Computational Genomics       

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Computational Genomics - Publications


   

2017

 
Enhancing Next‐Generation Sequencing‐Guided Cancer Care Through Cognitive Computing. N.M. Patela, V.V. Michelini, J.M. Snell, S. Balua, A.P. Hoyle, J.S. Parker, M.C. Hayward, D.A. Eberhard, A.H. Salazar, P. McNeillieg, J. Xu, C.S. Huettner, T. Koyama, F. Utro, K. Rhrissorrakrai, R. Norel, E. Bilal, A. Royyuru, L. Parida, H.S. Earp, J.E. Grilley‐Olson, D.N. Hayes, S.J. Harvey, N.E. Sharpless, W.Y. Kim, The Oncologist, 2017.
 
Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases. J. A. Romero Navarro, W. Phillips-Mora , A. Arciniegas-Leal, A. Mata-Quirós, N. Haiminen, G. Mustiga, D. Livingstone III, H. van Bakel, D. N. Kuhn, L. Parida, A. Kasarskis, J.C. Motamayor, Frontiers in Plant Science, 2017.
 
The SeqAn C++ template library for efficient sequence analysis: A resource for programmers. K. Reinert, T. H. Dadi, M. Ehrhardt, H. Hauswedell, S. Mehringer, R. Rahn, J. Kim, C. Pockrandt, J. Winkler, E. Siragusa, G. Urgese, D. Weese, Journal of Biotechnology, Elsevier, 2017.
 
Full-Text Indexes for High-Throughput Sequencing. D. Weese, E. Siragusa, Algorithms for Next-Generation Sequencing Data, Springer, 2017.
 
 
Association of waterpipe smoking with myocardial infarction and determinants of metabolic syndrome among catheterized patients. D.E. Platt, E. Hariri , P. Salameh, M. Merhi, N. Sabbah, M. Helou, F. Mouzaya, R. Nemer, Y. Al-Sarraj, H. El-Shanti, A.B. Abchee, P.A. Zalloua, Diabetology & Metabolic Syndrome, BioMed Central Ltd, 2017.
 
Host Phenotype Prediction from Differentially Abundant Microbes Using RoDEO. A.C. Carrieri, N. Haiminen, L. Parida, Lecture Notes in Computer Science, Springer, 2017.
 
Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma. K.O. Wrzeszczynski, M.O. Frank, T. Koyama, K. Rhrissorrakrai, N. Robine, F. Utro, A.-K. Emde, B.-J. Chen, K. Arora, M. Shah, V. Vacic, R. Norel, E. Bilal, E.A. Bergmann, J.L. Moore Vogel, J.N. Bruce, A.B. Lassman, P. Canoll, C. Grommes, S. Harvey, L. Parida, V.V. Michelini, M.C. Zody, V. Jobanputra, A.K. Royyuru, R.B. Darnell, Neurology Genetics, AAN Enterprises, 2017.
 
Type II diabetes mellitus and hyperhomocysteinemia: a complex interaction. D.E. Platt, E. Hariri , P. Salameh, M. Helou, N. Sabbah, M. Merhi, E. Chammas, W. Ammar, A.B. Abchee, P.A. Zalloua, Inhalation Toxicology, 2017.
 
Mapping Post-Glacial expansions: The Peopling of Southwest Asia. D.E. Platt, M. Haber, M.B. Dagher-Kharrat, B. Douaihy, G. Khazen, M.A. Bonab, A. Salloum, F. Mouzaya, D. Luiselli, C. Tyler-Smith, C. Renfrew, E. Matisoo-Smith, P.A. Zalloua, Scientific Reports, Nature, 2017.

2016

 
Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins. Z. Waks, O. Weissbrod, B. Carmeli, R. Norel, F. Utro, Y. Goldschmidt, Scientific Reports, Nature, 2016.
 
Design of the MCAW compute service for food safety bioinformatics. S.B. Edlund, K.L. Beck, N. Haiminen, L. Parida, D.B. Storey, B.C. Weimer, J.H. Kaufman, D.D. Chambliss, IBM Journal of Research and Development, 2016.
 
