Maciek Sasinowski

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As part of an international effort to sequence the rice genome, the Clemson University Genomics Institute is developing a sequence-tagged-connector (STC) framework. This framework includes the generation of deep-coverage BAC libraries from O. sativa ssp. japonica c.v. Nipponbare and the sequencing of both ends of the genomic DNA insert of the BAC clones.(More)
BACKGROUND Measurement of peptide/protein concentrations in biological samples for biomarker discovery commonly uses high-sensitivity mass spectrometers with a surface-processing procedure to concentrate the important peptides. These time-of-flight (TOF) instruments typically have low mass resolution and considerable electronic noise associated with their(More)
The rice blast fungus Magnaporthe grisea is a highly destructive plant pathogen and one of the most important for studying various aspects of host-plant interactions. It has been widely adopted as a model organism because it is ideally suited for genetic and biological studies. To facilitate map-based cloning, chromosome walking, and genome organization(More)
We have developed an algorithm which combines data obtained from restriction digestion experiments and hybridization experiments to construct robust physical maps of whole chromosomes. The algorithm has been incorporated into a program which accepts hybridization data consisting of an unordered hybridization matrix and fingerprinting data containing band(More)
mzXML (extensible markup language) is one of the pioneering data formats for mass spectrometry-based proteomics data collection. It is an open data format that has benefited and evolved as a result of the input of many groups, and it continues to evolve. Due to its dynamic history, its structure, purpose and applicability have all changed with time, meaning(More)
We have developed an automated procedure for aligning peaks in multiple TOF spectra that eliminates common timing errors and small variations in spectrometer output. Our method incorporates high-resolution peak detection, re-binning, and robust linear data fitting in the time domain. This procedure aligns label-free (uncalibrated) peaks to minimize the(More)
We have developed a peak deconvolution strategy that is applicable to the full mass range of a time-of-flight (TOF) spectrum. This strategy involves resampling a spectrum to create a time series that has equal peak widths (in time) across the entire spectrum, and then using the deconvolution filters we have previously described. We use this technique to(More)
OBJECTIVE Serum α-hydroxybutyrate (α-HB) is elevated in insulin resistance and diabetes. We tested the hypothesis that the α-HB level predicts abnormal 1 h glucose levels and β-cell dysfunction inferred from plasma insulin kinetics during a 75 g oral glucose tolerance test (OGTT). RESEARCH DESIGN AND METHODS This cross-sectional study included 217(More)
Currently there is a lack of targeted therapies that lead to long-term attenuation or regression of disease in patients with advanced clear cell renal cell carcinoma (ccRCC). Our group has implemented a high-throughput genetic analysis coupled with a high-throughput proliferative screen in order to investigate the genetic contributions of a large cohort of(More)
By applying time-domain filters to time-of-flight (TOF) mass spectrometry signals, we have simultaneously smoothed and narrowed spectra resulting in improved resolution and increased signal-to-noise ratios. This filtering procedure has an advantage over detailed curve fitting of spectra in the case of large dense spectra, when neither the location nor the(More)