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Publications in 2013

  1. Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling.

    Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA.
    PLoS Comput Biol. 2013 May;9(5):e1003047. doi: 10.1371/journal.pcbi.1003047. Epub 2013 May 9.

  2. Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue.

    Califano A, Kellis M, Stolovitzky G.
    J Comput Biol. 2013 May;20(5):373-4. doi: 10.1089/cmb.2013.008p.

  3. UV-radiation Induced Disruption of Dry-Cavities in Human γD-crystallin Results in Decreased Stability and Faster Unfolding.

    Xia Z, Yang Z, Huynh T, King JA, Zhou R.
    Sci Rep. 2013 Mar 27;3:1560. doi: 10.1038/srep01560.

  4. Ultrametric networks: a new tool for phylogenetic analysis.

    Apostolico A, Comin M, Dress A, Parida L.
    Algorithms Mol Biol. 2013 Mar 5;8(1):7. [Epub ahead of print]

  5. Seeking the Wisdom of Crowds Through Challenge-Based Competitions in Biomedical Research.

    Costello JC, Stolovitzky G.
    Clin Pharmacol Ther. 2013 Feb 20. doi: 10.1038/clpt.2013.36. [Epub ahead of print]

  6. Metallofullerenol Gd@C(82)(OH)(22) distracts the proline-rich-motif from putative binding on the SH3 domain.

    Kang SG, Huynh T, Zhou R.
    Nanoscale. 2013 Feb 19. [Epub ahead of print]

  7. Critical assessment of automated flow cytometry data analysis techniques.

    Aghaeepour N, Finak G; The FlowCAP Consortium, Dougall D, Khodabakhshi AH, Mah P, Obermoser G, Spidlen J, Taylor I, Wuensch SA, Bramson J, Eaves C, Weng AP, Iii ES, Ho K, Kollmann T, Rogers W, De Rosa S, Dalal B, Azad A, Pothen A, Brandes A, Bretschneider H, Bruggner R, Finck R, Jia R, Zimmerman N, Linderman M, Dill D, Nolan G, Chan C, Khettabi FE, O'Neill K, Chikina M, Ge Y, Sealfon S, Sugár I, Gupta A, Shooshtari P, Zare H, De Jager PL, Jiang M, Keilwagen J, Maisog JM, Luta G, Barbo AA, Májek P, Vilček J, Manninen T, Huttunen H, Ruusuvuori P, Nykter M, McLachlan GJ, Wang K, Naim I, Sharma G, Nikolic R, Pyne S, Qian Y, Qiu P, Quinn J, Roth A; The DREAM Consortium, Meyer P, Stolovitzky G, Saez-Rodriguez J, Norel R, Bhattacharjee M, Biehl M, Bucher P, Bunte K, Di Camillo B, Sambo F, Sanavia T, Trifoglio E, Toffolo G, Dimitrieva S, Dreos R, Ambrosini G, Grau J, Grosse I, Posch S, Guex N, Keilwagen J, Kursa M, Rudnicki W, Liu B, Maienschein-Cline M, Manninen T, Huttunen H, Ruusuvuori P, Nykter M, Schneider P, Seifert M, Strickert M, Vilar JM, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH.
    Nat Methods. 2013 Feb 10. doi: 10.1038/nmeth.2365. [Epub ahead of print]

  8. Sum of parts is greater than the whole: inference of common genetic history of populations.

    Utro F, Pybus M, Parida L.
    BMC Genomics. 2013 Jan 21;14 Suppl 1:S10. doi: 10.1186/1471-2164-14-S1-S10. Epub 2013 Jan 21.

  9. Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations.

    Badro DA, Douaihy B, Haber M, Youhanna SC, Salloum A, Ghassibe-Sabbagh M, Johnsrud B, Khazen G, Matisoo-Smith E, Soria-Hernanz DF, Wells RS, Tyler-Smith C, Platt DE, Zalloua PA; Genographic Consortium.
    PLoS One. 2013;8(1):e54616. doi: 10.1371/journal.pone.0054616. Epub 2013 Jan 30.

  10. Large Domain Motions in Ago Protein Controlled by the Guide DNA-Strand Seed Region Determine the Ago-DNA-mRNA Complex Recognition Process.

    Xia Z, Huynh T, Ren P, Zhou R.
    PLoS One. 2013;8(1):e54620. doi: 10.1371/journal.pone.0054620. Epub 2013 Jan 29.

  11. Evaluation of methods for modeling transcription factor sequence specificity.

    Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium, Agius P, Arvey A, Bucher P, Callan CG Jr, Chang CW, Chen CY, Chen YS, Chu YW, Grau J, Grosse I, Jagannathan V, Keilwagen J, Kiełbasa SM, Kinney JB, Klein H, Kursa MB, Lähdesmäki H, Laurila K, Lei C, Leslie C, Linhart C, Murugan A, Myšičková A, Noble WS, Nykter M, Orenstein Y, Posch S, Ruan J, Rudnicki WR, Schmid CD, Shamir R, Sung WK, Vingron M, Zhang Z, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.
    Nat Biotechnol. 2013 Jan 27. doi: 10.1038/nbt.2486. [Epub ahead of print]

Publications in 2012

  1. Erratum: ERRATUM: Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets.

    Xia Z, Clark P, Huynh T, Loher P, Zhao Y, Chen HW, Ren P, Rigoutsos I, Zhou R.
    Sci Rep. 2012;2:909. Epub 2012 Nov 28.

  2. Schizophrenia as a network disease: disruption of emergent brain function in patients with auditory hallucinations.

    Rish I, Cecchi G, Thyreau B, Thirion B, Plaze M, Paillere-Martinot ML, Martelli C, Martinot JL, Poline JB.
    PLoS One. 2013;8(1):e50625. doi: 10.1371/journal.pone.0050625. Epub 2013 Jan 21.

  3. ARG-based genome-wide analysis of cacao cultivars.

    Utro F, Cornejo OE, Livingstone D, Motamayor JC, Parida L.
    BMC Bioinformatics. 2012;13 Suppl 19:S17. doi: 10.1186/1471-2105-13-S19-S17. Epub 2012 Dec 19.

  4. Non-destructive Inhibition of Metallofullerenol Gd@C(82)(OH)(22) on WW domain: Implication on Signal Transduction Pathway.

    Kang SG, Huynh T, Zhou R.
    Sci Rep. 2012;2:957. doi: 10.1038/srep00957. Epub 2012 Dec 11.

  5. Molecular mechanism of pancreatic tumor metastasis inhibition by Gd@C82(OH)22 and its implication for de novo design of nanomedicine.

    Kang SG, Zhou G, Yang P, Liu Y, Sun B, Huynh T, Meng H, Zhao L, Xing G, Chen C, Zhao Y, Zhou R.
    Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):15431-6. Epub 2012 Sep 4.

  6. Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System.

    Arunkumar G, Soria-Hernanz DF, Kavitha VJ, Arun VS, Syama A, Ashokan KS, Gandhirajan KT, Vijayakumar K, Narayanan M, Jayalakshmi M, Ziegle JS, Royyuru AK, Parida L, Wells RS, Renfrew C, Schurr TG, Smith CT, Platt DE, Pitchappan R; The Genographic Consortium.
    PLoS One. 2012;7(11):e50269. Epub 2012 Nov 28.

  7. In silico cardiac risk assessment in patients with long QT syndrome: type 1: clinical predictability of cardiac models.

    Hoefen R, Reumann M, Goldenberg I, Moss AJ, O-Uchi J, Gu Y, McNitt S, Zareba W, Jons C, Kanters JK, Platonov PG, Shimizu W, Wilde AA, Rice JJ, Lopes CM.
    J Am Coll Cardiol. 2012 Nov 20;60(21):2182-91. doi: 10.1016/j.jacc.2012.07.053.

