelina La Civita, Daniela Terracciano, Ferdinando Febbraio, Amelia Cimmino
Software Mentions: 3
Published: almost 4 years ago

10.3390/cancers12061642

The Liver Microbiome Is Implicated in Cancer Prognosis and Modulated by Alcohol and Hepatitis B
Cited by: 13
Author(s): Jaideep Chakladar, Lauren Wong, Selena Z. Kuo, Wei Tse Li, Michael Yu, Eric Y. Chang, Xiao Qi Wang, Weg M. Ongkeko
Software Mentions: 3
Published: over 4 years ago

10.3389/fonc.2020.01029

Abnormal Food Timing Promotes Alcohol-Associated Dysbiosis and Colon Carcinogenesis Pathways
Cited by: 5
Author(s): Faraz Bishehsari, Shirin Moossavi, Phillip A. Engen, Xiaohan Liu, Yue Zhang
Software Mentions: 3
Published: over 4 years ago

10.1186/s13287-016-0370-8

Identification and validation of multiple cell surface markers of clinical-grade adipose-derived mesenchymal stromal cells as novel release criteria for good manufacturing practice-compliant production
Cited by: 120
Author(s): Emily T. Camilleri, Michael P. Gustafson, Amel Dudakovic, Scott M. Riester, Catalina Galeano Garces, Christopher R. Paradise, Hideki Takai, Marcel Karperien, Simon M. Cool, Hee Jeong Im Sampen, A. Noelle Larson, Wenchun Qu, Jay Smith, Allan B. Dietz, André J. van Wijnen
Software Mentions: 3
Published: over 8 years ago

10.3390/cancers11060887

Utility of Circulating Cell-Free RNA Analysis for the Characterization of Global Transcriptome Profiles of Multiple Myeloma Patients
Cited by: 20
Author(s): Maoshan Chen, Sridurga Mithraprabhu, Malarmathy Ramachandran, Kawa Choi, Tiffany Khong, Andrew Spencer
Software Mentions: 3
Published: over 5 years ago

10.3390/cancers13071585

Aberrations of Chromosomes 1 and 16 in Breast Cancer: A Framework for Cooperation of Transcriptionally Dysregulated Genes
Cited by: 8
Author(s): Anna Privitera, Vincenza Barresi, D. F. Condorelli
Software Mentions: 3
Published: over 3 years ago

10.3390/cancers11111668

Transcription Factor and miRNA Interplays Can Manifest the Survival of ccRCC Patients
Cited by: 41
Author(s): Si Qin, Xuejia Shi, Canbiao Wang, Jin Park, Fei Ma
Software Mentions: 3
Published: about 5 years ago

10.1186/s13071-016-1341-8

Reconstruction of the insulin-like signalling pathway of Haemonchus contortus
Cited by: 14
Author(s): Namitha Mohandas, Min Hu, Andreas J. Stroehlein, Neil D. Young, Paul W. Sternberg, James B. Lok, Robin B. Gasser
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13071-017-2326-y

Differential gene expression in Anopheles stephensi following infection with drug-resistant Plasmodium yoelii
Cited by: 4
Author(s): Jingru Zhang, Jiacheng Huang, Feng Zhu, Jian Zhang
Software Mentions: 3
Published: over 7 years ago

10.3390/cancers12061635

Circulating miRNAs in Small Extracellular Vesicles Secreted by a Human Melanoma Xenograft in Mouse Brains
Cited by: 9
Author(s): Loredana Guglielmi, Marta Nardella, Carla Musa, Ingrid Cifola, Manuela Porru, Beatrice Cardinali, Ilaria Iannetti, Chiara Di Pietro, Giulia Bolasco, Valentina Palmieri, Laura Vilardo, Nicolò Panini, Fabrizio Bonaventura, Massimiliano Papi, Ferdinando Scavizzi, Marcello Raspa, Carlo Leonetti, Germana Falcone, Armando Felsani, Igea D’Agnano
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-018-33807-y

