2017
Mutational Analysis of Gene Fusions Predicts Novel MHC Class I-Restricted T cell Epitopes and Immune Signatures in a Subset of Prostate Cancer

Clin Cancer Res

PRESAGE - PRivacy-preserving gEnetic testing via SoftwAre Guard Extension

BMC Med Genomics

HIT'nDRIVE - Patient-specific multi-driver gene prioritization for precision oncology

Genome Research, July 18 2017.

ReMixT - clone-specific genomic structure estimation in cancer

Genome Biol, Jul 27 2017.

Stromal Gene Expression is Predictive for Metastatic Primary Prostate Cancer

Eur Urol, Mar 19 2017.

Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data

Journal of Computational Biology. June 2017, 24(6), 515-523.

SRRM4 Drives Neuroendocrine Transdifferentiation of Prostate Adenocarcinoma Under Androgen Receptor Pathway Inhibition

European Urology. 2017 Jan 31

Genomic Hallmarks of Localized, Non-Indolent Prostate Cancer

Nature. 2017 Jan 9

PRINCESS - Privacy-protecting Rare disease International Network Collaboration via Encryption through Software Guard extensionS

Bioinformatics. 2017 Jan 8

2016
Comparison of High-Throughput Sequencing Data Compression Tools

Nature Methods. 2016 Oct 24

The lncRNA Landscape of Breast Cancer Reveals a Role for DSCAM-AS1 in Breast Cancer Progression

Nature Communications. 2016 Sep 26

SiNVICT - Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA

Bioinformatics. 2016 Aug 16. pii, btw536

Enabling Privacy-Preserving GWAS in Heterogeneous Human Populations

Cell Systems. 2016 Jul 17

ICGC in the Cloud

Cancer Research. 2016 Jul 15

CoLoRMap - Correcting Long Reads by Mapping short reads

Bioinformatics. 2016 Sep 1;32(17),i545-i551

2015
Cypiripi - exact genotyping of CYP2D6 using high-throughput sequencing data

Bioinformatics. 2015 Jun 15;31(12),i27-34

Spatial genomic heterogeneity within localized, multifocal prostate cancer

Nature Genetics. 2015 May doi,10.1038/ng.3315

Clonality Inference in Multiple Tumor Samples using Phylogeny

Bioinformatics. 2015 May 1;31(9),1349-56

2014
Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa

BMC Genomics. 2014 Nov 7;15,963. doi, 10.1186/1471-2164-15-963

DeeZ - reference-based compression by local assembly

Nature Methods, 2014 Nov; 11(11),1082–4

mrsFAST-Ultra - a compact, SNP-aware mapper for high performance sequencing applications

Nucl. Acids Res. (1 July 2014) 42 (W1), W494-W500.

HIT’nDRIVE - Multi-driver Gene Prioritization Based on Hitting Time

Proc. of RECOMB 2014,293-306

2013
Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms

Bioinformatics. 2014 Mar 1;30(5),644-51

Barnacle - detecting and characterizing tandem duplications and fusions in transcriptome assemblies

BMC Genomics. 2013 Aug 14;14,550. doi, 10.1186/1471-2164-14-550.

2012
CLIIQ - Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population

Proc. of WABI 2012, 178-189

Dissect - detection and characterization of novel structural alterations in transcribed sequences

Bioinformatics. 2012 Jun 15;28(12),i179-87

From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer

J Pathol. 2012 Jul;227(3),286-97

The 1000 Genomes Project - data management and community access

Nat Methods. 2012 Apr 27;9(5),459-62

Mirroring co-evolving trees in the light of their topologies

Bioinformatics. 2012 May 1;28(9),1202-8

Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer

J Pathol. Volume 227, Issue 1, pages 53-61, May 2012

SCALCE - boosting Sequence Compression Algorithms using Locally Consistent Encoding

Bioinformatics (2012) 28 (23), 3051-3057.

nFuse - Discovery of complex genomic rearrangements in cancer using high-throughput sequencing

Genome Res. 2012. 22, 2250-2261

Poly-gene fusion transcripts and chromothripsis in prostate cancer

Genes Chromosomes Cancer. 2012 Dec;51(12),1144-53

2011
Simultaneous structural variation discovery among multiple paired-end sequenced genomes

Genome Res. 2011. 21, 2203-2212

Optimally Discriminative Subnetwork Markers Predict Response To Chemotherapy

Bioinformatics (2011) 27 (13), i205-i213

deFuse - An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

PLoS Comput Biol. 2011 May;7(5),e1001138. Epub 2011 May 19.

Sensitive and fast mapping of di-base encoded reads

Bioinformatics. 2011 Jul 15;27(14),1915-21.