  8. Molecular mechanism of surface-assisted epitaxial self-assembly of amyloid-like peptides.

    Kang SG, Li H, Huynh T, Zhang F, Xia Z, Zhang Y, Zhou R.
    ACS Nano. 2012 Oct 23;6(10):9276-82. doi: 10.1021/nn303740j. Epub 2012 Sep 28.

  9. Predictive dynamics of human pain perception.

    Cecchi GA, Huang L, Hashmi JA, Baliki M, Centeno MV, Rish I, Apkarian AV.
    PLoS Comput Biol. 2012 Oct;8(10):e1002719. doi: 10.1371/journal.pcbi.1002719. Epub 2012 Oct 25.

  10. Dynamics of DNA translocation in a solid-state nanopore immersed in aqueous glycerol.

    Luan B, Wang D, Zhou R, Harrer S, Peng H, Stolovitzky G.
    Nanotechnology. 2012 Oct 12;23(45):455102. [Epub ahead of print]

  11. Nanopore-Based Sensors for Detecting Toxicity of a Carbon Nanotube to Proteins.

    Luan B, Zhou R.
    J Phys Chem Lett. 2012 Aug 8;2012(3):2337-2341.

  12. Molecular mechanism of pancreatic tumor metastasis inhibition by Gd@C82(OH)22 and its implication for de novo design of nanomedicine.

    Kang SG, Zhou G, Yang P, Liu Y, Sun B, Huynh T, Meng H, Zhao L, Xing G, Chen C, Zhao Y, Zhou R.
    Proc Natl Acad Sci U S A. 2012 Sep 4. [Epub ahead of print]

  13. Direct characterization of hydrophobic hydration during cold and pressure denaturation.

    Das P, Matysiak S.
    J Phys Chem B. 2012 May 10;116(18):5342-8. Epub 2012 May 2.

  14. Is cancer a metabolic rebellion against host aging? In the quest for immortality, tumor cells try to save themselves by boosting mitochondrial metabolism.

    Ertel A, Tsirigos A, Whitaker-Menezes D, Birbe RC, Pavlides S, Martinez-Outschoorn UE, Pestell RG, Howell A, Sotgia F, Lisanti MP.
    Cell Cycle. 2012 Jan 15;11(2):253-63. Epub 2012 Jan 15.

  15. Hyperactivation of oxidative mitochondrial metabolism in epithelial cancer cells in situ: visualizing the therapeutic effects of metformin in tumor tissue.

    Whitaker-Menezes D, Martinez-Outschoorn UE, Flomenberg N, Birbe RC, Witkiewicz AK, Howell A, Pavlides S, Tsirigos A, Ertel A, Pestell RG, Broda P, Minetti C, Lisanti MP, Sotgia F.
    Cell Cycle. 2011 Dec 1;10(23):4047-64. Epub 2011 Dec 1.

  16. Y-Chromosome Analysis in Individuals Bearing the Basarab Name of the First Dynasty of Wallachian Kings.

    Martínez-Cruz B, Ioana M, Calafell F, Arauna LR, Sanz P, Ionescu R, Boengiu S, Kalaydjieva L, Pamjav H, Makukh H, Plantinga T, van der Meer JW, Comas D, Netea MG; the Genographic Consortium.
    PLoS One. 2012;7(7):e41803.

  17. Wisdom of crowds for robust gene network inference.

    Marbach D, Costello JC, Kuffner R, Vega NM, Prill RJ, Camacho DM, Allison KR; The DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G.
    Nat Methods. 2012 Jul 15;9(8):796-804.

  18. The Basque paradigm: genetic evidence of a maternal continuity in the Franco-Cantabrian region since pre-Neolithic times.

    Behar DM, Harmant C, Manry J, van Oven M, Haak W, Martínez-Cruz B, Salaberria J, Oyharcabal B, Bauduer F, Comas D, Quintana-Murci L; Genographic Consortium.
    Am J Hum Genet. 2012 Mar 9;90(3):486-93.

  19. Dynamics of confined reactive water in smectite clay-zeolite composites.

    Pitman MC, van Duin AC.
    J Am Chem Soc. 2012 Feb 15;134(6):3042-53.

  20. Autophagy and senescence in cancer-associated fibroblasts metabolically supports tumor growth and metastasis via glycolysis and ketone production.

    Capparelli C, Guido C, Whitaker-Menezes D, Bonuccelli G, Balliet R, Pestell TG, Goldberg AF, Pestell RG, Howell A, Sneddon S, Birbe R, Tsirigos A, Martinez-Outschoorn U, Sotgia F, Lisanti MP.
    Cell Cycle. 2012 Jun 15;11(12):2285-302.

  21. Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations.

    Dulik MC, Owings AC, Gaieski JB, Vilar MG, Andre A, Lennie C, Mackenzie MA, Kritsch I, Snowshoe S, Wright R, Martin J, Gibson N, Andrews TD, Schurr TG; Genographic Consortium.
    Proc Natl Acad Sci U S A. 2012 May 29;109(22):8471-6.

  22. Mitochondrial origin of the matrilocal Mosuo people in China.

    Lu Y, Wang C, Qin Z, Wen B, Farina SE, Jin L, Li H; Genographic Consortium.
    Mitochondrial DNA. 2012 Feb;23(1):13-9.

  23. Clan, language, and migration history has shaped genetic diversity in Haida and Tlingit populations from Southeast Alaska.

    Schurr TG, Dulik MC, Owings AC, Zhadanov SI, Gaieski JB, Vilar MG, Ramos J, Moss MB, Natkong F; The Genographic Consortium.
    Am J Phys Anthropol. 2012 Jul;148(3):422-435.

  24. Afghanistan's Ethnic Groups Share a Y-Chromosomal Heritage Structured by Historical Events.

    Haber M, Platt DE, Ashrafian Bonab M, Youhanna SC, Soria-Hernanz DF, Martínez-Cruz B, Douaihy B, Ghassibe-Sabbagh M, Rafatpanah H, Ghanbari M, Whale J, Balanovsky O, Wells RS, Comas D, Tyler-Smith C, Zalloua PA; The Genographic Consortium.
    PLoS One. 2012;7(3):e34288. Epub 2012 Mar 28.

  25. Effect of cosolvents on nano-confined water: a molecular dynamics study.

    Das P.
    Nanoscale. 2012 Apr 28;4(9):2931-6. Epub 2012 Mar 22.

  26. Free-Energy Simulations Reveal that Both Hydrophobic and Polar Interactions Are Important for Influenza Hemagglutinin Antibody Binding.

    Xia Z, Huynh T, Kang SG, Zhou R.
    Biophys J. 2012 Mar 21;102(6):1453-61. Epub 2012 Mar 20.

  27. Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia.

    Ntziachristos P, Tsirigos A, Van Vlierberghe P, Nedjic J, Trimarchi T, Flaherty MS, Ferres-Marco D, da Ros V, Tang Z, Siegle J, Asp P, Hadler M, Rigo I, De Keersmaecker K, Patel J, Huynh T, Utro F, Poglio S, Samon JB, Paietta E, Racevskis J, Rowe JM, Rabadan R, Levine RL, Brown S, Pflumio F, Dominguez M, Ferrando A, Aifantis I.
    Nat Med. 2012 Feb 6;18(2):298-301. doi: 10.1038/nm.2651.

  28. Industrial Methodology for Process Verification in Research (IMPROVER): Towards Systems Biology Verification.

    Meyer P, Hoeng J, Norel R, Sprengel J, Stolle K, Bonk T, Corthesy S, Royyuru A, Peitsch MC, Rice JJ, Stolovitzky G.
    Bioinformatics. 2012 May 1;28(9):1193-201. doi: 10.1093/bioinformatics/bts116. Epub 2012 Mar 14. Review.

  29. Evidence of pre-Roman tribal genetic structure in Basques from uniparentally inherited markers.

    Martínez-Cruz B, Harmant C, Platt DE, Haak W, Manry J, Ramos-Luis E, Soria-Hernanz DF, Bauduer F, Salaberria J, Oyharcabal B, Quintana-Murci L, Comas D; the Genographic Consortium.
    Mol Biol Evol. 2012 Mar 12. [Epub ahead of print]

  30. Nonredundant representation of ancestral recombinations graphs.

    Parida L.
    Methods Mol Biol. 2012;856:315-32.