Characterization of the miRNA regulators of the human ovulatory cascade
Cited by: 23
Author(s): Gil M. Yerushalmi, Mali Salmon‐Divon, Libby Ophir, Yuval Yung, Micha Baum, Giovanni Coticchio, Rubens Fadini, Mario Mignini-Renzini, Mariabeatrice Dal Canto, Ronit Machtinger, Ettie Maman, Ariel Hourvitz
Software Mentions: 3
Published: about 6 years ago

10.1590/0074-02760190378

Computational prediction and characterisation of miRNAs and their pathway genes in human schistosomiasis caused by Schistosoma haematobium
Cited by: 3
Author(s): Thaís Cunha de Sousa Cardoso, Carlos Bruno de Araújo, Laysa Gomes Portilho, Luiz Guilherme Alves Mendes, Tamires Caixeta Alves, Gustavo Caetano Silva, Thales Henrique Cherubino Ribeiro, Peterson Elizandro Gandolfi, Enyara Rezende Morais, Laurence Rodrigues do Amaral, Matheus de Souza Gomes
Software Mentions: 3
Published: almost 5 years ago

10.3390/cancers13040632

MicroRNA Profile for Diagnostic and Prognostic Biomarkers in Thyroid Cancer
Cited by: 9
Author(s): Jong‐Lyul Park, Seon‐Kyu Kim, Sora Jeon, Chan Kwon Jung, Yong‐Sung Kim
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.26575

Human embryonic lung epithelial tips are multipotent progenitors that can be expanded in vitro as long-term self-renewing organoids
Cited by: 206
Author(s): Marko Nikolić, Oriol Caritg, Quitz Jeng, Jo-Anne Johnson, Dawei Sun, Kate J. Howell, Jane Brady, Usua Laresgoiti, George E. Allen, Richard J. Butler, Matthias Zilbauer, Adam Giangreco, Emma L. Rawlins
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.57519

The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression program to control neurite outgrowth
Cited by: 20
Author(s): Baisakhi Mondal, Hong Jin, Satish Kallappagoudar, Yurii Sedkov, Tanner Martinez, Monica F. Sentmanat, Greg J Poet, Chunliang Li, Yiping Fan, Shondra M. Pruett-Miller, Hans‐Martin Herz
Software Mentions: 3
Published: over 4 years ago

10.1186/s12870-019-1795-x

Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)
Cited by: 19
Author(s): Daniel R. Kohlhase, Jamie A. O’Rourke, Micheal D. K. Owen, Michelle A. Graham
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-40754-9

Genome analysis of Pseudomonas syringae pv. actinidiae biovar 6, which produces the phytotoxins, phaseolotoxin and coronatine
Cited by: 34
Author(s): Takashi Fujikawa, Hiroyuki Sawada
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12920-021-00975-2

Identification and validation of signal recognition particle 14 as a prognostic biomarker predicting overall survival in patients with acute myeloid leukemia
Cited by: 3
Author(s): Lingling Shi, Rui Huang, Yongrong Lai
Software Mentions: 3
Published: over 3 years ago

10.1186/s13071-018-2817-5

Genetic variation associated with increased insecticide resistance in the malaria mosquito, Anopheles coluzzii
Cited by: 21
Author(s): Bradley J. Main, Amanda Everitt, Anthony J. Cornel, Fereydoun Hormozdiari, Gregory C. Lanzaro
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2020.554759

Integrated Analysis of lncRNA–Mediated ceRNA Network in Lung Adenocarcinoma
Cited by: 90
Author(s): Xianxian Wu, Zhilin Sui, Hongdian Zhang, Ying Wang, Zhentao Yu
Software Mentions: 3
Published: over 4 years ago

10.1098/rsob.160330

Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress
Cited by: 10
Author(s): Erica Acton, Ahwon Lee, Pei Zhao, Stéphane Flibotte, Mauricio Neira, Sunita Sinha, Jennifer Chiang, Patrick Flaherty, Corey Nislow, Guri Giaever
Software Mentions: 3
Published: over 7 years ago

10.3389/fonc.2021.659201

Prognostic Prediction of Cytogenetically Normal Acute Myeloid Leukemia Based on a Gene Expression Model
Cited by: 4
Author(s): Yang Liu, Houyu Zhang, Xue Yang, Ting Lu, Shihui Ma, Hui Cheng, Kuangyu Yen, Tao Cheng
Software Mentions: 3
Published: over 3 years ago

