{"id":1784,"date":"2017-10-11T15:20:50","date_gmt":"2017-10-11T19:20:50","guid":{"rendered":"https:\/\/sites.bu.edu\/phenogeno\/?page_id=1784"},"modified":"2021-03-03T18:24:52","modified_gmt":"2021-03-03T23:24:52","slug":"network-biology","status":"publish","type":"page","link":"https:\/\/sites.bu.edu\/phenogeno\/research\/network-biology\/","title":{"rendered":"Network Systems Biology"},"content":{"rendered":"

Selected References<\/strong><\/p>\n

PUBMED PUBLICATIONS<\/a><\/p>\n

Google Scholar Publications<\/a><\/p>\n

Journal Publications<\/strong><\/p>\n

    \n
  1. Reconstructing and reprogramming the developmental hierarchy of glioblastoma<\/a>, Mario L. Suv\u00e0*, Esther Rheinbay* et al, Cell, 2014.<\/li>\n
  2. An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma<\/a>. Rheinbay E, Suv\u00e0 ML, Gillespie SM, Wakimoto H, Patel AP, Shahid M, Oksuz O, Rabkin SD, Martuza RL, Rivera MN, Louis DN, Kasif S, Chi AS, Bernstein BE. Cell Reports. 2013 May 30;3(5):1567-79.\u00a0 2013.04.021. Epub 2013 May 23. PMID: 23707066<\/li>\n
  3. The COMBREX project: design, methodology, and initial results<\/a>. Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Cr\u00e9cy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova\u00a0 IA, Rudd KE, S\u00f6ll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O’Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sj\u00f6lander K, Salzberg, SL, Vitkup D, Letovsky S, Segr\u00e8 D, DeLisi C, Roberts RJ, Steffen M, Kasif S. PLoS Biology. 2013 Aug;11(8):e1001638. doi: 10.1371\/journal.pbio.1001638. Epub 2013 Aug 27. PMID: 24013487<\/li>\n
  4. Systems biology characterization of engineered tissues<\/a>. Rajagopalan P, Kasif S, Murali TM. Annu Rev Biomed Eng. 2013;15:55-70. doi: 10.1146\/annurev-bioeng-071811-150120. PMID: 23862675<\/li>\n
  5. To supplement or not to supplement: a metabolic network framework for human nutritional supplements<\/a>. Nogiec CD, Kasif S. PLoS One. 2013;8(8):e68751. doi: 10.1371\/journal.pone.0068751. PMID: 23967053<\/li>\n
  6. Deep sequencing of the oral microbiome reveals s signatures of periodontal disease<\/a>, Bo Liu1,2<\/sup>*, Lina Faller3<\/sup>*, Niels Klitgord3<\/sup>*, Varun Mazumdar3<\/sup>*, Mohammad Ghodsi1,2<\/sup>,Daniel D. Sommer1<\/sup>, Theodore R. Gibbons1,4<\/sup>, Todd J. Treangen1,10<\/sup>, Yi-Chien Chang3<\/sup>,Shan Li5<\/sup>, O. Colin Stine5<\/sup>, Hatice Hasturk8<\/sup>, Simon Kasif3,7,9<\/sup>, Daniel Segr\u00e83,6,7<\/sup>#,\u00a0 Mihai Pop1,2,4<\/sup>#, Salomon Amar3,8<\/sup>#,, PLOS One, 2012<\/li>\n
  7. Network Signatures of Insulin Resistance and Life Span, M. Liu, M. Mori, IS. Kohane, ME Patti, A. Goldfine, CR Kahn, S. Kasif, in preparation.<\/li>\n
  8. Chris Nogiec, Allison Burkhart, Simon Kasif* and ME Patti*, Metabolic Analysis of Insulin Resistance, in revision (contributed equally authors).<\/li>\n
  9. Bridging Computation and Experiments: Using Computers to Drive Biology, (in revision), Science.<\/li>\n
  10. Towards a Personal Repeatome: A Genome-Wide Survey of Length Variation in Short Tandem Repeats in Human Gene Transcripts, in preparation.<\/li>\n
  11. A Critical Assessment of Genomic and Clinical Breast Cancer Biomarkers. Chang-Jiun Wu, Tianxi Cai, Zoltan Szallasi, Kamila Naxerova, Martin Steffen, L.J. Wei, Isaac S. Kohane*, Simon Kasif*, co-corresponding authors, in revision.<\/li>\n