  31. Discovering patterns in gene order.

    Parida L, Haiminen N.
    Methods Mol Biol. 2012;855:431-55.

  32. Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis.

    Martinez MR, Corradin A, Klein U, Alvarez MJ, Toffolo GM, di Camillo B, Califano A, Stolovitzky GA.
    Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2672-7. Epub 2012 Jan 30.

  33. Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 Special Issue.

    Califano A, Kellis M, Stolovitzky G.
    J Comput Biol. 2012 Feb;19(2):101. No abstract available.

  34. Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations.

    Yang Z, Wang Z, Tian X, Xiu P, Zhou R.
    J Chem Phys. 2012 Jan 14;136(2):025103.

Publications in 2011

  1. Threshold-avoiding proteomics pipeline.

    Suits F, Hoekman B, Rosenling T, Bischoff R, Horvatovich P.
    Anal Chem. 2011 Oct 15;83(20):7786-94.

  2. Performance of hybrid programming models for multiscale cardiac simulations: preparing for petascale computation.

    Pope BJ, Fitch BG, Pitman MC, Rice JJ, Reumann M.
    IEEE Trans Biomed Eng. 2011 Oct;58(10):2965-9.

  3. Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes.

    Cai X, Qin Z, Wen B, Xu S, Wang Y, Lu Y, Wei L, Wang C, Li S, Huang X, Jin L, Li H; The Genographic Consortium.
    PLoS One. 2011;6(8):e24282.

  4. Petascale computation performance of lightweight multiscale cardiac models using hybrid programming models.

    Pope BJ, Fitch BG, Pitman MC, Rice JJ, Reumann M.
    Conf Proc IEEE Eng Med Biol Soc. 2011 Aug;2011:433-6.

  5. Full-brain auto-regressive modeling (FARM) using fMRI.

    Garg R, Cecchi GA, Rao AR.
    Neuroimage. 2011 Sep 15;58(2):416-41. Epub 2011 Mar 22.

  6. GenomicTools: a computational platform for developing high-throughput analytics in genomics.

    Tsirigos A, Haiminen N, Bilal E, Utro F.
    Bioinformatics. 2012 Jan 15;28(2):282-3. Epub 2011 Nov 22.

  7. Slowing and controlling the translocation of DNA in a solid-state nanopore.

    Luan B, Stolovitzky G, Martyna G.
    Nanoscale. 2012 Feb 21;4(4):1068-77. Epub 2011 Nov 14.

  8. Characterizing and Controlling the Motion of ssDNA in a Solid-State Nanopore.

    Luan B, Martyna G, Stolovitzky G.
    Biophys J. 2011 Nov 2;101(9):2214-22. Epub 2011 Nov 1.

  9. mtDNA Lineages Reveal Coronary Artery Disease-Associated Structures in the Lebanese Population.

    Haber M, Youhanna SC, Balanovsky O, Saade S, Martínez-Cruz B, Ghassibe-Sabbagh M, Shasha N, Osman R, El Bayeh H, Koshel S, Zaporozhchenko V, Balanovska E, Soria-Hernanz DF, Platt DE, Zalloua PA.
    Ann Hum Genet. 2011 Oct 20. [Epub ahead of print].

  10. Recombination networks as genetic markers in a human variation study of the Old World.

    Javed A, Melé M, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Arunkumar G, Pitchappan R, Bertranpetit J, Calafell F, Parida L; The Genographic Consortium.
    Hum Genet. 2012 Apr;131(4):601-13. Epub 2011 Oct 18.

  11. Modeling mutations of influenza virus with IBM Blue Gene.

    Xia Z, Das P, Huynh T, Royyuru AK, Zhou R.
    IBM J Res & Dev. 55:7:1-11 (2011). doi 10.1147/JRD.2011.2163276

  12. The self-assessment trap: can we all be better than average?

    Norel R, Rice JJ, Stolovitzky G.
    Mol Syst Biol. 2011 Oct 11;7:537.

  13. An Ultrascalable Solution to Large-scale Neural Tissue Simulation.

    Kozloski J, Wagner J.
    Front Neuroinform. 2011;5:15.

  14. Verification of systems biology research in the age of collaborative competition.

    Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G.
    Nat Biotechnol. 2011 Sep 8;29(9):811-5. No abstract available.

  15. Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results.

    Haiminen N, Kuhn DN, Parida L, Rigoutsos I.
    PLoS One. 2011;6(9):e24182.

  16. Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge.

    Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G.
    Sci Signal. 2011 Sep 6;4(189).

  17. Recombination gives a new insight in the effective population size and the history of the Old World human populations.

    Melé M, Javed A, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Pitchappan R, Arunkumar G, Parida L, Calafell F, Bertranpetit J; The Genographic Consortium.
    Mol Biol Evol. 2012 Jan;29(1):25-30. Epub 2011 Sep 1.

  18. Cardiac electromechanical models: from cell to organ.

    Trayanova NA, Rice JJ.
    Front Physiol. 2011;2:43.

  19. Sequencing of a QTL-rich Region of the Theobroma cacao Genome using Pooled BACs and the Identification of Trait Specific Candidate Genes.

    Feltus FA, Saski CA, Mockaitis K, Haiminen N, Parida L, Smith Z, Ford J, Staton ME, Ficklin SP, Blackmon BP, Cheng CH, Schnell RJ, Kuhn DN, Motamayor JC.
    BMC Genomics. 2011 Jul 27;12(1):379.

  20. IRiS*: Construction of ARG networks at genomic scales.

    Javed A, Pybus M, Melé M, Utro F, Bertranpetit J, Calafell F, Parida L.
    Bioinformatics. 2011 Jul 15. [Epub ahead of print]

  21. Aggregation of γ-crystallins associated with human cataracts via domain swapping at the C-terminal β-strands.

    Das P, King JA, Zhou R.
    Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10514-9.

  22. Orthogonal recursive bisection as data decomposition strategy for massively parallel cardiac simulations.

    Reumann M, Fitch BG, Rayshubskiy A, Pitman MC, Rice JJ.
    Biomed Tech (Berl). 2011 Jun;56(3):129-45.

  23. Electrochemical protection of thin film electrodes in solid state nanopores.

    Harrer S, Waggoner PS, Luan B, Afzali-Ardakani A, Goldfarb DL, Peng H, Martyna G, Rossnagel SM, Stolovitzky GA.
    Nanotechnology. 2011 Jul 8;22(27):275304. Epub 2011 May 20.

  24. Parallel Evolution of Genes and Languages in the Caucasus Region.

    Balanovsky O, Dibirova K, Dybo A, Mudrak O, Frolova S, Pocheshkhova E, Haber M, Platt D, Schurr T, Haak W, Kuznetsova M, Radzhabov M, Balaganskaya O, Romanov A, Zakharova T, Soria Hernanz DF, Zalloua P, Koshel S, Ruhlen M, Renfrew C, Wells RS, Tyler-Smith C, Balanovska E; The Genographic Consortium.
    Mol Biol Evol. 2011 May 13. [Epub ahead of print]

  25. Automated Reconstruction of Neural Tissue and the Role of Large-Scale Simulation.

    Kozloski J.
    Neuroinformatics. 2011 Sep;9(2-3):132-42 No abstract available.

