S. Chakraborty

发表

Active Site Detection by Spatial Conformity and Electrostatic Analysis—Unravelling a Proteolytic Function in Shrimp Alkaline Phosphatase

B. Rao, S. Chakraborty, R. Minda, 2011, PloS one.

The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa

S. Lindow, B. Phinney, B. Durbin-Johnson, 2016, Scientific Reports.

Unifying the two different classes of plant non-specific lipid-transfer proteins allergens classified in the WHO/IUIS allergen database through a motif with conserved sequence, structural and electrostatic features

S. Chakraborty, 2016, bioRxiv.

Computational analysis of perturbations in the post-fusion Dengue virus envelope protein highlights known epitopes and conserved residues in the Zika virus

S. Chakraborty, 2016, F1000Research.

PREMONITION - Preprocessing motifs in protein structures for search acceleration

B. Rao, R. Venkatramani, B. Ásgeirsson, 2014 .

DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations

S. Chakraborty, 2014, F1000Research.

DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations

S. Chakraborty, 2014, F1000Research.

The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment

Shina Caroline Lynn Kamerlin, P. Weber, B. Rao, 2013, F1000Research.

Dipeptidyl peptidase-IV inhibitors used in type-2 diabetes inhibit a phospholipase C: a case of promiscuous scaffolds in proteins.

F. Goñi, B. Rao, R. Venkatramani, 2013, F1000Research.

Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms

B. Rao, R. Venkatramani, B. Ásgeirsson, 2013, F1000Research.

The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment.

B. Rao, R. Venkatramani, B. Ásgeirsson, 2013, F1000Research.

A Computational Module Assembled from Different Protease Family Motifs Identifies PI PLC from Bacillus cereus as a Putative Prolyl Peptidase with a Serine Protease Scaffold

F. Goñi, B. Rao, B. Ásgeirsson, 2013, PloS one.

Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator

Nathan A. Baker, B. Rao, B. Ásgeirsson, 2013, Intrinsically disordered proteins.

A Quantitative Measure of Electrostatic Perturbation in Holo and Apo Enzymes Induced by Structural Changes

S. Chakraborty, 2013, PloS one.

Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms

B. Rao, R. Venkatramani, B. Ásgeirsson, 2013, F1000Research.

A Measure of the Broad Substrate Specificity of Enzymes Based on ‘Duplicate’ Catalytic Residues

B. Rao, B. Ásgeirsson, S. Chakraborty, 2012, PloS one.

Enumerating Pathways of Proton Abstraction Based on a Spatial and Electrostatic Analysis of Residues in the Catalytic Site

S. Chakraborty, 2012, PloS one.

A Measure of the Promiscuity of Proteins and Characteristics of Residues in the Vicinity of the Catalytic Site That Regulate Promiscuity

B. Rao, S. Chakraborty, 2012, PloS one.

Inhibition of a cold‐active alkaline phosphatase by imipenem revealed by in silico modeling of metallo‐β‐lactamase active sites

J. Frère, B. Rao, B. Ásgeirsson, 2012, FEBS letters.

An Automated Flow for Directed Evolution Based on Detection of Promiscuous Scaffolds Using Spatial and Electrostatic Properties of Catalytic Residues

S. Chakraborty, 2012, PloS one.

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols.

Sandeep Chakraborty, Daniela Puiu, Charis Cardeno, 2016, The Plant journal : for cell and molecular biology.

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

S. Salzberg, D. Neale, A. Zimin, 2019, bioRxiv.

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

S. Salzberg, D. Neale, A. Zimin, 2019, bioRxiv.

GRASSLAND PLANT DISEASES: MANAGEMENT AND CONTROL

S. Chakraborty, 2001 .

Final amendment: Ambiguous specification of EGFR mutations compounded by nil or negligible fragmented gene counts and erroneous application of the Kappa statistic reiterates doubts on the veracity of the TEP-study

S. Chakraborty, 2017, bioRxiv.

The Interaction Affinity between Vascular Cell Adhesion Molecule-1 (VCAM-1) and Very Late Antigen-4 (VLA-4) Analyzed by Quantitative FRET

A. Karmenyan, Shuhan Wu, A. Chiou, 2015, PloS one.

Previously titled : A fragmented alignment method detects a phosphorylation site and a new BRC repeat in the BRCA 2 protein , and a new HAT repeat in Utp 6 from yeast Drosophila melanogaster

S. Chakraborty, 2016 .

A fragmented alignment method detects a phosphorylation site and a new BRC repeat in the Drosophila melanogaster BRCA2 protein, and a new HAT repeat in Utp6 from yeast.

S. Chakraborty, 2013, F1000Research.

The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment.