  12. Integrative Pheno-genomic module discovery with application to breast cancer, Chang-Jiun Wu, Tianxi Cai, Isaac S. Kohane*, Simon Kasif*, in revision.<\/li>\n
  13. A Systems Biology Approach Links Inflammation to the Predisposition to Metabolic Diseases in Mouse Strains<\/a>, Marcelo Mori*, Manway Liu*, Simon Kasif, Ron Kahn, Diabetes 2010.<\/li>\n
  14. Transcriptome Analysis Reveals Parallel Dysregulation of Oxidative Metabolism and Inflammation in Muscle and Adipose Tissue With Progression of Insulin Resistance in Humans, Mary-Elizabeth Patti, Manway Liu, Wanzhu Jin, Carles Lerin, Jonathan Dreyfuss, Martha Vokes, Joshua Schroeder, Elizabeth Tatro, Peter Park, Isaac Kohane, Igor Leykin, Simon Kasif, and Allison Goldfine, in preparation.<\/li>\n
  15. COMBREX: a project to accelerate the functional annotation of prokaryotic genomes<\/a>. Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG,\u00a0\u00a0 Osmani L, Swaminathan R, Tao KR, Letovsky S, Vitkup D, Segr D, Salzberg , SL, Delisi C, Steffen M, Kasif S. Nucleic Acids Res. 2010 Nov 21. PMID: 21097892<\/li>\n
  16. Drug Response Phosphorylation Signatures of Lung Cancer, Chang-Jiun Wu, Martin Steffen, Simon Kasif in preparation.<\/li>\n
  17. The Evolution of Gene Annotation<\/a>, Simon Kasif and Martin Steffen, Nature Chemical Biology, Jan 2010.<\/li>\n
  18. A Predictive phosphorylation signature of lung cancer<\/a>. Chang-Jiun Wu, Tianxi Cai, Klarisa Rikova, David Merberg, Simon Kasif,* Martin Steffen*, co-corresponding authors,\u00a0 PLoS ONE, Nov 2009.<\/li>\n
  19. Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance<\/a>. Park PJ, Kong SW, Tebaldi T, Lai WR, Kasif S, Kohane IS. Bioinformatics. 2009 Dec 1;25(23):3121-7. Epub 2009 Sep 28.PMID: 19786482<\/li>\n
  20. Seeing the Forest for the Trees: Using the Gene Ontology to Restructure Hierarchical clustering<\/a>.\u00a0 Dotan-Cohen D, Kasif S, Melkman AA, Kasif S, Bioinformatics, 2009<\/li>\n
  21. Biological process linkage networks<\/a>. Dotan-Cohen D, Letovsky S, Melkman AA, Kasif S. PLoS ONE. 2009;4(4):e5313. Epub 2009 Apr 23. PMID 19390589<\/li>\n
  22. Accelerated postnatal growth increases lipogenic gene expression and adipocyte size in low-birth weight mice<\/a>. Isganaitis E, Jimenez-Chillaron J, Woo M, Chow A, DeCoste J, Vokes M, Liu M, Kasif S, Zavacki AM, Leshan RL, Myers MG, Patti ME. Diabetes. 2009 May;58(5):1192-200. Epub 2009 Feb 10. PMID: 19208909<\/li>\n
  23. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains<\/a>. Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE. PLoS Genet. 2008 Oct;4(10):e1000242. Epub 2008 Oct 31. PMID: 18974828<\/li>\n
  24. Formula dissection: A parallel algorithm for constraint satisfaction<\/a>. Reif, J. H., Kasif, S., and Sherlekar, D.\u00a0 Comput. Math. Appl. 55, 6 (Mar. 2008), 1170- 1177 (republished from a 1987 conference version).<\/li>\n
  25. Integration of relational and hierarchical network information for protein function prediction<\/a>. Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED. BMC Bioinformatics. 2008 Aug 22; 9:350. PMID: 18721473<\/li>\n
  26. Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers<\/a>. Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S, Kohane IS. Genome Biol. 2008;9(7):R108. Epub 2008 Jul 8. PMID: 18611264<\/li>\n
