The Simons Center for Systems Biology - Research

Research interests at The Simons Center for Systems Biology include genetics and genomics, polymorphisms and molecular aspects of evolution, signal transduction pathways and networks, stress responses and pharmacogenomics in cancer biology. Members of the group explore the linkage between theoretical and experimental biology. The group has developed algorithms that have led to the discovery of correlations and signals that are characteristic of viruses, diseases such as cancer, and traits such as embryonic development and longevity. Researchers also are investigating protein-protein interaction networks, including the prediction of protein-protein interactions from sequence analysis, and the dynamics of mRNA and protein expression in gene circuits.

Using tools from statistical mechanics and information theory, Members are addressing problems in population genetics and association studies, haplotype structure and gene selection in the p53 pathway, and uncovering epistatic interactions between single nucleotide polymorphisms related to cell apoptosis as well as developing protocols for molecular profiling of cancer; studying evolutionary genetics, and patterns of mutations correlated with longevity. They are exploring the bioinformatics of DNA and RNA sequences with applications including patterns of re-assortment in viruses, optimal RNA expression for vaccines and chromatin structure as a function of DNA sequence; and developing numerically efficient theoretical methods to describe quantum effects experimentally observed in enzymatic reactions.

Other areas of activity include molecular coding theory and the physics of proteins. Members are exploring how the unique physico-chemical properties of large biomolecules are determined by the sequential information of DNA, the relationship between physical properties of proteins and their function as information processors; correlations between amino acid frequencies and position in multiple sequence alignments, and the dimensionality of the phenotype space in which biological functions evolve. There is also research focused on the physical processes of thermodynamic equilibrium based on information handling that relate to the basic workings of life––maintenance, growth, and reproduction; the impact of microscopic noise on the collective properties of biological systems at the “network” level; and the evolutionary mechanisms for microbial populations to adapt to varying environments.

The Center’s first publication from research on genetic predispositions to cancer, A Single Nucleotide Polymorphism in the MDM2 Promoter Attenuates the p53 Tumor Suppressor Pathway and Accelerates Tumor Formation in Humans, appeared in the journal Cell in November 2004.

A selection of other papers includes:

Krotov D, Hopfield, JJ "Unsupervised learning by competing hidden units" PNAS April 16, 2019, vol. 116, no. 16, 7723-7731. doi/10.1073/pnas.1820458116

Krotov D, Hopfield JJ "Dense Associative Memory is Robust to Adversarial Inputs" Neural Computation 30, 3151-3167 (2018). doi:10.1162/neco_a_01143

Luksza M, Riaz N, Makarov V, Balachandran VP, Hellmann MD, Solovyov A, Rizvi NA, Merghoub T, Levine AJ, Chan TA, Wolchok JD, Greenbaum BD "A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy" Nature 2017, doi:10.1038/nature24473

Balachandran VP, Luksza M, Zhao JN, Makarov V, Moral JA, Remark R, Herbst B, Askan G, Bhanot U, Senbabaoglu Y, Wells DK, Ormsby Cary CI, Grbovic-Huezo O, Attiyeh M, Medina B, Zhang J, Loo J, Saglimbeni J, Abu-Akeel M, Zappasodi R, Riaz N, Smoragiewicz M, Z. Larkin Kelley, Basturk O, Australian Pancreatic Cancer Genome Initiative, Gonen M, Levine AJ, Allen PJ, Fearon DT, Merad M, Gnjatic S, Iacobuzio-Donahue CA, Wolchok JD, DeMatteo RP, Chan TA, Greenbaum BD, Merghoub T, Leach, SD "Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer" Nature 2017, doi:10.1038/nature24462

Xue B & Leibler S "Bet Hedging against Demographic Fluctuations" Phys. Rev. Lett. 119, 108103 (2017)

Xue B & Leibler S “Evolutionary learning of adaptation to varying environments through a transgenerational feedback” PNAS Oct. 4, 2016, 113 (40) 11266-11271. doi:10.1073/pnas.1608756113

Mitchell MR, Tlusty T, Leibler S "Strain analysis of protein structures and low dimensionality of mechanical allosteric couplings" PNAS Oct 4, 2016, 113(40):E5847-E5855.doi:10.1073/pnas.1609462113

Pandey PP & Jain S "Analytical derivation of bacterial growth laws from a simple model of intracellular chemical dynamics" Theory Biosci. (2016) 135: 121-130. doi:10.1007/s12064-016-0227-9

