Fereydoun Hormozdiari, Michael Hsing, Raheleh Salari, Er Schönhuth, Simon K. Chan, S. Cenk Sahinalp, ...
Although insertions and deletions (indels) are a common type of sequence variation, their origin and their functional consequences have not yet been fully understood. It has been known that indels...
Hsing, Michael, Byler, Kendall, Cherkasov, Artem
Abstract Background Protein-protein interactions mediate a wide range of cellular functions and responses and have been studied rigorously through recent large-scale proteomics experiments and...
Hsing, Michael, Cherkasov, Artem
Abstract Background Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown...
Christopher D. Fjell, Artem Cherkasov
Motivation: Increasing antibiotics resistance in human pathogens represents a pressing public health issue worldwide for which novel antibiotic therapies based on antimicrobial peptides (AMPs) may...
The Current State of Biological Data (2008)
Michael Hsing, Artem Cherkasov
Abstract: In recent years, the broad utilization of high-throughput experimental techniques resulted in a vast amount of expression and interaction data, accompanied by information on metabolic, cell...
Relationship between insertion/deletion (indel) frequency of proteins and essentiality (2007)
Chan, Simon K, Hsing, Michael, Hormozdiari, Fereydoun, Cherkasov, Artem
Abstract Background In a previous study, we demonstrated that some essential proteins from pathogenic organisms contained sizable insertions/deletions (indels) when aligned to human proteins of high...
AMPer: a database and an automated discovery tool for antimicrobial peptides (2007)
Fjell, Christopher D., Hancock, Robert E.W., Cherkasov, Artem
Motivation: Increasing antibiotics resistance in human pathogens represents a pressing public health issue worldwide for which novel antibiotic therapies based on antimicrobial peptides (AMPs) may...
766 Combinatorial QSAR Modeling of Chemical Toxicants Tested against (2007)
Tetrahymena Pyriformis, Hao Zhu, Er Tropsha, Denis Fourches, Re Varnek, Ester Papa, ...
Selecting most rigorous quantitative structure-activity relationship (QSAR) approaches is of great importance in the development of robust and predictive models of chemical toxicity. To address this...
AMPer: A Database and an Automated Discovery Tool for Antimicrobial Peptides. (2007)
Fjell, Christopher D., Hancock, Robert E.W., Cherkasov, Artem
Motivation: Increasing antibiotics resistance in human pathogens represents a pressing public health issue worldwide for which novel antibiotic therapies based on antimicrobial peptides (AMPs) may...
Distance Based Algorithms for Small Biomolecule Classification (2006)
And Structural Similarity, Emre Karakoc, Artem Cherkasov, S. Cenk Sahinalp
Structural similarity search among small molecules is a standard tool used in molecular classification and insilico drug discovery. The effectiveness of this general approach depends on how well the...
Comparative QSAR- and Fragments Distribution Analysis of Drugs (2006)
Emre Karakoc, S. Cenk Sahinalp, Artem Cherkasov
A number of binary QSAR models have been developed using methods of artificial neural networks, k-nearest neighbors, linear discriminative analysis, and multiple linear regression and have been...
Karakoc, Emre, Cherkasov, Artem, Sahinalp, S. Cenk
Motivation: Structural similarity search among small molecules is a standard tool used in molecular classification and in-silico drug discovery. The effectiveness of this general approach depends on...
Prediction of HLA-A2 binding peptides using Bayesian network (2005)
Vadim Astakhov, Artem Cherkasov
Prediction of peptides binding to HLA (human leukocyte antigen) finds application in peptide vaccine design. A number of statistical and structural models have been developed in recent years for HLA...
Abstract: On the basis of the previous models of inductive and steric effects, ‘inductive’ electronegativity and molecular capacitance, a range of new...
Abstract: On the basis of the previous models of inductive and steric effects, ‘inductive’ electronegativity and molecular capacitance, a range of new ‘inductive ’ QSAR descriptors has been...
Modeling of cell signaling pathways in macrophages by semantic networks (2004)
Hsing, Michael, Bellenson, Joel L, Shankey, Conor, Cherkasov, Artem
Abstract Background Substantial amounts of data on cell signaling, metabolic, gene regulatory and other biological pathways have been accumulated in literature and electronic databases....
