Selected Bioinformatics Publications  

PUBMED Computational Biology / Bioinformatics Publications   


21. 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;


21. 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;

22. 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

23. Nariai N, Kolaczyk ED, Kasif S. Probabilistic protein function prediction from heterogeneous genome-wide data. PLoS ONE. 2007 Mar 28;2:e337. PMID: 17396164

24. 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

25. 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. Erratum in: J Biol Chem. 2007 May 11;282(19):14684. PMID: 17277356

26. 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

27. 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

28. Murali TM, Wu CJ, Kasif S. The art of gene function prediction. Nat Biotechnol. 2006 Dec;24(12):1474-5. PMID: 17160037

29. 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 30. Lee S, Kasif S. The complete genome sequence of a dog: a perspective. Bioessays. 2006 Jun;28(6):569-73. PMID: 16700068

31. 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

32. 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

33. 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

34. 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

35. 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

36. 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

37. 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

38. Zheng Y, Roberts RJ, Kasif S, Guan C. Characterization of two new aminopeptidases in Escherichia coli. J Bacteriol. 2005 Jun;187(11):3671-7. PMID: 15901689

39. Noga Alon, Richard Beigel and Simon Kasif and Steven Rudich and Benny Sudakov, "Learning a Hidden Matching", SIAM Journal of Computing, 2004.

40. 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

41. 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

42. 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

43. 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

44. 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

45. Wu CJ, Fu Y, Murali TM, Kasif S. Gene expression module discovery using Gibbs sampling. Genome Inform. 2004;15(1):239-48. PMID: 15712126

46. 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

47. 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

Murali TM, Kasif S. Extracting conserved gene expression motifs from gene expression data. Pac Symp Biocomput. 2003;:77-88. PMID: 12603019

48. 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

49. 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

50. 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

52. Letovsky S, Kasif S. Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics. 2003;19 Suppl 1:i197-204. PMID: 12855458

53. Murali TM, Kasif S. Extracting conserved gene expression motifs from gene expression data. Pac Symp Biocomput. 2003;:77-88. PMID: 12603019

54. 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

55. 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

56. 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

57. 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

58. Pavlovic V, Garg A, Kasif S. A Bayesian framework for combining gene predictions. Bioinformatics. 2002 Jan;18(1):19-27. PMID: 11836207

59. Lander ES et al, Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921.

60. Cai D, Delcher A, Kao B, Kasif S. Modeling splice sites with Bayes networks. Bioinformatics. 2000 Feb;16(2):152-8. PMID: 10842737

61. 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

62. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999 Dec 1;27(23):4636-41. PMID: 10556321

63. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL. Alignment of whole genomes. Nucleic Acids Res. 1999 Jun 1;27(11):2369-76. PMID: 10325427

64. Salzberg SL, Delcher AL, Kasif S, White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 1998 Jan 15;26(2):544-8. PMID: 9421513

Delcher AL, Kasif S, Goldberg HR, Hsu WH. Protein secondary structure modelling with probabilistic networks. Proc Int Conf Intell Syst Mol Biol. 1993;1:109-17. PMID: 7584325

 

Salzberg,S., D. Searl and S. Kasif,  Computational Methods in Molecular Biology;,Elsevier Publ., 1998.

S. Letovsky, S. Kasif, "A Probabilistic Approach to Gene Function Assignment and Propagation in Protein Interaction Networks", Bioinformatics 2003. ,  

International Human Genome Consortium,    Lander et al, Initial Sequencing and Analysis of the Human Genome,  Nature, February 2001

Delcher, A., S. Kasif, H. Goldberg and W. Xsu,  Protein Secondary-Structure Modeling with Probabilistic Networks, International Conference on Intelligent Systems and Molecular Biology, pp. 109--117, 1993. One of the first applications of Hidden Markov models and first application of probabilistic networks (Bayes Nets) to modeling proteins.

Salzberg, S., A. Delcher, S. Kasif and O. White,  Microbial Gene Identification Using Interpolated Markov Models;,  Nucleic Acids, 1997,  a widely used system for gene finding in microbial DNA.

Delcher, A.,  S. Kasif,  R. Fleischmann,  O. White and  S. Salzberg, Whole Genome Alignment,   Nucleic Acids Research, pp. 2369--2376, 1999,  used in the Minimal Organism study at TIGR (Science 10/1999), used to detect chromosomal duplications in Arabodopsis (Nature 12/2000), used to detect inversions and large scale duplications in microbial genomes.