Krotov D, Hopfield, JJ "Dense Associative Memory for Pattern Recognition" Advances in Neural Information Processing Systems 29, 1172-1180.arXiv:1606.01164 [cs.NE](2016)

Riccardo R, Peliti L “Thermodynamics of accuracy in kinetic proofreading: dissipation and efficiency trade-offs” Journal of Statistical Mechanics: Theory and Experiment 1 June 2015. Online at doi:10.1088/1742-5468/2015/06/P06001

Murugan A, Huse DA, Leibler S “Discriminatory Proofreading Regimes in Nonequilibrium Systems” PHYSICAL REVIEW X 2014 APR 25; 4(2): Article 021016

Thierry M, Peliti, L, Rivoire, O. “JSP Special Issue on Information Processing in Living Systems” J Stat Phys (2016) 162:1085-1087.DOI 10.1007/s10955-016-1459-2

Tlusty T "Self-referring DNA: a remark on physical and geometrical aspects" Phil Trans Roy Soc A 374: 20150070 (2016)

Lampert A & Tlusty T "Where two are fighting the third wins: Stronger selection implies greater polymorphism" (2016) PLoS one 11(2): e0147970

Savir Y, Kagan J & Tlusty T "Binding of transcription factors adapts to resolve information-energy trade-off" J Stat Phys 1-12 (2015)

Tesileanu T, Colwell LJ, Leibler S (2015) "Protein Sectors: Statistical Coupling Analysis versus Conservation" PLoS Computational Biology 11(2), e1004091. doi:10.1371/journal.pcbi.1004091

Pugatch, Rami "Greedy scheduling of cellular self-replication leads to optimal doubling times with a log-Frechet distribution" PNAS February 24, 2015 Vol. 112, no. 8, 2611-2616. Doi:10.1073/pnas.1418738112

Greenbaum BD, Kumar P, Libchaber A (2014) "Using First Passage Statistics to Extract Environmentally Dependent Amino Acid Correlations" PLoS ONE 9(7):e101665. doi:10.1371/journal.pone.0101665

Wagh K, Bhatia A, Greenbaum BD, Bhanot G (2014) "Bird to Human Transmission Biases and Vaccine Escape Mutants in H5N1 Infections" PLoS ONE 9(7):e100754. doi:10.1371/journal.pone.0100754

Shani I, Beatus T, Bar-Ziv RH, Tlusty T (February 2014) "Long-range orientational order in two-dimensional microfluidic dipoles" Nature Physics 10(2), 140-144. DOI:10.1038/NPHYS2843

Dwyer RS, Ricci DP, Colwell LJ, Silhavy TJ, Wingreen NS "Predicting Functionally Informative Mutations in Escherichia coli BamA Using Evolutionary Covariance Analysis" Genetics 2013 Aug 9 [Epub ahead of print] PMID: 23934888

Friedlander T, Mayo AE, Tlusty T, Alon U (August 2013) "Mutation Rules and the Evolution of Sparseness and Modularity in Biological Systems" PLoS ONE 8(8):e70444.doi:10.1371/journal.pone.0070444

Ponulak F, Hopfield JJ "Rapid, parallel path planning by propagating wavefronts of spiking neural activity" Front Comput Neurosci. 2013 July 18;7:98. doi: 10.3389/fncom.2013.00098. PMID: 23882213

Chin AW, Greenbaum BD, Li OT, Webby RJ, Poon LL "A statistical strategy to identify recombinant viral ribonucleoprotein of avian, human, and swine influenza A viruses with elevated polymerase activity" Influenza Other Respi Viruses 2013 May 2. doi: 10.1111/irv.12117. PMID: 23634764

Savir Y, Tlusty T "The ribosome as an optimal decoder: a lesson in molecular recognition" Cell 2013 Apr 11;153(2):471-9. doi: 10.1016/j.cell.2013.03.032. PMID: 23582332

Giacobbe A, Bongiorno-Borbone L, Bernassola F, Terrinoni A, Markert EK, Levine AJ, Feng Z, Agostini M, Zolla L, Agro AF, Notterman DA, Merlino G, Peschiaroli A "p63 regulates glutaminase 2 expression" Cell Cycle 2013 May 1;12(9):1395-405. doi: 10.4161/cc.24478. Epub 2013 Apr 10. PMID: 23574722

