Biomolecular Network Motif Counting and Discovery by Color Coding (2009)
Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, S. Cenk Sahinalp
Protein protein interaction (PPI) networks of many organisms share global topological features such as degree distribution, k − hop reachability, betweenness and closeness. Yet some of these...
Fereydoun Hormozdiari, Michael Hsing, Raheleh Salari, Er Schönhuth, Simon K. Chan, S. Cenk Sahinalp, ...
Although insertions and deletions (indels) are a common type of sequence variation, their origin and their functional consequences have not yet been fully understood. It has been known that indels...
Fereydoun Hormozdiari, Petra Berenbrink, S. Cenk Sahinalp
The (asymptotic) degree distributions of the best known “scale free ” network models are all similar and are independent of the seed graph used. Hence it has been tempting to assume that networks...
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data (2009)
Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, S. Cenk Sahinalp, Evan E. Eichler
The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5 % of sequence generated as part of primate genome sequencing projects consists of this material, which is...
Hormozdiari, Fereydoun, Alkan, Can, Eichler, Evan E., Sahinalp, S. Cenk
Recent studies show that along with single nucleotide polymorphisms and small indels, larger structural variants among human individuals are common. The Human Genome Structural Variation Project aims...
A partition function algorithm for interacting nucleic acid strands (2009)
Chitsaz, Hamidreza, Salari, Raheleh, Sahinalp, S. Cenk, Backofen, Rolf
Recent interests, such as RNA interference and antisense RNA regulation, strongly motivate the problem of predicting whether two nucleic acid strands interact. Motivation: Regulatory non-coding RNAs...
Optimal spaced seeds for faster approximate string matching (2008)
Martin Farach-Colton, Gad M. Landau, S. Cenk Sahinalp, Dekel Tsur
Filtering is a standard technique for fast approximate string matching in practice. In filtering, a quick first step is used to rule out almost all positions of a text as possible starting positions...
COMPARATIVE QSAR ANALYSIS OF BACTERIAL-, FUNGAL- PLANT- AND HUMAN METABOLITES. (2008)
Emre Karakoc, S. Cenk Sahinalp
Several QSAR models have been developed using a linear optimization approach that enabled distinguishing metabolic substances isolated from human-, bacterial-, plant- and fungal- cells. Seven binary...
Periodicity Testing with Sublinear Samples and Space (2008)
Funda Ergun, S. Muthukrishnan, S. Cenk Sahinalp
Abstract In this work, we are interested in finding representative trends in long large data streamsin the presence of computational constraints; to this end we present algorithms for discovering...
Daniel P. Miranker, Willard J. Briggs, Rui Mao, Shulin Ni, Weijia Xu, Arthur Kaufmann, ...
The Bulletin of the Technical Committee on Data Engineering is published quarterly and is distributed to all TC members. Its scope includes the design, implementation, modelling, theory and...
Emre Karakoc, Z. Meral Ozsoyoglu, Murat Tasan, Xiang Zhang, S. Cenk Sahinalp
In many biomolecular database applications involving string/sequence data, it is common to have similarity search in the form of near neighbor queries or nearest neighbor queries. The similarity...
Fereydoun Hormozdiari, Petra Berenbrink, S. Cenk Sahinalp
The (asymptotic) degree distributions of the best known “scale free ” network models are all similar and are independent of the seed graph used, hence it has been tempting to assume that networks...
Martin Farach-colton, Gad M. L, S. Cenk Sahinalp, Dekel Tsur
spaced seeds for faster approximate string matching
COMPARATIVE QSAR ANALYSIS OF BACTERIAL-, FUNGAL- PLANT- AND HUMAN METABOLITES. (2008)
Emre Karakoc, S. Cenk Sahinalp
Several QSAR models have been developed using a linear optimization approach that enabled distinguishing metabolic substances isolated from human-, bacterial-, plant- and fungal- cells. Seven binary...
Locally Consistent Parsing and Applications to (2008)
Approximate String Comparisons, S. Cenk Sahinalp
Locally consistent parsing (LCP) is a context sensitive partitioning method which achieves partition consistency in (almost) linear time. When iteratively applied, LCP followed by consistent block...
Improved Duplication Models (2008)
For Proteome Network, Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, ...
Protein-protein interaction networks, particularly that of the yeast S. Cerevisiae, have recently been studied extensively. These networks seem to satisfy the small world property and their (1-hop)...
Conifers have a unique small RNA silencing signature (2008)
Downloaded From, Elena V. Dolgosheina, Ryan D. Morin, Gozde Aksay, S. Cenk Sahinalp, Vincent Magrini, ...
Access the most recent version at doi: 10.1261/rna.1052008
The relation between indel length and functional divergence: a formal study (2008)
Raheleh Salari, Er Schönhuth, Fereydoun Hormozdiari, S. Cenk Sahinalp
Abstract. Although insertions and deletions (indels) are a common type of evolutionary sequence variation, their origins and their functional consequences have not been comprehensively understood....
