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Discovering novel cancer therapies: A computational modeling and search approach

Arthur W. Mahoney, Brian G. Smith, Nicholas S. Flann, Gregory J. Podgorski
2008 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology  
This paper presents a massively parallel computational search-based approach for the discovery of novel potential cancer treatments using a high fidelity simulation of angiogenesis.  ...  Results show the effectiveness of the search process in finding interventions that are currently in use and more interestingly, discovering some new approaches that are counter intuitive yet effective.  ...  Reviewing the results, it is clear that the Monte Carlo improving search is capable of quickly discovering novel and potentially important cancer therapies.  ... 
doi:10.1109/cibcb.2008.4675785 dblp:conf/cibcb/MahoneySFP08 fatcat:ykwisz4iwrbubn72b2xbol2vbu

Strategies for discovering novel cancer biomarkers through utilization of emerging technologies

Vathany Kulasingam, Eleftherios P Diamandis
2008 Nature Clinical Practice Oncology  
in discovering novel biomarkers for cancer.  ...  strategies represent a central component and a paradigm shift in the search for novel biomarkers (Box 3).  ...  CP Vega, University of California, Irvine, CA, is the author of and is solely responsible for the content of the learning objectives, questions and answers of the Medscapeaccredited continuing medical  ... 
doi:10.1038/ncponc1187 pmid:18695711 fatcat:cjuz2eqw25aoxbv4mvg67mrlze

RGD-Binding Integrins Revisited: How Recently Discovered Functions and Novel Synthetic Ligands (Re-)Shape an Ever-Evolving Field

Beatrice S. Ludwig, Horst Kessler, Susanne Kossatz, Ute Reuning
2021 Cancers  
For this, refined approaches are demanded aiming at alternative and improved preclinical models, optimized selectivity and pharmacological properties of integrin ligands, as well as more sophisticated  ...  Although integrin-targeted (cancer) therapy trials did not meet the high expectations yet, integrins are still valid and promising targets due to their elevated expression and surface accessibility on  ...  cancer models in vitro and in vivo [289] .  ... 
doi:10.3390/cancers13071711 pmid:33916607 fatcat:gy4tdc65zzakpgdxdlu4zhbphm

Towards precision medicine: discovering novel gynecological cancer biomarkers and pathways using linked data

Alokkumar Jha, Yasar Khan, Muntazir Mehdi, Md Rezaul Karim, Qaiser Mehmood, Achille Zappa, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
2017 Journal of Biomedical Semantics  
Next Generation Sequencing (NGS) is playing a key role in therapeutic decision making for the cancer prognosis and treatment.  ...  Consequently, the process of sharing and aggregating multisite sequencing datasets are thwarted by issues such as the need to discover relevant data from different sources, built scalable repositories,  ...  Second, the linking component searches and discovers links between selected datasets.  ... 
doi:10.1186/s13326-017-0146-9 pmid:28927463 pmcid:PMC5606033 fatcat:2ndn3yplorb7jfuu4iwqokphni

Discovering novel driver mutations from pan-cancer analysis of mutational and gene expression profiles

Houriiyah Tegally, Kevin H. Kensler, Zahra Mungloo-Dilmohamud, Anisah W. Ghoorah, Timothy R. Rebbeck, Shakuntala Baichoo, Sophia N. Karagiannis
2020 PLoS ONE  
Our approach allows for the identification of novel putative driver genes that are common across cancer sites using an unbiased approach without any a priori knowledge on pathways or gene interactions  ...  Our driver selection method successfully identified 116 probable novel cancer-causing genes, with 4 discovered in patients having no alterations in any known driver genes: MXRA5, OBSCN, RYR1, and TG.  ...  discover and validate novel cancer driver genes.  ... 
doi:10.1371/journal.pone.0242780 pmid:33232371 fatcat:cju7lhkgcveitf6zuqqkp22ozi

Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies

Paul Geeleher, Zhenyu Zhang, Fan Wang, Robert F. Gruener, Aritro Nath, Gladys Morrison, Steven Bhutra, Robert L. Grossman, R. Stephanie Huang
2017 Genome Research  
R.S.H. also received support from NIH/ NIGMS grant K08GM089941, NIH/NCI grant R21 CA139278, NIH/NIGMS grant U01GM61393, and a Circle of Service Foundation Early Career Investigator award.  ...  Acknowledgments This work was supported by a research grant from the Avon Foundation for Women.  ...  ., a genome-wide screen) (Geeleher et al. 2014b (Geeleher et al. , 2016a Gray and Mills 2015) , and se-verely limits our ability to discover novel drug biomarkers directly in cancer patients.  ... 
doi:10.1101/gr.221077.117 pmid:28847918 pmcid:PMC5630037 fatcat:3aptr7aovba27bakjyekwr5ps4

DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with In Silico Analysis to Identify Novel Therapeutic Targets

A. R. Hanaford, T. C. Archer, A. Price, U. D. Kahlert, J. Maciaczyk, G. Nikkhah, J. W. Kim, T. Ehrenberger, P. A. Clemons, V. Dancik, B. Seashore-Ludlow, V. Viswanathan (+10 others)
2016 Clinical Cancer Research  
Purpose: We used human stem and progenitor cells to develop a genetically accurate novel model of MYC-driven Group 3 medulloblastoma.  ...  Conclusions: We present a new method to generate genetically accurate models of rare tumors, and a companion computational methodology to find therapeutic interventions that target them.  ...  neural stem cell model of medulloblastoma was used as a test subject for a novel computational analysis technique, DiSCoVER, that we briefly describe here (additional details in Materials and Methods)  ... 
doi:10.1158/1078-0432.ccr-15-3011 pmid:27012813 pmcid:PMC5055054 fatcat:kn6zuyhzsba7vgososphojehdm

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy

Vachiranee Limviphuvadh, Chee Seng Tan, Fumikazu Konishi, Piroon Jenjaroenpun, Joy Shengnan Xiang, Yuliya Kremenska, Yar Soe Mu, Nicholas Syn, Soo Chin Lee, Ross A. Soo, Frank Eisenhaber, Sebastian Maurer-Stroh (+1 others)
2018 BMC Cancer  
The purpose of this study is to develop a systematic pathway approach to accurately and efficiently predict novel non-synonymous SNPs (nsSNPs) that could be causative to gemcitabine-based chemotherapy  ...  Conclusions: Our computational SNP candidate enrichment workflow approach was able to identify several high confidence biomarkers predictive for personalized drug treatment outcome while providing a rationale  ...  Therefore, the purpose of this study is to develop a systematic pathway approach to accurately and efficiently predict novel nonsynonymous SNPs (nsSNPs) that could be causative to gemcitabine-based chemotherapy  ... 
doi:10.1186/s12885-018-4471-x pmid:29751792 pmcid:PMC5948914 fatcat:5265if2wvfgmpoks7hch6akkwu

A Novel Galectin-1 Inhibitor Discovered through One-Bead Two-Compound Library Potentiates the Antitumor Effects of Paclitaxel in vivo

Tsung-Chieh Shih, Ruiwu Liu, Gabriel Fung, Gaurav Bhardwaj, Paramita M. Ghosh, Kit S. Lam
2017 Molecular Cancer Therapeutics  
Through the one-bead two-compound (OB2C) ultra-high-throughput screening method, we discovered a new small-molecule compound LLS2 that can kill a variety of cancer cells.  ...  Our results presented here indicate that the OB2C combinatorial technology is a highly efficient drug screening platform, and LLS2 discovered through this method can be further optimized for anticancer  ...  Utilization of the Combinatorial Chemistry Shared Resource was supported by the UC Davis Comprehensive Cancer Center support grant (NCI P30CA093373).  ... 
doi:10.1158/1535-7163.mct-16-0690 pmid:28396365 pmcid:PMC5516795 fatcat:djbemlfsj5ckjkgwa7nyytmj6q

