In comparison to the oceans, freshwater environments represent a more diverse community of microorganisms, exhibiting comparatively high levels of variability both temporally and spatially Maranger and Bird, Microb. Ecol. 31 (1996)... more
In comparison to the oceans, freshwater environments represent a more diverse community of microorganisms, exhibiting comparatively high levels of variability both temporally and spatially Maranger and Bird, Microb. Ecol. 31 (1996) 141-151. This level of variability is likely to extend to the world of viruses as well, in particular bacteria-infecting viruses (bacteriophages). Phages are known to influence bacterial diversity, and therefore key processes, in environmental niches across the globe Clokie et al., Bacteriophage 1 (2011) 31-45; Jacquet et al., Adv. Ocean Limn. 1 (2010) 97-141; Wilhelm and Suttle, Bioscience 49 (1999) 781-788; Bratback et al., Microb. Ecol. 28 (1994) 209-221. Despite their prevalence and likely critical role in freshwater environments, very few viral species have been characterized. Metagenomic approaches, however, have allowed for a glimpse into phage diversity. We collected surface water samples from four Chicago area beaches - Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach - every two weeks from May 13 through August 5, 2014. Sampling was conducted with four biological replicates for each sampling date and location, resulting in 112 samples. DNA isolated from each of the individual samples for a given collection date/location was pooled together, with one exception - Calumet Beach on August 5, 2014 - in which each biological replicate was sequenced individually. Raw sequence data is available via NCBI's SRA database (part of BioProject PRJNA248239).
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... Catherine Putonti1,2, Meizhuo Zhang1, Lennart Johnsson1, and Yuriy Fofanov1,2 ... C. Brown, Iowa (1994) 8. Robinson, J., Waller, MJ, Parham, P., de Groot, N., Bontrop, R., Kennedy, LJ, Stoehr, P., Marsh, SGE: IMGT/HLA and IMGT/MHC:... more
... Catherine Putonti1,2, Meizhuo Zhang1, Lennart Johnsson1, and Yuriy Fofanov1,2 ... C. Brown, Iowa (1994) 8. Robinson, J., Waller, MJ, Parham, P., de Groot, N., Bontrop, R., Kennedy, LJ, Stoehr, P., Marsh, SGE: IMGT/HLA and IMGT/MHC: sequence databases for the study of the ...
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The NCI-60 human tumor cell line panel has been used in a broad range of cancer research over the last two decades. A landmark 2013 whole exome sequencing study of this panel added an exceptional new resource for cancer biologists. The... more
The NCI-60 human tumor cell line panel has been used in a broad range of cancer research over the last two decades. A landmark 2013 whole exome sequencing study of this panel added an exceptional new resource for cancer biologists. The complementary analysis of the sequencing data produced by this study suggests the presence of Propionibacterium acnes genomic sequences in almost half of the datasets, with the highest abundance in the leukemia (RPMI-8226) and central nervous system (SF-295, SF-539, and SNB-19) cell lines. While the origin of these contaminating bacterial sequences remains to be determined, observed results suggest that computational control for the presence of microbial genomic material is a necessary step in the analysis of the high throughput sequencing (HTS) data.
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Glucocorticoidal steroids (GC) are capable of causing apoptotic death of many varieties of lymphoid cells; consequently, GC are used in therapy for many lymphoid malignancies. Gene transcription in the GC-treated cells is required for... more
Glucocorticoidal steroids (GC) are capable of causing apoptotic death of many varieties of lymphoid cells; consequently, GC are used in therapy for many lymphoid malignancies. Gene transcription in the GC-treated cells is required for subsequent apoptosis, but only a few of the actual genes involved have been identified. We employed gene microarray analysis to find the network of genes involved in GC-evoked cell death, using three clones derived from the CEM lymphoid leukemia cell line. Clone C1-15 was resistant to GC-evoked apoptosis, although not necessarily to GC-induced gene transcription; the other two underwent apoptosis in the presence of GC. Clone C7-14 was subcloned from the apoptosis-sensitive parental C7 clone to establish karyotypic uniformity. The second sensitive clone, C1-6, was a spontaneous revertant from parental resistant clone C1. A period of > or = 24 h in the constant presence of receptor-occupying concentrations of synthetic GC dexamethasone (Dex) was neces...
