Simon Kasif

Summary

Affiliation: Boston University
Country: USA

Publications

  1. pmc GEMS: a web server for biclustering analysis of expression data
    Chang Jiun Wu
    Program in Bioinformatics, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 33:W596-9. 2005
  2. pmc Genomic functional annotation using co-evolution profiles of gene clusters
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Genome Biol 3:RESEARCH0060. 2002
  3. pmc Thousands of missed genes found in bacterial genomes and their analysis with COMBREX
    Derrick E Wood
    Department of Computer Science, University of Maryland, College Park, MD 20742, USA
    Biol Direct 7:37. 2012
  4. pmc A computational framework for optimal masking in the synthesis of oligonucleotide microarrays
    Simon Kasif
    Center for Advanced Genomic Technology, Bioinformatics Program and Biomedical Engineering Department, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 30:e106. 2002
  5. pmc Computational tradeoffs in multiplex PCR assay design for SNP genotyping
    John Rachlin
    Bioinformatics Program, Boston University, MA 02215, USA
    BMC Genomics 6:102. 2005
  6. pmc Towards the identification of essential genes using targeted genome sequencing and comparative analysis
    Adam M Gustafson
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215 USA
    BMC Genomics 7:265. 2006
  7. pmc Segmentally variable genes: a new perspective on adaptation
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA
    PLoS Biol 2:E81. 2004
  8. pmc Phylogenetic detection of conserved gene clusters in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA, USA
    BMC Bioinformatics 6:243. 2005
  9. pmc Immediate-early and delayed primary response genes are distinct in function and genomic architecture
    John W Tullai
    Department of Biology, Boston University, Boston, Massachusetts 02215, USA
    J Biol Chem 282:23981-95. 2007
  10. pmc Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes
    SooHyun Lee
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    BMC Genomics 6:168. 2005