Scalable Algorithms at Genomic Resolution to fit LD Distributions. L. Parida, N. Haiminen, Proceedings of the 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 2016.
 
A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis. D.P. Noren, B.L. Long, R. Norel, K. Rhrissorrakrai, K. Hess, C.W. Hu, A.J. Bisberg, A. Schultz, E. Engquist, L. Liu, X. Lin, G.M. Chen, H. Xie, G.A.M. Hunter, P.C. Boutros, O. Stepanov, DREAM 9 AML-OPC Consortium, T. Norman, S.H. Friend, G. Stolovitzky, S. Kornblau, A.A. Qutub , PLoS Computational Biology, Public Library of Science, 2016.
 
Caffeine Impact on Metabolic Syndrome Components Is Modulated by a CYP1A2 Variant. D.E. Platt, M. Ghassibe-Sabbagh, P. Salameh, A.K. Salloum, M. Haber, F. Mouzaya, D. Gauguier, Y. Al-Sarraj, H. El-Shanti, P.A. Zalloua, A.B. Abchee, Ann Nutr Metab, 2016.
 
 
Shared genetic variants between serum levels of high-density lipoprotein cholesterol and wheezing in a cohort of children from Cyprus. K.Y. Panayiotis, P. Kouis, K. Ourania, Y. Sonia, C.S. Savvas, D. Kleanthi, Z. Aikaterini, D.E. Platt, M. Nicos, Z. Pierre, Italian Journal of Pediatrics, BioMed Central Ltd, 2016.
 
 
 

2015

 
Variable-Selection Emerges on Top in Empirical Comparison of Whole-Genome Complex-Trait Prediction Methods. D.C. Haws, I. Rish , S. Teyssedre, D. He, A.C. Lozano, P. Kambadur, Z. Karaman, L. Parida, PLOS One, 2015.
 
 
Host Trait Prediction of Metagenomic Data for Topology-based Visualization. L. Parida, N. Haiminen, D. Haws, J. Suchodolski, Lecture Notes in Computer Science,Springer, 2015.
 
MINT: Mutual Information based Transductive Feature Selection for Genetic Trait Prediction. D. He, I. Rish, D. Haws, L. Parida IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015.
 
Data-driven encoding for quantitative genetic trait prediction. D. He, Z. Wang, L. Parida, BMC Bioinformatics, BioMed Central Ltd, 2015.
 
 
 
Topological Signatures for Population Admixture. L. Parida, F. Utro, D. Yorukoglu, A.P. Carrieri, D. Kuhn, S. Basu, Research in Computational Molecular Biology, Elsevier, 2015.
 
Circulating lipid levels and risk of coronary artery disease in a large group of patients undergoing coronary angiography. D.E. Platt, M. Ghassibe-Sabbagh, S. Youhanna, J. Hager, J.-B. Cazier, Y. Kamatani, A.K. Salloum, M. Haber, J. Romanos, B. Doueihy, F. Mouzaya, S. Kibbani, H. Sbeite, M.E. Deeb, E. Chammas, H. el Bayeh, G. Khazen, D. Gauguier, P.A. Zalloua, A.B. Abchee, FGENTCARD Consortium, Journal of Thrombosis and Thrombolysis, Springer, 2015.
 
ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis. R. Giancarlo, D. Scaturro, F. Utro, Computer Methods and Programs in Biomedicine, Elsevier, 2015.

2014

 
T2DM GWAS in the Lebanese population confirms the role of TCF7L2 and CDKAL1 in disease susceptibility. M. Ghassibe-Sabbagh, M. Haber, A.K. Salloum, Y. Al-Sarraj, Y. Akle, K. Hirbli, J. Romanos, F. Mouzaya, D. Gauguier, D.E. Platt, H. El-Shanti, P.A. Zalloua, Scientific Reports, Nature, 2014.
 
Identifying Genetic Relatives without Compromising Privacy. D. He, N.A. Furlotte, R. Ostrovsky, A. Sahai, E. Eskin, Genome Research, 2014.
 
Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies. M.G. Vilar, C. Melendez, A.B. Sanders, A. Walia, J.B. Gaieski, A.C. Owings, T.G. Schurr, Genographic Consortium, Am. J. Phys. Anthropol, 2014.
 
Association of hypertension with coronary artery disease onset in the Lebanese population. A. Milane, J. Abdallah, R. Kanbar, G. Khazen, M. Ghassibe-Sabbagh, A.K. Salloum, S. Youhanna, A. Saad, H. El Bayeh, E. Chammas, D.E. Platt, J. Hager, D. Gauguier, P. Zalloua, A. Abchee, FGENTCARD Consortium, Springerplus, 2014.
 
Geographic population structure analysis of worldwide human populations infers their biogeographical origins. E. Elhaik, T. Tatarinova, D. Chebotarev, I.S. Piras, C.M. CalÚ, A. De Montis, M. Atzori, M. Marini, S. Tofanelli, P. Francalacci, L. Pagani, C. Tyler-Smith, Y. Xue, F. Cucca, T.G. Schurr, J.B. Gaieski, C. Melendez, M.G. Vilar, A.C. Owings, R. GÛmez, R. Fujita, F.R. Santos, D. Comas, O. Balanovsky, E. Balanovska, P. Zalloua, H. Soodyall, R. Pitchappan, A. GaneshPrasad, M. Hammer, L. Matisoo-Smith, R.S. Wells, The Genographic Consortium, Nature Communications, 2014.
 
Comparative exomics of Phalaris cultivars under salt stress. N. Haiminen, M. Klass, Z. Zhou, F. Utro, P. Cormican, T. Didion, C.S. Jensen, C.E. Mason, S. Barth, L. Parida, BMC Genomics, BioMed Central Ltd, 2014.
 
Multivariate epidemiologic analysis of type 2 diabetes mellitus risks in the Lebanese population. M. Ghassibe-Sabbagh, M. Deeb, A.K. Salloum, F. Mouzaya, M. Haber, Y. Al-Sarraj, Y. Chami, Y. Akle, K. Hirbli, R. Nemr, R. Ahdab1, D.E. Platt, A.B. Abchee, H. El-Shanti, P.A. Zalloua, Diabetology & Metabolic Syndrome, BioMed Central Ltd, 2014.
 
IPED2: Inheritance path based pedigree reconstruction algorithm for complicated pedigrees. D. He, Z. Wang, L. Parida, E. Eskin , Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 2014.
 
Transductive HSIC Lasso. D. He, I. Rish, L. Parida, Proceedings of the 2014 SIAM International Conference on Data Mining, 2014.
 
BAC Sequencing Using Pooled Methods. C.A. Saski, F.A. Feltus, L. Parida, N. Haiminen, Methods in Molecular Biology, Springer, 2014.
 
Best-Fit in Linear Time for Non-generative Population Simulation. N. Haiminen, C. Lebreton, L. Parida, Lecture Notes in Computer Science, Springer, 2014.
 
Mitochondrial genome sequencing in Mesolithic North East Europe Unearths a new sub-clade within the broadly distributed human haplogroup C1. C. Der Sarkissian, P. Brotherton, O. Balanovsky, J.E. Templeton, B. Llamas, J. Soubrier, V. Moiseyev, V. Khartanovich, A. Cooper, W. Haak, Genographic Consortium, PLoS One, 2014.
 
From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes. A.C. Clarke, S. Prost, J.A. Stanton, W.T. White, M.E. Kaplan, E.A. Matisoo-Smith, Genographic Consortium, BMC Genomics, 2014.
 
Bayesian versus data driven model selection for microarray data. R. Giancarlo, G. Lo Bosco, F. Utro, Natural Computing, Springer, 2014.
 

