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Ron Elber

dblp:29/1978 · DBLP profile ↗
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2ranked-venue papers
0as first author
0since 2021 · last 2007
0000-0001-7849-415XORCID · corroborated

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

Applied, interdisciplinary, general and emerging computing · 2

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
2 papers
Bioinformatics and computational biology · 100%
Theoretical computer science
1 paper
Algorithms and data structures · 100%

Topics — the 4 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › protein sequence analysis
protein alignment
0.112007
Support Vector Training of Protein Alignment Models · RECOMB 2007
Bioinformatics and computational biology
protein structure analysis
0.012004
The evolutionary capacity of protein structures · RECOMB 2004
Bioinformatics and computational biology
structural bioinformatics
0.012004
The evolutionary capacity of protein structures · RECOMB 2004
Algorithms and data structures
randomized algorithms
0.012004
The evolutionary capacity of protein structures · RECOMB 2004

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

randomized algorithm · 0.1markov chain mixing · 0.1knapsack problem reduction · 0.1support vector machine · 0.1
YearPublicationVenuePosition
2007 Support Vector Training of Protein Alignment Models
Chun-Nam John Yu, Thorsten Joachims, Ron Elber, Jaroslaw Pillardy
RECOMB3
2004 The evolutionary capacity of protein structures
abstract
In nature, one finds large collections of different protein sequences exhibiting roughly the same three-dimensional structure, and this observation underpins the study of structural protein families. In studying such families at a global level, a natural question to ask is how close to "optimal" the native sequences are in terms of their energy. We therefore define and compute the evolutionary capacity of a protein structure as the total number of sequences whose energy in the structure is below that of the native sequence. An important aspect of our definition is that we consider the space of all possible protein sequences, i.e. the exponentially large set of all strings over the 20-letter amino acid alphabet, rather than just the set of sequences found in nature.In order to make our approach computationally feasible, we develop randomized algorithms that perform approximate enumeration in sequence space with provable performance guarantees. We draw on the area of rapidly mixing Markov chains, by exhibiting a connection between the evolutionary capacity of proteins and the number of feasible solutions to the Knapsack problem. This connection allows us to design an algorithm for approximating the evolutionary capacity, extending a recent result of Morris and Sinclair on the Knapsack problem. We present computational experiments that show the method to be effective in practice on large collections of protein structures. In addition, we show how to use approximations to the evolutionary capacity to compute a statistical mechanics notion of "evolutionary temperature" on sequence space.
Leonid Meyerguz, David Kempe 0001, Jon M. Kleinberg, Ron Elber
RECOMB4