  26. Molecular profiling of a lethal tumor microenvironment, as defined by stromal caveolin-1 status in breast cancers.

    Witkiewicz AK, Kline J, Queenan M, Brody JR, Tsirigos A, Pavlides S, Sotgia F, Lisanti MP.
    Cell Cycle. 2011 Jun 1;10(11). [Epub ahead of print]

  27. An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4.

    Yan S, Wang CC, Li H, Li SL, Jin L; The Genographic Consortium, Schurr TG, Santos FR, Quintana-Murci L, Bertranpetit J, Comas D, Tyler-Smith C, Zalloua PA, Balanovska E, Balanovsky O, John Mitchell R, Jin L, Soodyall H, Pitchappan R, Cooper A, Matisoo-Smith L, Royyuru AK, Platt DE, Parida L, Blue-Smith J, Soria Hernanz DF, Spencer Wells R.
    Eur J Hum Genet. 2011 Apr 20. [Epub ahead of print]

  28. Assessing Pooled BAC and Whole Genome Shotgun Strategies for Assembly of Complex Genomes.

    Haiminen N, Feltus FA, Parida L.
    BMC Genomics. 2011 Apr 15;12(1):194. [Epub ahead of print]

  29. Ketones and lactate increase cancer cell "stemness," driving recurrence, metastasis, and poor clinical outcome in breast cancer: Achieving personalized medicine via Metabolo-Genomics.

    Martinez-Outschoorn UE, Prisco M, Ertel A, Tsirigos A, Lin Z, Pavlides S, Wang C, Flomenberg N, Knudsen ES, Howell A, Pestell RG, Sotgia F, Lisanti MP.
    Cell Cycle. 2011 Apr 15;10(8):1271-86.

  30. Use of Mutant-Specific Ion Channel Characteristics for Risk Stratification of Long QT Syndrome Patients.

    Jons C, O-Uchi J, Moss AJ, Reumann M, Rice JJ, Goldenberg I, Zareba W, Wilde AA, Shimizu W, Kanters JK, McNitt S, Hofman N, Robinson JL, Lopes CM.
    Sci Transl Med. 2011 Mar 30;3(76):76ra28.

  31. A minimal descriptor of an ancestral recombinations graph.

    Parida L, Palamara PF, Javed A.
    BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S6. PMID: 21342589 [PubMed - in process]

  32. A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data.

    Ahmad I, Suits F, Hoekman B, Swertz MA, Byelas H, Dijkstra M, Hooft R, Katsubo D, van Breukelen B, Bischoff R, Horvatovich P.
    Bioinformatics. 2011 Feb 23. [Epub ahead of print]

  33. Setting the standards for signal transduction research.

    Saez-Rodriguez J, Alexopoulos LG, Stolovitzky G.
    Sci Signal. 2011 Feb 15;4(160):pe10. PMID: 21325202 [PubMed - in process]

Publications in 2010

  1. Tribological Effects on DNA Translocation in a Nanochannel Coated with a Self-Assembled Monolayer.

    Luan B, Afzali A, Harrer S, Peng H, Waggoner P, Polonsky S, Stolovitzky G, Martyna G.
    J Phys Chem B. 2010 Dec 3. [Epub ahead of print]

  2. A New Method to Reconstruct Recombination Events at a Genomic Scale.

    Melé M, Javed A, Pybus M, Calafell F, Parida L, Bertranpetit J; The Genographic Consortium.
    PLoS Comput Biol. 2010 Nov 24;6(11):e1001010.

  3. Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon.

    Haber M, Platt DE, Badro DA, Xue Y, El-Sibai M, Bonab MA, Youhanna SC, Saade S, Soria-Hernanz DF, Royyuru A, Wells RS, Tyler-Smith C, Zalloua PA.
    Eur J Hum Genet. 2010 Dec 1. [Epub ahead of print]

  4. Electrochemical Characterization of Thin Film Electrodes Toward Developing a DNA Transistor.

    Harrer S, Ahmed S, Afzali-Ardakani A, Luan B, Waggoner PS, Shao X, Peng H, Goldfarb DL, Martyna GJ, Rossnagel SM, Deligianni L, Stolovitzky GA.
    Langmuir. 2010 Nov 22. [Epub ahead of print].

  5. Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities.

    Haak W, Balanovsky O, Sanchez JJ, Koshel S, Zaporozhchenko V, Adler CJ, Der Sarkissian CS, Brandt G, Schwarz C, Nicklisch N, Dresely V, Fritsch B, Balanovska E, Villems R, Meller H, Alt KW, Cooper A; the Genographic Consortium.
    PLoS Biol. 2010 Nov 9;8(11):e1000536.

  6. Key Residues that Play a Critical Role in Urea-Induced Lysozyme Unfolding.

    Gao M, She ZS, Zhou R.
    J Phys Chem B. 2010 Nov 5. [Epub ahead of print]

  7. When the optimal is not the best: parameter estimation in complex biological models.

    Fernández Slezak D, Suárez C, Cecchi GA, Marshall G, Stolovitzky G.
    PLoS One. 2010 Oct 25;5(10):e13283.

  8. VARUN: Discovering Extensible Motifs under Saturation Constraints.

    Apostolico A, Comin M, Parida L.
    IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):752-26.

  9. Ancestral recombinations graph: a reconstructability perspective using random-graphs framework.

    Parida L.
    J Comput Biol. 2010 Oct;17(10):1345-70.

  10. OmiR: Identification of associations between OMIM diseases and microRNAs.

    Rossi S, Tsirigos A, Amoroso A, Mascellani N, Rigoutsos I, Calin GA, Volinia S.
    Genomics. 2010 Oct 22. [Epub ahead of print]

  11. Statistics of natural scenes and cortical color processing.

    Cecchi GA, Rao AR, Xiao Y, Kaplan E.
    J Vis. 2010 Sep 1;10(11):21.

  12. Base-by-base ratcheting of single stranded DNA through a solid-state nanopore.

    Luan B, Peng H, Polonsky S, Rossnagel S, Stolovitzky G, Martyna G.
    Phys Rev Lett. 2010 Jun 11;104(23):238103. Epub 2010 Jun 10.

  13. Integrative modeling of the cardiac ventricular myocyte.

    Winslow RL, Cortassa S, O'Rourke B, Hashambhoy YL, Rice JJ, Greenstein JL.
    Wiley Interdiscip Rev Syst Biol Med. 2011 Jul;3(4):392-413.

  14. The autophagic tumor stroma model of cancer: Role of oxidative stress and ketone production in fueling tumor cell metabolism.

    Pavlides S, Tsirigos A, Migneco G, Whitaker-Menezes D, Chiavarina B, Flomenberg N, Frank PG, Casimiro MC, Wang C, Pestell RG, Martinez-Outschoorn UE, Howell A, Sotgia F, Lisanti MP.
    Cell Cycle. 2010 Nov;9(21):4297-306.

  15. Understanding the "lethal" drivers of tumor-stroma co-evolution: Emerging role(s) for hypoxia, oxidative stress and autophagy/mitophagy in the tumor micro-environment.

    Lisanti MP, Martinez-Outschoorn UE, Chiavarina B, Pavlides S, Whitaker-Menezes D, Tsirigos A, Witkiewicz A, Lin Z, Balliet R, Howell A, Sotgia F.
    Cancer Biol Ther. 2010 Sep 19;10(6). [Epub ahead of print]

  16. Ketones and lactate "fuel" tumor growth and metastasis: Evidence that epithelial cancer cells use oxidative mitochondrial metabolism.

    Bonuccelli G, Tsirigos A, Whitaker-Menezes D, Pavlides S, Pestell RG, Chiavarina B, Frank PG, Flomenberg N, Howell A, Martinez-Outschoorn UE, Sotgia F, Lisanti MP.
    Cell Cycle. 2010 Sep 21;9(17). [Epub ahead of print]

  17. Simple and versatile methods to integrate directed self-assembly with optical lithography using a polarity-switched photoresist.

    Cheng JY, Sanders DP, Truong HD, Harrer S, Friz A, Holmes S, Colburn M, Hinsberg WD.
    ACS Nano. 2010 Aug 24;4(8):4815-23.

  18. Distribution of Electromechanical Delay in the Heart: Insights from a Three-Dimensional Electromechanical Model.

    Gurev V, Constantino J, Rice JJ, Trayanova NA.
    Biophys J. 2010 Aug 4;99(3):745-754.