2013

 
JNK1 stress signaling is hyper-activated in high breast density and the tumor stroma: Connecting fibrosis, inflammation, and stemness for cancer prevention. M.P. Lisanti, A. Tsirigos, S. Pavlides, K.J. Reeves, M. Peiris-Pag&eacutes, A.L. Chadwick, R. Sanchez-Alvarez, R. Lamb, A. Howell, U.E. Martinez-Outschoorn, F. Sotgia, Cell Cycle, 2013.
 
Compressive biological sequence analysis and archival in the era of high-throughput sequencing technologies. R. Giancarlo, S.E. Rombo, F. Utro, Briefings in bioinformatics, Oxford Univ Press, 2013.
 
Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata. A. Boattini, B. Martinez-Cruz, S. Sarno, C. Harmant, A. Useli, P. Sanz, D. Yang-Yao, J. Manry, G. Ciani, D. Luiselli, L. Quintana-Murci, D. Comas, D. Pettener, Genographic Consortium, PLoS One, 2013.
 
Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations. D.A. Badro, B. Douaihy, M. Haber, S.C. Youhanna, A. Salloum, M. Ghassibe-Sabbagh, B. Johnsrud, G. Khazen, E. Matisoo-Smith, D.F. Soria-Hernanz, R.S. Wells, C. Tyler-Smith, D.E. Platt, P.A. Zalloua, Genographic Consortium., PLoS One, 2013.
 
Genetic History of Populations: Limits to Inference. D.E. Platt, F. Utro, M.Pybus, L. Parida, Models and Algorithms for Genome Evolution , Springer London, 2013.
 
 
Using Random Graphs in Population Genomics. L. Parida, The Nature of Computation. Logic, Algorithms, Applications (Lecture Notes in Computer Science), Springer Verlag, 2013.
 
iXora: Exact haplotype inferencing and trait association. F. Utro, N. Haiminen, D. Livingstone, O.E. Cornejo, S. Royaert, J.C. Motamayor, D.N. Kuhn and L. Parida, BMC Genetics, BioMed Central Ltd, 2013.
 
The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. J.C. Motamayor, K. Mockaitis, J. Schmutz, N. Haiminen, D. Livingstone, O.E. Cornejo, S. Findley, P. Zheng, F. Utro, S. Royaert, C. Saski, J. Jenkins, R. Podicheti, M. Zhao, B. Scheffler, J. Stack, F. Feltus, G. Mustiga, F. Amores, W. Phillips, J.P. Marelli, G. May, H. Shapiro, J. Ma, C. Bustamante, R. Schnell, D. Main, D. Gilbert, L. Parida and D.N. Kuhn, Genome Biology, BioMed Central Ltd, 2013.
 
Ultrametric networks: a new tool for phylogenetic analysis. A. Apostolico, M. Comin, A. Dress, L. Parida, Algorithms for Molecular Biology, BioMed Central Ltd, 2013.
 
 

2012

 
ARG-based genome-wide analysis of cacao cultivars. F. Utro, O.E. Cornejo, D. Livingstone, J.C. Motamayor, L. Parida, BMC Bioinformatics, BioMed Central Ltd, 2012.
 
Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System. G. ArunKumar , D.F. Soria-Hernanz , V. John Kavitha , V.S. Arun, A. Syama, K.S. Ashokan, K.T. Gandhirajan, K. Vijayakumar, M. Narayanan, M. Jayalakshmi, J.S. Ziegle, A.K. Royyuru, L. Parida, R.S. Wells, C. Renfrew, T.G. Schurr, C.T. Smith, D.E. Platt, R. Pitchappan, PLoS One, 2012.
 
GenomicTools: a computational platform for developing high-throughput analytics in genomics. A. Tsirigos, N. Haiminen, E. Bilal, F. Utro, Open source software in life science research: Practical solutions to common challenges in the pharmaceutical industry and beyond, Woodhead Publishing (Series in Biomedicine No. 16), 2012.
 
 
Evidence of pre-Roman tribal genetic structure in Basques from uniparentally inherited markers. B. Martìnez-Cruz, C. Harmant, D.E. Platt, W. Haak, J. Manry, E. Ramos-Luis, D.F. Soria-Hernanz, F. Bauduer, J. Salaberria, B. Oyharçabal, L. Quintana-Murci, D. Comas and the Genographic Consortium, Molecular Biology and Evolution, 2012.
 