Downloaded From, Ryan D. Morin, Gozde Aksay, Elena Dolgosheina, H. Alex, Er Ebhardt, ...
Comparative analysis of the small RNA transcriptomes of Pinus
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa (2008)
Morin, Ryan D., Aksay, Gozde, Dolgosheina, Elena, Ebhardt, H. Alexander, Magrini, Vincent, Mardis, Elaine R., ...
The diversity of microRNAs and small-interfering RNAs has been extensively explored within angiosperms by focusing on a few key organisms such as Oryza sativa and Arabidopsis thaliana. A deeper...
Conifers have a unique small RNA silencing signature (2008)
Dolgosheina, Elena V., Morin, Ryan D., Aksay, Gozde, Sahinalp, S. Cenk, Magrini, Vincent, Mardis, Elaine R., ...
Plants produce small RNAs to negatively regulate genes, viral nucleic acids, and repetitive elements at either the transcriptional or post-transcriptional level in a process that is referred to as...
Biomolecular network motif counting and discovery by color coding (2008)
Alon, Noga, Dao, Phuong, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Sahinalp, S. Cenk
Protein–protein interaction (PPI) networks of many organisms share global topological features such as degree distribution, k-hop reachability, betweenness and closeness. Yet, some of these...
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies (2008)
Hajirasouliha, Iman, Hormozdiari, Fereydoun, Sahinalp, S. Cenk, Birol, Inanc
New generation sequencing technologies offer unique opportunities and challenges for re-sequencing studies. In this article, we focus on re-sequencing experiments using the Solexa technology, based...
Cation Of Uniformly, S. Cenk Sahinalp, Evan Eichler, Paul Goldberg, Petra Berenbrink, Tom Friedetzky, ...
Given a long string of characters from a constant size (w.l.o.g. binary) alphabet we present an algorithm to determine whether its characters have been generated by a single i.i.d. random source....
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data (2007)
Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, S. Cenk Sahinalp, Evan E. Eichler
The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5% of sequence generated as part of primate genome sequencing projects consists of this material, which is...
taveRNA: a web suite for RNA algorithms and applications (2007)
Aksay, Cagri, Salari, Raheleh, Karakoc, Emre, Alkan, Can, Sahinalp, S. Cenk
We present taveRNA, a web server package that hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is a new alternative for RNA secondary structure prediction. It is based on a dynamic...
Fereydoun Hormozdiari, Petra Berenbrink, Nataša Prulj, S. Cenk Sahinalp
The (asymptotic) degree distributions of the best-known “scale-free” network models are all similar and are independent of the seed graph used; hence, it has been tempting to assume that networks...
The intelligence in developing systems for molecular biology (2007)
A report on the 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, 6-10 August 2006.
Fereydoun Hormozdiari, Petra Berenbrink, S. Cenk Sahinalp
The (asymptotic) degree distributions of the best-known ‘‘scale-free’ ’ network models are all similar and are independent of the seed graph used; hence, it has been tempting to assume that...
Fereydoun Hormozdiari, Petra Berenbrink, S. Cenk Sahinalp
The (asymptotic) degree distributions of the best-known ‘‘scale-free’ ’ network models are all similar and are independent of the seed graph used; hence, it has been tempting to assume that...
RNA secondary structure prediction via energy density minimization (2006)
Can Alkan, Emre Karakoc, S. Cenk Sahinalp, Peter Unrau, H. Alex, Kaizhong Zhang, ...
Abstract. There is a resurgence of interest in RNA secondary structure prediction problem (a.k.a. the RNA folding problem) due to the discovery of many new families of non-coding RNAs with a variety...
RNA Secondary Structure Prediction via Energy Density Minimization (2006)
Can Alkan, Emre Karakoc, S. Cenk Sahinalp, Peter Unrau, H. Alexander Ebhardt, H. Alex, ...
There is a resurgence of interest in RNA secondary structure prediction problem (a.k.a. the RNA folding problem) due to the discovery of many new families of non-coding RNAs with a variety of...
Distance Based Algorithms for Small Biomolecule Classification (2006)
And Structural Similarity, Emre Karakoc, Artem Cherkasov, S. Cenk Sahinalp
Structural similarity search among small molecules is a standard tool used in molecular classification and insilico drug discovery. The effectiveness of this general approach depends on how well the...
Improved duplication models for proteome network evolution (2006)
Gürkan Bebek, Petra Berenbrink, Colin Cooper, Joseph H. Nadeau, S. Cenk Sahinalp
Abstract. Protein-protein interaction networks, particularly that of the yeast S. Cerevisiae, have recently been studied extensively. These networks seem to satisfy the small world property and their...
Comparative QSAR- and Fragments Distribution Analysis of Drugs (2006)
Emre Karakoc, S. Cenk Sahinalp, Artem Cherkasov
A number of binary QSAR models have been developed using methods of artificial neural networks, k-nearest neighbors, linear discriminative analysis, and multiple linear regression and have been...