  27. Anton BP, Saleh L, Benner JS, Raleigh EA, Kasif S, Roberts RJ.RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli<\/a>. Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1826-31. Epub 2008 Feb 5. PMID: 18252828<\/li>\n
  28. Context specific protein function prediction<\/a>. Nariai N, Kasif S. Genome Inform. 2007; 18:173-82. PMID: 18546485<\/li>\n
  29. Tullai JW, Schaffer ME, Mullenbrock S, Sholder G, Kasif S, Cooper GM.\u00a0Immediate-early and delayed primary response genes are distinct in function and genomic architecture<\/a>, J Biol Chem. 2007 Jun 15;<\/li>\n
  30. Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S.\u00a0Network-based analysis of affected biological processes in type 2 diabetes models<\/a>. PLoS Genet. 2007 Jun 15;3(6):e96. PMID: 17571924<\/li>\n
  31. Nariai N, Kolaczyk ED, Kasif S.\u00a0Probabilistic protein function prediction from heterogeneous genome-wide data<\/a>. PLoS ONE. 2007 Mar 28;2:e337. PMID: 17396164<\/li>\n
  32. Zhang L, Kasif S, Cantor AC.\u00a0Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy<\/a>. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3061-6. Epub 2007 Feb 20. PMID: 17360609<\/li>\n
  33. Tullai JW, Chen J, Schaffer ME, Kamenetsky E, Kasif S, Cooper GM.\u00a0Glycogen synthase kinase-3 represses cyclic AMP response element-binding protein (CREB)-targeted immediate early genes in quiescent cells<\/a>. J Biol Chem. 2007 Mar 30;282(13):9482-91. Epub 2007 Feb 3. PMID: 17277356<\/li>\n
  34. Alon N, Asodi V, Cantor C, Kasif S, Rachlin J.\u00a0Multi-node graphs: a framework for multiplexed biological assays<\/a>. J Comput Biol. 2006 Dec;13(10):1659-72. PMID: 17238837<\/li>\n
  35. Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS.\u00a0Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles<\/a>., PLoS Biol. 2007 Jan 9;5(1):e8 PMID: 17214507<\/li>\n
  36. Murali TM, Wu CJ, Kasif S.\u00a0The art of gene function prediction<\/a>. Nature Biotechnology. 2006 Dec;24(12):1474-5. PMID: 17160037<\/li>\n
  37. Gustafson AM, Snitkin ES, Parker SC, DeLisi C, Kasif S.\u00a0Towards the identification of essential genes using targeted genome sequencing and comparative analysis<\/a>. BMC Genomics. 2006 Oct 19;7:265. PMID: 17052348<\/li>\n
  38. Rachlin J, Cohen DD, Cantor C, Kasif S.\u00a0Biological context networks: a mosaic view of the interactome<\/a>. Nature\/Embo. Mol Syst Biol. 2006;2:66. Epub 2006 Nov 28. PMID: 17130868<\/li>\n
  39. Lee S, Kohane I, Kasif S.\u00a0Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes<\/a>. BMC Genomics. 2005 Nov 27;6:168. PMID: 16309559<\/li>\n
  40. Zheng Y, Anton BP, Roberts RJ, Kasif S.\u00a0Phylogenetic detection of conserved gene clusters in microbial genomes<\/a>. BMC Bioinformatics. 2005 Oct 3;6:243. PMID: 16202130<\/li>\n
  41. Szustakowski JD, Kasif S, Weng Z. Less is more: towards an optimal universal description of protein folds. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii66-ii71. PMID: 16204127<\/li>\n
  42. Rachlin J, Ding C, Cantor C, Kasif S.\u00a0Computational tradeoffs in multiplex PCR assay design for SNP genotyping<\/a>. BMC Genomics. 2005 Jul 25;6:102.PMID: 16042802<\/li>\n
  43. Wu CJ, Kasif S.\u00a0\u00a0GEMS: a web server for biclustering analysis of expression data<\/a>. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W596-9. PMID: 15980544<\/li>\n
