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Sheetal Chainraj

dblp:93/3941 · DBLP profile ↗
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1ranked-venue papers
0as first author
0since 2021 · last 2004
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%
Theoretical computer science
1 paper
Graph algorithms and graph theory · 100%

Topics — the 5 heaviest of 5, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › structural biology
NMR spectroscopy
0.012004
A random graph approach to NMR sequential assignment · RECOMB 2004
Bioinformatics and computational biology › structural biology
resonance assignment
0.012004
A random graph approach to NMR sequential assignment · RECOMB 2004
Bioinformatics and computational biology
structural bioinformatics
0.012004
A random graph approach to NMR sequential assignment · RECOMB 2004
Graph algorithms and graph theory
graph algorithms
0.012004
A random graph approach to NMR sequential assignment · RECOMB 2004
Graph algorithms and graph theory
random graph models
0.012004
A random graph approach to NMR sequential assignment · RECOMB 2004

Methods — techniques the papers use, named apart from their topics

randomized algorithm · 0.1random graph theory · 0.1
YearPublicationVenuePosition
2004 A random graph approach to NMR sequential assignment
abstract
Nuclear magnetic resonance (NMR) spectroscopy allows scientists to study protein structure, dynamics, and interactions in solution. A necessary first step for such applications is determining the resonance assignment, mapping spectral data to atoms and residues in the primary sequence. Automated resonance assignment algorithms rely on information regarding connectivity (e.g. through-bond atomic interactions) and amino acid type, typically using the former to determine strings of connected residues and the latter to map those strings to positions in the primary sequence. Significant ambiguity exists in both connectivity and amino acid type, and different algorithms have combined the information in two phases (find short unambiguous strings then align) or simultaneously (align while extending strings). This paper focuses on the information content available in connectivity alone, allowing for ambiguity rather than handling only unambiguous strings, and complements existing work on the information content in amino acid type.In this paper, we develop a novel random-graph theoretic framework for algorithmic analysis of NMR sequential assignment. Our random graph model captures the structure of chemical shift degeneracy (a key source of connectivity ambiguity). We then give a simple and natural randomized algorithm for finding an optimum sequential cover. The algorithm naturally and efficiently reuses substrings while exploring connectivity choices; it overcomes local ambiguity by enforcing global consistency of all choices. We employ our random graph model to analyze our algorithm, and show that it can provably tolerate a relatively large ambiguity while still giving expected optimal performance in polynomial time. To study the algorithm's performance in practice, we tested it on experimental data sets from a variety of proteins and experimental set-ups. The algorithm was able to overcome significant noise and local ambiguity and consistently identify significant sequential fragments.
Chris Bailey-Kellogg, Sheetal Chainraj, Gopal Pandurangan
RECOMB2