Biological Networks


Selected References




Google Scholar Publications



Journal Publications

  1. Analysis of brain region-specific co-expression networks reveals clustering of established and novel genes associated with Alzheimer disease.
    Lancour D, Dupuis J, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg GC, Crovella M, Farrer LA, Kasif S.
    Alzheimers Res Ther. 2020 Sep 2;12(1):103. doi: 10.1186/s13195-020-00674-7.
  2. Identifying Human Interactors of SARS-CoV-2 Proteins and Drug Targets for COVID-19 using Network-Based Label Propagation, Jeffrey Law et al, aRxiv, 2020
  3. Rate Estimation and Identification of COVID-19 Infections: Towards Rational Policy Making During Early and Late Stages of Epidemics, Richard Beigel, Simon Kasif, medRxiv 2020
  4. Single-cell transcriptional networks in differentiating preadipocytes suggest drivers associated with tissue heterogeneity.Ramirez AK, Dankel SN, Rastegarpanah B, Cai W, Xue R, Crovella M, Tseng YH, Kahn CR, Kasif S.Nat Commun. 2020 Apr 30;11(1):2117. doi: 10.1038/s41467-020-16019-9.PMID: 32355218
  5. Evolution of Knowledge Networks: Towards Reproducibility, Provenance and Causal Paths in Biology and Medicine, Kasif S. Roberts, RJ., in review.
  6. Novel mediation analysis of human plasma proteome and metabolome reveals
    mediators of improved glycemia after gastric bypass surgery Jonathan M Dreyfuss, Yixing Yuchi, Hui Pan, Xuehong Dong, Donald C. Simonson, Ashley Vernon, Pratik Aryal, Anish Konkar, Yinong Sebastian, Brandon W Higgs, Joseph Grimsby, Cristina M. Rondinone, Simon Kasif , Barbara B. Kahn, Kathleen Foster, Allison Goldfine, Mary-Elizabeth Patti, in review.
  7. Membrane Metallo-Endopeptidase (Neprilysin) Regulates Inflammatory Response and Insulin Signaling in White Preadipocytes Ramirez AK, Dankel S, Cai W, Sakaguchi M, Kasif S, Kahn CR. Mol Metab. 2019 Apr;22:21-36. doi: 10.1016/j.molmet.2019.01.006. Epub 2019 Jan 25. PMID: 30795914
  8. One for all and all for One: Improving replication of genetic studies through network diffusion. Lancour D, Naj A, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg GD, Crovella M, Farrer LA, Kasif S. PLoS Genet. 2018 Apr 23;14(4):e1007306. doi: 10.1371/journal.pgen.1007306. eCollection 2018 Apr. PMID: 29684019
  9. Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Differences between Brown and White Adipocytes. Ramirez AK, Lynes MD, Shamsi F, Xue R, Tseng YH, Kahn CR, Kasif S, Dreyfuss JM. Cell Rep. 2017 Dec 12;21(11):3040-3048. doi: 10.1016/j.celrep.2017.11.065. PMID: 29241534 (Best Graduate Student Paper award to Alfred Ramirez).
