#### Filter Results:

#### Publication Year

2006

2013

#### Co-author

#### Key Phrase

#### Publication Venue

Learn More

Kinship analysis using genetic data is important for many biological applications, including many in conservation biology. Wide availability of microsatellites has boosted studies in wild populations that rely on the knowledge of kinship, particularly sibling relationships (sibship). While there exist many methods for reconstructing sibling relationships,… (More)

Predicting the folding of an RNA sequence, while allowing general pseudoknots (PK), consists in finding a minimal free-energy matching of its n positions. Assuming independently contributing base-pairs, the problem can be solved in Θ(n 3)-time using a variant of the maximal weighted matching. By contrast, the problem was previously proven NP-Hard in the… (More)

A software suite KINALYZER reconstructs full-sibling groups without parental information using data from codominant marker loci such as microsatellites. KINALYZER utilizes a new algorithm for sibling reconstruction in diploid organisms based on combinatorial optimization. KINALYZER makes use of a Minimum 2-Allele Set Cover approach based on Mendelian… (More)

- Saad I Sheikh, Tanya Y Berger-Wolf, Ashfaq A Khokhar, Isabel C Caballero, Mary V Ashley, Wanpracha Chaovalitwongse +1 other
- 2009

While full sibling group reconstruction from microsatellite data is a well studied problem, reconstruction of half sibling groups is much less studied, theoretically challenging, and a computationally intense problem. In this paper, we present two different formulations of the half-sib reconstruction problem and prove their NP-hardness. We also present… (More)

- Saad I Sheikh, Tanya Y Berger-Wolf, Ashfaq A Khokhar, Bhaskar Dasgupta
- 2008

Kinship analysis using genetic data is important for many biological applications, including many in conservation biology. A number of methods have been proposed for this problem. However, in absence of a true answer, biologists today find it challenging to consolidate different reconstructions into one solution. Towards this end, consensus based… (More)

—Transmembrane β-barrel (TMB) proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of TMB proteins with known structures is very small. Over the years, a number of learning-based methods have been introduced for recognition and structure prediction of TMB… (More)

We describe the broad outline of a new thermodynamics-based algorithm, FFTbor, that uses the fast Fourier transform to perform polynomial interpolation to compute the Boltzmann probability that secondary structures differ by k base pairs from an arbitrary reference structure of a given RNA sequence. The algorithm, which runs in quartic time O(n 4) and… (More)

- Saad I Sheikh, Tanya Y Berger-Wolf, Ashfaq A Khokhar, Isabel C Caballero, Mary V Ashley, Wanpracha Chaovalitwongse +2 others
- 2010

While full-sibling group reconstruction from microsatellite data is a well-studied problem , reconstruction of half-sibling groups is much less studied, theoretically challenging, and computationally demanding. In this paper, we present a formulation of the half-sibling reconstruction problem and prove its APX-hardness. We also present exact solutions for… (More)

- Mary Ashley, Tanya Berger-Wolf, Piotr Berman, Wanpracha Chaovalitwongse, Bhaskar Dasgupta, Ming-Yang Kao +9 others
- 2009

In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: a r t i c l e i n f o a b s t r a c t In this paper, we consider approximability… (More)