Lampert A, Tlusty T "Resonance-induced multimodal body-size distributions in ecosystems" Proc Natl Acad Sci USA 2013 Jan 2;110(1):205-9. doi: 10.1073/pnas.1211761110. Epub 2012 Dec 17. PMID: 23248320

Levine AJ, Greenbaum B "The Maintenance of Epigenetic States by p53: The Guardian of the Epigenome" Oncotarget 2012 Dec 11; 3 (12): 1503-1504. PMID: 23237909

Maeda YT, Tlusty T, Libchaber A "Effects of long DNA folding and small RNA stem-loop in thermophoresis" Proc Natl Acad Sci USA 2012 Oct 30;109(44):17972-7. doi: 10.1073/pnas.1215764109. Epub 2012 Oct 15. PMID: 23071341

Markert, EK, Levine, AJ, Vazquez A “Proliferation and tissue remodeling: the hallmarks revisited” Cell Death and Disease 2012. Oct 4; 3:e397. doi: 10.1038/cddis.2012.140. PMCID: PMC3481128

Wagh K, Bhatia A, Alexe G, Reddy A, Ravikumar V, Seiler M, Boemo M, Yao M, Cronk L, Naqvi A, Ganesan S. Levine AJ, Bhanot G “Lactase Persistence and Lipid Pathway Selection in the Maasai” PLoS One 2012;7(9):e44751. doi: 10.1371/ journal.pone. 0044751. Epub 2012 Sep 28. PMCID: PMC3461017

Levary D, Eckmann J-P, Moses E, Tlusty T (2012) "Loops and Self-Reference in the Construction of Dictionaries" Phys Rev X, 2(3): 031018.DOI:10.1103/PhysRevX.2.031018

Savir Y, Waysbort N, Antebi YE, Tlusty T, Friedman N "Balancing speed and accuracy of polyclonal T cell activation: a role for extracellular feedback" BMC Syst Biol. 2012 Aug 27;6:111. doi: 10.1186/1752-0509-6-111. PMID: 22925037

Lukic S, Hey J "Demographic inference using spectral methods on SNP data, with an analysis of the human out-of-Africa expansion" Genetics 2012 Oct;192(2):619-39. doi: 10.1534/genetics.112.141846. Epub 2012 Aug 3

Murugan A, Huse DA, Leibler S “Speed, dissipation, and error in kenetic proofreading” PNAS 2012 doi/10.1073/pnas.1119911109

Yu X, Vazquez A, Levine AJ, Carpizo DR “Allele-Specific p53 Mutant Reactivation” Cancer Cell, 2012 May 15; 21 (5): 614-625. PMCID: PMC3366694, NIHMS372800

Levine, AJ “Damage that Precedes Parkinson Symptoms” Proc. Natl. Acad. Sci. (February 28, 2012) 109 (9) 3191–3192. doi/10.1073/iti0912109

Greenbaum BD, Li OT, Poon LL, Levine AJ, Rabadan R “Viral reassortment as an information exchange between viral segments” PNAS (Feb. 28, 2012) 109 (9):3341-3346, doi/10.1073/pnas.1113300109, PMCID: PMC3295259

Melnikov A, Murugan A, Zhang X, Tesileanu T, Wang L, Rogov P, Feizi S, Gnirke A, Callan CG Jr, Kinney JB, Kellis M, Lander ES, Mikkelsen TS "Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay" Nat Biotechnol. 2012 Feb 26;30(3):271-7. doi: 10.1038/nbt.2137. PMID: 22371084

Markert EK, Mizuno H, Vazquez A, Levine AJ “Molecular classification of prostate cancer using curated expression signatures” PNAS (Dec. 27, 2011) 108(52) 21276-21281, doi/10.1073/pnas.1117029108. Published online 2011 November 28. PMCID: PMC3248553

Vazquez A, Rual JF, Venkatesan K “Quality control methodology for high-throughput protein-protein interaction screening” Methods Mol Biol. 2011; 781:279-94. doi: 10.1007/978-1-61779-276-2_13. PMID: 21877286

Feng Z, Zhang C, Kang H, Sun Y, Wang H, Naqvi A, Frank A, Rosenwaks Z, Murphy, M, Levine AJ, Hu W (2011) “Regulation of female reproduction by p53 and its family members” FASEB J. (July 2011) 25 (7): 2245-55. Epub 2011 March 14. PMCID: PMC3114525

