Research Topics
Genomes and Genes | Simon KasifSummaryAffiliation: Boston University Country: USA Publications
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Publications
A computational framework for optimal masking in the synthesis of oligonucleotide microarraysSimon 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...- Computational tradeoffs in multiplex PCR assay design for SNP genotypingJohn Rachlin
Bioinformatics Program, Boston University, MA 02215, USA
BMC Genomics 6:102. 2005.... - Towards the identification of essential genes using targeted genome sequencing and comparative analysisAdam M Gustafson
Bioinformatics Graduate Program, Boston University, Boston, MA 02215 USA
BMC Genomics 7:265. 2006.... - Segmentally variable genes: a new perspective on adaptationYu 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... - Phylogenetic detection of conserved gene clusters in microbial genomesYu Zheng
Bioinformatics Graduate Program, Boston University, Boston, MA, USA
BMC Bioinformatics 6:243. 2005.... - Immediate-early and delayed primary response genes are distinct in function and genomic architectureJohn 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... - Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomesSooHyun 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... - Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profilesJeremiah 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... - GEMS: a web server for biclustering analysis of expression dataChang-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/... 
Identification of functional links between genes using phylogenetic profilesJie Wu
Department of Biomedical Engineering, USA Bioinformatics Graduate Program, Boston University, 44 Cummington St, Boston, MA, 02215, USA
Bioinformatics 19:1524-30. 2003....- Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistancePeter 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..Top candidates obtained from our analysis have been confirmed in recent laboratory studies... - Characterization of two new aminopeptidases in Escherichia coliYu 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... - Identification of genes with fast-evolving regions in microbial genomesYu 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... - Quantitative analysis of single nucleotide polymorphisms within copy number variationSooHyun 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... - Probabilistic protein function prediction from heterogeneous genome-wide dataNaoki 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... - Whole-genome annotation by using evidence integration in functional-linkage networksUlas 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... - Triplet repeat length bias and variation in the human transcriptomeMichael 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.... - RankGene: identification of diagnostic genes based on expression dataYang 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... - A predictive phosphorylation signature of lung cancerChang Jiun Wu
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
PLoS ONE 4:e7994. 2009.... - A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic diseaseMarcelo 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... - Genomic functional annotation using co-evolution profiles of gene clustersYu 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... - Biological context networks: a mosaic view of the interactomeJohn 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... - Less is more: towards an optimal universal description of protein foldsJoseph D Szustakowski
Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
Bioinformatics 21:ii66-71. 2005..Dictionaries generated using the training set had high coverage over the folds in the testing set, suggesting that dictionary entries reflect general features of protein structures and should be capable of describing novel protein folds... - Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopyLingang 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... - Human-mouse gene identification by comparative evidence integration and evolutionary analysisLingang 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... - MuPlex: multi-objective multiplex PCR assay designJohn 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... - Computational identification of operons in microbial genomesYu 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... - Gene expression module discovery using gibbs samplingChang 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... - Integration of relational and hierarchical network information for protein function predictionXiaoyu 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... - GC/AT-content spikes as genomic punctuation marksLingang 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... - Glycogen synthase kinase-3 represses cyclic AMP response element-binding protein (CREB)-targeted immediate early genes in quiescent cellsJohn 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... - A comparative genomic method for computational identification of prokaryotic translation initiation sitesMegon 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... - The complete genome sequence of a dog: a perspectiveSooHyun 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).. - Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathwaysJohn 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... - On the normalization of RNA equilibrium free energy to the length of the sequenceDmitri 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... - Accelerated postnatal growth increases lipogenic gene expression and adipocyte size in low-birth weight miceElvira 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)... - Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancersKamila 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.... - Context specific protein function predictionNaoki Nariai
Boston University, Boston, MA 02215, USA
Genome Inform 18:173-82. 2007..Finally, we predicted 57 unknown genes as "ribosome biogenesis" proteins... - Network-based analysis of affected biological processes in type 2 diabetes modelsManway Liu
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
PLoS Genet 3:e96. 2007.... - COMBREX: a project to accelerate the functional annotation of prokaryotic genomesRichard 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... - Predicting protein function from protein/protein interaction data: a probabilistic approachStanley Letovsky
Bioinformatics Program and Department of Biomedical Engineering, Boston University, 44 Cummington St, Boston, MA 02215, USA
Bioinformatics 19:i197-204. 2003..The method reconstructed known GO term assignments with high precision, and produced putative GO assignments to 320 proteins that currently lack GO annotation, which represents about 10% of the unlabeled proteins in S. cerevisiae... - A Bayesian framework for combining gene predictionsVladimir Pavlovic
Bioinformatics Program, Department of Bioengineering, Boston University, Boston, MA 02215, USA
Bioinformatics 18:19-27. 2002..We show that our approach is promising to improve the prediction accuracy and provides a systematic and flexible framework for incorporating multiple sources of evidence into gene prediction systems... - RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coliBrian 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... - topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease associationNathan 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... - Multi-node graphs: a framework for multiplexed biological assaysNoga 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... - Hierarchical tree snipping: clustering guided by prior knowledgeDikla 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... - The art of gene function predictionT M Murali
Nat Biotechnol 24:1474-5; author reply 1475-6. 2006 - Structural location of disease-associated single-nucleotide polymorphismsNathan 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...
Research Grants
- Comparative Cross-Species Genomic Analysis SystemSimon Kasif; Fiscal Year: 2006....
- Gene Annotation Using Evidence Integration & Propagation in Functional LinkageSimon Kasif; Fiscal Year: 2007....