Discovering Patterns in Gene Order. L. Parida, N. Haiminen, Evolutionary genomics: statistical and computational methods (in series Methods in Molecular Biology), 2012.
 
Non-redundant Representation of Ancestral Recombinations Graphs. L. Parida, Evolutionary genomics: statistical and computational methods (in series Methods in Molecular Biology), 2012.
 
 
Is cancer a metabolic rebellion against host aging? In the quest for immortality, tumor cells try to save themselves by boosting mitochondrial metabolism. A. Ertel, A. Tsirigos, D. Whitaker-Menezes, R.C. Birbe, S. Pavlides, U.E. Martinez-Outschoorn, R.G. Pestell, A. Howell, F. Sotgia, M.P. Lisanti , Cell Cycle, 2012.
 
Textual data compression in computational biology: Algorithmic techniques. R. Giancarlo, D. Scaturro, F. Utro, Computer Science Review, Elsevier, 2012.
 
Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia. P. Ntziachristos, A. Tsirigos, P. Van Vlierberghe, J. Nedjic, T. Trimarchi, M. Sol Flaherty, D. Ferres-Marco, V. da Ros, Z. Tang, J. Siegle, P. Asp, M. Hadler, I. Rigo, K. De Keersmaecker, J. Patel, T. Huynh, F. Utro, S. Poglio, J.B. Samon, E. Paietta, J. Racevskis, J.M. Rowe, R. Rabadan, R.L. Levine, S. Brown, F. Pflumio, M. Dominguez, A. Ferrando, I. Aifantis, Nature Medicine, Nature Publishing Group, 2012.
 

2011

 
Large Scale Association Analysis Identifies Three Susceptibility Loci for Coronary Artery Disease. S. Saadè, J.-B. Cazier, M. Ghassibe-Sabbagh, S. Youhanna, D.A. Badro, Y. Kamatani, J. Hager, J.S. Yeretzian, G. El-Khazen, M. Haber, A.K. Salloum, B. Douaihy, R. Othman, N. Shasha, S. Kabbani, H. El Bayeh, E. Chammas, M. Farrall, D. Gauguier, D.E. Platt, P.A. Zalloua and The FGENTCARD Consortium, PLoS ONE, 2011.
 
Hyperactivation of oxidative mitochondrial metabolism in epithelial cancer cells in situ: Visualizing the therapeutic effects of metformin in tumor tissue.. D. Whitaker-Menezes, U.E. Martinez-Outschoorn, N. Flomenberg, R.C. Birbe, A.K. Witkiewicz, A. Howell, S. Pavlides, A. Tsirigos, A. Ertel, R.G. Pestell, P. Broda, C. Minetti, M.P. Lisanti, F. Sotgia, Cell Cycle, 2011.
 
 
Molecular profiling of a lethal tumor microenvironment, as defined by stromal caveolin-1 status in breast cancers.. A.K. Witkiewicz, J. Kline, M. Queenan, J.R. Brody, A. Tsirigos, E. Bilal, A. Ertel, F. Sotgia, M.P. Lisanti, Cell Cycle, 2011.
 
Ketones and lactate increase cancer cell "stemness," driving recurrence, metastasis and poor clinical outcome in breast cancer: achieving personalized medicine via Metabolo-Genomics.. U.E. Martinez-Outschoorn, M. Prisco, A. Ertel, A. Tsirigos, Z. Lin, S. Pavlides, C. Wang, N. Flomenberg, E.S. Knudsen, A. Howell, R.G. Pestell, F. Sotgia, M.P. Lisanti, Cell Cycle, 2011.
 
Randomization techniques for assessing the significance of gene periodicity results. A. Kallio, N. Vuokko, M. Ojala, N. Haiminen, H. Mannila, BMC Bioinformatics, BioMed Central Ltd, 2011.
 