Vazquez, A, Oltvai, ZN “Molecular Crowding Defines a Common Origin for the Warburg Effect in Proliferating Cells and the Lactate Threshold in Muscle Physiology” PLoS ONE 2011 Apr 29;6(4): e19538. doi: 10.1371/journal.pone.0019538. PMID: 21559344

Cocco S, Monasson R "Adaptive Cluster Expansion for Inferring Boltzmann Machines with Noisy Data" Phys Rev Lett. 2011 Mar 4;106(9):090601. Epub 2011 Mar 2. doi: 10.1103/PhysRevLett.106.090601. PMID: 21405611

Greenbaum B, Trifonov V, Khiabanian H, Levine AJ, Rabadan R “The Emergence of 2009 H1N1 Pandemic Influenza” Influenza Vaccines of the Future, 2nd Edition Eds. R. Rappuoli and G. Del Giudice. Basel: Birkhaeuser (2011), DOI 10.1007/978-3-0346-0279-2_5

Mehta MS, Vazquez A, Kulkarni DA, Kerrigan JE, Atwal G, Metsugi S, Toppmeyer DL, Levine AJ, Hirshfield KM “Polymorphic variants in TSC1 and TSC2 and their association with breast cancer phenotypes” Breast Cancer Res Treat (2011) 125:861-868, Published online: Jul 25, 2010, doi:10.1007/s10549-010-1062-1, PMID: 2058316

Mizuno H, Spike BT, Wahl GM, Levine AJ “Inactivation of p53 in breast cancers correlates with stem cell transcriptional signatures” PNAS (Dec. 28, 2010) 107(52): 22745-50, doi/10.1073/pnas.1017001108, Epub 2010 Dec 13. PMID: 21149740 PMCID: PMC3012457

Mizuno H, Atwal G, Wang H, Levine AJ, Vazquez A “Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome” BMC Genetics 2010; 11:27

Belyi VA, Levine AJ, Skalka AM “Sequences from Ancestral Single Stranded DNA Viruses in Vertebrate Genomes: The Parvoviridae and Circoviridae Are More Than 40-50 Million Years Old” J. Virology (December 2010) 84 (23), 12458-12462, doi:10.1128/JVI.01789-10, PMID 20861255, PMCID: PMC2976387

Vazquez A, Kulkarni D, Grochola LF, Bond GL, Barnard N, Toppmeyer D, Levine AJ, Hirshfield KM “A genetic variant in a PP2A regulatory subunit encoded by the PPP2R2B gene associates with altered breast cancer risk and recurrence” Int J Cancer 2010 Jul 28 [Epub ahead of print] PMID: 20669227

Belyi VA, Levine AJ, Skalka AM “Unexpected Inheritance: Multiple Integrations of Ancient Bornavirus and Ebolavirus/Marburgvirus Sequences in Vertebrate Genomes” PLoS Pathogens (July 2010), 6 (7): e1001030. PMCID: PMC2912400

Belyi VA, Ak P, Markert E, Wang H, Hu W, Puzio-Kuter A, Levine AJ 2010 "The Origins and Evolution of the p53 Family of Genes" The P53 Family: Chapter 1, Cold Spring Harbor Perspectives in Biology, Cold Spring Harbor Laboratory Press

Hu W, Chan CS, Wu R, Zhang C, Sun Y, Song JS, Tang LH, Levine AJ, Feng Z “Negative Regulation of Tumor Suppressor p53 by MicroRNA miR-504” Molecular Cell (June 11, 2010) 38, 689-699

Mizuno H, Atwal G, Wang H, Levine AJ, Vazquez A “Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome” BMC Genetics 2010, 11:27, doi: 10.1186/1471-2156-11-27

Markert EK, Baas N, Levine AJ, Vazquez A, 2010 “Higher order Boolean networks as models of cell state dynamics” Journal of Theoretical Biology 2010 264 (3):945-951, doi:10.1016/j.jtbi.2010.03.015

Solovyov A, Greenbaum B, Palacios G, Lipkin WI, Rabadan R “Host Dependent Evolutionary Patterns and the Origin of 2009 H1N1 Influenza Pandemic Virus” PLoS Currents Influenza, RRN1147 (January 2010)

Jeong BS, Hu W, Belyi V, Rabadan R, Levine AJ 2010 “Differential levels of transcription of p53-regulated genes by the arginine/proline polymorphism: p53 with arginine at codon 72 favors apoptosis” FASEB J. 24 1347-53