B. Rao, R. Venkatramani, B. Ásgeirsson, 2013, F1000Research.

A fragmented alignment method detects a putative phosphorylation site and a putative BRC repeat in the Drosophila melanogaster BRCA2 protein

S. Chakraborty, 2013, F1000Research.

RNA-seq assembler artifacts can bias expression counts and differential expression analysis - case study on the chickpea transcriptome emphasizes importance of freely accessible data for reproducibility

S. Chakraborty, 2016 .

RNA-seq assembler artifacts can bias expression counts and differential expression analysis - application of YeATS on the chickpea transcriptome

S. Chakraborty, 2016 .

PAGAL - Properties and corresponding graphics of alpha helical structures in proteins

B. Rao, A. Dandekar, S. Chakraborty, 2014, F1000Research.

Dipeptidyl peptidase-IV inhibitors used in type-2 diabetes inhibit a phospholipase C: a case of promiscuous scaffolds in proteins.

F. Goñi, B. Rao, R. Venkatramani, 2013, F1000Research.

The PDB database is a rich source of alpha-helical antimicrobial peptides to combat disease causing pathogens [version 1; peer review: 1 approved]

B. Rao, B. Ásgeirsson, A. Dandekar, 2022 .

YeATSAM analysis of the walnut and chickpea transcriptome reveals key genes undetected by current annotation tools

A. Dandekar, P. Martínez-García, S. Chakraborty, 2016, F1000Research.

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut [version 2; peer review: 3 approved]

D. Neale, B. Rao, A. Dandekar, 2019 .

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

D. Neale, B. Rao, A. Dandekar, 2015, F1000Research.

Corrigendum: The Type II Secreted Lipase/Esterase LesA is a Key Virulence Factor Required for Xylella fastidiosa Pathogenesis in Grapevines

G. Bruening, B. Rao, P. Feldstein, 2016, Scientific Reports.

The Type II Secreted Lipase/Esterase LesA is a Key Virulence Factor Required for Xylella fastidiosa Pathogenesis in Grapevines

G. Bruening, B. Rao, P. Feldstein, 2016, Scientific Reports.

The profile of Cβ atoms applied to protein structure quality assessment.

B. Rao, R. Venkatramani, B. Ásgeirsson, 2014 .

Quantification of the Metabolic State in Cell-Model of Parkinson’s Disease by Fluorescence Lifetime Imaging Microscopy

Sandeep Chakraborty, Jin-Wu Tsai, Artashes Karmenyan, 2016, Scientific Reports.

Elucidation of microstructural changes in leaves during senescence using spectral domain optical coherence tomography

T. Anna, W. Kuo, V. Srivastava, 2019, Scientific Reports.

Final amendment: A plausible explanation for in silico reporting of erroneous MET gene expression in tumor-educated platelets (TEP) intended for "liquid biopsy" of non-small cell lung carcinoma still refutes the TEP-study

S. Chakraborty, 2017, bioRxiv.

No evidence of MET and HER2 over-expression in non-small cell lung carcinoma and breast cancer, respectively, raises serious doubts on using RNA-seq profiles of tumor-educated platelets as a ‘liquid biopsy’ source

S. Chakraborty, 2017 .

No supporting evidence of classification based on FFPE samples, ambiguity in classification of EGFR mutants, and inclusion of bona-fide platelet genes in discriminator sets indicate no biological basis for using RNA-seq from tumor-educated platelets as a source in ”liquid biopsy”

S. Chakraborty, 2017, bioRxiv.

Genomic Variation Among and Within Six Juglans Species

S. Salzberg, D. Neale, Kristian Stevens, 2018, G3: Genes, Genomes, Genetics.

A single amino acid substitution in the Ω-like loop of E. coli PBP5 disrupts its ability to maintain cell shape and intrinsic beta-lactam resistance.

S. Chakraborty, Mouparna Dutta, A. Ghosh, 2015, Microbiology.

Inhibitory effects of curcumin and cyclocurcumin in 1-methyl-4-phenylpyridinium (MPP+) induced neurotoxicity in differentiated PC12 cells

A. Karmenyan, Arthur Chiou, A. Chiou, 2017, Scientific Reports.

Cataloguing over-expressed genes in Epstein Barr Virus immortalized lymphoblastoid cell lines through consensus analysis of PacBio transcriptomes corroborates hypomethylation of chromosome 1

S. Chakraborty, 2017, bioRxiv.

Shorter unreported sequences in a RACE-Seq study involving seven tissues confirms ∼150 novel transcripts identified in MCF-7 cell line PacBio transcriptome, leaving ∼100 non-redundant transcripts exclusive to the cancer cell line

S. Chakraborty, 2017, bioRxiv.

MCF-7 breast cancer cell line PacBio generated transcriptome has ~300 novel transcribed regions, un-annotated in both RefSeq and GENCODE, and absent in the liver, heart and brain transcriptomes