Collaborators

Detail Information

Publications49

  1. pmc GEMS: a web server for biclustering analysis of expression data
    Chang Jiun Wu
    Program in Bioinformatics, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 33:W596-9. 2005
    ..The web server provides a flexible and an useful platform for the discovery of co-expressed and potentially co-regulated gene modules. GEMS is an open source software and is available at http://genomics10.bu.edu/terrence/gems/...
  2. pmc Genomic functional annotation using co-evolution profiles of gene clusters
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Genome Biol 3:RESEARCH0060. 2002
    ..The gene cluster phylogenetic profile integrates chromosomal proximity information and phylogenetic profile information and allows us to infer functional dependences between the gene clusters even at great distance on the chromosome...
  3. pmc Thousands of missed genes found in bacterial genomes and their analysis with COMBREX
    Derrick E Wood
    Department of Computer Science, University of Maryland, College Park, MD 20742, USA
    Biol Direct 7:37. 2012
    ..Annotation methods vary considerably and may fail to identify some genes. Here we draw attention to a large number of likely genes missing from annotations using common tools such as Glimmer and BLAST...
  4. pmc A computational framework for optimal masking in the synthesis of oligonucleotide microarrays
    Simon Kasif
    Center for Advanced Genomic Technology, Bioinformatics Program and Biomedical Engineering Department, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 30:e106. 2002
    ..The problem was introduced by Hubbell et al. Here, we formalize the problem, obtain precise bounds on its complexity and devise several computational solutions...
  5. pmc Computational tradeoffs in multiplex PCR assay design for SNP genotyping
    John Rachlin
    Bioinformatics Program, Boston University, MA 02215, USA
    BMC Genomics 6:102. 2005
    ....
  6. pmc Towards the identification of essential genes using targeted genome sequencing and comparative analysis
    Adam M Gustafson
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215 USA
    BMC Genomics 7:265. 2006
    ....
  7. pmc Segmentally variable genes: a new perspective on adaptation
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA
    PLoS Biol 2:E81. 2004
    ..Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment...
  8. pmc Phylogenetic detection of conserved gene clusters in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA, USA
    BMC Bioinformatics 6:243. 2005
    ....
  9. pmc Immediate-early and delayed primary response genes are distinct in function and genomic architecture
    John W Tullai
    Department of Biology, Boston University, Boston, Massachusetts 02215, USA
    J Biol Chem 282:23981-95. 2007
    ..These findings suggest that genomic features of immediate-early genes, in contrast to the delayed primary response genes, are selected for rapid induction, consistent with their regulatory functions...
  10. pmc Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes
    SooHyun Lee
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    BMC Genomics 6:168. 2005
    ..We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories...
  11. pmc Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance
    Peter J Park
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology, Center of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 25:3121-7. 2009
    ..We asked whether these heterogeneous models can be integrated to provide consistent and robust biological insights into the biology of insulin resistance...
  12. pmc Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    Jeremiah J Faith
    Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
    PLoS Biol 5:e8. 2007
    ..The compendium of expression data compiled in this study, coupled with RegulonDB, provides a valuable model system for further improvement of network inference algorithms using experimental data...
  13. ncbi request reprint Identification of functional links between genes using phylogenetic profiles
    Jie Wu
    Department of Biomedical Engineering, USA Bioinformatics Graduate Program, Boston University, 44 Cummington St, Boston, MA, 02215, USA
    Bioinformatics 19:1524-30. 2003
    ..Function is then inferred at any desired level of confidence...
  14. ncbi request reprint RankGene: identification of diagnostic genes based on expression data
    Yang Su
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Bioinformatics 19:1578-9. 2003
    ..This flexibility makes RankGene a useful tool in gene expression analysis and feature selection...
  15. pmc Computational identification of operons in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts 02215, USA
    Genome Res 12:1221-30. 2002
    ..We looked further into the conservation of operons across genomes. A trp operon alignment is analyzed in depth to show gene loss and rearrangement in different organisms during operon evolution...
  16. pmc Quantitative analysis of single nucleotide polymorphisms within copy number variation
    SooHyun Lee
    Bioinformatics Program, Boston University, Boston, MA, USA
    PLoS ONE 3:e3906. 2008
    ..This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE...
  17. pmc Characterization of two new aminopeptidases in Escherichia coli
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Massachusetts 02215, USA
    J Bacteriol 187:3671-7. 2005
    ..ypdE is the immediate downstream gene of ypdF, and its start codon overlaps with the stop codon of ypdF by 1 base. YpdE is shown to be a metalloaminopeptidase and has a broad exoaminopeptidase activity...