Grochola LF, Vazquez A, Bond EE, Würl P, Taubert H, Müller TH, Levine AJ, Bond GL “Recent Natural Selection Identifies a Genetic Variant in a Regulatory Subunit of Protein Phosphatase 2A that Associates with Altered Cancer Risk and Survival” Clin Cancer Res (October 1, 2009) 15 (19), 6301-6308, doi: 10.1158/1078-0432.CCR-09-0797

Kulkarni DA, Vazquez A, Haffty BG, Bandera EV, Hu W, Sun YY, Toppmeyer DL, Levine AJ, Hirshfield KM “A polymorphic variant in human MDM4 associates with accelerated age of onset of estrogen receptor negative breast cancer” Carcinogenesis 2009, vol. 30, no. 11, pp. 1910-1915, doi: 10.1093/carcin/bgp224

Belyi VA, Ak P, Markert E, Wang H, Hu W, Puzio-Kuter A, Levine AJ “The Origins and Evolution of the p53 Family of Genes” Cold Spring Harb Perspect Biol 2010; 2(6):a001198 doi: 10.1101/cshperspect.a001198. Published online December 16, 2009. PMID:20516129

Cocco S, Monasson R “Inference of a random potential from random walk realizations: Formalism and application to the one-dimensional Sinai model with a drift” International Workshop on Statistical-Mechanical Informatics, IOP Publishing, Journal of Physics: Conference Series 197 (2009) 012005. doi:10.1088/1742-6596/197/1/012005

Vazquez A “Optimal Drug Combinations and Minimal Hitting Sets” BMC Systems Biology (August 6, 2009) 3:81 doi:10.1186/1752-0509-3-81

Belyi VA, Levine AJ “One Billion Years of p53/p63/p73 Evolution” Proc. Natl. Acad. Sci. (October 20, 2009) 106 (42) 17609-17610. doi: 10.1073/pnas.0910634106

Greenbaum B, Rabadan R, Levine AJ “Patterns of Oligonucleotide Sequences in Viral and Host Cell RNA Identify Mediators of the Host Innate Immune System” PLoS ONE (June 18, 2009) 4 (6): e5969. doi:10.1371/journal.pone.0005969

Trifonov V, Khiabanian H, Greenbaum B, Rabadan R “The origin of the recent swine influenza A (H1N1) virus infecting humans” Euro Surveill. (April 30, 2009); 14 (17):pii=19193

Vazquez A, Bond EE, Levine AJ, Bond GL “The genetics of the p53 pathway, apoptosis and cancer therapy” Nature Reviews Drug Discovery (December 2008) 7: 979-987

Chan CS, Song JS “CCCTC-Binding Factor Confines the Distal Action of Estrogen Receptor” Cancer Research (November 1, 2008) 68: (21), 9041-9049

Alexe G, Satya RV, Seiler M, Platt D, Bhanot T, Hui S, Tanaka M, Levine AJ, Bhanot G “PCA and Clustering Reveal Alternate mtDNA Phylogeny of N and M Clades” J Mol Evol (2008) 67: 465-487 (published online October 15, 2008); DOI 10.1007/s00239-008-9148-7

Yu H, Vazquez A et al “High-Quality Binary Protein Interaction Map of the Yeast Interactome Network” Science (October 3, 2008) 322: 104-110 (DOI: 10.1126/science.1158684)

Vazquez A, de Menezes MA, Barabási A-L, Oltvai ZN “Impact of Limited Solvent Capacity on Metabolic Rate, Enzyme Activities, and Metabolite Concentrations of S. cerevisiae Glycolysis” PLoS Computational Biology (October 10, 2008) 4 (10): e1000195 (doi:10.1371/journal.pcbi.1000195)

Krasnitz M, Rabadan R, Levine AJ “Anomalies in the Influenza Virus Genome Database: New Biology or Laboratory Errors?” Journal of Virology (September 2008) 82 (17): 8947-8950

Huang Y, Krasnitz M, Rabadan R, Witten DM, Song Y, Levine AJ, Ho DD, Robins H, “A recoding method to improve the humoral immune response to an HIV DNA vaccine” PLoS ONE (September 15, 2008), 3 (9): e3214

Holmes KA, Song JS, Liu XS, Brown M, Carroll JS “Nkx3-1 and LEF-1 Function as Transcriptional Inhibitors of Estrogen Receptor Activity” Cancer Research (September 15, 2008) 68: (18), 7380-7385