10.1098/rsob.190141

Identification of a novel regulatory pathway for PPARα by RNA-seq characterization of the endothelial cell lipid peroxidative injury transcriptome
Cited by: 4
Author(s): Fangfang Dou, Beiling Wu, Sun Liang, Jiulin Chen, Te Liu, Zhihua Yu, Chuan Chen
Software Mentions: 3
Published: about 5 years ago

10.3389/fneur.2015.00045

Long Non-Coding RNA Expression during Aging in the Human Subependymal Zone
Cited by: 37
Author(s): Guy Barry, Boris Guennewig, Samantha J. Fung, Dominik C. Kaczorowski, Cynthia Shannon Weickert
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13578-019-0356-1

Transcriptome analysis reveals an important candidate gene involved in both nodal metastasis and prognosis in lung adenocarcinoma
Cited by: 42
Author(s): Xiao Zhu, Hui Luo, Ying Xu
Software Mentions: 3
Published: about 5 years ago

10.3389/fneur.2020.573575

Differential Glial Activation in Early Epileptogenesis—Insights From Cell-Specific Analysis of DNA Methylation and Gene Expression in the Contralateral Hippocampus
Cited by: 4
Author(s): Toni Berger, Magnus Dehli Vigeland, Hanne Sagsveen Hjorthaug, Cecilie G. Nome, Erik Taubøll, Kaja Kristine Selmer, Kjell Heuser
Software Mentions: 3
Published: about 4 years ago

10.7150/jca.38796

A Combined four-mRNA Signature Associated with Lymphatic Metastasis for Prognosis of Colorectal Cancer
Cited by: 7
Author(s): Xueping Li, Zhang Qiang, Liang Zhao, Longyang Jiang, Aoshuang Qi, Wei Qian, Xinyue Song, Wei Lin, Liwen Zhang, Yimeng Zhao, Xuemei Lv, Lin Zhao
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12964-019-0332-8

Low levels of pyruvate induced by a positive feedback loop protects cholangiocarcinoma cells from apoptosis
Cited by: 12
Author(s): Mingming Zhang, Yida Pan, Dehua Tang, Robert Dorfman, Lei Xu, Qian Zhou, Lixing Zhou, Yuming Wang, Li Yang, Yuyao Yin, Bo Kong, Helmut Frieß, Shimin Zhao, Jian‐Lin Wu, Lei Wang, Xiaoping Zou
Software Mentions: 3
Published: almost 6 years ago

10.7150/jca.34723

Signatures of circulating microRNA in four sarcoma subtypes
Cited by: 11
Author(s): Hanna Koseła-Paterczyk, Agnieszka Paziewska, Maria Kulecka, Aneta Bałabas, Anna Kluska, Michalina Dąbrowska, Magdalena Piątkowska, Natalia Żeber‐Lubecka, Filip Ambrożkiewicz, Jakub Karczmarski, Michał Mikula, Piotr Rutkowski, Jerzy Ostrowski
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12964-016-0142-1

Normalization of TAM post-receptor signaling reveals a cell invasive signature for Axl tyrosine kinase
Cited by: 26
Author(s): Stanley Kimani, Sushil Kumar, Viralkumar Davra, Yun‐Juan Chang, Canan Kasikara, Ke Geng, Wen-I Tsou, Shenyan Wang, Mainul Hoque, Andrej Boháč, Anita Lewis-Antes, Mariana S. De Lorenzo, Sergei V. Kotenko, Raymond B. Birge
Software Mentions: 3
Published: over 8 years ago

10.7150/jca.35801

Identification of a six-lncRNA signature based on a competing endogenous RNA network for predicting the risk of tumour recurrence in bladder cancer patients
Cited by: 8
Author(s): Danfeng Zhao, Qiang Peng, Lu Wang, Cong Li, Yulin Lv, Yong Liu, Zhichao Wang, Ruizhe Fang, Jiaqi Wang, Zhongqing Liu, Wanhai Xu
Software Mentions: 3
Published: almost 5 years ago