  19. Glycolytic cancer associated fibroblasts promote breast cancer tumor growth, without a measurable increase in angiogenesis: Evidence for stromal-epithelial metabolic coupling.

    Migneco G, Whitaker-Menezes D, Chiavarina B, Castello-Cros R, Pavlides S, Pestell RG, Fatatis A, Flomenberg N, Tsirigos A, Howell A, Martinez-Outschoorn UE, Sotgia F, Lisanti MP.
    Cell Cycle. 2010 Jun 6;9(12). [Epub ahead of print]

  20. Single Mutation Effects on Conformational Change and Membrane Deformation of Influenza Hemagglutinin Fusion Peptides.

    Li J, Das P, Zhou R.
    J Phys Chem B. 2010 Jun 16;[Epub ahead of print].

  21. Base-By-Base Ratcheting of Single Stranded DNA through a Solid-State Nanopore

    Luan B, Peng H, Polonsky S, Rossnagel S, Stolovitzky G, Martyna.
    Phys. Rev. Lett. 2010 Jun 10;104(23):8103.

  22. 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.

    Pavlides S, Tsirigos A, Vera I, Flomenberg N, Frank PG, Casimiro MC, Wang C, Fortina P, Addya S, Pestell RG, Martinez-Outschoorn UE, Sotgia F, Lisanti MP.
    Cell Cycle. 2010 Jun 1;9(11):2201-19.

  23. 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".

    Pavlides S, Tsirigos A, Vera I, Flomenberg N, Frank PG, Casimiro MC, Wang C, Pestell RG, Martinez-Outschoorn UE, Howell A, Sotgia F, Lisanti MP.
    Aging (Albany NY). 2010 Apr;2(4):185-99.

  24. Urea-induced drying of carbon nanotubes suggests existence of a dry globule-like transient state during chemical denaturation of proteins.

    Das P, Zhou R.
    J Phys Chem B 2010 Apr 29;114(16):5427-30.

  25. Revealing strengths and weaknesses of methods for gene network inference.

    Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G.
    Proc Natl Acad Sci U S A 2010 Apr 6;107(14):6286-91. Epub 2010 Mar 22.

  26. A theory of loop formation and elimination by spike timing-dependent plasticity.

    Kozloski J, Cecchi GA.
    Front Neural Circuits 2010 Mar 10;4:7.

  27. Dynamic changes in the human methylome during differentiation.

    Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J, Wei CL.
    Genome Res 2010 Mar;20(3):320-31. Epub 2010 Feb 4.

  28. Time alignment algorithms based on selected mass traces for complex LC-MS data.

    Christin C, Hoefsloot HC, Smilde AK, Suits F, Bischoff R, Horvatovich PL.
    J Proteome Res. 2010 Mar 5;9(3):1483-95.

  29. Towards a rigorous assessment of systems biology models: the DREAM3 challenges.

    Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G.
    PLoS One 2010 Feb 23;5(2):e9202.

  30. APBC 2010. The Eighth Asia Pacific Bioinformatics Conference Bangalore, India, 18-21 January 2010.

    Parida L, Myers G.
    BMC Bioinformatics 2010 Jan 18;11 Suppl 1:I1. No abstract available.

  31. A conserved activation element in BMP signaling during Drosophila development.

    Weiss A, Charbonnier E, Ellertsdóttir E, Tsirigos A, Wolf C, Schuh R, Pyrowolakis G, Affolter M.
    Nat Struct Mol Biol 2010 Jan;17(1):69-76. Epub 2009 Dec 13.

  32. MULTI-RESOLUTION MODELING OF BIOLOGICAL MACROMOLECULES - Session Introduction.

    Flores S, Bernauer J, Huang X, Zhou R, Shin S.
    Pac Symp Biocomput. 2010;15:201-204.

  33. beta-Strand interactions at the domain interface critical for the stability of human lens gammaD-crystallin.

    Das P, King JA, Zhou R.
    Protein Sci 2010 Jan;19(1):131-40.

Publications in 2009

  1. Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes.

    Tsirigos A, Rigoutsos I.
    PLoS Comput Biol 2009 Dec;5(12):e1000610. Epub 2009 Dec 18.

  2. Geographical structure of the Y-chromosomal genetic landscape of the Levant: a coastal-inland contrast.

    El-Sibai M, Platt DE, Haber M, Xue Y, Youhanna SC, Wells RS, Izaabel H, Sanyoura MF, Harmanani H, Bonab MA, Behbehani J, Hashwa F, Tyler-Smith C, Zalloua PA; Genographic Consortium.
    Ann Hum Genet 2009 Nov;73(Pt 6):568-81. Epub 2009 Aug 16.

  3. Water-mediated signal multiplication with Y-shaped carbon nanotubes.

    Tu Y, Xiu P, Wan R, Hu J, Zhou R, Fang H.
    Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18120-4. Epub 2009 Oct 8.

  4. Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus.

    Xia Z, Jin G, Zhu J, Zhou R.
    Bioinformatics. 2009 Sep 15;25(18):2309-17. Epub 2009 Aug 25.

  5. Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity.

    Das P, Li J, Royyuru AK, Zhou R.
    J Comput Chem 2009 Aug;30(11):1654-63.

  6. Glass microneedles for force measurements: a finite-element analysis model.

    Ayittey PN, Walker JS, Rice JJ, de Tombe PP.
    Pflugers Arch 2009 Apr;457(6):1415-22. Epub 2008 Dec 23.

  7. High-Throughput Image Reconstruction and Analysis.

    (Editors) A. Ravishankar Rao and Guillermo A. Cecchi
    Artech House, 2009.

  8. Anterior-posterior positional information in the absence of a strong Bicoid gradient.

    Ochoa-Espinosa A, Yu D, Tsirigos A, Struffi P, Small S.
    Proc Natl Acad Sci U S A 2009 Mar 10;106(10):3823-8. Epub 2009 Feb 23.

  9. Lessons from the DREAM2 Challenges.

    Stolovitzky G, Prill RJ, Califano A.
    Ann N Y Acad Sci 2009 Mar;1158:159-95.

  10. Recognition mechanism of siRNA by viral p19 suppressor of RNA silencing: a molecular dynamics study.

    Xia Z, Zhu Z, Zhu J, Zhou R.
    Biophys J. 2009 Mar 4;96(5):1761-9.

  11. The challenges of systems biology. Preface.

    Stolovitzky G, Kahlem P, Califano A.
    Ann N Y Acad Sci 2009 Mar;1158:ix-xii. No abstract available.

  12. Urea's action on hydrophobic interactions.

    Zangi R, Zhou R, Berne BJ.
    J Am Chem Soc. 2009 Feb 4;131(4):1535-41.

  13. Minimizing recombinations in consensus networks for phylogeographic studies.

    Parida L, Javed A, Melé M, Calafell F, Bertranpetit J; Genographic Consortium.
    BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S72.

  14. ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes.

    Margolin AA, Palomero T, Sumazin P, Califano A, Ferrando AA, Stolovitzky G.
    Proc Natl Acad Sci U S A 2009 Jan 6;106(1):244-9. Epub 2008 Dec 31.

  15. Orthogonal recursive bisection data decomposition for high performance computing in cardiac model simulations: dependence on anatomical geometry.

    Reumann M, Fitch BG, Rayshubskiy A, Keller DU, Seemann G, Dossel O, Pitman MC, Rice JJ.
    Conf Proc IEEE Eng Med Biol Soc 2009;2009:2799-802.

  16. Strong scaling and speedup to 16,384 processors in cardiac electro-mechanical simulations.

    Reumann M, Fitch BG, Rayshubskiy A, Keller DU, Seemann G, Dossel O, Pitman MC, Rice JJ.
    Conf Proc IEEE Eng Med Biol Soc 2009;2009:2795-8.