Review on ''Bioinformatics, Biocomputing and Perl'' by Michael Moorhouse and Paul Barry (2004)
No abstract available.
Cherkasov, Artem, Ho Sui, Shannan J, Brunham, Robert C, Jones, Steven JM
Abstract Background We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted...
Cherkasov, Artem, Jones, Steven JM
Abstract Background A new sequence independent bioinformatics approach allowing genome-wide search for proteins with similar three dimensional structures has been developed. By utilizing the...
Structural characterization of genomes by large scale sequence-structure threading (2004)
Cherkasov, Artem, Jones, Steven JM
Abstract Background Using sequence-structure threading we have conducted structural characterization of complete proteomes of 37 archaeal, bacterial and eukaryotic organisms (including worm, fly,...
Artem Cherkasov, Bojana Jankovic
On the basis of the inductive QSAR descriptors we have created a neural network-based solution enabling quantification of antibacterial activity in the series of 101 synthetic cationic polypeptides...
BMC Bioinformatics BioMed Central (2004)
Artem Cherkasov, Steven Jm Jones
Research article Structural characterization of genomes by large scale sequence-structure threading
Brinkman, Fiona S.L., Blanchard, Jeffrey L., Cherkasov, Artem, Av-Gay, Yossef, Brunham, Robert C., Fernandez, Rachel C., ...
Brinkman, Fiona S.L., Blanchard, Jeffrey L., Cherkasov, Artem, Av-Gay, Yossef, Brunham, Robert C., Fernandez, Rachel C., ...
Molecular Analysis of the Multiple GroEL Proteins of Chlamydiae
Karunakaran, Karuna P., Noguchi, Yasuyuki, Read, Timothy D., Cherkasov, Artem, Kwee, Jeffrey, Shen, Caixia, ...
Genome sequencing revealed that all six chlamydiae genomes contain three groEL-like genes (groEL1, groEL2, and groEL3). Phylogenetic analysis of groEL1, groEL2, and groEL3 indicates that these genes...
Brinkman, Fiona S.L., Blanchard, Jeffrey L., Cherkasov, Artem, Av-Gay, Yossef, Brunham, Robert C., Fernandez, Rachel C., ...
An unusually high proportion of proteins encoded in Chlamydia genomes are most similar to plant proteins, leading to proposals that a Chlamydia ancestor obtained genes from a plant or plant-like host...
Modeling of cell signaling pathways in macrophages by semantic networks
Hsing, Michael, Bellenson, Joel L, Shankey, Conor, Cherkasov, Artem
Molecular Analysis of the Multiple GroEL Proteins of Chlamydiae
Karunakaran, Karuna P., Noguchi, Yasuyuki, Read, Timothy D., Cherkasov, Artem, Kwee, Jeffrey, Shen, Caixia, ...
Genome sequencing revealed that all six chlamydiae genomes contain three groEL-like genes (groEL1, groEL2, and groEL3). Phylogenetic analysis of groEL1, groEL2, and groEL3 indicates that these genes...
Brinkman, Fiona S.L., Blanchard, Jeffrey L., Cherkasov, Artem, Av-Gay, Yossef, Brunham, Robert C., Fernandez, Rachel C., ...
An unusually high proportion of proteins encoded in Chlamydia genomes are most similar to plant proteins, leading to proposals that a Chlamydia ancestor obtained genes from a plant or plant-like host...
Modeling of cell signaling pathways in macrophages by semantic networks
Hsing, Michael, Bellenson, Joel L, Shankey, Conor, Cherkasov, Artem
Prediction of HLA-A2 binding peptides using Bayesian network
Astakhov, Vadim, Cherkasov, Artem
Prediction of peptides binding to HLA (human leukocyte antigen) finds application in peptide vaccine design. A number of statistical and structural models have been developed in recent years for HLA...
Relationship between insertion/deletion (indel) frequency of proteins and essentiality
Chan, Simon K, Hsing, Michael, Hormozdiari, Fereydoun, Cherkasov, Artem