  18. pmc Identification of genes with fast-evolving regions in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 32:6347-57. 2004
    ..Gene sets reported from our method provide a measure of the phenotypic divergence between two closely related genomes...
  19. pmc MuPlex: multi-objective multiplex PCR assay design
    John Rachlin
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 33:W544-7. 2005
    ..The server is available at http://genomics14.bu.edu:8080/MuPlex/MuPlex.html...
  20. ncbi request reprint Gene expression module discovery using gibbs sampling
    Chang Jiun Wu
    Boston University Bioinformatics Program, Boston, MA 02215, USA
    Genome Inform 15:239-48. 2004
    ..In our preliminary studies comparing GEMS with other bi-clustering software we show that GEMS is a reliable, flexible and computationally efficient approach for bi-clustering gene expression data...
  21. pmc Probabilistic protein function prediction from heterogeneous genome-wide data
    Naoki Nariai
    Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
    PLoS ONE 2:e337. 2007
    ..Surprisingly, in some contexts integration hurts overall prediction accuracy. Lastly, we provide a comprehensive assignment of putative GO terms to 463 proteins that currently have no assigned function...
  22. pmc Whole-genome annotation by using evidence integration in functional-linkage networks
    Ulas Karaoz
    Bioinformatics Program, Boston University, 48 Cummington Street, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 101:2888-93. 2004
    ..Our results contain a number of predictions and furnish strong evidence that integration of functional information is indeed a promising direction for improving the accuracy and robustness of functional genomics...
  23. pmc Triplet repeat length bias and variation in the human transcriptome
    Michael Molla
    Department of Biomedical Engineering and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 106:17095-100. 2009
    ....
  24. pmc A predictive phosphorylation signature of lung cancer
    Chang Jiun Wu
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
    PLoS ONE 4:e7994. 2009
    ....
  25. pmc A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic disease
    Marcelo A Mori
    Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts, USA
    Diabetes 59:2960-71. 2010
    ..Our goal was to identify early molecular signatures predicting genetic risk to these metabolic diseases using two strains of mice that differ greatly in disease susceptibility...
  26. pmc A comparative genomic method for computational identification of prokaryotic translation initiation sites
    Megon Walker
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 30:3181-91. 2002
    ..The novel architecture has a number of attractive features that distinguish it from previous comparative models such as pair-HMMs...
  27. pmc Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy
    Lingang Zhang
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Bioinformatics Program, and Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 104:3061-6. 2007
    ..By using the commercially available homogeneous MassEXTEND platform (SEQUENOM), it is scalable for high-throughput DNA-TF binding applications, including genome-wide TF binding site mapping and analyses of SNPs in promoter regions...
  28. pmc Biological context networks: a mosaic view of the interactome
    John Rachlin
    Department of Computer Science, Boston University, Boston, MA 02215, USA
    Mol Syst Biol 2:66. 2006
    ..We show that such context-sensitive measures are significantly better predictors of knockout lethality than node degree, reaching better than 70% accuracy among the top scoring proteins...
  29. pmc Human-mouse gene identification by comparative evidence integration and evolutionary analysis
    Lingang Zhang
    Center for Advanced Biotechnology, Boston University, Boston, Massachusetts 02215, USA
    Genome Res 13:1190-202. 2003
    ..Finally, we experiment with Bayesian networks for the integration of comparative and compositional evidence...
  30. ncbi request reprint Less is more: towards an optimal universal description of protein folds
    Joseph D Szustakowski
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Bioinformatics 21:ii66-71. 2005
    ..Here we focus on an intermediate level of regularity. We have developed automated methods to systematically construct a dictionary of supersecondary structures that can be used as 'protein parts' to describe fold-sized structures...
  31. pmc Integration of relational and hierarchical network information for protein function prediction
    Xiaoyu Jiang
    Department of Mathematics and Statistics, Boston University, Boston, MA 02215, USA
    BMC Bioinformatics 9:350. 2008
    ..Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions...
  32. pmc Glycogen synthase kinase-3 represses cyclic AMP response element-binding protein (CREB)-targeted immediate early genes in quiescent cells
    John W Tullai
    Department of Biology, Boston University, MA 02215, USA
    J Biol Chem 282:9482-91. 2007
    ..These results indicate that GSK-3 actively represses gene expression in quiescent cells, with inhibition of CREB playing a key role in this transcriptional response...
  33. pmc GC/AT-content spikes as genomic punctuation marks
    Lingang Zhang
    Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 101:16855-60. 2004
    ..The GC-content spikes at transcription boundaries may reflect a general principle of genomic punctuation. Our analysis also provides means for identifying these GC-content spikes in individual genomic sequences...
  34. ncbi request reprint The complete genome sequence of a dog: a perspective