  17. Prediction and interpretation of distributed neural activity with sparse models.

    Carroll MK, Cecchi GA, Rish I, Garg R, Rao AR.
    Neuroimage 2009 Jan 1;44(1):112-22. Epub 2008 Aug 27.

  18. Dewetting and hydrophobic interaction in physical and biological systems.

    Berne BJ, Weeks JD, Zhou R.
    Annu Rev Phys Chem. 2009;60:85-103. Review.

Publications in 2008

  1. Single mutation induced H3N2 hemagglutinin antibody neutralization: a free energy perturbation study.

    Zhou R, Das P, Royyuru AK.
    J Phys Chem B 2008 Dec 11;112(49):15813-20.

  2. Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks.

    Ma'ayan A, Cecchi GA, Wagner J, Rao AR, Iyengar R, Stolovitzky G.
    Proc Natl Acad Sci U S A 2008 Dec 9;105(49):19235-40. Epub 2008 Nov 25.

  3. Identifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean.

    Zalloua PA, Platt DE, El Sibai M, Khalife J, Makhoul N, Haber M, Xue Y, Izaabel H, Bosch E, Adams SM, Arroyo E, López-Parra AM, Aler M, Picornell A, Ramon M, Jobling MA, Comas D, Bertranpetit J, Wells RS, Tyler-Smith C; Genographic Consortium.
    Am J Hum Genet 2008 Nov;83(5):633-42. Epub 2008 Oct 30.

  4. Maximum-likelihood estimation of site-specific mutation rates in human mitochondrial DNA from partial phylogenetic classification.

    Rosset S, Wells RS, Soria-Hernanz DF, Tyler-Smith C, Royyuru AK, Behar DM; Genographic Consortium.
    Genetics 2008 Nov;180(3):1511-24. Epub 2008 Sep 14.

  5. Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding.

    Hua L, Zhou R, Thirumalai D, Berne BJ.
    Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):16928-33. Epub 2008 Oct 28.

  6. Estimating the ancestral recombinations graph (ARG) as compatible networks of SNP patterns.

    Parida L, Melé M, Calafell F, Bertranpetit J; Genographic Consortium.
    J Comput Biol 2008 Nov;15(9):1133-54.

  7. Approximate model of cooperative activation and crossbridge cycling in cardiac muscle using ordinary differential equations.

    Rice JJ, Wang F, Bers DM, de Tombe PP.
    Biophys J 2008 Sep;95(5):2368-90. Epub 2008 Jan 30.

  8. Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin.

    Grossfield A, Pitman MC, Feller SE, Soubias O, Gawrisch K.
    J Mol Biol 2008 Aug 29;381(2):478-86. Epub 2008 May 22.

  9. Role of water in mediating the assembly of Alzheimer amyloid-beta Abeta16-22 protofilaments.

    Krone MG, Hua L, Soto P, Zhou R, Berne BJ, Shea JE.
    J Am Chem Soc. 2008 Aug 20;130(33):11066-72. Epub 2008 Jul 29.

  10. Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs.

    Tsirigos A, Rigoutsos I.
    Nucleic Acids Res 2008 Jun;36(10):3484-93. Epub 2008 May 1.

  11. The dawn of human matrilineal diversity.

    Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, Metspalu E, Scozzari R, Makkan H, Tzur S, Comas D, Bertranpetit J, Quintana-Murci L, Tyler-Smith C, Wells RS, Rosset S; Genographic Consortium.
    Am J Hum Genet 2008 May;82(5):1130-40. Epub 2008 Apr 24.

  12. Two-dimensional method for time aligning liquid chromatography-mass spectrometry data.

    Suits F, Lepre J, Du P, Bischoff R, Horvatovich P.
    Anal Chem 2008 May 1;80(9):3095-104. Epub 2008 Apr 9.

  13. Sequence-based protein domain boundary prediction using BP neural network with various property profiles.

    Ye L, Liu T, Wu Z, Zhou R.
    Proteins. 2008 Apr;71(1):300-7.

  14. A noise model for mass spectrometry based proteomics.

    Du P, Stolovitzky G, Horvatovich P, Bischoff R, Lim J, Suits F.
    Bioinformatics 2008 Apr 15;24(8):1070-7. Epub 2008 Mar 18.

  15. Y-chromosomal diversity in Lebanon is structured by recent historical events.

    Zalloua PA, Xue Y, Khalife J, Makhoul N, Debiane L, Platt DE, Royyuru AK, Herrera RJ, Hernanz DF, Blue-Smith J, Wells RS, Comas D, Bertranpetit J, Tyler-Smith C; Genographic Consortium.
    Am J Hum Genet 2008 Apr;82(4):873-82. Epub 2008 Mar 27.

  16. Preventive ablation strategies in a biophysical model of atrial fibrillation based on realistic anatomical data.

    Reumann M, Bohnert J, Seemann G, Osswald B, Dössel O.
    IEEE Trans Biomed Eng 2008 Feb;55(2 Pt 1):399-406.

  17. Assessing learning progress and quality of teaching in large groups of students.

    Reumann M, Mohr M, Diez A, Dössel O.
    Conf Proc IEEE Eng Med Biol Soc 2008;2008:2877-80.

  18. Large scale cardiac modeling on the Blue Gene supercomputer.

    Reumann M, Fitch BG, Rayshubskiy A, Keller DU, Weiss DL, Seemann G, Dössel O, Pitman MC, Rice JJ.
    Conf Proc IEEE Eng Med Biol Soc 2008;2008:577-80.

  19. Unsupervised segmentation with dynamical units.

    Rao AR, Cecchi GA, Peck CC, Kozloski JR.
    IEEE Trans Neural Netw 2008 Jan;19(1):168-82.

  20. Spatially-compressed cardiac myofilament models generate hysteresis that is not found in real muscle.

    Rice JJ, Tu Y, Poggesi C, De Tombe PP.
    Pac Symp Biocomput 2008:366-77.

Publications in 2007

  1. Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference.

    Stolovitzky G, Monroe D, Califano A.
    Ann N Y Acad Sci 2007 Dec;1115:1-22. Epub 2007 Oct 9. Review.

  2. Statistical significance of large gene clusters.

    Parida L.
    J Comput Biol 2007 Nov;14(9):1145-59.

  3. Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells.

    Roach JC, Smith KD, Strobe KL, Nissen SM, Haudenschild CD, Zhou D, Vasicek TJ, Held GA, Stolovitzky GA, Hood LE, Aderem A.
    Proc Natl Acad Sci U S A 2007 Oct 9;104(41):16245-50. Epub 2007 Oct 3.

  4. Nanoscale dewetting transition in protein complex folding.

    Hua L, Huang X, Liu P, Zhou R, Berne BJ.
    J Phys Chem B. 2007 Aug 2;111(30):9069-77. Epub 2007 Jul 4.

  5. Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.

    Yu H, Jansen R, Stolovitzky G, Gerstein M.
    Bioinformatics 2007 Aug 15;23(16):2163-73. Epub 2007 May 31.

  6. High performance computing environment for multidimensional image analysis.

    Rao AR, Cecchi GA, Magnasco M.
    BMC Cell Biol 2007 Jul 10;8 Suppl 1:S9.

  7. Identifying directed links in large scale functional networks: application to brain fMRI.

    Cecchi GA, Rao AR, Centeno MV, Baliki M, Apkarian AV, Chialvo DR.
    BMC Cell Biol 2007 Jul 10;8 Suppl 1:S5.

  8. The Genographic Project public participation mitochondrial DNA database.

    Behar DM, Rosset S, Blue-Smith J, Balanovsky O, Tzur S, Comas D, Mitchell RJ, Quintana-Murci L, Tyler-Smith C, Wells RS; Genographic Consortium.
    PLoS Genet 2007 Jun;3(6):e104. Erratum in: PLoS Genet. 2007 Sep 14;3(9):1785.

  9. Destruction of long-range interactions by a single mutation in lysozyme.

    Zhou R, Eleftheriou M, Royyuru AK, Berne BJ.
    Proc Natl Acad Sci U S A 2007 Apr 3;104(14):5824-9. Epub 2007 Mar 26. Erratum in: Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11507.