10.3389/fonc.2021.707066

Cystatin-B Negatively Regulates the Malignant Characteristics of Oral Squamous Cell Carcinoma Possibly Via the Epithelium Proliferation/Differentiation Program
Cited by: 3
Author(s): Tiantian Xu, Xiao‐Wen Zeng, Xinhong Wang, Luxi Yang, Gang Luo, Ting Yu
Software Mentions: 3
Published: over 3 years ago

10.7150/jca.31675

Comprehensive investigation of the clinical significance and molecular mechanisms of plasmacytoma variant translocation 1 in sarcoma using genome-wide RNA sequencing data
Cited by: 9
Author(s): Jianwei Liu, Rong Li, Xiwen Liao, Bang-li Hu, Jia Yu
Software Mentions: 3
Published: almost 6 years ago

10.3390/v13081603

Characterization of the SARS-CoV-2 Host Response in Primary Human Airway Epithelial Cells from Aged Individuals
Cited by: 9
Author(s): Subramaniyan Bharathiraja, Jason L. Larabee, Manish Bodas, Andrew R. Moore, Anthony W. G. Burgett, Dean A. Myers, Constantin Georgescu, Jonathan D. Wren, James F. Papin, Matthew S. Walters
Software Mentions: 3
Published: over 3 years ago

10.1186/s12867-017-0099-7

An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing
Cited by: 42
Author(s): Parisa Amini, Julia Ettlin, Lennart Opitz, Elena Clementi, Alexandra Malbon, Enni Markkanen
Software Mentions: 3
Published: over 7 years ago

10.3390/metabo11060369

Plant Transcriptome Reprograming and Bacterial Extracellular Metabolites Underlying Tomato Drought Resistance Triggered by a Beneficial Soil Bacteria
Cited by: 17
Author(s): Rafael J. L. Morcillo, Juan Ignacio Vílchez, Song Zhang, Rajesh Kaushal, Danxia He, Hailing Zi, Renyi Liu, Karsten Niehaus, Avtar K. Handa, Huiming Zhang
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-98420-y

Short-term transcriptomic response to plasma membrane injury
Cited by: 3
Author(s): Swantje Christin Häger, Catarina Dias, Stine Lauritzen Sønder, André Vidas Olsen, Isabelle da Piedade, Anne Sofie Busk Heitmann, Elena Papaleo, Jesper Nylandsted
Software Mentions: 3
Published: about 3 years ago

10.1074/jbc.RA120.014960

mTOR kinase inhibition disrupts neuregulin 1-ERBB3 autocrine signaling and sensitizes NF2-deficient meningioma cellular models to IGF1R inhibition
Cited by: 7
Author(s): Roberta L. Beauchamp, Serkan Erdin, Luke Witt, Justin T. Jordan, Scott R. Plotkin, James F. Gusella, Vijaya Ramesh
Software Mentions: 3
Published: almost 4 years ago

10.1186/s40168-021-01117-7

Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria
Cited by: 23
Author(s): Wisnu Adi Wicaksono, Tomislav Cernava, Christian Berg, Gabriele Berg
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2020.01765

Identification of TYROBP and C1QB as Two Novel Key Genes With Prognostic Value in Gastric Cancer by Network Analysis
Cited by: 26
Author(s): Junjie Jiang, Yongfeng Ding, Mengjie Wu, Xiadong Lyu, Haifeng Wang, Yanyan Chen, Haiyong Wang, Lisong Teng
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2017.01784

Analyzing the Complex Regulatory Landscape of Hfq – an Integrative, Multi-Omics Approach
Cited by: 14
Author(s): Lucia Grenga, Govind Chandra, Gerhard Saalbach, Carla V. Galmozzi, Günter Krämer, Jacob G. Malone
Software Mentions: 3
Published: about 7 years ago

10.18632/oncotarget.13346

Differentiated regulation of immune-response related genes between LUAD and LUSC subtypes of lung cancers
Cited by: 51
Author(s): Mengzhu Chen, Xiu Ying Liu, Jie Du, Xiu‐Jie Wang, Xia Lei
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-34591-5