  10. Not All Experimental Questions Are Created Equal: Accelerating Biological Data to Knowledge Transformation (BD2K) via Science Informatics, Active Learning and Artificial Intelligence, Kasif,S, Letovsky S, Roberts, RJ,  Steffen,M,  bioRxiv, 2017 (**Can computers help biologists come up with high impact biology questions**)
  11. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps. Chang YC, Hu Z, Rachlin J, Anton BP, Kasif S, Roberts RJ, Steffen M.Nucleic Acids Res. 2015 Dec 3. pii: gkv1324. [Epub ahead of print] PMID: 26635392. (**first database that allows searching of knowledge gaps – SEARCHING THE SPACE THAT WE DON’T KNOW **)
  12. Metabolic modeling of muscle metabolism identifies key reactions linked to insulin resistance phenotypes. Nogiec C, Burkart A, Dreyfuss JM, Lerin C, Kasif S, Patti ME. Mol Metab. 2015 Jan 2;4(3):151-63. doi: 10.1016/j.molmet.2014.12.012. eCollection 2015 Mar. PMID: 25737951 (COVER). (** first FBA modeling modeling of insulin resistance with experimental validations **) 
  13. Identification of rare germline copy number variations over-represented in five human cancer types. Park RW, Kim TM, Kasif S, Park PJ. Mol Cancer. 2015 Feb 3;14(1):25. [Epub ahead of print] PMID: 25644941
  14. Objective: Biochemical Function. Anton BP, Kasif S, Roberts RJ, Steffen M. Nature Frontiers in Genetics, 2014
  15. Hypermutable DNA chronicles the evolution of human colon cancer. Naxerova K, Brachtel E, Salk JJ, Seese AM, Power K, Abbasi B, Snuderl M, Chiang, S, Kasif S, Jain RK. Proc Natl Acad Sci U S A. 2014 PMID: 24753616
  16. Reconstructing and reprogramming the developmental hierarchy of glioblastoma, Mario L. Suvà*, Esther Rheinbay* et al, Cell, 2014. (** reprogramming cancer stem cells along the malignancy axis based on clues provided by epigenomic signatures and analysis **)
  17. An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Rheinbay E, Suvà 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.  20
  18. Reconstructing and reprogramming the developmental hierarchy of glioblastoma, Mario L. Suvà*, Esther Rheinbay* et al, Cell, 2014.
  19. An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Rheinbay E, Suvà 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.  2013.04.021. Epub 2013 May 23. PMID: 23707066
  20. The COMBREX project: design, methodology, and initial results. 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 Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova  IA, Rudd KE, Söll 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, Sjölander K, Salzberg, SL, Vitkup D, Letovsky S, Segrè 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
  21. Systems biology characterization of engineered tissues. Rajagopalan P, Kasif S, Murali TM. Annu Rev Biomed Eng. 2013;15:55-70. doi: 10.1146/annurev-bioeng-071811-150120. PMID: 23862675
  22. To supplement or not to supplement: a metabolic network framework for human nutritional supplements. Nogiec CD, Kasif S. PLoS One. 2013;8(8):e68751. doi: 10.1371/journal.pone.0068751. PMID: 23967053
  23. Deep sequencing of the oral microbiome reveals s signatures of periodontal disease, Bo Liu1,2*, Lina Faller3*, Niels Klitgord3*, Varun Mazumdar3*, Mohammad Ghodsi1,2,Daniel D. Sommer1, Theodore R. Gibbons1,4, Todd J. Treangen1,10, Yi-Chien Chang3,Shan Li5, O. Colin Stine5, Hatice Hasturk8, Simon Kasif3,7,9, Daniel Segrè3,6,7#,  Mihai Pop1,2,4#, Salomon Amar3,8#,, PLOS One, 2012
  24. Network Signatures of Insulin Resistance and Life Span, M. Liu, M. Mori, IS. Kohane, ME Patti, A. Goldfine, CR Kahn, S. Kasif, in preparation.
  25. Chris Nogiec, Allison Burkhart, Simon Kasif* and ME Patti*, Metabolic Analysis of Insulin Resistance, in revision (contributed equally authors).
  26. Bridging Computation and Experiments: Using Computers to Drive Biology, (in revision), Science.
  27. Towards a Personal Repeatome: A Genome-Wide Survey of Length Variation in Short Tandem Repeats in Human Gene Transcripts, in preparation.
  28. 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.
  29. Integrative Pheno-genomic module discovery with application to breast cancer, Chang-Jiun Wu, Tianxi Cai, Isaac S. Kohane*, Simon Kasif*, in revision.
  30. A Systems Biology Approach Links Inflammation to the Predisposition to Metabolic Diseases in Mouse Strains, Marcelo Mori*, Manway Liu*, Simon Kasif, Ron Kahn, Diabetes 2010.
  31. 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.