Delcher, A., D. Harmon,  S. Kasif,  O. White and S. Salzberg,  Improved Microbial Gene Identification with Glimmer,   Nucleic Acids, Vol. 27, No. 23, pp. 4636--4641, 1999.  Glimmer II.

Tettelin, H. D. Radune, S. Kasif, H. Khouri, and S. Salzberg,   Pipette Optimal Multiplexed PCR: Efficiently Closing Whole Genome Shotgun Sequencing Project;, Genomics, Vol. 62, pp. 500--507, 1999.

Kasif,S., S. Salzberg, D. Waltz, J. Rachlin and D. Aha,  ; Towards a ProbabilisticFramework for Memory-Based Reasoning ,  Artificial Intelligence, November 1998.A early proposal for for combining generative models and supevised learning (classification).

S. Kasif,  ; Datascope: Mining Biological Sequences ;, IEEE Intelligent Systems,  pp. 38--46,  1999.

Cai, D., B. Kao, S. Kasif and A. Delcher,  "Modeling Splice Sites Using Bayes Networks'', Bioinformatics, 2000.

Pavlovic, V., A. Garg and S. Kasif, "A Bayesian Framework for Combining Gene Predictions",  Computational Genomics Nov. 2000.

A. Delcher, A. Grove, S. Kasif and J. Pearl, Logarithmic Time Query-Update Inference Algorithms in Bayesian Networks", Journal of Artificial Intelligence, 1996. An early theoretical proposal for deploying Bayesian Networks for Perturbational Analysis in Biological Systems

Beigel, R., N. Alon, S.M. Apaydin, L. Fortnow and S. Kasif,  "An Optimal Multiplex PCR Protocol for Closing Gaps in Whole Genomes",  Computational Genomics, Nov 2000.

B. Logan, P. Moreno, B. Suzek, Z. Weng and Simon Kasif,   "Remote-Homology Detection Using Feature Vectors", in review.

B. Suzek, S. Kasif, B. Logan and P. Moreno,  "Remote-Homology Detection Using Feature Vectors", in review.

Beigel, R., N. Alon, S.M. Apaydin, L. Fortnow and S.Kasif,  "An Optimal Multiplex PCR Protocol for Closing Gaps in Whole Genomes",  RECOMB 2001, ,  a theoretical treatment of multiplex PCR for GAP closing in whole genome assembly.

S. Kasif, "Efficient Gene Discovery by Database Matching",  by request.

Kasif, S., S. Banerjee, A. Delcher and G.Sullivan,  "Some Results on the Complexity of Symmetric Connectionist Networks",  Annals of Mathematics and Artificial Intelligence,  327-344,  Nov. 1993. Hopfield Networks  

Murthy, S., S. Kasif and S. Salzberg, "A System for Induction of Oblique Decision Trees'', Journal of Artificial Intelligence Research, 2:1 (1994),1--33,   a popular decision tree system.

Very early paper on voting of committees of decision trees, D. Heath, S. Kasif, S. Salzberg, " Committees of decision trees "., Conference on Multi-strategy Learning, 1993  

A full version of the above on bagged committees of decision trees. Voting (Bagging) decision trees have proven to be rather useful as proven by the seminal research and software produced by Leo Breiman -- Random-Forest ----- D. Heath, S. Kasif, S. Salzberg, " Committees of decision trees "., In Gorayanska and J. Mey (Eds) Cognitive Technology: In search of a Humane Interface, Elsevier Science, 1996.  

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NEW PAPER WATCH

 

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ANNOTATED RECENT PAPERS

1*. Walker, M., V. Pavlovic, and S. Kasif "A Comparative genomic method for the identification of prokaryotic translation sites", Nucleic Acid Research, 2002.

An application of comparative product HMMs (a new methodology for comparative genomics) for bacterial start-site identification. This is an increasingly important problem because of the opportunity to use comparative analysis of up-stream sequences for binding site identification leading to understand regulation in bacteria.

2*. Zheng, Y., R. Roberts and S. Kasif, "Computational identification of operons in microbial genomes", Genome Research, 2002

Identification of complex operons in bacterial genomes. Applications include identification of polyketides for production of antibiotics.