Brassica yellows virus’ movement protein upregulates anthocyanin accumulation, leading to the development of purple leaf symptoms on Arabidopsis thaliana
Cited by: 18
Author(s): Xiangru Chen, Ying Wang, Hang-Hai Zhao, Xiaoyan Zhang, Xianbing Wang, Dawei Li, Jialin Yu, Chenggui Han
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-021-95698-w

PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients
Cited by: 9
Author(s): Kota Fujisawa, Mamoru Shimo, Y-h. Taguchi, Shinya Ikematsu, Ryota Miyata
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2019.01914

Soil Metatranscriptomes Under Long-Term Experimental Warming and Drying: Fungi Allocate Resources to Cell Metabolic Maintenance Rather Than Decay
Cited by: 28
Author(s): Adriana L. Romero‐Olivares, Germán Meléndrez-Carballo, Asunción Lago‐Lestón, Kathleen K. Treseder
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.19531

Evolution of herbivore-induced early defense signaling was shaped by genome-wide duplications in Nicotiana
Cited by: 24
Author(s): Wenwu Zhou, Thomas Brockmöller, Zhihao Ling, Ashton Omdahl, Ian Thomas Baldwin, Shuqing Xu
Software Mentions: 3
Published: about 8 years ago

10.1038/s41419-020-2381-8

MOB2 suppresses GBM cell migration and invasion via regulation of FAK/Akt and cAMP/PKA signaling
Cited by: 41
Author(s): Ke Jiang, Gang Yao, Lulu Hu, Yumei Yan, Jia Liu, Jingwei Shi, Youwei Chang, Ye Zhang, Dapeng Liang, Dachuan Shen, Guirong Zhang, Meng Shao, Haozhe Piao
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2018.00445

Comparative mRNA-Seq Analysis Reveals the Improved EPS Production Machinery in Streptococcus thermophilus ASCC 1275 During Optimized Milk Fermentation
Cited by: 25
Author(s): Qinglong Wu, Nagendra P. Shah
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41419-021-03641-8

LDHA induces EMT gene transcription and regulates autophagy to promote the metastasis and tumorigenesis of papillary thyroid carcinoma
Cited by: 44
Author(s): Xiukun Hou, Xianle Shi, Wei Zhang, Dapeng Li, Linfei Hu, Jihong Yang, Jingzhu Zhao, Songfeng Wei, Xi Wei, Xianhui Ruan, Xiangqian Zheng, Ming Gao
Software Mentions: 3
Published: over 3 years ago

10.1038/s41419-021-03566-2

CircSPI1 acts as an oncogene in acute myeloid leukemia through antagonizing SPI1 and interacting with microRNAs
Cited by: 19
Author(s): Xiaoling Wang, Peng Jin, Yi Zhang, Kankan Wang
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-96150-9

Transcriptomic analysis of the mouse retina after acute and chronic normobaric and hypobaric hypoxia
Cited by: 10
Author(s): Lynn J. A. Ebner, Marijana Samardzija, Federica Storti, Vyara Todorova, Duygu Karademir, Julian Behr, Fraser Simpson, Markus Thiersch, Christian Grimm
Software Mentions: 3
Published: over 3 years ago

10.1074/jbc.RA120.016009

Human genetic variants disrupt RGS14 nuclear shuttling and regulation of LTP in hippocampal neurons
Cited by: 9
Author(s): Katherine E. Squires, Kyle J. Gerber, Matthew Tillman, Daniel Lustberg, Carolina Montañez-Miranda, Mei Zhao, Suneela Ramineni, Christopher D. Scharer, Ramendra N. Saha, Shu Fang, Jeanne L. Schroeder, Eric A. Ortlund, David Weinshenker, Serena M. Dudek, John R. Hepler
Software Mentions: 3
Published: almost 4 years ago

10.3390/v13061140

Global mRNA and miRNA Analysis Reveal Key Processes in the Initial Response to Infection with WSSV in the Pacific Whiteleg Shrimp
Cited by: 8
Author(s): Rebecca S. Millard, Lisa K. Bickley, Kelly S. Bateman, Audrey Farbos, Diana Minardi, Karen Moore, Stuart Ross, Grant D. Stentiford, Charles R. Tyler, Ronny van Aerle, Eduarda M. Santos
Software Mentions: 3
Published: over 3 years ago