Song JS, Liu X, Liu S, He X “A high-resolution map of nucleosome positioning on a fission yeast centromere” Genome Research (2008) 18:1064-1072 (Published online before print doi/10.1101/gr.075374.107)

Robins H, Krasnitz M, Levine AJ “The Computational Detection of Functional Nucleotide Sequence Motifs in the Coding Regions of Organisms” Exp Biol and Med. (2008) 233: 665-673

Bilal E, Rabadan R, Alexe G, Fuku N, Ueno H, Nishigaki Y, Fujita Y, Ito M, Arai Y, Hirose N, Ruckenstein A, Bhanot G, Tanaka M “Mitochondrial DNA Haplogroup D4a is a Marker for Extreme Longevity in Japan” PLoS ONE (June 11, 2008) 3 (6): e2421

Greenbaum BD, Levine AJ, Bhanot G, Rabadan R “Patterns of Evolution and Host Gene Mimicry in Influenza and other RNA Viruses” PLoS Pathogens (June 6, 2008) 4 (6): 1-9.

Atwal G, Rabadan R, Lozano G, Strong LC, Ruijs MWG, Schmidt MK, van ´t Veer LJ, Nevanlinna H, Tommiska J, Aittomäki K, Bougeard G, Frebourg T, Levine AJ, Bond GL “An Information-Theoretic Analysis of Genetics, Gender and Age in Cancer Patients” PLoS ONE (April 9, 2008) 3 (4): e1951

Murphy E, Vanicek J, Robins H, Shenk T, Levine AJ "Suppression of immediate-early viral gene expression by herpesvirus-coded microRNAs: Implications for latency" PNAS (April 8, 2008) 105 (14), 5453-5458

Borghuis BG, Ratliff CP, Smith RG, Sterling P, Balasubramanian V “Design of a Neuronal Array” The Journal of Neuroscience (March 19, 2008) 28 (12): 3178-3189

Marsh GA, Rabadan R, Levine AJ, Palese P “Highly conserved regions of influenza A virus polymerase gene segments are critical for efficient viral RNA packaging” Journal of Virology (March 2008) 82 (5): 2295-2304 (published online ahead of print on December 19, 2007; doi:10.1128/JVI.02267-07)

Rabadan R, Levine AJ, Krasnitz M “Non-random reassortment in human influenza A viruses” Influenza and Other Respiratory Viruses (2008) 2 (1), 9-22. (doi:10.1111/j.1750-2659.2007.00030.x)

Johnson DS, Song JS et al “Systematic evaluation of variability in simulated ChIP-chip experiments using predefined DNA targets” Genome Research (2008) 18: 393-403 (Published online before print doi/10.1101/gr.7080508)

Rabadan R, Robins H “Evolution of the Influenza A Virus: Some New Advances” Evolutionary Bioinformatics Online 2007: 299-307

Yeang C-H, Haussler D “Detecting Coevolution in and among Protein Domains” PLoS Computational Biology (November 2007) 3(11):e211

Beg, QK, Vazquez A, Ernst J, de Menezes MA, Bar-Joseph Z, Barabási A-L, Oltvai ZN “Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity” PNAS (July 31, 2007) vol. 104 no. 31 (12663-12668)

Atwal GS, Bond, GL, Metsuyanim S, Papa M, Friedman E, Distelman-Menachem, T, Asher EB, Lancet D, Ross DA, Sninsky J, White TJ, Levine AJ, Yarden R “Haplotype structure and selection of the MDM2 oncogene in humans” PNAS (March 13, 2007) vol. 104 no. 11 (4525-4529)

Bond GL, Levine AJ “A single nucleotide polymorphism in the p53 pathway interacts with gender, environmental stresses and tumor genetics to influence cancer in humans” Oncogene (2007) 26, 1317-1323

Vazquez A “Epidemic outbreaks on structured populations” Journal of Theoretical Biology 245 (2007) 125-129 (published online ahead of print on 23 September 2006. doi:10.1016/j.jtbi.2006.09.018)

Rabadan R, Levine AJ, Robins H “Comparison of Avian and Human Influenza A Viruses Reveals a Mutational Bias on the Viral Genomes” Journal of Virology, (December 2006) vol. 80, no. 23 (11887-11891) (published online ahead of print on 20 September 2006. doi:10.1128/JVI.01414-06)