3*. Zheng, Y., R. Roberts and S. Kasif, "Genomic functional annotation using co-evolution profiles of gene clusters, Genome Biology 2002.

Continued collaboration with Dr. Richard Roberts.

4*. Simon Kasif+, Zhiping Weng+, Richard Beigel, Charles DeLisi, "A Computational Framework for Optimal Masking in the Synthesis of Oligonucleotide Microarrays", Nucleic Acid Research 2002 (+ - contributed equally).

10-20% improvement in number of rounds needed to synthesize a microarray.

5*. Noga Alon, Richard Beigel and Simon Kasif and Steven Rudich and Benny Sudakov, "Learning a Hidden Matching", Proc. of Foundations of Computer Science (FOCS 2002), a theoretical treatment of multiplex PCR to close gaps in shot gun sequencing of genomes, joint project with Princeton Institute for Advanced Studies. Previous version of this algorithm has been used at MIT Genome Center and The Institute for Genomic Research to close the gaps in several major pathogens and archea.

6. Joseph D. Szustakowski, Ulas Karaoz, Serafim Batzouglou, James Galagan, Tarjei Mikkelsen, Zhiping Weng, Joel H. Graber, S. Kasif, On the Organization of Ancient and Modern Genes in the Human Genome, in review. (joint project with MIT Genome Center).

7. B. Logan, P. Moreno, B, Suzek and S. Kasif, "Learning Remote-Homology Using Probabilistic Feature Vectors", in review.

A new approach for classification of proteins into structural families.

8*. Yang Su, T. M. Murali S. Kasif, "RankGene", Bioinformatics, 2003.

A system to identify diagnostic genes in microarray data.

9*. T. M. Murali and S. Kasif, "Discovering Conserved Gene Expression Motifs in Microarray Data", PSB 2002.

Identifying groups of genes whose expression profile is relatively conserved across a collection of conditions.

10*. J. Zhang, V. Pavlovic, C. Cantor, S. Kasif, "Cross Species Gene Identification in Human and Mouse Sequences using Evidence Integration Frameworks", Genome Research 2003.

joint project with Charles Cantor, Sequenom.

A new approach for gene prediction using multiple related genomes. The first evolutionary analysis of error based on evolutionary distance between organisms.

11. Y. Zheng, R. Roberts, S. Kasif, "Identification of the Adaptivity Layer of Microbial Organisms using Whole-Genome Variability Profiless", to be submitted, continued comparative genomics research with Rich Roberts on the structure of microbial organisms.

12*. N. O. Stitziel, J. Tseng, D. Pervouchine, D. Goddeau, S. Kasif, J. Liang, "Structural Location of Disease-Associated Single Nucleotide Polymorphisms", Journal of Molecular Biology, 2003.

A approach for classifying SNPs using a novel structural analysis tool and conservation analysis. A database with this information

13*. J. Wu, Simon Kasif, and Charles DeLisi, "Identification of functional links between genes using phylogenetic profiles", Bioinformatics 2003.

A rigorous methodology for assigning function based on phylogenetic profiles.

14*. D. Pervouchine, J. Graber and S. Kasif, "On the normalization of RNA equllibrium to sequence length", NAR , 2003.

An efficient method for whole genome RNA analysis.

15. T. M. Murali and S. Kasif, "Discovering Conserved Gene Expression Motifs in Microarray Data", in review.

16. S. Letovsky, S. Kasif, "A Probabilistic Approach to Gene Function Assignment and Propagation in Protein Interaction Networks", Bioinformatics 2003. ".,  

Prediction of Protein Function from Protein Protein Interaction Networks A systematic approach for Functional Gene Annotation using Protein-Protein interaction graphs. 30-40% of genes in newly sequenced organisms have not been assigned function. This approach is highly promising for functional annotation.

17. V. Pavlovic, J. Zhang, C. Cantor, S. Kasif, "The Effect of Evolution: on the Performance of Comparative Gene Finders" , in

20. M. Schaffer, J. Tullai, S. Kasif and G. Cooper, Cold Spring Harbor Meeting on System Biology.

21. Noga Alon, Richard Beigel and Simon Kasif and Steven Rudich and Benny Sudakov, "Learning a Hidden Matching", in press SIAM Journal of Computing.

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