Alexander Pozhitkov - Profile on Academia.edu (original) (raw)

Papers by Alexander Pozhitkov

Additional file 13: of Cryptic sequence features in the active postmortem transcriptome

Multiple sheets in MS Excel file. The first sheet provides a detailed Readme that describes the s... more Multiple sheets in MS Excel file. The first sheet provides a detailed Readme that describes the sheets. Rows differ by mer length. The matrix file consists of 5117 columns and 333 rows. (XLSX 40047 kb)

Additional file 11: of Cryptic sequence features in the active postmortem transcriptome

11 sheets in MS Excel file. It is similar to the Online Resource_9 mouse file except the raw data... more 11 sheets in MS Excel file. It is similar to the Online Resource_9 mouse file except the raw data is missing to reduce matrix size. The purpose of the sheets is to calculate over- and under-abundant mers that are 5 X the standard deviation of the CP for each mer. The first sheet provides a detailed Readme that describes the sheets. Rows differ by mer length. (XLSX 69035 kb)

Additional file 10: of Cryptic sequence features in the active postmortem transcriptome

11 sheets in MS Excel file. It is similar to the Online Resource_8 zebrafish file except the raw ... more 11 sheets in MS Excel file. It is similar to the Online Resource_8 zebrafish file except the raw data is missing to reduce matrix size. The purpose of the sheets is to calculate over- and under-abundant mers that are 5 X the standard deviation of the CP for each mer. The first sheet provides a detailed Readme that describes the sheets. Rows differ by mer length. (XLSX 65834 kb)

Additional file 9: of Cryptic sequence features in the active postmortem transcriptome

Nine sheets in MS Excel file of mouse data. The first sheet provides a detailed Readme that descr... more Nine sheets in MS Excel file of mouse data. The first sheet provides a detailed Readme that describes the sheets. Basically, first column is abundance of mer in OP, second column is average abundance in CP, third column is standard deviation in CP, and remaining 30 columns are abundances of 30 random draws from CP. Rows differ by mer length. (XLSX 62431 kb)

Additional file 8: of Cryptic sequence features in the active postmortem transcriptome

Nine sheets in MS Excel file of zebrafish data. The first sheet provides a detailed Readme that d... more Nine sheets in MS Excel file of zebrafish data. The first sheet provides a detailed Readme that describes the sheets. Basically, first column is abundance of mer in OP, second column is average abundance in CP, third column is standard deviation in CP, and remaining 30 columns are abundances of 30 random draws from CP. Rows differ by mer length. (XLSX 61046 kb)

Additional file 5: of Cryptic sequence features in the active postmortem transcriptome

Two columns in text file of the control pool (CP) for the mouse. One column is Agilent Probe ID l... more Two columns in text file of the control pool (CP) for the mouse. One column is Agilent Probe ID linked to Annotated Gene Name and second column is cDNA sequence. Total of 32,611 rows. (FNA 81851 kb)

Additional file 4: of Cryptic sequence features in the active postmortem transcriptome

Two columns in text file of the over-abundant pool (OP) for the zebrafish. One column is Agilent ... more Two columns in text file of the over-abundant pool (OP) for the zebrafish. One column is Agilent Probe ID linked to Annotated Gene Name and second column is cDNA sequence. Total of 230 rows. (FNA 546 kb)

Additional file 3: of Cryptic sequence features in the active postmortem transcriptome

Two columns in text file of the over-abundant pool (OP) for the mouse. One column is Agilent Prob... more Two columns in text file of the over-abundant pool (OP) for the mouse. One column is Agilent Probe ID linked to Annotated Gene Name and second column is cDNA sequence. Total of 330 rows. (FNA 926 kb)

Additional file 2: of Cryptic sequence features in the active postmortem transcriptome

Two sheets in MS Excel file: (i) zebrafish_probes_PM, and (ii) mouse_probes_PM. PM, perfect match... more Two sheets in MS Excel file: (i) zebrafish_probes_PM, and (ii) mouse_probes_PM. PM, perfect match probes. Each sheet has two columns: first column is Agilent Probe ID and second column is DNA sequence. (XLSX 31 kb)

Additional file 1: of Cryptic sequence features in the active postmortem transcriptome

Proof that using the 'Chaos Genome Representation' method to extract mers from transcript... more Proof that using the 'Chaos Genome Representation' method to extract mers from transcript sequences is more practical (computational efficient) than string-based search algorithms. (DOCX 20 kb)

Additional file 15: of Cryptic sequence features in the active postmortem transcriptome

Four sheets in MS Excel file. The first sheet provides a detailed Readme that describes the sheet... more Four sheets in MS Excel file. The first sheet provides a detailed Readme that describes the sheets. The second and third sheets have the number of mer hits by transcript sequence length for the zebrafish and mouse. The fourth sheet has the summarize RegRNA2 output for 10 samples. (XLS 117 kb)

Additional file 14: of Cryptic sequence features in the active postmortem transcriptome

Two sheets in MS Excel file. The first sheet is the collapsed data of the Zebrafish and the secon... more Two sheets in MS Excel file. The first sheet is the collapsed data of the Zebrafish and the second sheet is the collapsed data of the Mouse. Each sheet shows how the data was log normalized for making the heatmaps. The collapsed data was based on two way cluster groups using Wards linkage methods. (XLS 108 kb)