  10. Replica exchange with solute tempering: efficiency in large scale systems.

    Huang X, Hagen M, Kim B, Friesner RA, Zhou R, Berne BJ.
    J Phys Chem B. 2007 May 17;111(19):5405-10. Epub 2007 Apr 17.

  11. Discovering topological motifs using a compact notation.

    Parida L.
    J Comput Biol 2007 Apr;14(3):300-23.

  12. Convergence of molecular dynamics simulations of membrane proteins.

    Grossfield A, Feller SE, Pitman MC.
    Proteins 2007 Apr 1;67(1):31-40.

  13. A single nucleotide polymorphism in the MDM2 gene disrupts the oscillation of p53 and MDM2 levels in cells.

    Hu W, Feng Z, Ma L, Wagner J, Rice JJ, Stolovitzky G, Levine AJ.
    Cancer Res 2007 Mar 15;67(6):2757-65.

  14. Electrostatic gating of a nanometer water channel.

    Li J, Gong X, Lu H, Li D, Fang H, Zhou R.
    Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3687-92. Epub 2007 Feb 27.

  15. PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory.

    Zhou R, Parida L, Kapila K, Mudur S.
    Bioinformatics 2007 Jan 1;23(1):99-106. Epub 2006 Oct 24.

  16. Gapped permutation pattern discovery for gene order comparisons.

    Parida L.
    J Comput Biol 2007 Jan-Feb;14(1):45-55.

  17. Accurate phylogenetic classification of variable-length DNA fragments.

    McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I.
    Nat Methods 2007 Jan;4(1):63-72. Epub 2006 Dec 10.

  18. Replica exchange molecular dynamics method for protein folding simulation.

    Zhou R.
    Methods Mol Biol. 2007;350:205-23.

Publications in 2006

  1. Using PQ structures for genomic rearrangement phylogeny.

    Parida L.
    J Comput Biol 2006 Dec;13(10):1685-700.

  2. Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields.

    Eleftheriou M, Germain RS, Royyuru AK, Zhou R.
    J Am Chem Soc 2006 Oct 18;128(41):13388-95.

  3. Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent.

    Liu P, Huang X, Zhou R, Berne BJ.
    J Phys Chem B. 2006 Sep 28;110(38):19018-22.

  4. Hydration and dewetting near fluorinated superhydrophobic plates.

    Li X, Li J, Eleftheriou M, Zhou R.
    J Am Chem Soc. 2006 Sep 27;128(38):12439-47.

  5. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes.

    Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I.
    Cell 2006 Sep 22;126(6):1203-17.

  6. Constructing near-perfect phylogenies with multiple homoplasy events.

    Satya RV, Mukherjee A, Alexe G, Parida L, Bhanot G.
    Bioinformatics 2006 Jul 15;22(14):e514-22.

  7. Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes.

    Rigoutsos I, Huynh T, Miranda K, Tsirigos A, McHardy A, Platt D.
    Proc Natl Acad Sci U S A 2006 Apr 25;103(17):6605-10. Epub 2006 Apr 24.

  8. A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids.

    Grossfield A, Feller SE, Pitman MC.
    Proc Natl Acad Sci U S A 2006 Mar 28;103(13):4888-93. Epub 2006 Mar 17.

  9. Mining, compressing and classifying with extensible motifs.

    Apostolico A, Comin M, Parida L.
    Algorithms Mol Biol 2006 Mar 23;1(1):4.

  10. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.

    Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A.
    BMC Bioinformatics 2006 Mar 20;7 Suppl 1:S7.

  11. Dynamics of water confined in the interdomain region of a multidomain protein.

    Hua L, Huang X, Zhou R, Berne BJ.
    J Phys Chem B. 2006 Mar 2;110(8):3704-11.

  12. Magnitude and spatial orientation of the hydrophobic moments of multi-domain proteins.

    Zhou R, Royyuru A, Athma P, Suits F; B. David Silverman.
    Int J Bioinform Res Appl 2006;2(2):161-76.

  13. Is Poisson-Boltzmann theory insufficient for protein folding simulations?

    Lwin TZ, Zhou R, Luo R.
    J Chem Phys. 2006 Jan 21;124(3):034902.

  14. Comparison of Amersham and Agilent microarray technologies through quantitative noise analysis.

    Held GA, Duggar K, Stolovitzky G.
    OMICS 2006 Winter;10(4):532-44.

Publications in 2005

  1. A wavelet approach for the analysis of folding trajectory of protein Trp-cage.

    Ye L, Chen H, Liu T, Wu Z, Li J, Zhou R.
    J Bioinform Comput Biol. 2005 Dec;3(6):1351-70.

  2. Gene proximity analysis across whole genomes via PQ trees.

    Landau GM, Parida L, Weimann O.
    J Comput Biol 2005 Dec;12(10):1289-306.

  3. A plausible model for the digital response of p53 to DNA damage.

    Ma L, Wagner J, Rice JJ, Hu W, Levine AJ, Stolovitzky GA.
    Proc Natl Acad Sci U S A 2005 Oct 4;102(40):14266-71. Epub 2005 Sep 26.

  4. Adaptive diagnosis in distributed systems.

    Rish I, Brodie M, Ma S, Odintsova N, Beygelzimer A, Grabarnik G, Hernandez K.
    IEEE Trans Neural Netw 2005 Sep;16(5):1088-109.

  5. p53-Mdm2 loop controlled by a balance of its feedback strength and effective dampening using ATM and delayed feedback.

    Wagner J, Ma L, Rice JJ, Hu W, Levine AJ, Stolovitzky GA.
    Syst Biol (Stevenage) 2005 Sep;152(3):109-18.

  6. Observation of a dewetting transition in the collapse of the melittin tetramer.

    Liu P, Huang X, Zhou R, Berne BJ.
    Nature. 2005 Sep 1;437(7055):159-62.

  7. Formation of regulatory patterns during signal propagation in a Mammalian cellular network.

    Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong NJ, Weng G, Ram PT, Rice JJ, Kershenbaum A, Stolovitzky GA, Blitzer RD, Iyengar R.
    Science 2005 Aug 12;309(5737):1078-83.

  8. Hydration and dewetting near graphite-CH(3) and graphite-COOH plates.

    Li J, Liu T, Li X, Ye L, Chen H, Fang H, Wu Z, Zhou R.
    J Phys Chem B. 2005 Jul 21;109(28):13639-48.

  9. A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes.

    Tsirigos A, Rigoutsos I.
    Nucleic Acids Res 2005 Jul 8;33(12):3699-707. Print 2005.

  10. Report: workshop on mediastinal grey zone lymphoma.

    Poppema S, Kluiver JL, Atayar C, van den Berg A, Rosenwald A, Hummel M, Lenze D, Lammert H, Stein H, Joos S, Barth T, Dyer M, Lichter P, Klein U, Cattoretti G, Gloghini A, Tu Y, Stolovitzky GA, Califano A, Carbone A, Dalla-Favera R, Melzner I, Bucur AJ, Brüderlein S, Dorsch K, Hasel C, Barth TF, Leithäuser F, Möller P.
    Eur J Haematol Suppl 2005 Jul;(66):45-52.

  11. Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers.

    Pitman MC, Suits F, Gawrisch K, Feller SE.
    J Chem Phys 2005 Jun 22;122(24):244715.

  12. Molecular dynamics investigation of the structural properties of phosphatidylethanolamine lipid bilayers.

    Suits F, Pitman MC, Feller SE.
    J Chem Phys 2005 Jun 22;122(24):244714.

  13. Conservative extraction of over-represented extensible motifs.

    Apostolico A, Comin M, Parida L.
    Bioinformatics 2005 Jun;21 Suppl 1:i9-18.