  32. COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. 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,   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
  33. Drug Response Phosphorylation Signatures of Lung Cancer, Chang-Jiun Wu, Martin Steffen, Simon Kasif in preparation.
  34. The Evolution of Gene Annotation, Simon Kasif and Martin Steffen, Nature Chemical Biology, Jan 2010.
  35. A Predictive phosphorylation signature of lung cancer. Chang-Jiun Wu, Tianxi Cai, Klarisa Rikova, David Merberg, Simon Kasif,* Martin Steffen*, co-corresponding authors,  PLoS ONE, Nov 2009.
  36. Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. 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
  37. Seeing the Forest for the Trees: Using the Gene Ontology to Restructure Hierarchical clustering.  Dotan-Cohen D, Kasif S, Melkman AA, Kasif S, Bioinformatics, 2009
  38. Biological process linkage networks. Dotan-Cohen D, Letovsky S, Melkman AA, Kasif S. PLoS ONE. 2009;4(4):e5313. Epub 2009 Apr 23. PMID 19390589
  39. Accelerated postnatal growth increases lipogenic gene expression and adipocyte size in low-birth weight mice. 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
  40. Quantitative analysis of single nucleotide polymorphisms within copy number variation. Lee S, Kasif S, Weng Z, Cantor CR. PLoS ONE. 2008;3(12):e3906. Epub 2008 Dec 18. PMID: 19093001
  41. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. 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
  42. Formula dissection: A parallel algorithm for constraint satisfaction. Reif, J. H., Kasif, S., and Sherlekar, D.  Comput. Math. Appl. 55, 6 (Mar. 2008), 1170- 1177 (republished from a 1987 conference version).
  43. Integration of relational and hierarchical network information for protein function prediction. Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED. BMC Bioinformatics. 2008 Aug 22; 9:350. PMID: 18721473
  44. Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. 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
  45. 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. Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1826-31. Epub 2008 Feb 5. PMID: 18252828
  46. Context specific protein function prediction. Nariai N, Kasif S. Genome Inform. 2007; 18:173-82. PMID: 18546485
  47. Tullai JW, Schaffer ME, Mullenbrock S, Sholder G, Kasif S, Cooper GM. Immediate-early and delayed primary response genes are distinct in function and genomic architecture, J Biol Chem. 2007 Jun 15;
  48. Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S. Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet. 2007 Jun 15;3(6):e96. PMID: 17571924
  49. Nariai N, Kolaczyk ED, Kasif S. Probabilistic protein function prediction from heterogeneous genome-wide data. PLoS ONE. 2007 Mar 28;2:e337. PMID: 17396164
  50. Zhang L, Kasif S, Cantor AC. Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3061-6. Epub 2007 Feb 20. PMID: 17360609
  51. Tullai JW, Chen J, Schaffer ME, Kamenetsky E, Kasif S, Cooper GM. Glycogen synthase kinase-3 represses cyclic AMP response element-binding protein (CREB)-targeted immediate early genes in quiescent cells. J Biol Chem. 2007 Mar 30;282(13):9482-91. Epub 2007 Feb 3. PMID: 17277356
  52. Alon N, Asodi V, Cantor C, Kasif S, Rachlin J. Multi-node graphs: a framework for multiplexed biological assays. J Comput Biol. 2006 Dec;13(10):1659-72. PMID: 17238837
  53. Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles., PLoS Biol. 2007 Jan 9;5(1):e8 PMID: 17214507
  54. Murali TM, Wu CJ, Kasif S. The art of gene function prediction. Nature Biotechnology. 2006 Dec;24(12):1474-5. PMID: 17160037
  55. Gustafson AM, Snitkin ES, Parker SC, DeLisi C, Kasif S. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics. 2006 Oct 19;7:265. PMID: 17052348
  56. Rachlin J, Cohen DD, Cantor C, Kasif S. Biological context networks: a mosaic view of the interactome. Nature/Embo. Mol Syst Biol. 2006;2:66. Epub 2006 Nov 28. PMID: 17130868
  57. Lee S, Kohane I, Kasif S. Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes. BMC Genomics. 2005 Nov 27;6:168. PMID: 16309559
  58. Zheng Y, Anton BP, Roberts RJ, Kasif S. Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinformatics. 2005 Oct 3;6:243. PMID: 16202130
  59. 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
  60. Rachlin J, Ding C, Cantor C, Kasif S. Computational tradeoffs in multiplex PCR assay design for SNP genotyping. BMC Genomics. 2005 Jul 25;6:102.PMID: 16042802
  61. Wu CJ, Kasif S.  GEMS: a web server for biclustering analysis of expression data. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W596-9. PMID: 15980544
  62. Rachlin J, Ding C, Cantor C, Kasif S.  MuPlex: multi-objective multiplex PCR assay design. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W544-7. PMID: 15980531
  63. Noga Alon, Richard Beigel and Simon Kasif and Steven Rudich and Benny Sudakov, “Learning a Hidden Matching“, SIAM Journal of Computing, 2004.