DISCOVERY OF MOLECULARLY TARGETED THERAPIES

KELLY REGAN, ZACHARY ABRAMS, MICHAEL SHARPNACK, ARUNIMA SRIVASTAVA, KUN HUANG, NIGAM SHAH, PHILIP R.O. PAYNE
2015 Biocomputing 2016  
They discovered that by filtering out variance from low functional regions of the genome they could conduct a pair-wise search using linear regression analysis to identify associations.  ...  the identification of molecularly targeted therapies as noted above, have been explored in a number of instances by the biology, computer science and translational bioinformatics communities.  ... 
doi:10.1142/9789814749411_0001 fatcat:5zfvhqmbhzb6zcqyo3zezsoyeu

DISCOVERY OF MOLECULARLY TARGETED THERAPIES

Kelly Regan, Zachary Abrams, Michael Sharpnack, Arunima Srivastava, Kun Huang, Nigam Shah, Philip R O Payne
2016 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
They discovered that by filtering out variance from low functional regions of the genome they could conduct a pair-wise search using linear regression analysis to identify associations.  ...  the identification of molecularly targeted therapies as noted above, have been explored in a number of instances by the biology, computer science and translational bioinformatics communities.  ... 
pmid:26776168 pmcid:PMC4874173 fatcat:ccbs2avjdja3lahhjnaifrqgjq

Drug combination therapy increases successful drug repositioning

Wei Sun, Philip E. Sanderson, Wei Zheng
2016 Drug Discovery Today  
Drug combinations of two or more compounds with different mechanisms of action are an alternative approach to increase the success rate of drug repositioning.  ...  Repositioning of approved drugs has recently gained new momentum for rapid identification and development of new therapeutics for diseases that lack effective drug treatment.  ...  The authors would like to thank DeeAnn Visk for reading and critiquing the manuscript.  ... 
doi:10.1016/j.drudis.2016.05.015 pmid:27240777 pmcid:PMC4907866 fatcat:2u65tf7g3bghpom2nye7atpa2e

INGOT: Towards network-driven in silico combination therapy

Sourav S Bhowmick, Huey-Eng Chua, Jie Zheng
2014 2014 International Conference on Big Data and Smart Computing (BIGCOMP)  
In this paper, we take a step towards this grand goal by laying out the vision of a novel in silico, datadriven combination therapy framework called ingot for complex network diseases.  ...  Combination therapy, where several drugs interact with multiple targets, holds tremendous promise for effective clinical outcomes in the management of chronic, complex diseases such as cancer.  ...  Examples of such a strategy can be found in the combination therapy of aids, cancer, and hypercholesterolaemia [24] .  ... 
doi:10.1109/bigcomp.2014.6741401 dblp:conf/bigcomp/BhowmickCZ14 fatcat:my6ou66ghrb2tf4tjj3cf3qgaa

Novel Holistic Approaches for Overcoming Therapy Resistance in Pancreatic and Colon Cancers

Fazlul H. Sarkar
2015 Medical Principles and Practice  
This short review article provides an overview of the different challenges involved in the understanding of the GI resistome, and how novel computational biology can help in the design of effective therapies  ...  Natural agents (dietary agents or their synthetic derivatives) can individually alter miRNA profiles, suppress EMT pathways and eliminate cancer stem-like cells that derive from pancreatic cancer and colon  ...  of complex and therapy-resistant disease models such as GI cancer.  ... 
doi:10.1159/000435814 pmid:26228733 pmcid:PMC5588517 fatcat:fl4rjep5gvhibkxm5a3xxxlmpm

Targeting p53-MDM2-MDMX Loop for Cancer Therapy [chapter]

Qi Zhang, Shelya X. Zeng, Hua Lu
2014 Sub-cellular biochemistry  
The tumor suppressor p53 plays a central role in anti-tumorigenesis and cancer therapy.  ...  In this chapter, we review the approaches for screening and discovering efficient and selective MDM2 inhibitors with emphasis on the most advanced synthetic small molecules that interfere with the p53-  ...  Acknowledgements This work was supported in part by NIH-NCI grants CA095441, CA 079721, CA129828, and CA172468, as well as the LLL fund to H.L.  ... 
doi:10.1007/978-94-017-9211-0_16 pmid:25201201 pmcid:PMC4472007 fatcat:j7y4hhaaqrdcfkegzexvewuetm
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