Karakoc, Emre, Cherkasov, Artem, Sahinalp, S. Cenk
Motivation: Structural similarity search among small molecules is a standard tool used in molecular classification and in-silico drug discovery. The effectiveness of this general approach depends on...
Manipulating multiple sequence alignments via MaM and WebMaM. (2005)
Alkan, Can, T Z N, Eray, Buard, Jerome, Lethiec, Franck, Eichler, Evan E., Bailey, Jeffrey A., ...
MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned...
Manipulating multiple sequence alignments via MaM and (2005)
Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, ...
MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned...
Manipulating multiple sequence alignments via MaM and WebMaM (2005)
Alkan, Can, Tüzün, Eray, Buard, Jerome, Lethiec, Franck, Eichler, Evan E., Bailey, Jeffrey A., ...
MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned...
Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. (2003)
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Comparing sequences with segment rearrangements (2003)
Funda Ergun, S. Muthukrishnan, S. Cenk Sahinalp
Abstract. Computational genomics involves comparing sequences based on "similarity " for detecting evolutionary and functional relation-ships. Until very recently, available...
Comparing sequences with segment rearrangements (2003)
Funda Ergun, S. Muthukrishnan, S. Cenk Sahinalp
Center for Comp. Genomics, CWRU.
Distance based indexing for string proximity search (2003)
In many database applications involving string data, it is common to have near neighbor queries (asking for strings that are similar to a query string) or nearest neighbor queries (asking for strings...
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome (2003)
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Manipulating multiple sequence alignments via MaM and WebMaM
Alkan, Can, Tüzün, Eray, Buard, Jerome, Lethiec, Franck, Eichler, Evan E., Bailey, Jeffrey A., ...
MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned...
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Manipulating multiple sequence alignments via MaM and WebMaM
Alkan, Can, Tüzün, Eray, Buard, Jerome, Lethiec, Franck, Eichler, Evan E., Bailey, Jeffrey A., ...
MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned...
The intelligence in developing systems for molecular biology
A report on the 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, 6-10 August 2006.
Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution
Hormozdiari, Fereydoun, Berenbrink, Petra, Pržulj, Nataša, Sahinalp, S. Cenk
The (asymptotic) degree distributions of the best-known “scale-free” network models are all similar and are independent of the seed graph used; hence, it has been tempting to assume that networks...
taveRNA: a web suite for RNA algorithms and applications
Aksay, Cagri, Salari, Raheleh, Karakoc, Emre, Alkan, Can, Sahinalp, S. Cenk
We present taveRNA, a web server package that hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is a new alternative for RNA secondary structure prediction. It is based on a dynamic...
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
Alkan, Can, Ventura, Mario, Archidiacono, Nicoletta, Rocchi, Mariano, Sahinalp, S. Cenk, Eichler, Evan E
The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5% of sequence generated as part of primate genome sequencing projects consists of this material, which is...
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa
Morin, Ryan D., Aksay, Gozde, Dolgosheina, Elena, Ebhardt, H. Alexander, Magrini, Vincent, Mardis, Elaine R., ...
The diversity of microRNAs and small-interfering RNAs has been extensively explored within angiosperms by focusing on a few key organisms such as Oryza sativa and Arabidopsis thaliana. A deeper...
Conifers have a unique small RNA silencing signature
Dolgosheina, Elena V., Morin, Ryan D., Aksay, Gozde, Sahinalp, S. Cenk, Magrini, Vincent, Mardis, Elaine R., ...
Plants produce small RNAs to negatively regulate genes, viral nucleic acids, and repetitive elements at either the transcriptional or post-transcriptional level in a process that is referred to as...
smyRNA: A Novel Ab Initio ncRNA Gene Finder
Salari, Raheleh, Aksay, Cagri, Karakoc, Emre, Unrau, Peter J., Hajirasouliha, Iman, Sahinalp, S. Cenk
A partition function algorithm for interacting nucleic acid strands
Chitsaz, Hamidreza, Salari, Raheleh, Sahinalp, S. Cenk, Backofen, Rolf
Recent interests, such as RNA interference and antisense RNA regulation, strongly motivate the problem of predicting whether two nucleic acid strands interact.
Biomolecular network motif counting and discovery by color coding
Alon, Noga, Dao, Phuong, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Sahinalp, S. Cenk
Protein–protein interaction (PPI) networks of many organisms share global topological features such as degree distribution, k-hop reachability, betweenness and closeness. Yet, some of these...
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies
Hajirasouliha, Iman, Hormozdiari, Fereydoun, Sahinalp, S. Cenk, Birol, Inanc
New generation sequencing technologies offer unique opportunities and challenges for re-sequencing studies. In this article, we focus on re-sequencing experiments using the Solexa technology, based...