A5082737444- Advanced Proteomics Techniques and Applications
- Machine Learning in Bioinformatics
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Advanced Biosensing Techniques and Applications
- Medical Imaging Techniques and Applications
- Intraocular Surgery and Lenses
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- DNA Repair Mechanisms
- Corneal surgery and disorders
- Ophthalmology and Visual Impairment Studies
- Sarcoma Diagnosis and Treatment
- Advanced MRI Techniques and Applications
- Advanced Radiotherapy Techniques
- Cardiovascular Syncope and Autonomic Disorders
- Bone Tumor Diagnosis and Treatments
- Meta-analysis and systematic reviews
- Retinal Diseases and Treatments
- Muscle Physiology and Disorders
- Retinal Development and Disorders
- Oral and Maxillofacial Pathology
- Axon Guidance and Neuronal Signaling
- Retinal and Optic Conditions
- Advanced X-ray Imaging Techniques
University of Michigan
2020-2025
McMaster University
2023
Vanderbilt University Medical Center
2020
Eye Institute of Utah
2016
University of Utah
2016
Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments relies on computational algorithms for matching acquired MS/MS spectra against sequences of candidate peptides using database search tools, such as MSFragger. Here, we present a new tool, MSBooster, rescoring peptide-to-spectrum matches additional features incorporating deep learning-based predictions peptide properties, LC retention time, ion mobility, and spectra. We demonstrate the utility...
Abstract Data-independent acquisition has become a widely used strategy for peptide and protein quantification in liquid chromatography-tandem mass spectrometry-based proteomics studies. The integration of ion mobility separation into data-independent analysis, such as the diaPASEF technology available on Bruker’s timsTOF platform, further improves accuracy depth achievable using acquisition. We introduce diaTracer, spectrum-centric computational tool optimized data. diaTracer performs...
Abstract Recent developments in machine-learning (ML) and deep-learning (DL) have immense potential for applications proteomics, such as generating spectral libraries, improving peptide identification, optimizing targeted acquisition modes. Although new ML/DL models various properties are frequently published, the rate at which these adopted by community is slow, mostly due to technical challenges. We believe that, make better use of state-of-the-art models, more attention should be spent on...
Abstract Bulky DNA lesions in transcribed strands block RNA polymerase II (RNAPII) elongation and induce a genome-wide transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking lesions, but how transcription is restored the genome following remains unresolved. Here, we find that TCR-specific CSB protein loads PAF1 complex (PAF1C) onto RNAPII promoter-proximal regions response to damage. Although dispensable for TCR-mediated repair,...
Abstract Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments relies on computational algorithms for matching acquired MS/MS spectra against sequences of candidate peptides using database search tools, such as MSFragger. Here, we present a new tool, MSBooster, rescoring peptide-to-spectrum matches additional features incorporating deep learning-based predictions peptide properties, LC retention time, ion mobility, and spectra. We demonstrate the...
Purpose: To develop a method for predicting postoperative anterior chamber depth (ACD) in cataract surgery patients based on preoperative biometry, demographics, and intraocular lens (IOL) power. Methods: Patients who underwent had both biometry measurements were included. Patient demographics IOL power collected from the Sight Outcomes Research Collaborative (SOURCE) database. A gradient-boosting decision tree model was developed to predict ACD. The mean absolute error (MAE) median (MedAE)...
Abstract Manganese (Mn) is an essential micronutrient required for the proper function of several enzymes. Accumulating evidence demonstrates a selective decrease bioavailable Mn in vulnerable cell types Huntington’s Disease (HD), inherited progressive neurodegenerative disorder with no cure. Amelioration underlying pathophysiology, such as alterations Mn-dependent biology, may be therapeutic. We therefore sought to investigate global and Mn-responsive biology following various exposures...
Abstract Data-independent acquisition (DIA) has become a widely used strategy for peptide and protein quantification in mass spectrometry-based proteomics studies. The integration of ion mobility separation into DIA analysis, such as the diaPASEF technology available on Bruker’s timsTOF platform, further improves accuracy depth achievable using DIA. We introduce diaTracer, new spectrum-centric computational tool optimized data. diaTracer performs three-dimensional (m/z, retention time,...
For parallel beam geometry the Fourier reconstruction works via slice theorem (or central theorem, projection theorem). fan situation, can be extended to a generalized (GFST) for fan-beam image reconstruction. We have briefly introduced this method in conference. This paper reintroduces GFST details. The described as following: plane is filled by adding up contributions from all fanbeam projections individually; thereby values are directly calculated Cartesian coordinates such avoiding...
Abstract The coordinated transcription of genes involves the regulated release RNA polymerase II (RNAPII) from promoter-proximal sites into active elongation. DNA lesions in transcribed strands block elongation and induce a strong transcriptional arrest. transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking lesions, but this is not sufficient to resume transcription. Through proteomics screens, we find that TCR-specific CSB protein loads evolutionary conserved...
Abstract Purpose To develop a method for predicting postoperative anterior chamber depth (ACD) in cataract surgery patients based on preoperative biometry, demographics, and intraocular lens (IOL) power. Methods Patients who underwent had both biometry measurements were included. Patient demographics IOL power collected from the Sight Outcomes Research Collaborative (SOURCE) database. A gradient boosting decision tree model was developed to predict ACD. The mean absolute error (MAE) median...
The iterative refinement method (IRM) has been very successfully applied in many different fields for examples the modern quantum chemical calculation and CT image reconstruction. It is proved that can create an exact inverse from approximate with a few iterations. IRM used reconstruction to lower radiation dose. utilize errors between original measured data recalculated correct reconstructed images. However if it not smooth inside object, there often over-correction along boundary of organs...