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KAOS: a new automated computational method for the identification of overexpressed genes

Angelo Nuzzo, Giovanni Carapezza, Sebastiano Di Bella, Alfredo Pulvirenti, Antonella Isacchi, Roberta Bosotti
2016 BMC Bioinformatics  
Results: We propose a computational method aimed at the automatic identification of genes which are selectively over-expressed in a very small fraction of samples within a specific tissue.  ...  The search for novel rearrangements of kinases or other druggable genes may contribute to understanding the biology of cancerogenesis, as well as lead to the identification of new candidate targets for  ...  Angelo Nuzzo is currently affiliated with the Department of Bioengineering, University of Applied Sciences, Vienna, 1190, Austria.  ... 
doi:10.1186/s12859-016-1188-1 pmid:28185541 pmcid:PMC5123341 fatcat:h5oz5n46mva7pcnn5dbmdoovna

Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)

Chun-Nan Hsu, Jin-Mei Lai, Chia-Hung Liu, Huei-Hun Tseng, Chih-Yun Lin, Kuan-Ting Lin, Hsu-Hua Yeh, Ting-Yi Sung, Wen-Lian Hsu, Li-Jen Su, Sheng-An Lee, Chang-Han Chen (+7 others)
2007 BMC Bioinformatics  
The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers  ...  To further highlight the potential new targets in the inferred network from EHCO, we combine comparative genomics and interactomics approaches to analyze 120 evolutionary conserved and overexpressed genes  ...  and migration of the web system.  ... 
doi:10.1186/1471-2105-8-66 pmid:17326819 pmcid:PMC1828168 fatcat:bredj7xrcrajvbbujgmt35z6wa

BITS 2015: the annual meeting of the Italian Society of Bioinformatics

Luciano Milanesi, Alessandro Guffanti, Giancarlo Mauri, Marco Masseroli
2016 BMC Bioinformatics  
This preface introduces the content of the BioMed Central journal Supplements related to the BITS 2015 meeting, held in Milan, Italy, from the 3 th to the 5 th of June, 2015.  ...  The Supplement Editors wish to thank the helpful suggestions received by the editors of the previous BITS supplements. We also thank the BMC Editorial Office for its efficient and kind support.  ...  Acknowledgements We are extremely grateful to all the referees for their dedication and effort in peer reviewing the manuscripts.  ... 
doi:10.1186/s12859-016-1187-2 pmid:28185548 pmcid:PMC5123416 fatcat:zmpnv3ap6bcq3n6rardvn5tkzq

Detection of Brain Tumor Cells in the Peripheral Blood by a Telomerase Promoter-Based Assay

Kelly M. MacArthur, Gary D. Kao, Sanjay Chandrasekaran, Michelle Alonso-Basanta, Christina Chapman, Robert A. Lustig, E. Paul Wileyto, Stephen M. Hahn, Jay F. Dorsey
2014 Cancer Research  
These results support further development of this assay as a generalized method to detect CTC in patients with cancer.  ...  For patients with brain tumors, such as aggressive glioblastoma multiforme, CTC assays are needed that do not rely on expression of cancer cell surface biomarkers like epithelial cell adhesion molecules  ...  The authors also thank the Department of Radiation Oncology Clinical Research Coordinators for their assistance with sample collections and they acknowledge Oncolys Biopharma (Tokyo, Japan) for providing  ... 
doi:10.1158/0008-5472.can-13-0813 pmid:24525740 pmcid:PMC4144786 fatcat:st7saixyang5pltxhvtm4nedzq

Endoplasmic reticulum aminopeptidase 2 involvement in metastasis of oral cavity squamous cell carcinoma discovered by proteome profiling of primary cancer cells

I-Chun Kuo, Huang-Kai Kao, Yenlin Huang, Chun-I Wang, Jui-Shan Yi, Ying Liang, Chun-Ta Liao, Tzu-Chen Yen, Chih-Ching Wu, Kai-Ping Chang
2017 OncoTarget  
The overall survival rates of patients without and with the ERAP2 overexpression were 71.9% and 56.0%, respectively (P = 0.029).  ...  Oral cavity squamous cell carcinoma (OSCC) is a leading cause of cancer-related deaths worldwide and associated with poor prognosis and mortality.  ...  proteome analysis of primary oral epithelial cells is a feasible strategy for OSCC biomarker identification, and that ERAP2 is a potentially useful tissue marker for the prognosis of OSCC.  ... 
doi:10.18632/oncotarget.18680 pmid:28977897 pmcid:PMC5617457 fatcat:rpo4imzkvrelvnmmudjmjo746i