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Finding relations among gene expressions involves the definition of the similarity between experimental data. A simplest similarity measure is the Correlation Coefficient. It is able to identify linear dependences only; moreover, is... more
Finding relations among gene expressions involves the definition of the similarity between experimental data. A simplest similarity measure is the Correlation Coefficient. It is able to identify linear dependences only; moreover, is sensitive to experimental errors. An alternative measure, the Shannon Mutual Information (MI), is free from the above mentioned weaknesses. However, the calculation of MI for continuous variables from the finite number of experimental points, N, involves an ambiguity arising when one divides the range of values of the continuous variable into boxes. Then the distribution of experimental points among the boxes (and, therefore, MI) depends on the box size. An algorithm for the calculation of MI for continuous variables is proposed. We find the optimum box sizes for a given N from the condition of minimum entropy variation with respect to the change of the box sizes. We have applied this technique to the gene expression dataset from Stanford, containing mic...
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Human space travelers experience a unique environment that affects homeostasis and physio-logic adaptation. One of the important regulatory biology interactions affected by space flight is the alteration of the immune response. As such,... more
Human space travelers experience a unique environment that affects homeostasis and physio-logic adaptation. One of the important regulatory biology interactions affected by space flight is the alteration of the immune response. As such, the impairment of the immune system may lead to higher risk of bacterial and/or viral infection during human space flight missions. Mi-crobiological contaminants have been a source
Research Interests: Immune response, Scanning Electron Microscopy, Gene expression, Environmental Change, Extracellular Matrix, and 11 moreFunctional Genomics, Space flight, Escherichia coli, Cellular Network, Shear Stress, Physiological Response, Knowledge base, Immune system, Viral Infection, Virulence factor, and Long Term Effect
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Research Interests: Evolutionary Biology, Genetics, Molecular Biology, Genomics, Molecular Evolution, and 12 moreHorizontal Gene Transfer, Software, Escherichia coli, Molecular biology and evolution, Dimensional, Visual Representation, Genome sequence, Large Scale, Species Specificity, Lateral Gene Transfer, Biochemistry and cell biology, and Yersinia pseudotuberculosis
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Research Interests: Engineering, Algorithms, Thermodynamics, Technology, Computational Biology, and 24 moreBiotechnology, Dengue Virus, Biological Sciences, real time PCR, PCR, Identification, Humans, Polymerase Chain Reaction, Genome Analysis, Genome, Plasmids, Bp, Molecular cloning, Human Genome, Snp, Primer, cDNA, Experimental Tests, Reproducibility of Results, RT PCR, Species Specificity, Flaviviridae, Nucleotides, and Serotyping
Reliable detection and identification of pathogens in complex biological samples, in the presence of contaminating DNA from a variety of sources, is an important and challenging diagnostic problem for the development of field tests. The... more
Reliable detection and identification of pathogens in complex biological samples, in the presence of contaminating DNA from a variety of sources, is an important and challenging diagnostic problem for the development of field tests. The problem is compounded by the difficulty of finding a single, unique genomic sequence that is present simultaneously in all genomes of a species of closely related pathogens and absent in the genomes of the host or the organisms that contribute to the sample background. Here we describe 'host-blind probe design'- a novel strategy of designing probes based on highly frequent genomic signatures found in the pathogen genomes of interest but absent from the host genome. Upon hybridization, an array of such informative probes will produce a unique pattern that is a genetic fingerprint for each pathogen strain. This multiprobe approach was applied to 83 dengue virus genome sequences, available in public databases, to design and perform in silico m...
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Yuriy Fofanov,1 Yi Luo,1 Charles Katili,1 Jim Wang,1 Yuri Y. Belosludtsev,3 Thomas F. ... Powdrill,3 Viacheslav Fofanov,1 Tong-Bin Li,1 Sergey Chumakov,1,4 and B. Montgomery ... 1Department of Computer Science University of Houston,... more
Yuriy Fofanov,1 Yi Luo,1 Charles Katili,1 Jim Wang,1 Yuri Y. Belosludtsev,3 Thomas F. ... Powdrill,3 Viacheslav Fofanov,1 Tong-Bin Li,1 Sergey Chumakov,1,4 and B. Montgomery ... 1Department of Computer Science University of Houston, Houston, Texas 3Vitruvius ...