S. Chakraborty, 2017, bioRxiv.

Screening of Selected Hosts for Sandalwood Seedlings at Nursery Stage Based on Host Cation Exchange Capacity

S. Chakraborty, S. Viswanath, A. Devakumar, 2020, Indian Forester.

FRET Based Quantification and Screening Technology Platform for the Interactions of Leukocyte Function-Associated Antigen-1 (LFA-1) with InterCellular Adhesion Molecule-1 (ICAM-1)

A. Karmenyan, A. Chiou, S. Chakraborty, 2014, PloS one.

Transcriptome from saffron (Crocus sativus) plants in Jammu and Kashmir reveals abundant soybean mosaic virus transcripts and several putative pathogen bacterial and fungal genera

S. Chakraborty, 2016, bioRxiv.

Molecular Profiling of Pierce’s Disease Outlines the Response Circuitry of Vitis vinifera to Xylella fastidiosa Infection

A. Dandekar, D. Cantu, L. Goulart, 2018, Front. Plant Sci..

Metagenome of SARS-Cov2 patients in Shenzhen with travel to Wuhan shows a wide range of species - Lautropia, Cutibacterium, Haemophilus being most abundant - and Campylobacter explaining diarrhea

S. Chakraborty, 2020 .

Quantitative analysis of chromosome localization in the nucleus.

B. Rao, S. Chakraborty, I. Mehta, 2015, Methods in molecular biology.

Chromosome territories reposition during DNA damage-repair response

Sandeep Chakraborty, Basuthkar J Rao, Ullas Kolthur-Seetharam, 2013, Genome Biology.

IMACULAT — An Open Access Package for the Quantitative Analysis of Chromosome Localization in the Nucleus

B. Rao, S. Chakraborty, I. Mehta, 2013, PloS one.

A fragmented alignment method detects a phosphorylation site and a new BRC repeat in the BRCA 2 Drosophila melanogaster protein , and a new HAT repeat in Utp 6 from yeast

S. Chakraborty, 2016 .

Promiscuous scaffolds in proteins - non-native, non-additive and non-trivial

Sandeep Chakraborty, Ravindra Venkatramani, Basuthkar J. Rao, 2013 .

The plant-based chimeric antimicrobial protein SlP14a-PPC20 protects tomato against bacterial wilt disease caused by Ralstonia solanacearum.

A. Dandekar, L. Goulart, P. A. Zaini, 2019, Plant science : an international journal of experimental plant biology.

Potential impact of climate change on plant diseases of economic significance to Australia

R. Sutherst, K. Old, M. Dudzinski, 1998, Australasian Plant Pathology.

Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species

J. Dvorak, M. Luo, Tingting Zhu, 2019, Horticulture Research.

Correlating the ability of VP24 protein from Ebola and Marburg viruses to bind human karyopherin to their immune suppression mechanism and pathogenicity using computational methods

B. Ásgeirsson, A. Dandekar, S. Chakraborty, 2014 .

Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions.

B. Rao, B. Ásgeirsson, A. Dandekar, 2014, F1000Research.

Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions

B. Rao, B. Ásgeirsson, A. Dandekar, 2014, F1000Research.

Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions.

B. Rao, B. Ásgeirsson, A. Dandekar, 2014, F1000Research.

MEPPitope: spatial, electrostatic and secondary structure perturbations in the post-fusion Dengue virus envelope protein highlights known epitopes and conserved residues in the Zika virus.

S. Chakraborty, 2016, F1000Research.

The PDB database is a rich source of alpha-helical anti-microbial peptides to combat disease causing pathogens

B. Rao, B. Ásgeirsson, A. Dandekar, 2014, F1000Research.

The PDB database is a rich source of alpha-helical anti-microbial peptides to combat disease causing pathogens

B. Rao, B. Ásgeirsson, A. Dandekar, 2014, F1000Research.

Open Peer Review , Sgit -inia (deputy

A. Dandekar, P. Martínez-García, S. Chakraborty, 2022 .

The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins

F. Goñi, B. Rao, R. Venkatramani, 2015, F1000Research.

Deep RNA-Seq profile reveals biodiversity, plant–microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues

A. Dandekar, P. Martínez-García, M. Britton, 2016, AMB Express.

Distributed under Creative Commons Cc-by 4.0

B. Rao, A. Dandekar, L. Goulart, 2022 .

Sequencing data from Massachusetts General Hospital shows Cas9 integration into the genome, highlighting a serious hazard in gene-editing therapeutics

S. Chakraborty, 2019, F1000Research.

A fragmented alignment method detects a phosphorylation site and a new BRC repeat in the BRCA2 Drosophila melanogaster