  44. Rachlin J, Ding C, Cantor C, Kasif S. \u00a0MuPlex: multi-objective multiplex PCR assay design<\/a>. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W544-7. PMID: 15980531<\/li>\n
  45. Noga Alon, Richard Beigel and Simon Kasif and Steven Rudich and Benny Sudakov, “Learning a Hidden Matching<\/a>“, SIAM Journal of Computing, 2004.<\/li>\n
  46. Zheng Y, Roberts RJ, Kasif S. \u00a0Identification of genes with fast-evolving regions in microbial genomes<\/a>. Nucleic Acids Res. 2004 Dec 2;32(21):6347-57. Print 2004. PMID: 15576679<\/li>\n
  47. Zhang L, Kasif S, Cantor CR, Broude NE.\u00a0GC\/AT-content spikes as genomic punctuation marks<\/a>. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16855-60. Epub 2004 Nov 17. PMID: 15548610<\/li>\n
  48. Tullai JW, Schaffer ME, Mullenbrock S, Kasif S, Cooper GM.\u00a0Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK\/ERK signaling pathways<\/a>. J Biol Chem. 2004 May 7;279(19):20167-77. Epub 2004 Feb 9. PMID: 14769801<\/li>\n
  49. Zheng Y, Roberts RJ, Kasif S. \u00a0Segmentally variable genes: a new perspective on adaptation<\/a>. PLoS Biol. 2004 Apr;2(4):E81. Epub 2004 Apr 13. PMID: 15094797<\/li>\n
  50. Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2888-93. Epub 2004 Feb 23. PMID: 4981259<\/li>\n
  51. Wu CJ, Fu Y, Murali TM, Kasif S. \u00a0Gene expression module discovery using Gibbs sampling<\/a>. Genome Inform. 2004;15(1):239-48. PMID: 15712126<\/li>\n
  52. Stitziel NO, Binkowski TA, Tseng YY, Kasif S, Liang J. \u00a0topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association<\/a>. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D520-2. PMID: 14681472<\/li>\n
  53. Su Y, Murali TM, Pavlovic V, Schaffer M, Kasif S.\u00a0RankGene: identification of diagnostic genes based on expression data<\/a>. Bioinformatics. 2003 Aug 12;19(12):1578-9. PMID: 12912841<\/li>\n
  54. Wu J, Kasif S, DeLisi C.\u00a0\u00a0Identification of functional links between genes using phylogenetic profiles<\/a>. Bioinformatics. 2003 Aug 12;19(12):1524-30. PMID: 12912833<\/li>\n
  55. Zhang L, Pavlovic V, Cantor CR, Kasif S.\u00a0Human-mouse gene identification by comparative evidence integration and evolutionary analysis.<\/a>\u00a0Genome Res. 2003 Jun;13(6A):1190-202. Epub 2003 May 12. PMID: 12743024<\/li>\n
  56. Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, Liang J.\u00a0\u00a0Structural location of disease-associated single-nucleotide polymorphisms<\/a>. J Mol Biol. 2003 Apr 11;327(5):1021-30. PMID: 12662927<\/li>\n
  57. Letovsky S, Kasif S.\u00a0\u00a0Predicting protein function from protein\/protein interaction data: a probabilistic approach<\/a>.\u00a0 Bioinformatics. 2003;19 Suppl 1:i197-204. PMID: 12855458<\/li>\n
  58. Zheng Y, Roberts RJ, Kasif S.\u00a0Genomic functional annotation using co-evolution profiles of gene clusters<\/a>. Genome Biol. 2002 Oct 10;3(11):RESEARCH0060. Epub 2002 Oct 10. PMID: 12429059<\/li>\n
  59. Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S.\u00a0\u00a0Computational identification of operons in microbial genomes<\/a>. Genome Res. 2002 Aug;12(8):1221-30. PMID: 12176930<\/li>\n
  60. Pavlovic V, Garg A, Kasif S.\u00a0A Bayesian framework for combining gene predictions<\/a>. Bioinformatics. 2002 Jan;18(1):19-27. PMID: 11836207<\/li>\n
  61. Cai D, Delcher A, Kao B, Kasif S.\u00a0Modeling splice sites with Bayes networks<\/a>. Bioinformatics. 2000 Feb;16(2):152-8. PMID: 10842737<\/li>\n