P2X7 Purinoceptor Affects Ectopic Calcification of Dystrophic Muscles

Robin M. H. Rumney, Justyna Róg, Natalia Chira, Alexander P. Kao, Rasha Al-Khalidi, Dariusz C. Górecki
2022 Frontiers in Pharmacology  
Total loss of P2X7 increased EC, indicating that P2X7 overexpression is a protective mechanism against dystrophic mineralisation.  ...  a protective role for P2X7 against ectopic mineralisation in dystrophic muscle.  ...  Understanding this alteration may lead to the development of new therapies for this debilitating disease but also for other pathologies where EC presents a real problem (Proudfoot 2019; Daniela, Federica  ... 
doi:10.3389/fphar.2022.935804 pmid:35910348 pmcid:PMC9333129 fatcat:67pugt4hmzaf7psf7equsfg4mi

DNA Hypomethylation Is Associated with the Overexpression of INHBA in Upper Tract Urothelial Carcinoma

Chien-Chang Kao, Yin-Lun Chang, Hui-Ying Liu, Sheng-Tang Wu, En Meng, Tai-Lung Cha, Guang-Huan Sun, Dah-Shyong Yu, Hao-Lun Luo
2022 International Journal of Molecular Sciences  
Together, these results are the first evidence of INHBA promoter hypomethylation and INHBA overexpression in UTUC.  ...  Interestingly, a positive correlation was found between SMAD binding and extracellular structure organization with INHBA using gene set enrichment analysis and gene ontology analysis.  ...  Acknowledgments: We thank the Genomics & Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital for technical support.  ... 
doi:10.3390/ijms23042072 pmid:35216189 pmcid:PMC8877459 fatcat:gvdafaxrqvel5m46voth44go3u

Factors associated with survival in a large series of patients with malignant pleural mesothelioma in New South Wales

A Linton, N Pavlakis, R O'Connell, M Soeberg, S Kao, S Clarke, J Vardy, N van Zandwijk
2014 British Journal of Cancer  
Those results indicate that MARCO is probably important for the fast-phase uptake of MWCNT and there are other mechanisms (non-MARCO mediated) in the slow-phase cellular uptake of MWCNT.  ...  There may be a chance that MWCNT migrate from the alveolar space to thoracic cavity.  ...  Since Gene-X and THBS-2 are associated with cell proliferation, the regulation of these genes has a possibility to develop a new molecular target treatment.  ... 
doi:10.1038/bjc.2014.478 pmid:25188323 pmcid:PMC4453733 fatcat:cvajfefqozcuxcvzv2z54d664e

The need for calcium imaging in nonhuman primates: New motor neuroscience and brain-machine interfaces

Daniel J. O'Shea, Eric Trautmann, Chandramouli Chandrasekaran, Sergey Stavisky, Jonathan C. Kao, Maneesh Sahani, Stephen Ryu, Karl Deisseroth, Krishna V. Shenoy
2017 Experimental Neurology  
These limitations have spurred the development of all-optical methods for neural circuit interrogation.  ...  We review here several of the key opportunities and challenges for calcium-based optical imaging in NHPs.  ...  We thank the Deisseroth and Shenoy lab for their helpful discussions.  ... 
doi:10.1016/j.expneurol.2016.08.003 pmid:27511294 pmcid:PMC5154795 fatcat:vkud53m5fneu3ob7xsuqhybqe4

A long noncoding RNA contributes to neuropathic pain by silencing Kcna2 in primary afferent neurons

Xiuli Zhao, Zongxiang Tang, Hongkang Zhang, Fidelis E Atianjoh, Jian-Yuan Zhao, Lingli Liang, Wei Wang, Xiaowei Guan, Sheng-Chin Kao, Vinod Tiwari, Yong-Jing Gao, Paul N Hoffman (+4 others)
2013 Nature Neuroscience  
Long noncoding RNAs (lncRNAs) are emerging as new players in gene regulation, but how lncRNAs operate in the development of neuropathic pain is unclear.  ...  RESULTS Identification of natural Kcna2 antisense RNA in DRG neurons To detect Kcna2 antisense RNA, we first searched a database using the complete published Kcna2 cDNA sequence.  ...  Samulski (University of North Carolina) for the rAAV5 plasmid, J. Zhou (Institute of Biochemistry of Cell Biology, Chinese Academy of Sciences) for the full-length EGFP-MZF1 plasmid and D.Y.H.  ... 
doi:10.1038/nn.3438 pmid:23792947 pmcid:PMC3742386 fatcat:27htnypaujhzpj4swqboyjaej4

ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing [article]

Ricardo F Frausto, Doug D Chung, Payton M. Boere, Vinay S. Swamy, Huong N.V. Duong, Liyo Kao, Rustam Azimov, Wenlin Zhang, Liam Carrigan, Davey Wong, Marco Morselli, Marina Zakharevich (+5 others)
2019 bioRxiv   pre-print
The zinc finger e-box binding homeobox 1 (ZEB1) transcription factor is a master regulator of the epithelial to mesenchymal transition (EMT), and of the reverse mesenchymal to epithelial transition (MET  ...  Posterior polymorphous corneal dystrophy (PPCD), associated with ZEB1 insufficiency, provides a new biological context in which to understand and evaluate the classic EMT/MET paradigm.  ...  been determined for a majority of these genes.  ... 
doi:10.1101/547927 fatcat:nko4uhmnijamndhowlrdguhbs4

Omics-based natural product discovery and the lexicon of genome mining

Henrique Machado, Robert N Tuttle, Paul R Jensen
2017 Current Opinion in Microbiology  
The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.  ...  Acknowledgements Research reported in this publication was supported by the National Institutes of Health under Award Number R01GM085770 and 2U19TW007401.  ...  Genome mining has benefited from a better understanding of the biosynthetic logic of natural products [7, 8] and enhanced computational approaches that automate the process by which BGCs are detected  ... 
doi:10.1016/j.mib.2017.10.025 pmid:29175703 pmcid:PMC5732065 fatcat:ikpc7kcw2zflfluqulgtlqhfs4

Arrival of carbapenem-hydrolyzing-oxacillinases in Acinetobacter baumannii in Bosnia and Herzegovina

Tanja Petrović, Selma Uzunović, Ivan Barišić, Josefa Luxner, Andrea Grisold, Gernot Zarfel, Amir Ibrahimagić, Sanja Jakovac, Domagoj Slaćanac, Branka Bedenić
2018 Infection, Genetics and Evolution  
This prompted us to analyze these isolates with regards to genotypic diversity, antibiotic susceptibility and occurrence of acquired carbapenem resistance genes.  ...  the dynamic changes in  ...  out to the introduction of a new clone..  ... 
doi:10.1016/j.meegid.2017.12.021 pmid:29277554 fatcat:6c6wwie52rb7fgahzus66bt4fq

Kinase/phosphatase overexpression reveals pathways regulating hippocampal neuron morphology

William J Buchser, Tatiana I Slepak, Omar Gutierrez-Arenas, John L Bixby, Vance P Lemmon
2010 Molecular Systems Biology  
We undertook a gain-offunction analysis to determine the functions of kinases and phosphatases in the regulation of neuron morphology.  ...  Development and regeneration of the nervous system requires the precise formation of axons and dendrites.  ...  We thank Nirupa Chaudhari for providing the cDNA encoding the human PKA catalytic a subunit.  ... 
doi:10.1038/msb.2010.52 pmid:20664637 pmcid:PMC2925531 fatcat:5lisnujag5a2lifrwamekjyudq

Multicenter Validation of a 1,550-Gene Expression Profile for Identification of Tumor Tissue of Origin

Federico A. Monzon, Maureen Lyons-Weiler, Ljubomir J. Buturovic, C. Ted Rigl, W. David Henner, Christin Sciulli, Catherine I. Dumur, Fabiola Medeiros, Glenda G. Anderson
2009 Journal of Clinical Oncology  
, Raji Pillai, PhD, for the biologic plausibility analysis (supplemental methods), Shawn Becker for helpful advice and Jane Seck for editorial support.  ...  Acknowledgment We thank Amelia Hensler and Aprel Delo for tissue procurement and preparation, Jill Hagenkord and Melissa Price for retrieval of pathology information, Rebecca Deeter for statistical analyses  ...  The Pearson correlation between the SE values, a continuous variable, and the class label, a binary variable, was computed for probe set #1.  ... 
doi:10.1200/jco.2008.17.9762 pmid:19332734 fatcat:mmne5cgs5rgfredhoyluzdjnom
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