Publications

Please find some of our work below


Published Papers & Letters


Phylogenetic Cladograms: Tools for Analyzing Biomedical Data.


Abu-Asab MS, and Jim DeLeo.


In Springer Handbook of Bio-/Neuroinformatics


Editors: Nikola Kasabov


ISBN: 978-3-642-30573-3 (Print) 978-3-642-30574-0 (Online)

Manuscript: | Abstract




Systems Biology Profiling of AMD on the Basis of Gene Expression.


Abu-Asab MS, Salazar J, Tuo J, Chan CC.


PMID: 24349763

Published in final edited form as: J Ophthalmol. 2013;2013:453934. doi: 10.1155/2013/453934. Epub 2013 Nov 14.

Manuscript: | Abstract | Full Text | PDF




Identifying Early Events of Gene Expression in Breast Cancer with Systems Biology Phylogenetics


Abu-Asab MS, Abu-Asab N, Loffredo CA, Clarke R, Amri H.


PMID: 23548567

Published in final edited form as: Cytogenet Genome Res. 2013 Apr 2:206-214.

Manuscript: | Abstract | Full Text | PDF




Analyzing heterogeneous complexity in complementary and alternative medicine research: a systems biology solution via parsimony phylogenetics


Abu-Asab M, Koithan M, Shaver J, Amri H.


PMID: 22327551

Published in final edited form as: Forsch Komplementmed. 2012;19 Suppl 1:42-8. Epub 2012 Jan 20.

Manuscript: | Abstract | Full Text | PDF




Endometriosis gene expression heterogeneity and biosignature: a phylogenetic analysis


Abu-Asab M, Zhang M, Amini D, Abu-Asab N, Amri H.


PMID: 22203846

Published in final edited form as: Obstet Gynecol Int. 2011;2011:719059. Epub 2011 Dec 13.

Manuscript: | Abstract | Full Text | PDF




Biomarkers in the Age of Omics: Time for a Systems Biology Approach


Abu-Asab MS, Chaouchi M, Alesci S, Galli S, Laassri M, Cheema AK, Atouf F, Vanmeter J, Amri H.


PMID: 21319991

Published in final edited form as: OMICS. 2011 Feb 14.

Manuscript: | Abstract | Full Text | PDF




Algorithmic assessment of vaccine-induced selective pressure and its implications on future vaccine candidates


Abu-Asab MS, Laassri M, Amri H.


PMID: 20150957

Published in final edited form as: Adv Bioinformatics. 2010;2010:178069. Epub 2010 Feb 1.

Manuscript: | Abstract | Full Text | PDF




Microarrays Need Phylogenetics


Mones Abu-Asab


Science Signaling

Published in final edited form as: Sci. STKE (E-Letter, 30 January 2009) http://stke.sciencemag.org/cgi/eletters/sigtrans;1/51/eg11.

Manuscript: | Letter




Phylogenetic Modeling of Heterogeneous Gene-Expression Microarray Data from Cancerous Specimens


Mones Abu-Asab, Mohamed Chaouchi, and Hakima Amri


OMICS: A Journal of Integrative Biology. Author manuscript available in PMC 2008 November 17.


PMCID: PMC2583934

Published in final edited form as: Omics 2008 Sept; 12(3): 183-199.


doi: 10.1089/omi.2008.0010.

Manuscript: | Abstract | Full Text | PDF�1mb




Evolutionary medicine: A meaningful connection between omics, disease, and treatment


Mones Abu-Asab, Mohamed Chaouchi, and Hakima Amri


Proteomics Clin Appl. Author manuscript; available in PMC 2008 May 5.


PMCID: PMC2367146

Published in final edited form as: Proteomics Clin Appl. 2008 February; 2(2): 122�134.


doi: 10.1002/prca.200780047.

Manuscript: | Abstract | Full Text | PDF�685K |




Phyloproteomics: What Phylogenetic Analysis Reveals about Serum Proteomics


Mones Abu-Asab, Mohamed Chaouchi, and Hakima Amri


J Proteome Res. Author manuscript available in PMC 2008 March 20.


PMCID: PMC2270414

Published in final edited form as: J Proteome Res. 2006 September; 5(9): 2236�2240.


doi: 10.1021/pr0504485.

Manuscript: | Abstract | Full Text | PDF�523K |




Published Abstracts


2010: Modeling cancer heterogeneity using parsimony phylogenetics: a systems biology approach. Amri H, Abu-Asab MS, Chaouchi M, Alesci S, Galli S, Laassri M, Cheema KA, Atouf F, VanMeter J. Days of Molecular Medicine 2010, Systems Biology Approaches to Cancer and Metabolic Disease, May 20-22, Karolinska Institutet, Stockholm, Sweden.


2008: A Phylogenetic Paradigm for Dynamic Systems Biology: An Integrative Modeling of the Heterogeneities of the Omics Data and Disease. USHUPO 4th Annual Conference, March 2008, Bethesda, MD.


2007: Phyloarray: a phylogenetic approach to cancer gene-expression microarray analysis. 98th Annual Meeting of the American Association for Cancer Research, April 2007, Los Angeles, CA


2006: Phyloproteomics: What Phylogenetic Analysis Reveals About Serum Proteomics. 97th Annual Meeting of the American Association for Cancer Research, April 2006, Washington, DC


Authors


Mones Abu-Asab, Mohamed Chaouchi, and Hakima Amri.






Recommended Readings




Vincent M.D.


Cancer: beyond speciation


Adv Cancer Res. 2011;112:283-350. PMID: 21925308






Berman, J.J. and Moore, G.W.


Precancer: The Beginning and the End of Cancer


Jones & Bartlett Publishers


Sudbury, MA 01776 2009.




Heng HH, Liu G, Stevens JB, Bremer SW, Ye KJ, Ye CJ.


Genetic and Epigenetic Heterogeneity in Cancer: The Ultimate Challenge for Drug Therapy.


Curr Drug Targets. 2010 Jul 1. PMID: 20594169



Ziliak ST.


The Validus Medicus and a new gold standard.


Lancet. 2010 Jul 31;376(9738):324-5. PMID: 20681063




Heng HH, Bremer SW, Stevens JB, Ye KJ, Liu G, Ye CJ.


Genetic and epigenetic heterogeneity in cancer: a genome-centric perspective.


J Cell Physiol. 2009 Sep;220(3):538-47. Review.PMID: 19441078



Randolph M. Nesse, Stephen C. Stearns (2008)


The great opportunity: Evolutionary applications to medicine and public health


Evolutionary Applications 1 (1) , 28�48






Albert, V. A. (Ed.),


Parsimony, phylogeny, and genomics


Oxford University Press,


Oxford, OX ; New York 2005.




Shibata, D.


Stem cells as common ancestors in a colorectal cancer ancestral tree.


Curr Opin Gastroenterol. 2008 Jan;24(1):59-63. Review. PMID: 18043234




Wong KM, Suchard MA, Huelsenbeck JP.


Alignment uncertainty and genomic analysis.


Science. 2008 Jan 25;319(5862):473-6.PMID: 18218900






Frank, S. A.. 2007.


Dynamics of Cancer: Incidence, Inheritance, and Evolution.


Princeton University Press,


Princeton, NJ.




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