  64. Zheng Y, Roberts RJ, Kasif S.  Identification of genes with fast-evolving regions in microbial genomes. Nucleic Acids Res. 2004 Dec 2;32(21):6347-57. Print 2004. PMID: 15576679
  65. Zhang L, Kasif S, Cantor CR, Broude NE. GC/AT-content spikes as genomic punctuation marks. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16855-60. Epub 2004 Nov 17. PMID: 15548610
  66. Tullai JW, Schaffer ME, Mullenbrock S, Kasif S, Cooper GM. Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways. J Biol Chem. 2004 May 7;279(19):20167-77. Epub 2004 Feb 9. PMID: 14769801
  67. Zheng Y, Roberts RJ, Kasif S.  Segmentally variable genes: a new perspective on adaptation. PLoS Biol. 2004 Apr;2(4):E81. Epub 2004 Apr 13. PMID: 15094797
  68. 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
  69. Wu CJ, Fu Y, Murali TM, Kasif S.  Gene expression module discovery using Gibbs sampling. Genome Inform. 2004;15(1):239-48. PMID: 15712126
  70. Stitziel NO, Binkowski TA, Tseng YY, Kasif S, Liang J.  topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D520-2. PMID: 14681472
  71. Su Y, Murali TM, Pavlovic V, Schaffer M, Kasif S. RankGene: identification of diagnostic genes based on expression data. Bioinformatics. 2003 Aug 12;19(12):1578-9. PMID: 12912841
  72. Wu J, Kasif S, DeLisi C.  Identification of functional links between genes using phylogenetic profiles. Bioinformatics. 2003 Aug 12;19(12):1524-30. PMID: 12912833
  73. Zhang L, Pavlovic V, Cantor CR, Kasif S. Human-mouse gene identification by comparative evidence integration and evolutionary analysis. Genome Res. 2003 Jun;13(6A):1190-202. Epub 2003 May 12. PMID: 12743024
  74. Pervouchine DD, Graber JH, Kasif S. On the normalization of RNA equilibrium free energy to the length of the sequence.  Nucleic Acids Res. 2003 May 1;31(9):e49. PMID: 12711694
  75. Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, Liang J.  Structural location of disease-associated single-nucleotide polymorphisms. J Mol Biol. 2003 Apr 11;327(5):1021-30. PMID: 12662927
  76. Letovsky S, Kasif S.  Predicting protein function from protein/protein interaction data: a probabilistic approach.  Bioinformatics. 2003;19 Suppl 1:i197-204. PMID: 12855458
  77. Kasif S, Weng Z, Derti A, Beigel R, DeLisi C. A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. Nucleic Acids Res. 2002 Oct 15;30(20):e106. PMID: 12384608
  78. Zheng Y, Roberts RJ, Kasif S. Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol. 2002 Oct 10;3(11):RESEARCH0060. Epub 2002 Oct 10. PMID: 12429059
  79. Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S.  Computational identification of operons in microbial genomes. Genome Res. 2002 Aug;12(8):1221-30. PMID: 12176930
  80. Walker M, Pavlovic V, Kasif S A comparative genomic method for computational identification of prokaryotic translation initiation sites. Nucleic Acids Res. 2002 Jul 15;30(14):3181-91. PMID: 12136100
  81. Pavlovic V, Garg A, Kasif S. A Bayesian framework for combining gene predictions. Bioinformatics. 2002 Jan;18(1):19-27. PMID: 11836207
  82. Lander ES et al,  Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921.
  83. Cai D, Delcher A, Kao B, Kasif S. Modeling splice sites with Bayes networks. Bioinformatics. 2000 Feb;16(2):152-8. PMID: 10842737
  84. Tettelin H, Radune D, Kasif S, Khouri H, Salzberg SL.  Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics. 1999 Dec 15;62(3):500-7. PMID: 10644449
  85. Bright, J., Kasif, L. Stiller, “Data Intensive Algorithms for Search Problems”, accepted for publication in IEEE Transactions on Computers.