10.1186/s12866-020-1722-1

Integrative analysis of outer membrane vesicles proteomics and whole-cell transcriptome analysis of eravacycline induced Acinetobacter baumannii strains
Cited by: 19
Author(s): Dinesh Kumar Kesavan, Aparna Vasudevan, Liang Wu, Jianguo Chen, Zhaoliang Su, Shengjun Wang, Huaxi Xu
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-95423-7

Evolutionary transition of doublesex regulation from sex-specific splicing to male-specific transcription in termites
Cited by: 14
Author(s): Shôzô Miyazaki, Kokuto Fujiwara, Keima Kai, Yudai Masuoka, Hiroki Gotoh, Teruyuki Niimi, Yoshinobu Hayashi, Shuji Shigenobu, Kazuyuki Maekawa
Software Mentions: 3
Published: over 3 years ago

10.7150/jca.49138

LINC00184 involved in the regulatory network of ANGPT2 via ceRNA mediated miR-145 inhibition in gastric cancer
Cited by: 13
Author(s): Haiyan Piao, Shuai Guo, Haoyi Jin, Yue Wang, Jun Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1038/cddis.2017.468

The histone code reader Spin1 controls skeletal muscle development
Cited by: 12
Author(s): Holger Greschik, Delphine Duteil, Nadia Messaddeq, Dominica Willmann, Laura Arrigoni, Manuela Sum, Manfred Jung, Daniel Metzger, Thomas Manke, Thomas Günther, Roland Schüle
Software Mentions: 3
Published: about 7 years ago

10.1038/s41419-019-1792-x

The Cornelia de Lange Syndrome-associated factor NIPBL interacts with BRD4 ET domain for transcription control of a common set of genes
Cited by: 32
Author(s): Noelia Luna-Peláez, Rosana March-Díaz, María Ceballos-Chávez, José A. Guerrero-Martínez, Paolo Grazioli, Pablo García-Gutiérrez, Thomas Vaccari, Valentina Massa, José Carlos Castañeda Reyes, Mario García-Domínguez
Software Mentions: 3
Published: over 5 years ago

10.1186/s13041-020-00702-5

Translational changes induced by acute sleep deprivation uncovered by TRAP-Seq
Cited by: 17
Author(s): Lisa C. Lyons, Snehajyoti Chatterjee, Yann Vanrobaeys, Marie E. Gaine, Ted Abel
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-018-34636-9

Gene set enrichment analysis of the bronchial epithelium implicates contribution of cell cycle and tissue repair processes in equine asthma
Cited by: 13
Author(s): Laurence Tessier, Olivier Côté, Mary E. Clark, Laurent Viel, Andrés Diaz-Méndez, Simon Anders, Dorothee Bienzle
Software Mentions: 3
Published: about 6 years ago

10.1074/jbc.M116.751644

Bromodomain and extraterminal inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps
Cited by: 25
Author(s): Kristin M. Keck, S. Moquin, Amanda He, Samantha G. Fernandez, Jessica J. Somberg, Stephanie M. Liu, Delsy M. Martinez, JJ L. Miranda
Software Mentions: 3
Published: over 7 years ago

10.1186/s12967-018-1732-z

Integrated analysis of dysregulated long non-coding RNAs/microRNAs/mRNAs in metastasis of lung adenocarcinoma
Cited by: 49
Author(s): Lifeng Li, Mengle Peng, Wenhua Xue, Zhirui Fan, Tian Wang, Jingyao Lian, Yunkai Zhai, Wenping Lian, Dongchun Qin, Jie Zhao
Software Mentions: 3
Published: about 6 years ago

10.7150/jca.50472

High Expression of RhoBTB3 Predicts Favorable Chemothrapy Outcomes in non-M3 Acute Myeloid Leukemia
Cited by: 3
Author(s): Shuanghui Yang, Wei Liu, Jie Peng, Yajing Xu, Yanfeng Liu, Yan Li, Minyuan Peng, Zhao Ouyang, Cong Chen, Enyi Liu
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-94386-z