The footprint of recombination gives a new insight in the effective population size and the history of the Old World human populations. M. Melè, A. Javed, M. Pybus, P. Zalloua, M. Haber, D. Comas, M. Netea, O. Balanovsky, E. Balanovska, L. Jin, Y. Yang, R.M. Pitchappan, G. Arunkumar, L. Parida, F. Calafell, J. Bertranpetit and The Genographic Consortium, Molecular Biology and Evolution, 2011.
 
Sequencing of a QTL-rich Region of the Theobroma cacao Genome using Pooled BACs and the Identification of Trait Specific Candidate Genes. F.A. Feltus, C.A. Saski, K. Mockaitis, N. Haiminen, L. Parida, Z. Smith, J. Ford, M.E. Staton, S.P. Ficklin, B.P. Blackmon, C.-H. Cheng, R.J. Schnell, D.N. Kuhn, J.-C. Motamayor, BMC Genomics, BioMed Central Ltd, 2011.
 
The Three Steps of Clustering in the Post-Genomic Era: A Synopsis. R. Giancarlo, G. Lo Bosco, L. Pinello, F. Utro, Computational Intelligence Methods for Bioinformatics and Biostatistics, Springer Berlin / Heidelberg, 2011.
 
IRiS: Construction of ARG networks at genomic scales. A. Javed, M. Pybus, M. Melè, F. Utro, J. Bertranpetit, F. Calafell and L. Parida, Bioinformatics, 2011.
 
Experiences with Mining Temporal Event Sequences from Electronic Medical Records: Initial Successes and Some Challenges. D. Patnaik, P. Butler, N. Ramakrishnan, L. Parida, B. J. Keller, D. A. Hanauer, The 17th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD-2011), 2011.
 
Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon. M. Haber, D. E. Platt, D. A. Badro, Y. Xue, M. El-Sibai, A. Bonb, S. C. Youhanna, S. Saadè, D. F. Soria-Hernanz, A. Royyuru, R. S. Wells, C. Tyler-Smith, P. A. Zalloua, The Genographic Consortium, European Journal of Human Genetics , 2011.
 
A Minimal Descriptor of an Ancestral Recombinations Graph. L. Parida, P. F. Palamara, A. Javed, BMC Bioinformatics, APBC, Inchon, Korea,, BioMed Central Ltd, 2011.
 
 
OMiR: Identification of associations between OMIM diseases and microRNAs. S. Rossi, A. Tsirigos, A. Amoroso, M. Mascellani, I. Rigoutsos, G.A. Calin, S. Volinia, Genomics, 2011.
 
Genomic Regions Tools for High-throughput Analytics in Genomics. A. Tsirigos, N. Haiminen, E. Bilal, IBM Technical Report RC25125, 2011.
 
Speeding up the Consensus Clustering methodology for microarray data analysis. R. Giancarlo, F. Utro, Algorithms for Molecular Biology, BioMed Central Ltd, 2011.

2010

 
 
The autophagic tumor stroma model of cancer or "battery-operated tumor growth": A simple solution to the autophagy paradox. U. E.Martinez-Outschoorn, D. Whitaker-Menezes, S. Pavlides, B. Chiavarina, G. Bonuccelli, T. Casey, A. Tsirigos, G. Migneco, A. Witkiewicz, R. Balliet, I. Mercier, C. Wang, N. Flomenberg, A. Howell, Z. Lin, J. Caro, R. G. Pestell, F. Sotgia, M. P. Lisanti, Cell Cycle, 2010.
 
The autophagic tumor stroma model of cancer: Role of oxidative stress and ketone production in fueling tumor cell metabolism. S. Pavlides, A. Tsirigos, G. Migneco, D. Whitaker-Menezes, B. Chiavarina, N. Flomenberg, P.G. Frank, M.C. Casimiro, C. Wang, R. G. Pestell, U. E. Martinez-Outschoorn, A. Howell, F. Sotgia, M. P. Lisanti, Cell Cycle, 2010.
 