Data from: Tracing the dynamics of gene transcripts after organismal death

In life, genetic and epigenetic networks precisely coordinate the expression of genes—but in deat... more In life, genetic and epigenetic networks precisely coordinate the expression of genes—but in death, it is not known if gene expression diminishes gradually or abruptly stops or if specific genes and pathways are involved. We studied this by identifying mRNA transcripts that apparently increase in relative abundance after death, assessing their functions, and comparing their abundance profiles through postmortem time in two species, mouse and zebrafish. We found mRNA transcript profiles of 1063 genes became significantly more abundant after death of healthy adult animals in a time series spanning up to 96 h postmortem. Ordination plots revealed non-random patterns in the profiles by time. While most of these transcript levels increased within 0.5 h postmortem, some increased only at 24 and 48 h postmortem. Functional characterization of the most abundant transcripts revealed the following categories: stress, immunity, inflammation, apoptosis, transport, development, epigenetic regulation and cancer. The data suggest a step-wise shutdown occurs in organismal death that is manifested by the apparent increase of certain transcripts with various abundance maxima and durations

Briefings in functional genomics & proteomics, 2007

Microarray technology, which has been around for almost two decades, now provides an indispensabl... more Microarray technology, which has been around for almost two decades, now provides an indispensable service to the biomedical research community. Soaring demand for high-throughput screening of genes potentially associated with cancer and other diseases, as well as the increased need for identifying microorganisms, have substantially opened up the application of this technology to many fields of science, including new ones such as array-based comparisons of whole genomes. Yet, despite this significant progress, the fundamental understanding of the pillars of this technology, have been largely unexplored, in particular for oligonucleotide-based microarrays. In fact, most of the current approaches for the design of microarrays are based on 'common-sense' parameters, such as guanine-cytosine content, secondary structure, melting temperature or possibility of minimizing the effects of nonspecific hybridization. However, recent experiments suggest that these are inadequate. Here w...

High‐throughput methods for analysis of the human oral microbiome

Periodontology 2000, 2010

The vast majority (ca. 90%) of cells in the human body are not human at all but rather microbia... more The vast majority (ca. 90%) of cells in the human body are not human at all but rather microbial (64). Many of these microbial cells play important roles in normal human physiology because they are involved in nutrient absorption (5, 6, 10), synthesis of vitamins and protection of ...

Nucleic Acids Research, 2006

Hybridization of rRNAs to microarrays is a promising approach for prokaryotic and eukaryotic spec... more Hybridization of rRNAs to microarrays is a promising approach for prokaryotic and eukaryotic species identification. Typically, the amount of bound target is measured by fluorescent intensity and it is assumed that the signal intensity is directly related to the target concentration. Using thirteen different eukaryotic LSU rRNA target sequences and 7693 short perfect match oligonucleotide probes, we have assessed current approaches for predicting signal intensities by comparing Gibbs free energy (DG ) calculations to experimental results. Our evaluation revealed a poor statistical relationship between predicted and actual intensities. Although signal intensities for a given target varied up to 70-fold, none of the predictors were able to fully explain this variation. Also, no combination of different free energy terms, as assessed by principal component and neural network analyses, provided a reliable predictor of hybridization efficiency. We also examined the effects of single-base pair mismatch (MM) (all possible types and positions) on signal intensities of duplexes. We found that the MM effects differ from those that were predicted from solution-based hybridizations. These results recommend against the application of probe design software tools that use thermodynamic parameters to assess probe quality for species identification. Our results imply that the thermodynamic properties of oligonucleotide hybridization are by far not yet understood.

Nucleic Acids Research, 2009

Microarray hybridization studies have attributed the nonlinearity of hybridization isotherms to p... more Microarray hybridization studies have attributed the nonlinearity of hybridization isotherms to probe saturation and post-hybridization washing. Both processes are thought to distort 'true' target abundance because immobilized probes are saturated with excess target and stringent washing removes loosely bound targets. Yet the paucity of studies aimed at understanding hybridization and dissociation makes it difficult to align physicochemical theory to microarray results. To fill the void, we first examined hybridization isotherms generated on different microarray platforms using a ribosomal RNA target and then investigated hybridization signals at equilibrium and after stringent wash. Hybridization signal at equilibrium was achieved by treating the microarray with isopropanol, which prevents nucleic acids from dissolving into solution. Our results suggest that (i) the shape of hybridization isotherms varied by microarray platform with some being hyperbolic or linear, and others following a power-law; (ii) at equilibrium, fluorescent signal of different probes hybridized to the same target were not similar even with excess of target and (iii) the amount of target removed by stringent washing depended upon the hybridization time, the probe sequence and the presence/absence of nonspecific targets. Possible physicochemical interpretations of the results and future studies are discussed.

Comment on “Discrimination of Shifts in a Soil Microbial Community Associated with TNT-Contamination Using a Functional ANOVA of 16S rRNA Hybridized to Oligonucleotide Microarrays”

Environmental Science & Technology, 2007

Eyers et al. (1) suggested that nonequilibrium thermal dissociation (NTD) curves could be used to... more Eyers et al. (1) suggested that nonequilibrium thermal dissociation (NTD) curves could be used to discriminate shifts of soil microbial communities. Our own experience with gel pad array technology (2 and refs within) suggests an alternative interpretation. In this correspondence, we ...

Environmental Microbiology, 2007