Press WH, Robins H “Isochores Exhibit Evidence of Genes Interacting With the Large-Scale Genomic Environment” Genetics (October 2006) vo. 174 (1029-1040)

Bond GL, Hirshfield KM, Kirchhoff T, Alexe G, Bond EE, Robins H, Bartel F, Taubert H, Wuerl P, Hait W, Toppmeyer D, Offit K, Levine AJ “MDM2 SNP309 Accelerates Tumor Formation in a Gender Specific and Hormonal Dependent Manner” Cancer Research (May 15, 2006) 66(10) (5104-10)

Vanicek J “Dephasing representation of quantum fidelity for general pure and mixed states” Physical Review E 73 (April 14, 2006) 046204

Alexe G, Dalgin GS, Ramaswamy R, Delisi C, Bhanot G “Data Perturbation Independent Diagnosis and Validation of Breast Cancer Subtypes Using Clustering and Patterns” Cancer Informatics, Online (2006) 2, 243-274

Bhanot G, Alexe G, Venkataraghavan B, Levine AJ “A robust meta-classification strategy for cancer detection from mass spectrometry data” Proteomics (2005) Dec 8; 6(2):592-604

Robins H, Krasnitz M, Barak H, Levine A “A Relative Entropy Algorithm for Genomic Fingerprinting Captures Host-Phage Similarities” Journal of Bacteriology (December 2005) vol. 187 no. 24 (8370-8374)

Harris S, Gil G, Robins H, Hu W, Hirshfield K, Bond E, Bond G, Levine A “Detection of functional single nucleotide polymorphisms that affect apoptosis” PNAS (November 8, 2005) vol. 102 no. 45 (16297-16302)

Robins H, Press WH “Human microRNAs target a functionally distinct population of genes with AT-rich 3’UTRs” PNAS (October 25, 2005) vol. 102 no. 43 (15557-15562)

Bond GL, Hu W, Levine AJ “A Single Nucleotide Polymorphism in the MDM2 Gene: From a Molecular and Cellular Explanation to Clinical Effect” Cancer Research (July 1, 2005) 65(13): (5481-5484) (Review)

Alexe G, Alexe S, Axelrod DE, Hammer PL, Weissmann D “Logical analysis of diffuse large B-cell lymphomas” Artificial Intelligence in Medicine (July 2005) vol. 34 issue 3 (235-267)

Robins H, Li Y, Padgett RW “Incorporating structure to predict microRNA targets” PNAS (March 15, 2005) vol. 102 no. 11 (4006-4009)

Ma B, Pan Y, Gunasekaran K, Venkataraghavan B, Levine AJ, Nussinov R “Comparison of the protein-protein interfaces in the p53-DNA crystal structures: Towards elucidation of the biological interface” PNAS (March 15, 2005) vol. 102 no. 11 (3988-3993)

Ramaswamy R “The natural effectiveness of mathematics in the biological sciences” Current Science (Bangalore) (10 Feb 2005) vol. 88 no. 3 (381-387)

Pan Y, Ma B, Venkataraghavan B, Levine AJ, Nussinov R “In the Quest for Stable Rescuing Mutants of p53: Computational Mutagenesis of Flexible Loop L1” Biochemistry (February 8, 2005) 44 (1423-1432)

Robins H, Alexe G, Harris S, Levine AJ “The first twenty five years of p53 research” In: 25 Years of P53 Research, Hainaut, Pierre; Wiman, Klas (Eds.) Ch 1, 2005

Alexe G, Bhanot G, Levine AJ, Stolovitzky G “Robust diagnosis of non-Hodgkin lymphoma phenotypes validated on gene expression data from different laboratories” Genome Informatics (2005) 16(1): 233-244

Levine AJ, Bargonetti J, Bond GL, Hoh J, Onel K, Overholtzer M, Stoffel A, Teresky, AK, Walsh CA, Jin S “The p53 Network” In: The p53 Tumor Suppressor. (2005) (ed.) G. Zambetti, Springer Science and Business Media, New York, pp. 1-23

Bond GL, Hu W, Levine AJ “Mdm2 is a Central Node in the p53 Pathway: 12 Years and Counting” Current Cancer Drug Targets (2005) (5): 3-8

Plotkin JB, Robins H, Levine, AJ “Tissue-specific codon usage and the expression of human genes” PNAS (August 24, 2004) vol. 101 no. 34 (12588-12591)