Süleyman Cenk Sahinalp

According to our database1, Süleyman Cenk Sahinalp authored at least 103 papers between 1994 and 2019.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of two.

Timeline

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PhD thesis 
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Bibliography

2019
Genomic Data Compression.
Proceedings of the Encyclopedia of Big Data Technologies., 2019

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data.
Bioinformatics, 2019

A multi-labeled tree dissimilarity measure for comparing "clonal trees" of tumor progression.
Algorithms for Molecular Biology, 2019

Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave.
Proceedings of the Research in Computational Molecular Biology, 2019

Protecting Genomic Data Privacy with Probabilistic Modeling.
Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019

2018
Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data.
IEEE Trans. Knowl. Data Eng., 2018

Preface: Selected Articles from RECOMB 2017.
Journal of Computational Biology, 2018

Computational identification of micro-structural variations and their proteogenomic consequences in cancer.
Bioinformatics, 2018

MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions.
Bioinformatics, 2018

A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression.
Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data.
Proceedings of the Research in Computational Molecular Biology, 2018

GTED: Graph Traversal Edit Distance.
Proceedings of the Research in Computational Molecular Biology, 2018

2017
SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA.
Bioinformatics, 2017

PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS.
Bioinformatics, 2017

2016
Edit Distance Under Block Operations.
Encyclopedia of Algorithms, 2016

CoLoRMap: Correcting Long Reads by Mapping short reads.
Bioinformatics, 2016

Clonality Inference from Single Tumor Samples Using Low Coverage Sequence Data.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

Enabling Privacy Preserving GWAS in Heterogeneous Human Populations.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015
Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data.
Bioinformatics, 2015

Clonality inference in multiple tumor samples using phylogeny.
Bioinformatics, 2015

Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples.
Proceedings of the Research in Computational Molecular Biology, 2015

2014
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.
Nucleic Acids Research, 2014

ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.
Bioinformatics, 2014

HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time.
Proceedings of the Research in Computational Molecular Biology, 2014

2012
Dissect: detection and characterization of novel structural alterations in transcribed sequences.
Bioinformatics, 2012

Sensitive and fast mapping of di-base encoded reads.
Bioinformatics, 2012

Mirroring co-evolving trees in the light of their topologies.
Bioinformatics, 2012

SCALCE: boosting sequence compression algorithms using locally consistent encoding.
Bioinformatics, 2012

CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population.
Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing.
Proceedings of the Research in Computational Molecular Biology, 2012

2011
deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data.
PLoS Computational Biology, 2011

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.
Bioinformatics, 2011

Sensitive and fast mapping of di-base encoded reads.
Bioinformatics, 2011

Optimally discriminative subnetwork markers predict response to chemotherapy.
Bioinformatics [ISMB/ECCB], 2011

Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes.
Proceedings of the Research in Computational Molecular Biology, 2011

2010
Periodicity testing with sublinear samples and space.
ACM Trans. Algorithms, 2010

Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set.
Journal of Chemical Information and Modeling, 2010

Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length.
Journal of Computational Biology, 2010

Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets.
Journal of Computational Biology, 2010

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
Bioinformatics, 2010

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.
Bioinformatics [ISMB], 2010

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.
Bioinformatics, 2010

Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties.
Proceedings of the Algorithms in Bioinformatics, 10th International Workshop, 2010

Sparsification of RNA Structure Prediction Including Pseudoknots.
Proceedings of the Algorithms in Bioinformatics, 10th International Workshop, 2010

Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding.
Proceedings of the Research in Computational Molecular Biology, 2010

Session Introduction.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Session Introduction.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009
The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study.
Journal of Computational Biology, 2009

A partition function algorithm for interacting nucleic acid strands.
Bioinformatics, 2009

Fast Prediction of RNA-RNA Interaction.
Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks.
Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

biRNA: Fast RNA-RNA Binding Sites Prediction.
Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes.
Proceedings of the Research in Computational Molecular Biology, 2009

Dense Graphlet Statistics of Protein Interaction and Random Networks.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

2008
Edit Distance Under Block Operations.
Proceedings of the Encyclopedia of Algorithms - 2008 Edition, 2008

The Relation between Indel Length and Functional Divergence: A Formal Study.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

Biomolecular network motif counting and discovery by color coding.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

2007
Novel approaches for small biomolecule classification and structural similarity search.
SIGKDD Explorations, 2007

Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution.
PLoS Computational Biology, 2007

Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data.
PLoS Computational Biology, 2007

taveRNA: a web suite for RNA algorithms and applications.
Nucleic Acids Research, 2007

Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites.
Proceedings of the Biocomputing 2007, 2007

2006
Preface.
Theor. Comput. Sci., 2006

The degree distribution of the generalized duplication model.
Theor. Comput. Sci., 2006

Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds.
Journal of Chemical Information and Modeling, 2006

Oblivious string embeddings and edit distance approximations.
Proceedings of the Seventeenth Annual ACM-SIAM Symposium on Discrete Algorithms, 2006

Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation.
Proceedings of the Systems Biology and Computational Proteomics, 2006

RNA Secondary Structure Prediction Via Energy Density Minimization.
Proceedings of the Research in Computational Molecular Biology, 2006

Distance based algorithms for small biomolecule classification and structural similarity search.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005
Manipulating multiple sequence alignments via MaM and WebMaM.
Nucleic Acids Research, 2005

Improved Duplication Models for Proteome Network Evolution.
Proceedings of the Systems Biology and Regulatory Genomics, 2005

RNA-RNA Interaction Prediction and Antisense RNA Target Search.
Proceedings of the Research in Computational Molecular Biology, 2005

Optimal Spaced Seeds for Faster Approximate String Matching.
Proceedings of the Automata, Languages and Programming, 32nd International Colloquium, 2005

Locally Consistent Parsing and Applications to Approximate String Comparisons.
Proceedings of the Developments in Language Theory, 9th International Conference, 2005

2004
An efficient algorithm for sequence comparison with block reversals.
Theor. Comput. Sci., 2004

The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis.
Journal of Computational Biology, 2004

Identifying Uniformly Mutated Segments within Repeats.
J. Bioinformatics and Computational Biology, 2004

Novel Approaches to Biomolecular Sequence Indexing.
IEEE Data Eng. Bull., 2004

Sublinear Methods for Detecting Periodic Trends in Data Streams.
Proceedings of the LATIN 2004: Theoretical Informatics, 2004

Hardness of String Similarity Search and Other Indexing Problems.
Proceedings of the Automata, Languages and Programming: 31st International Colloquium, 2004

2003
Distance Based Indexing for String Proximity Search.
Proceedings of the 19th International Conference on Data Engineering, 2003

Comparing Sequences with Segment Rearrangements.
Proceedings of the FST TCS 2003: Foundations of Software Technology and Theoretical Computer Science, 2003

2002
An Improved Algorithm for Sequence Comparison with Block Reversals.
Proceedings of the LATIN 2002: Theoretical Informatics, 2002

Statistical Identification of Uniformly Mutated Segments within Repeats.
Proceedings of the Combinatorial Pattern Matching, 13th Annual Symposium, 2002

Simple and Practical Sequence Nearest Neighbors with Block Operations.
Proceedings of the Combinatorial Pattern Matching, 13th Annual Symposium, 2002

2001
Biased dictionaries with fast insert/deletes.
Proceedings of the Proceedings on 33rd Annual ACM Symposium on Theory of Computing, 2001

A Dynamic Lookup Scheme for Bursty Access Patterns.
Proceedings of the Proceedings IEEE INFOCOM 2001, 2001

Permutation Editing and Matching via Embeddings.
Proceedings of the Automata, Languages and Programming, 28th International Colloquium, 2001

Biased Skip Lists for Highly Skewed Access Patterns.
Proceedings of the Algorithm Engineering and Experimentation, Third International Workshop, 2001

2000
Approximate nearest neighbors and sequence comparison with block operations.
Proceedings of the Thirty-Second Annual ACM Symposium on Theory of Computing, 2000

Communication complexity of document exchange.
Proceedings of the Eleventh Annual ACM-SIAM Symposium on Discrete Algorithms, 2000

On the temporal HZY compression scheme.
Proceedings of the Eleventh Annual ACM-SIAM Symposium on Discrete Algorithms, 2000

1999
Compact Grid Layouts of Multi-Level Networks.
Proceedings of the Thirty-First Annual ACM Symposium on Theory of Computing, 1999

On the Optimality of Parsing in Dynamic Dictionary Based Data Compression.
Proceedings of the Tenth Annual ACM-SIAM Symposium on Discrete Algorithms, 1999

The Complexity of Gene Placement.
Proceedings of the Tenth Annual ACM-SIAM Symposium on Discrete Algorithms, 1999

The Effect of Flexible Parsing for Dynamic Dictionary Based Data Compression.
Proceedings of the Data Compression Conference, 1999

1998
Implementation and Experimental Evaluation of Flexible Parsing for Dynamic Dictionary Based Data Compression.
Proceedings of the Algorithm Engineering, 1998

Layout of the Batcher Bitonic Sorter (Extended Abstract).
Proceedings of the Tenth Annual ACM Symposium on Parallel Algorithms and Architectures, 1998

Augmenting Suffix Trees, with Applications.
Proceedings of the Algorithms, 1998

1996
Efficient Approximate and Dynamic Matching of Patterns Using a Labeling Paradigm (extended abstract).
Proceedings of the 37th Annual Symposium on Foundations of Computer Science, 1996

1994
Symmetry breaking for suffix tree construction.
Proceedings of the Twenty-Sixth Annual ACM Symposium on Theory of Computing, 1994

On a Parallel-Algorithms Method for String Matching Problems.
Proceedings of the Algorithms and Complexity, Second Italian Conference, 1994


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