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Author

Gaurav Sharma

Other affiliations: Northeastern University, D. E. Shaw & Co., Hewlett-Packard  ...read more
Bio: Gaurav Sharma is an academic researcher from Shenzhen University. The author has contributed to research in topics: Medicine & Photocatalysis. The author has an hindex of 82, co-authored 1244 publications receiving 31482 citations. Previous affiliations of Gaurav Sharma include Northeastern University & D. E. Shaw & Co..


Papers
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Journal ArticleDOI
TL;DR: An R/Bioconductor package is developed, projectR, to perform TL for analyses of genomics data via TL of clustering, correlation, and factorization methods, and the utility TL for integrated data analysis is demonstrated.
Abstract: Motivation Dimension reduction techniques are widely used to interpret high-dimensional biological data. Features learned from these methods are used to discover both technical artifacts and novel biological phenomena. Such feature discovery is critically importent in analysis of large single-cell datasets, where lack of a ground truth limits validation and interpretation. Transfer learning (TL) can be used to relate the features learned from one source dataset to a new target dataset to perform biologically driven validation by evaluating their use in or association with additional sample annotations in that independent target dataset. Results We developed an R/Bioconductor package, projectR, to perform TL for analyses of genomics data via TL of clustering, correlation and factorization methods. We then demonstrate the utility TL for integrated data analysis with an example for spatial single-cell analysis. Availability and implementation projectR is available on Bioconductor and at https://github.com/genesofeve/projectR. Contact gsteinobrien@jhmi.edu or ejfertig@jhmi.edu. Supplementary information Supplementary data are available at Bioinformatics online.

34 citations

Journal ArticleDOI
TL;DR: In this article, the authors reported that inhibition of palmitoyl-protein thioesterase 1 (PPT1), a target of chloroquine derivatives like hydroxychloroquine (HCQ), enhances the antitumor efficacy of anti-PD-1 Ab in melanoma.
Abstract: New strategies are needed to enhance the efficacy of anti-programmed cell death protein antibody (anti-PD-1 Ab) in cancer. Here, we report that inhibiting palmitoyl-protein thioesterase 1 (PPT1), a target of chloroquine derivatives like hydroxychloroquine (HCQ), enhances the antitumor efficacy of anti-PD-1 Ab in melanoma. The combination resulted in tumor growth impairment and improved survival in mouse models. Genetic suppression of core autophagy genes, but not Ppt1, in cancer cells reduced priming and cytotoxic capacity of primed T cells. Exposure of antigen-primed T cells to macrophage-conditioned medium derived from macrophages treated with PPT1 inhibitors enhanced melanoma-specific killing. Genetic or chemical Ppt1 inhibition resulted in M2 to M1 phenotype switching in macrophages. The combination was associated with a reduction in myeloid-derived suppressor cells in the tumor. Ppt1 inhibition by HCQ, or DC661, induced cyclic GMP-AMP synthase/stimulator of interferon genes/TANK binding kinase 1 pathway activation and the secretion of interferon-β in macrophages, the latter being a key component for augmented T cell-mediated cytotoxicity. Genetic Ppt1 inhibition produced similar findings. These data provide the rationale for this combination in melanoma clinical trials and further investigation in other cancers.

34 citations

Proceedings ArticleDOI
18 Mar 2005
TL;DR: A pitch synchronous overlap and add (PSOLA) algorithm is used for pitch and duration modifications in the watermark embedding phase and experiments with multiple speech codecs show very good robustness with low data-rate speech coders.
Abstract: We propose a speech watermarking algorithm based on the modification of the pitch (fundamental frequency) and duration of the quasi-periodic speech segments. Natural variability of these speech features allows watermarking modifications to be imperceptible to the human observer. On the other hand, the significance of these features makes the system robust to common signal processing operations and low data-rate source excitation based speech coders. This class of coders is particularly obstructive for conventional audio watermarking algorithms when applied to speech signals. A pitch synchronous overlap and add (PSOLA) algorithm is used for pitch and duration modifications in the watermark embedding phase. Experiments with multiple speech codecs show very good robustness with low data-rate (5-8 kbps) speech coders.

34 citations

Journal ArticleDOI
TL;DR: Isothermal titration calorimetry and molecular docking studies suggested that inhibition of fibrillation by these naphthalene derivatives is mediated not just through hydrophobic forces, but also by disruption of π-π interactions between the aromatic residues together with the inter-polypeptide chain repulsion among negatively charged ANS/bis-ANS bound SB.

34 citations

Journal Article
TL;DR: In this article, a color calibration method for photographic input media that does not require a calibration target is presented, using characteristic spectral measurements from the image(s) to be scanned, a model for the spectra on the medium is obtained through a principal component analysis.
Abstract: The lack of a scanner calibration target representative of the image medium (substrate and colorants) often limits the accuracy of scanner color calibration. In this paper, a color calibration method is presented for photographic input media that does not require a calibration target. Using characteristic spectral measurements from the image(s) to be scanned, a model for the spectra on the medium is obtained through a principal component analysis. The spectral sensitivity of the scanner provides a model for its operation. By combining the models for the scanner and the medium, the spectral reflectance of the input corresponding to a given set of scanner RGB values can be determined. This provides a spectral calibration for the scanner, which can readily be transformed into a color calibration under any suitable viewing illuminant. Results from simulations and actual calibrations demonstrate the value of the new method.

34 citations


Cited by
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08 Dec 2001-BMJ
TL;DR: There is, I think, something ethereal about i —the square root of minus one, which seems an odd beast at that time—an intruder hovering on the edge of reality.
Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

33,785 citations

01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal ArticleDOI

7,335 citations

Journal ArticleDOI

6,278 citations