  86. Kasif, S., Salzberg, S., Waltz, D., J. Rachlin, and Aha, D., “Towards of a Framework for Memory-Based Reasoning”, Artificial Intelligence, pp. 287–311, 1998.
  87. Kasif, S., “Towards a Constraint-Based Engineering Framework for Algorithm Design and Application”, Journal of Constraints, 1997.
  88. Delcher, A, A. Grove, S. Kasif and J. Pearl, “Logarithmic Time Queries and Updates in Probabilistic Networks”, Journal of Artificial Intelligence Research, Vol. 4., pp. 37–59, 1996.
  89. Waltz, D. and S. Kasif, “On Reasoning from Data”, Computing Surveys, 1996.
  90. Salzberg, S., D. Heath, A. Delcher and S. Kasif, “Best Case Analysis of Nearest Neighbours Algorithms”, IEEE Transaction on Pattern Analysis and Machine Intelligence, 17:6, pp.599–608, June 1995.
  91. Delcher, A. and S. Kasif, “Term Matching on a Mesh-Connected Array of Processors”, Annals of Mathematics and Artificial Intelligence, Volume 14, pp.177–186, 1995.
  92. Murthy, S., S. Kasif and S. Salzberg, “ System for Induction of Oblique Decision Trees”, Journal of Artificial Intelligence Research, 2:1, pp.1–33, 1994.
  93. Heath, D., S. Kasif, S. R. Kosaraju, S. Salzberg and G. Sullivan, “Learning Nested Concept Classes with Limited Memory”, Journal of Experimental and Theoretical AI, 1996.
  94. Kasif, S., “Optimal Parallel Algorithms for Quad-Tree Problems”, Journal of Computer Vision and Image Processing, pp.281–285, May 1994.
  95. Kasif, S. and A. Delcher, “Analysis of Local Consistency in Parallel Constraint Networks”, Artificial Intelligence, 69, pp.307–327, 1994.
  96. Heath, D. and S. Kasif, “On Voronoi Covers with Applications to Machine Learning”, Computational Geometry: Theory and Applications, pp. 289-305, Nov. 1993.
  97. Kasif, S., S. Banerjee, A. Delcher and G. Sullivan, “Some Results on the Complexity of Symmetric Connectionist Networks”, Annals of Mathematics and Artificial Intelligence, pp.327-344, Nov. 1993.
  98. Delcher, A. and S. Kasif,  “Efficient Parallel Term Matching and Anti-Unification”, Journal of Automated Reasoning, pp.  391–406, 1992.
  99. Kasif, S., “On the Parallel Complexity of Discrete Relaxation in Constraint Networks”, Artificial Intelligence, pp. 275-286, October 1990.
  100. Delcher, A. and S. Kasif, “Some Results On the Complexity of Maintaining Data Flow Dependencies in Parallel Logic Programs”, Journal of Logic Programming, pp.229–241, April 1989.
  101. Kasif, S., “Control and Data Driven Execution of Logic Programs: A Comparison”, Journal of Parallel Programming.Vol.15, No.1, pp.73–100, February 1987.
  102. Kasif, S., L. Kitchen and A. Rosenfeld, “A Hough Transform Technique for Subgraph Isomorphism”, Pattern Recognition Letters. Vol.2, pp.83–88, December 1983.
  103. Kasif, S. and A. Rosenfeld, “Pyramid Linking as a Special Case of Isodata”, IEEE Transactions on Systems, Man and Cybernetics, Vol.SMC-13, No.1, January 1983.