S. Chakraborty, 2019 .

An atypical CRISPR-Cas locus in Symbiobacterium thermophilum flanked by a transposase, a reverse transcriptase, the endonuclease MutS2 and a putative Cas9-like protein

S. Chakraborty, 2018, bioRxiv.

Inhibitory effects of curcumin and cyclocurcumin in 1-methyl-4-phenylpyridinium (MPP+) induced neurotoxicity in differentiated PC12 cells

A. Karmenyan, A. Chiou, S. Chakraborty, 2017, Scientific Reports.

YeATSAM analysis of the chloroplast genome of walnut reveals several putative un-annotated genes and mis-annotation of the trans-spliced rps12 gene in other organisms

S. Chakraborty, 2016, bioRxiv.

Elucidation of microstructural changes in leaves during senescence using spectral domain optical coherence tomography

T. Anna, W. Kuo, V. Srivastava, 2019, Scientific Reports.

Revealing the cellular metabolism and microstructural changes in vivo in senescing Acer saccharum leaves using two-photon FLIM and full-field OCM

Wen-Chuan Kuo, Arthur Chiou, Sandeep Chakraborty, 2016, SPIE/COS Photonics Asia.

A comparative study of metabolic state of stem cells during osteogenic and adipogenic differentiations via fluorescence lifetime imaging microscopy

Arthur Chiou, Sandeep Chakraborty, Meng-Hsin Ou, 2016, SPIE/COS Photonics Asia.

Ripidomyxa australiensis nov. gen. nov. sp., a mycophagous amoeba from Australian soil

S. Chakraborty, M. Pussard, 1985 .

Promiscuity-based enzyme selection for rational directed evolution experiments.

Sandeep Chakraborty, Renu Minda, Lipika Salaye, 2013, Methods in molecular biology.

Enzymatic attributes of an l-isoaspartyl methyltransferase from Candida utilis and its role in cell survival

A. Ghosh, S. Chakraborty, Trina Dutta, 2015, Biochemistry and biophysics reports.

Inconclusive studies on possible CRISPR-Cas off-targets should moderate expectations about enzymes that have evolved to be non-specific

S. Chakraborty, 2018, Journal of Biosciences.

Reverse transcriptase fused CRISPR-Cas1 locus with RNA-seq expression necessitates revisiting hypothesis on acquisition of antibiotic resistance genes in multidrug-resistant Enterococcus faecalis V583

S. Chakraborty, 2018, bioRxiv.

Directed evolution induces tributyrin hydrolysis in a virulence factor of Xylella fastidiosa using a duplicated gene as a template

B. Rao, B. Ásgeirsson, A. Dandekar, 2014, F1000Research.

Directed evolution induces tributyrin hydrolysis in a virulence factor of using a duplicated gene as a template Xylella fastidiosa (v1; ref status: indexed, http://f1000r.es/48i)

B. Rao, B. Ásgeirsson, A. Dandekar, 2015 .

Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species

J. Dvorak, M. Luo, Tingting Zhu, 2019, Horticulture Research.

PAGAL - Properties and corresponding graphics of alpha helical structures in proteins

B. Rao, A. Dandekar, S. Chakraborty, 2014, F1000Research.

YeATS-a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut [version 1; peer review: 1 approved with reservations]

B. Rao, A. Dandekar, C. Leslie, 2021 .

Sequence/structural analysis of xylem proteome emphasizes pathogenesis-related proteins, chitinases and β-1, 3-glucanases as key players in grapevine defense against Xylella fastidiosa

B. Rao, A. Dandekar, L. Goulart, 2016, PeerJ.

The PDB database is a rich source of alpha-helical antimicrobial peptides to combat disease causing pathogens [version 1; peer review: 1 approved]

B. Rao, B. Ásgeirsson, A. Dandekar, 2021 .

En-face Tomographic Imaging of Scattering Objects Using Single Broadband Light Emitting Diode Based Full-Field Optical Coherence Microscopy

T. Anna, W. Kuo, A. Chiou, 2018 .

Inhibition of a cold‐active alkaline phosphatase by imipenem revealed by in silico modeling of metallo‐β‐lactamase active sites

J. Frère, B. Rao, B. Ásgeirsson, 2012, FEBS letters.

Secondary infection by anaerobic bacteria possibly ensues a battle for oxygen in SARS-Cov2 infected patients: anaerobe-targeting antibiotics (like doxycycline/Metronidazole) to supplement Azithromycin in the treatment regimen of COVID19?

S. Chakraborty, G. Das, 2020 .

Computational analysis of perturbations in the post-fusion Dengue virus envelope protein highlights known epitopes and conserved residues in the Zika virus

S. Chakraborty, 2016, F1000Research.