An epigenetic GPI anchor defect impairs TLR4 signaling in the B cell transdifferentiation model for primary human monocytes BLaER1
Cited by: 3
Author(s): Julia Wegner, Thomas Zillinger, Thais Marina Schlee-Guimarães, Eva Bartok, Martin Schlee
Software Mentions: 3
Published: over 3 years ago

10.7150/jca.59348

Long non-coding RNA RP4-694A7.2 Promotes Hepatocellular Carcinoma Cell Proliferation and Metastasis through the Regulation of PSAT1
Cited by: 5
Author(s): Yaoxin Fan, Lin Wang, Yang Ding, Qiuju Sheng, Chong Zhang, Yanwei Li, Chao Han, Bao-Liang Lu, Xiao-guang Dou
Software Mentions: 3
Published: almost 4 years ago

10.1172/jci.insight.149446

Combining multiomics and drug perturbation profiles to identify muscle-specific treatments for spinal muscular atrophy
Cited by: 5
Author(s): Katharina E. Meijboom, Viola Volpato, Jimena Monzón‐Sandoval, Joseph M. Hoolachan, Suzan M. Hammond, Frank Abendroth, Olivier G. de Jong, Gareth Hazell, Nina Ahlskog, Matthew J. Wood, Caleb Webber, Mélissa Bowerman
Software Mentions: 3
Published: over 3 years ago

10.1172/jci.insight.145607

A surgical method for continuous intraportal infusion of gut microbial metabolites in mice
Cited by: 5
Author(s): Danny Orabi, Lucas J Osborn, Kevin Fung, William Massey, Anthony Horak, Federico Aucejo, Ibrahim Choucair, Beckey DeLucia, Zeneng Wang, Jan Claesen, J. Mark Brown
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-93142-7

Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
Cited by: 3
Author(s): Zoltán Maróti, Dóra Tombácz, Norbert Moldován, Gábor Torma, Victoria A Jefferson, Zsolt Csabai, Gábor Gulyás, Ákos Dörmő, Miklós Boldogkői, Tibor Kalmár, Florencia Meyer, Zsolt Boldogköi
Software Mentions: 3
Published: over 3 years ago

10.1172/jci.insight.147929

Adipocyte-like signature in ovarian cancer minimal residual disease identifies metabolic vulnerabilities of tumor initiating cells
Cited by: 2
Author(s): Mara Artibani, Kenta Masuda, Zhiyuan Hu, Pascal C. Rauher, Garry Mallett, Nina Wietek, Matteo Morotti, Kay Y. Chong, Mohammad KaramiNejadRanjbar, Christos E. Zois, Sunanda Dhar, Salma El-Sahhar, Leticia Campo, Sarah P. Blagden, Stephen Damato, Pubudu Pathiraja, Shibani Nicum, Fergus Gleeson, A Laios, Abdulkhaliq Alsaadi, Laura Santana González, Takeshi Motohara, Ashwag Albukhari, Zhen Lü, Robert C. Bast, Adrian L. Harris, Christer S. Ejsing, Robin W. Klemm, Christopher Yau, Tatjana Sauka‐Spengler, Ashfaq Ahmed
Software Mentions: 3
Published: over 3 years ago

10.18632/oncotarget.14050

Genomic binding of PAX8-PPARG fusion protein regulates cancer-related pathways and alters the immune landscape of thyroid cancer
Cited by: 12
Author(s): Yanxiao Zhang, Jie Yu, Vladimir Grachtchouk, Tingting Qin, Carey N. Lumeng, Maureen A. Sartor, Ronald J. Koenig
Software Mentions: 3
Published: almost 8 years ago

10.1172/jci.insight.141690

Aging imparts cell-autonomous dysfunction to regulatory T cells during recovery from influenza pneumonia
Cited by: 20
Author(s): Luisa Morales‐Nebreda, Kathryn A. Helmin, Manuel A. Torres Acosta, Nikolay S. Markov, Jennifer Yuan Shih Hu, Anthony M. Joudi, Raul Piseaux‐Aillon, Hiam Abdala‐Valencia, Yuliya Politanska, Benjamin D. Singer
Software Mentions: 3
Published: over 3 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568