G. Sampath

Whole protein sequencing and quantification without proteolysis, terminal residue cleavage, or purification: A computational model

The paper models a computational method to sequence and quantify whole proteins without proteolysis, using nanopore translocation and signal analysis.

Identifying residues in unfolded whole proteins with a nanopore: a theoretical model based on linear inequalities

The paper proposes a theoretical model to identify amino acids in unfolded proteins using nanopore measurements by solving linear inequalities derived from exclusion volume differences.

Unbiased counting of whole proteins with nanopores over the full dynamic range of a proteome: a computational study

This paper presents a computational model for nanopore-based single-protein counting across the full proteome dynamic range without proteolysis or separation.

Horizontal detection of post-translational modifications to an amino acid with a nanopore based on analyte volume and translocation-time

The paper proposes a method to detect post-translational modifications in amino acids using nanopore measurements of current blockade and translocation time.

Slowing down an analyte in a nanopore

The paper describes a method to slow down analyte translocation through a nanopore by reversing voltage and adjusting pH, showing potential for improved nanopore sensing and sequencing.

Label-free amino acid identification for de novo protein sequencing via tRNA charging and current blockade in a nanopore

The paper introduces a label-free method to identify single amino acids for protein sequencing using tRNA charging and nanopore current blockade.

Protein identification with a nanopore and a binary alphabet

The paper describes a method to identify proteins using a binary alphabet derived from amino acid volumes, validated on H. pylori proteome data.

Peptide partitions and protein identification: a computational analysis

The paper analyzes peptide partitions to improve protein identification from sequences, showing high identification rates using specific partitioning strategies.

DNA sequencing with stacked nanopores and exonuclease: a simulation-based analysis

The paper simulates a modified nanopore sequencing setup with stacked pores and exonuclease to improve base calling accuracy by preventing base loss and out-of-order entry.

A digital approach to protein identification and quantity estimation using tandem nanopores, peptidases, and database search

The paper introduces a digital method for protein identification and quantification using nanopores, peptidases, and database search, achieving over 90% identification accuracy in the human proteome.

A circuit theory of protein structure

The paper models protein secondary and tertiary structures as electrical circuits, using impedance functions and pole-zero maps to analyze and synthesize protein structures.

A quasi-digital approach to peptide sequencing using tandem nanopores with endo- and exo-peptidases

The paper describes a peptide sequencing method using tandem nanopores and peptidases to generate an ordered list of residue counts, enabling sequence reconstruction through a quasi-digital approach.

Peptide sequencing in an electrolytic cell with two nanopores in tandem and exopeptidase

This paper proposes a nanopore-based peptide sequencing method using tandem pores and exopeptidase, showing it could enable label-free sequencing with error correction.

A Tandem Cell for Nanopore-based DNA Sequencing with Exonuclease

The paper proposes a tandem cell design for nanopore-based DNA sequencing using an exonuclease to cleave and identify bases, showing that bases enter the downstream nanopore in natural order without regression.