Ancestry informative markers for fine-scale individual assignment to worldwide populations. P. Paschou, J. Lewis, A. Javed, P. Drineas, Journal of Medical Genetics, BMJ Publishing Group Ltd, 2010.
 
Ketones and lactate "fuel" tumor growth and metastasis: Evidence that epithelial cancer cells use oxidative mitochondrial metabolism. G. Bonuccelli, A. Tsirigos, D. Whitaker-Menezes, S. Pavlides, R. G. Pestell, B. Chiavarina, P. G. Frank, N. Flomenberg, A. Howell, U. E. Martinez-Outschoorn, F. Sotgia, M. P. Lisanti, Cell Cycle, 2010.
 
VARUN: Discovering Extensible Motifs under Saturation Constraints. A. Apostolico, M. Comin, L. Parida, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010.
 
Y-chromosome R-M343 African lineages and sickle cell disease reveal structured assimilation in Lebanon. M. Haber, D. E. Platt, S. Khoury, D. A. Badro, M. Abboud, C. Tyler-Smith, P. A. Zalloua,Journal of Human Genetics , 2010.
 
Understanding the "lethal" drivers of tumor-stroma co-evolution: emerging role(s) for hypoxia, oxidative stress and autophagy/mitophagy in the tumor micro-environment. M. P. Lisanti, U. E. Martinez-Outschoorn, B. Chiavarina, S. Pavlides, D. Whitaker-Menezes, A. Tsirigos, A. Witkiewicz, Z. Lin , R. Balliet, A. Howell, F. Sotgia, Cancer Biology & Therapy, 2010.
 
A New Method to Reconstruct Recombination Events at a Genomic Scale. M. Melè, A. Javed, M. Pybus, F. Calafell, L. Parida, J. Bertranpetit, The Genographic Consortium, PLoS Computational Biology, Public Library of Science, 2010.
 
Glycolytic cancer associated fibroblasts promote breast cancer tumor growth, without a measurable increase in angiogenesis: Evidence for stromal-epithelial metabolic coupling. G. Migneco, D. Whitaker-Menezes, B. Chiavarina, R. Castello-Cros, S. Pavlides, R. G. Pestell, A. Fatatis, N. Flomenberg, A. Tsirigos, A. Howell, U. E. Martinez-Outschoorn, F. Sotgia, M. P. Lisanti, Cell Cycle, 2010.
 
Loss of Stromal Caveolin-1 Leads to Oxidative Stress, Mimics Hypoxia, and Drives Inflammation in the Tumor Microenvironment, Conferring the "Reverse Warburg Effect": A Transcriptional Informatics Analysis with Validation. S. Pavlides, A. Tsirigos, I. Vera, N. Flomenberg, P. G. Frank, M. C. Casimiro, C. Wang, P. Fortina, S. Addya, R. G. Pestell, U. E. Martinez-Outschoorn, F. Sotgia, M. P. Lisanti, Cell Cycle, 2010.
 
Ancestral Recombinations Graph: A Reconstructability Perspective using Random-Graphs Framework. L. Parida, Journal of Computational Biology, 2010.
 
Estimating the Ancestral Recombinations Graph (ARG) as compatible networks of SNP Patterns. L. Parida, M. Melè, F. Calafell, J. Bertranpetit, The Genographic Consortium, Journal of Computational Biology, 2010.
 
Graph Model of Coalescence with Recombinations. L. Parida, The Problem Solving Handbook for Computational Biology and Bioinformatics (Lecture notes in mathematics), Springer Verlag, 2010.
 
Transcriptional Evidence for the "Reverse Warburg Effect" in Human Breast Cancer Tumor Stroma and Metastasis: Similarities with Oxidative Stress, Inflammation, Alzheimer's Disease, and "Neuron-Glia Metabolic Coupling". S. Pavlides, A. Tsirigos, I. Vera, N. Flomenberg, P. G. Frank, M. C. Casimiro, C. Wang, R. G. Pestell, U. E. Martinez-Outschoorn, A. Howell, F. Sotgia, M. P. Lisanti, Aging, 2010.
 