  14. Combinatorial pattern discovery approach for the folding trajectory analysis of a beta-hairpin.

    Parida L, Zhou R.
    PLoS Comput Biol 2005 Jun;1(1):e8. Epub 2005 Jun 24.

  15. Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment.

    Pitman MC, Grossfield A, Suits F, Feller SE.
    J Am Chem Soc 2005 Apr 6;127(13):4576-7.

  16. Reverse engineering of regulatory networks in human B cells.

    Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A.
    Nat Genet 2005 Apr;37(4):382-90. Epub 2005 Mar 20.

  17. Reconstructing biological networks using conditional correlation analysis.

    Rice JJ, Tu Y, Stolovitzky G.
    Bioinformatics 2005 Mar;21(6):765-73. Epub 2004 Oct 14.

  18. Reconstructing biological networks using conditional correlation analysis.

    Rice JJ, Tu Y, Stolovitzky G.
    Bioinformatics 2005 Mar;21(6):765-73. Epub 2004 Oct 14.

  19. Drying and hydrophobic collapse of paraffin plates.

    Huang X, Zhou R, Berne BJ.
    J Phys Chem B. 2005 Mar 3;109(8):3546-52.

  20. A new computational method for the detection of horizontal gene transfer events.

    Tsirigos A, Rigoutsos I.
    Nucleic Acids Res 2005 Feb 16;33(3):922-33. Print 2005.

  21. Statistical analysis of MPSS measurements: application to the study of LPS-activated macrophage gene expression.

    Stolovitzky GA, Kundaje A, Held GA, Duggar KH, Haudenschild CD, Zhou D, Vasicek TJ, Smith KD, Aderem A, Roach JC.
    Proc Natl Acad Sci U S A 2005 Feb 1;102(5):1402-7. Epub 2005 Jan 24.

  22. Robust diagnosis of non-Hodgkin lymphoma phenotypes validated on gene expression data from different laboratories.

    Bhanot G, Alexe G, Levine AJ, Stolovitzky G.
    Genome Inform 2005;16(1):233-44.

  23. A robust meta-classification strategy for cancer diagnosis from gene expression data.

    Alexe G, Bhanot G, Venkataraghavan B, Ramaswamy R, Lepre J, Levine AJ, Stolovitzky G.
    Proc IEEE Comput Syst Bioinform Conf 2005:322-5.

Publications in 2004

  1. Tracking CD40 signaling during germinal center development.

    Basso K, Klein U, Niu H, Stolovitzky GA, Tu Y, Califano A, Cattoretti G, Dalla-Favera R.
    Blood 2004 Dec 15;104(13):4088-96. Epub 2004 Aug 26.

  2. Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol.

    Pitman MC, Suits F, Mackerell AD Jr, Feller SE.
    Biochemistry 2004 Dec 14;43(49):15318-28.

  3. Hydrophobic collapse in multidomain protein folding.

    Zhou R, Huang X, Margulis CJ, Berne BJ.
    Science 2004 Sep 10;305(5690):1605-9.

  4. The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update.

    Huynh T, Rigoutsos I.
    Nucleic Acids Res 2004 Jul 1;32(Web Server issue):W10-5.

  5. Approaches to modeling crossbridges and calcium-dependent activation in cardiac muscle.

    Rice JJ, de Tombe PP.
    Prog Biophys Mol Biol 2004 Jun-Jul;85(2-3):179-95. Review.

  6. Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm.

    Zhou R.
    J Mol Graph Model. 2004 May;22(5):451-63.

US Patents

  1. 7,761,715

    Semiotic system and method with privacy protection

  2. 7,756,691

    Establishing relationships between components in simulation systems

  3. 7,698,067

    Sequence pattern descriptors for transmembrane structural details

  4. 7,613,851

    Apparatus, method, and product of manufacture for transforming supply chain networks using pair-wise nodal analysis

  5. 7,613,662

    Apparatus, machine-readable medium, and system for the detection of atypical sequences via generalized compositional methods

  6. 7,587,516

    Class network routing

  7. 7,561,974

    System and method for identifying genes

  8. 7,558,768

    Topological motifs discovery using a compact notation

  9. 7,499,805

    Method and apparatus for protein structure analysis

  10. 7,496,550

    Techniques for reconstructing synthetic networks using pair-wise correlation analysis

  11. 7,479,905

    Apparatus, system and method for data compression using irredundant patterns

  12. 7,433,857

    Techniques for reconstructing supply chain networks using pair-wise correlation analysis

  13. 7,428,515

    Object classification using an optimized Boolean expression

  14. 7,356,415

    Similarity searching of molecules based upon descriptor vectors characterizing molecular regions

  15. 7,343,246

    Spatial profiling of proteins using hydrophobic moments

  16. 7,315,877

    Efficient implementation of a multidimensional fast fourier transform on a distributed-memory parallel multi-node computer

  17. 7,313,582

    Arithmetic functions in torus and tree networks

  18. 7,313,507

    System and method for spatially profiling a distribution of hydrophobicity of a transmembrane protein

  19. 7,287,015

    Methods and apparatus for transmitting signals through network elements for classification

  20. 7,259,701

    Method and structure for lossy compression of continuous data with extensible motifs

  21. 7,248,971

    Method and apparatus for discovering patterns in a set of sequences

  22. 7,233,906

    Progress notes model in a clinical information system

  23. 7,203,680

    System and method for encoding and detecting extensible patterns

  24. 7,158,892

    Genomic messaging system

  25. 7,096,167

    System and method for molecular dynamic simulation

  26. 7,085,613

    System for monitoring audio content in a video broadcast

  27. 7,062,121

    Method and apparatus for a scalable parallel computer based on optical fiber broadcast

  28. 7,043,476

    Method and apparatus for data mining to discover associations and covariances associated with data

  29. 7,031,921

    System for monitoring audio content available over a network

  30. 6,785,672

    Methods and apparatus for performing sequence homology detection

  31. 6,748,360

    System for selling a product utilizing audio content identification

  32. 6,671,626

    Determination and use of three-dimensional moments of molecular property fields

  33. 6,604,072

    Feature-based audio content identification

  34. 6,574,594

    System for monitoring broadcast audio content

  35. 6,571,199

    Method and apparatus for performing pattern dictionary formation for use in sequence homology detection

  36. 6,446,011

    Tandem repeat detection using pattern discovery

  37. 6,434,488

    Alignment free methodology for rapid determination of differences between a test data set and known data sets

  38. 6,408,321

    Method and apparatus for mapping components of descriptor vectors to a space that discriminates between groups

  39. 6,373,971

    Method and apparatus for pattern discovery in protein sequences

  40. 6,349,265

    Method and apparatus for mapping components of descriptor vectors for molecular complexes to a space that discriminates between groups

  41. 6,341,284

    Method and apparatus for exhaustive enumeration of correspondence in a set of descriptors

  42. 6,205,444

    Multiple sequence alignment system and method

  43. 6,108,666

    Method and apparatus for pattern discovery in 1-dimensional event streams

  44. 6,092,065

    Method and apparatus for discovery, clustering and classification of patterns in 1-dimensional event streams

  45. 6,064,753

    System and method for distortion control in live-scan inkless fingerprint images

  46. 6,041,133

    Method and apparatus for fingerprint matching using transformation parameter clustering based on local feature correspondences

  47. 5,977,890

    Method and apparatus for data compression utilizing efficient pattern discovery

  48. 5,802,525

    Two-dimensional affine-invariant hashing defined over any two-dimensional convex domain and producing uniformly-distributed hash keys

  49. 5,799,312

    Three-dimensional affine-invariant hashing defined over any three-dimensional convex domain and producing uniformly-distributed hash keys

  50. 5,787,279

    System and method for conformationally-flexible molecular recognition

  51. 5,784,294

    System and method for comparative molecular moment analysis (CoMMA)

  52. 5,752,019

    System and method for confirmationally-flexible molecular identification

  53. 5,577,249

    Method for finding a reference token sequence in an original token string within a database of token strings using appended non-contiguous substrings