    SooHyun Lee
    Bioinformatics Program, Boston University, MA 02215, USA
    Bioessays 28:569-73. 2006
    ..5 million single nucleotide polymorphisms within and between dog breeds, which can be used in evolutionary analysis, behavioral studies and disease gene mapping.(1)..
  35. ncbi request reprint Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways
    John W Tullai
    Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA
    J Biol Chem 279:20167-77. 2004
    ..These results indicate that groups of human genes regulated by discrete intracellular signaling pathways share common cis-regulatory elements...
  36. ncbi request reprint A Bayesian framework for combining gene predictions
    Vladimir Pavlovic
    Bioinformatics Program, Department of Bioengineering, Boston University, Boston, MA 02215, USA
    Bioinformatics 18:19-27. 2002
    ..As the number of such systems grows the need for a rigorous way to combine the predictions becomes more essential...
  37. pmc Network-based analysis of affected biological processes in type 2 diabetes models
    Manway Liu
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
    PLoS Genet 3:e96. 2007
    ....
  38. pmc COMBREX: a project to accelerate the functional annotation of prokaryotic genomes
    Richard J Roberts
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 39:D11-4. 2011
    ..It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support successful bids...
  39. ncbi request reprint Predicting protein function from protein/protein interaction data: a probabilistic approach
    Stanley Letovsky
    Bioinformatics Program and Department of Biomedical Engineering, Boston University, 44 Cummington St, Boston, MA 02215, USA
    Bioinformatics 19:i197-204. 2003
    ..A binomial model of local neighbor function labeling probability is combined with a Markov random field propagation algorithm to assign function probabilities for proteins in the network...
  40. pmc On the normalization of RNA equilibrium free energy to the length of the sequence
    Dmitri D Pervouchine
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 31:e49. 2003
    ..This method can be used for genome-wide detection of transcription termination signals, putative micro-RNAs, and other regulatory elements that involve stable RNA secondary structures...
  41. pmc Accelerated postnatal growth increases lipogenic gene expression and adipocyte size in low-birth weight mice
    Elvira Isganaitis
    Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts, USA
    Diabetes 58:1192-200. 2009
    ..To characterize the hormonal milieu and adipose gene expression in response to catch-up growth (CUG), a growth pattern associated with obesity and diabetes risk, in a mouse model of low birth weight (LBW)...
  42. pmc Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers
    Kamila Naxerova
    Children s Hospital Informatics Program, Harvard MIT Division of Health Sciences and Technology, Longwood Avenue, Boston, MA 02115, USA
    Genome Biol 9:R108. 2008
    ....
  43. ncbi request reprint Context specific protein function prediction
    Naoki Nariai
    Boston University, Boston, MA 02215, USA
    Genome Inform 18:173-82. 2007
    ..Finally, we predicted 57 unknown genes as "ribosome biogenesis" proteins...
  44. pmc topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association
    Nathan O Stitziel
    Department of Bioengineering, University of Illinois at Chicago, M C 063, 851 S Morgan Street, Chicago, IL 60607, USA
    Nucleic Acids Res 32:D520-2. 2004
    ..TopoSNP includes an interactive structural visualization web interface, as well as downloadable batch data. The database will be updated at regular intervals and can be accessed at: http://gila.bioengr.uic.edu/snp/toposnp...
  45. pmc RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli
    Brian P Anton
    New England Biolabs, Ipswich, MA 01938, USA
    Proc Natl Acad Sci U S A 105:1826-31. 2008
    ..The initial results presented here constitute a bioinformatics-driven prediction with preliminary experimental validation that should serve as the starting point for several interesting lines of further inquiry...
  46. ncbi request reprint Multi-node graphs: a framework for multiplexed biological assays
    Noga Alon
    Department of Mathematics, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 13:1659-72. 2006
    ..Our theoretical results suggest, however, that the resulting phase transition is a fundamental characteristic of the problem, implying intrinsic limits on the development of future assay design algorithms...
  47. ncbi request reprint Hierarchical tree snipping: clustering guided by prior knowledge
    Dikla Dotan-Cohen
    Department of Computer Science, Ben Gurion University, Beer Sheva 84105, Israel
    Bioinformatics 23:3335-42. 2007
    ..Next this tree is partitioned into subtrees by cutting all edges at some level, thereby inducing a clustering. Unfortunately, the resulting clusters often do not exhibit significant functional coherence...
  48. ncbi request reprint The art of gene function prediction
    T M Murali
    Nat Biotechnol 24:1474-5; author reply 1475-6. 2006
  49. ncbi request reprint Structural location of disease-associated single-nucleotide polymorphisms
    Nathan O Stitziel
    Department of Bioengineering SEO, MC 063, University of Illinois at Chicago, Room 218, 851, S Morgan Street, Chicago, IL 60607 7052, USA
    J Mol Biol 327:1021-30. 2003
    ..The approach of classifying nsSNPs with alpha shape and HMM developed in this study can be integrated with additional methods to improve the accuracy of predictions of whether a given nsSNP is likely to be disease-associated...