Parental consanguinity and family history of coronary artery disease strongly predict early stenosis. S. Youhanna, D. E. Platt, A. Rebeiz, M. Lauridsen, M. E. Deeb, A. Nasrallah, S. Alam, H. Puzantian, S. Kabbani, M. Ghoul, T. G. Zreik, H. el Bayeh, A. Abchee, P. A. Zalloua, Atherosclerosis , 2010.
 
Dynamic Changes in the Human Methylome During Differentiation. L. Laurent, E. Wong, G. Li, T. Huynh, A. Tsirigos, C. T. Ong, H. M. Low, K. W. Kin Sung, I. Rigoutsos, J. Loring, C. L. Wei, Genome Research, 2010.
 
ALOX5AP gene variants show differential association with coronary artery disease in different populations. A. Alwan, S. C. Youhanna, D. E. Platt , M. El-Sibai, J. S. Yerezian, M. E. Deeb, G. Khazen, S. Saadè, T. G. Zreik, H. el Bayeh, A. Maalouf, A. Abchee, P. A. Zalloua, Journal of Community Genetics , 2010.
 
 
Combinatorics in Recombinational Population Genomics. L. Parida, Bioinformatics Research and Applications (in series Lecture Notes in Computer Science), Springer Berlin / Heidelberg, 2010.

2009

 
 
 
A conserved activation element in BMP signaling during Drosophila development. A. Weiss, E. Charbonnier, E. Ellertsdòttir, A. Tsirigos, C. Wolf, R. Schuh, G. Pyrowolakis, M. Affolter, Nature Structural & Molecular Biology, 2009.
 
Minimizing recombinations in consensus networks for phylogeographic studies. L. Parida, A. Javed, M. Melè, F. Calafell, J. Bertranpetit, The Genographic Consortium, BMC Bioinformatics , APBC, Beijing, BioMed Central Ltd, 2009.
 
 
Geographical Structure of the Y-chromosomal Genetic Landscape of the Levant: A coastal-inland contrast. M. El-Sibai, D. E. Platt, M. Haber, Y. Xue, S. C. Youhanna, R. S. Wells, H. Izaabel, M. F. Sanyoura, H. Harmanani, M. A. Bonab, The Genographic Consortium, Annals of human genetics, John Wiley & Sons, 2009.

2008

 
Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns. L. Parida, M. Melè, F. Calafell, J. Bertranpetit, The Genographic Consortium, Journal of Computational Biology, 2008.
 
Identifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean. P. A. Zalloua, D. E. Platt, M. El-Sibai, J. Khalife, N. Makhoul, M. Haber, Y. Xue, H. Izaabel, E. Bosch, S. M. Adams, E. Arroyo, A. M. Lòpez-Parra, M. Aler, A. Picornell, M. Ramon, M. A. Jobling, D. Comas, J. Bertranpetit, R. S. Wells, C. Tyler-Smith, The Genographic Consortium1 The American Journal of Human Genetics, Elsevier, 2008.
 
Y-chromosome diversity in Lebanon is structured by recent historical events. P. A. Zalloua, Y. Xue, J. Khalife, N. Makhoul, L. Debiane, D. E. Platt, A. K. Royyuru, R. J. Herrera, D. F. Hernanz, J. Blue-Smith, R. S. Wells, D. Comas, J. Bertranpetit, C. Tyler-Smith, Am J. Human Genetics, 2008.
 
Detection of Subtle Variations as Consensus Motifs. M. Comin, L. Parida, Theoretical Computer Science, 2008.
 
 
PCA and clustering reveal alternate mtDNA phylogeny of N and M clades. G. Alexe, S. R. Vijaya, M Seller, D. E. Platt, T. Bhanot, S. Hui, M. Tanaka, A. J. Levine, Gyan Bhanot, Journal of Molecular Evolution, 2008.
 
A case for Recombinomics. L. Parida, A. Javed, M. Melè, J. Bertranpetit, IBM Technical Report RC24677, 2008.