  62. Tettelin H, Radune D, Kasif S, Khouri H, Salzberg SL.\u00a0\u00a0Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project<\/a>. Genomics. 1999 Dec 15;62(3):500-7. PMID: 10644449<\/li>\n
  63. Bright, J., Kasif, L. Stiller, \u201cData Intensive Algorithms for Search Problems\u201d, accepted for publication in IEEE Transactions on Computers.<\/li>\n
  64. Kasif, S., \u201cTowards a Constraint-Based Engineering Framework for Algorithm Design and Application<\/a>\u201d, Journal of Constraints, 1997.<\/li>\n
  65. Delcher, A, A. Grove, S. Kasif and J. Pearl, \u201cLogarithmic Time Queries and Updates in Probabilistic Networks<\/a>\u201d, Journal of Artificial Intelligence Research, Vol. 4., pp. 37–59, 1996.<\/li>\n
  66. Waltz, D. and S. Kasif, \u201cOn Reasoning from Data<\/a>\u201d, Computing Surveys, 1996.<\/li>\n
  67. Kasif, S. and A. Delcher, \u201cAnalysis of Local Consistency in Parallel Constraint Networks\u201d, Artificial Intelligence, 69, pp.307–327, 1994.<\/li>\n
  68. Kasif, S., S. Banerjee, A. Delcher and G. Sullivan, \u201cSome Results on the Complexity of Symmetric Connectionist Networks<\/a>\u201d, Annals of Mathematics and Artificial Intelligence, pp.327-344, Nov. 1993.<\/li>\n
  69. Kasif, S., \u201cOn the Parallel Complexity of Discrete Relaxation in Constraint Networks\u201d, Artificial Intelligence, pp. 275-286, October 1990.<\/li>\n
  70. Delcher, A. and S. Kasif, \u201cSome Results On the Complexity of Maintaining Data Flow Dependencies in Parallel Logic Programs\u201d, Journal of Logic Programming, pp.229–241, April 1989.<\/li>\n
  71. Kasif, S., \u201cControl and Data Driven Execution of Logic Programs: A Comparison\u201d, Journal of Parallel Programming.Vol.15, No.1, pp.73–100, February 1987.<\/li>\n
  72. Kasif, S., L. Kitchen and A. Rosenfeld, \u201cA Hough Transform Technique for Subgraph Isomorphism\u201d, Pattern Recognition Letters. Vol.2, pp.83–88, December 1983.<\/li>\n
  73. Kasif, S. and A. Rosenfeld, \u201cPyramid Linking as a Special Case of Isodata\u201d, IEEE Transactions on Systems, Man and Cybernetics, Vol.SMC-13, No.1, January 1983.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

    Selected References PUBMED PUBLICATIONS Google Scholar Publications Journal Publications Reconstructing and reprogramming the developmental hierarchy of glioblastoma, Mario L. Suv\u00e0*, Esther Rheinbay* et al, Cell, 2014. An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Rheinbay E, Suv\u00e0 ML, Gillespie SM, Wakimoto H, Patel AP, Shahid M, Oksuz O, […]<\/p>\n","protected":false},"author":8782,"featured_media":0,"parent":11,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages\/1784"}],"collection":[{"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/users\/8782"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/comments?post=1784"}],"version-history":[{"count":4,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages\/1784\/revisions"}],"predecessor-version":[{"id":2568,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages\/1784\/revisions\/2568"}],"up":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages\/11"}],"wp:attachment":[{"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/media?parent=1784"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}