Mapping copy number variation by population-scale genome sequencing

Nature. 2011 Feb 3;470(7332),59-65.

Comrad - a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data

Bioinformatics (2011) 27 (11), 1481-1488

Mapping the Protein Interaction Network in Methicillin-Resistant Staphylococcus aureus

J Proteome Res. 2011 Mar 4;10(3),1139-50

Alu repeat discovery and characterization within human genomes

Genome Res. 2011 Jun;21(6),840-9

2010
Sparsification of RNA structure prediction including pseudoknots

Algorithms Mol Biol. 2010 Dec 31;5(1),39.

Applicability Domains for Classification Problems - Benchmarking of Distance to Models for Ames Mutagenicity Set

J. Chem. Inf. Model., 2010, 50 (12), pp 2094–2111

A map of human genome variation from population-scale sequencing

Nature, 2010 Oct 28;467(7319),1061-73

Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties

Proc. of WABI 2010, 350-361

Sparsification of RNA Structure Prediction Including Pseudoknots

Proc. of WABI 2010, 40-51

mrsFAST - a cache-oblivious algorithm for short-read mapping

Nature Methods, 2010 Aug;7(8),576-7

Next Generation VariationHunter - Combinatorial Algorithms for Transposon Insertion Discovery

Bioinformatics 2010 Jun 15;26(12),i350-i357

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

Bioinformatics 2010 26(10),1277-1283

Periodicity testing with sublinear samples and space

ACM Transactions on Algorithms 6(2), (2010)

Protein protein interaction network evaluation for identifying potential drug targets

Journal of Computational Biology, 2010 May;17(5),669-84.

PSORTb 3.0 - improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

Bioinformatics 26(13), 1608-1615 (2010).

Time and space efficient RNA-RNA interaction prediction via sparse folding

Proc. of RECOMB 2010, 473-490

Towards improved assessment of functional similarity in large-scale screens - an indel study

Journal of Computational Biology, 2010 Jan;17(1),1-20.

2009
Personalized copy number and segmental duplication maps using next-generation sequencing

Nature Genetics,Oct, 41(10),1061-1067, 2009PubMed ID,

Quantifying systemic evolutionary changes by color coding confidence-sored PPI networks

Proc. of WABI 2009, 37-48

Fast prediction of RNA-RNA interaction

Algorithms for Molecular Biology 2010, 5,5

biRNA - Fast RNA-RNA Binding Sites Prediction

Proc. of WABI 2009, 25-36

Improved Small Molecule Activity Determination via Centroid Nearest Neighbors Classification

Proc. of LSS Comput Syst Bioinform Conf. August, 2009. Vol. 8, p. 251-262

smyRNA - A novel ab initio ncRNA gene finder

PLoS ONE 4(5), e5433, 2009.

A Partition Function Algorithm for Interacting Nucleic Acid Strands

Bioinformatics 25(12),i365-i373

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes

Genome Research, Jul, 19(7),1270-8, 2009.

Dense graphlet statistics of protein interaction networks and random networks

Proc. of Pac Symp Biocomput. 2009,178-89

2008
Edit distance under block operations

Encyclopedia of Algorithms 2008

The effect of insertion and deletions (indels) on wirings in protein interaction networks - a large scale study

Journal of Computational Biology, February 1, 2009, 16(2), 159-167

The relation between indel length and functional divergence - a formal study

WABI 2008, 330-341

Biomolecular Network Motif Counting and Discovery by Color Coding

Bioinformatics 2008 24, i241-i249

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies

Bioinformatics 2008 24, i32-i40

Conifers have a unique small RNA silencing signature

RNA 2008. 14, 1508-1515

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

Genome Res. 2008. 18, 571-584

Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis

J. Chem. Inf. Model., 2008, 48 (4), pp 766–784

2007
Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data

PLoS Comput Biol. 2007 Sep;3(9),1807-18.

Novel Approaches for Small Biomolecule Classification and Structural Similarity Search

ACM SIGKDD Explorations, Volume 9, Issue 1, pages 14-21, June 2007

Not all scale-free networks are born equal - The role of the seed graph in PPI network evolution

PLoS Computational Biology 3(7). July 2007,e118

taveRNA - a web suite for RNA algorithms and applications

Nucl. Acids Res. (2007) 35 (suppl 2), W325-W329

The intelligence in developing systems for molecular biology

Genome Biol. 2007;8(1),301

Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites

Proc. of Pacific Symposium on Biocomputing, 12,133-144, 2007

Relationship between insertion/deletion (indel) frequency of proteins and essentiality

BMC Bioinformatics 2007, 8,277

2006
RNA-RNA Interaction Prediction and Antisense RNA Target Search

J Comput Biol. 2006 Mar;13(2),267-82.

Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds

J. Chem. Inf. Model., 2006, 46 (5), pp 2167–2182

The Degree Distribution of the Generalized Duplication Model

Theor. Comput. Sci. 369(1-3), 239-249 (2006)

Distance Based Algorithms for Small Biomolecule Classification and Structural Similarity Search

Bioinformatics. 2006 Jul 15;22(14),e243-51

Not All Scale Free Networks are Born Equal - the Role of the Seed Graph in PPI Network Emulation

Proc. of Systems Biology and Computational Proteomics 2006, 1-13

RNA Secondary Structure Prediction via Energy Density Minimization

Proc. of RECOMB 2006, 130-142

String Embeddings and Edit Distance Approximations

Proc of SODA 2006, 792-801

2005
Manipulating Multiple Sequence Alignments via MaM and WebMaM

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue),W295-8.

Locally Consistent Parsing and Applications to Approximate String Comparisons

Proc. of Developments in Language Theory 2005, 22-35

Optimal Spaced Seeds for Faster Approximate String Matching

Proc. of ICALP 2005, 1251-1262

Improved Duplication Models for Proteome Network Evolution

Proc. of Systems Biology and Regulatory Genomics 2005, 119-137

RNA-RNA Interaction Prediction and Antisense RNA Target Search

Proc. of RECOMB 2005, 152-171

2004
The structure and evolution of centromeric transition regions within the human genome

Nature, 2004 Aug 19;430(7002),857-64, (2004)

Hardness of string similarity search and other indexing problems

Proc. of ICALP 2004, 1080-1098

Identifying uniformly mutated segments within repeats.

J Bioinform Comput Biol. 2004 Dec;2(4),657-68.

The Role of Unequal Crossover in Alpha-Satellite DNA Evolution - A Computational Analysis

Journal of Computational Biology 11(5), 933-944 (2004)

Novel approaches to Biomolecular Sequence Indexing

IEEE Data Eng. Bull. 27(3), 40-47 (2004)

Sublinear methods for detecting periodic trends in data streams

Proc. of LATIN 2004, 16-28

An Efficient Algorithm for Sequence Comparison with Block Reversals

Theor. Comput. Sci. 321(1), 95-101 (2004)

2003
Comparing Sequences with Segment Rearrangements

Proc. of FSTTCS 2003, 183-194

Distance Based Indexing for Sequence Proximity Search

Proc. of ICDE 2003, 125-136

Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome

Genome Res. 2003. 13, 358-368

2002
An algorithmic analysis of the role of unequal crossover in alpha satellite DNA evolution

Proc. of Genome Inform. 2002;13,93-102.

Statistical Identification of Uniformly Mutated Segments within Repeats

Proc. of CPM 2002, 249-261

Simple and Practical Sequence Nearest Neighbors Under Block Edit Operations

Proc. of CPM 2002, 262-278

An Improved Algorithm for Sequence Comparison with Block Reversals

Proc. of LATIN 2002, 319-325

Dictionary Based Data Compression

Handbook of Lossless Data Compression, K. Sayood (ed.), Academic Press, (2002).

2001
Divergent Origins and Concerted Expansion of Two Segmental Duplications on Chromosome 16

J Hered. 2001 Nov-Dec;92(6),462-8.

The Complexity of Gene Placement

J. Algorithms 41(2), 225-243 (2001)

The Effect of Flexible Parsing for Dynamic Dictionary-Based Data Compression

ACM Journal of Experimental Algorithmics 6, 10 (2001)

Biased Skip Lists for Highly Skewed Access Patterns

Proc. of ALENEX 2001, 216-230

Permutation editing and matching via embeddings

Proc. of ICALP 2001, 481-492

A Dynamic Lookup Scheme for Bursty Access Patterns

Proc. of INFOCOM 2001, 1444-1453

Biased Dictionaries with Fast Insert/ Deletes

Proc. of STOC 2001, 483-491

2000
On the temporal HZY data compression scheme

Proc. of SODA 2000, 185-186

Communication complexity of document exchange

Proc. of SODA 2000, 197-206

Robustness of Massively Parallel Sequencing Platforms

PLoS One. 2015 Sep 18

Approximate nearest neighbors and sequence comparison with block operations

Proc. of STOC 2000, 416-424

1999
Compact Grid Layouts of Multi-Level Networks

Proc. of STOC 1999, 455-463

The Effect of Flexible Parsing for Lempel-Ziv Dictionary Compression

Proc. of Data Compression Conference 1999, 238-246

On the Optimality of Parsing for Dynamic Dictionary Compression

Proc. of SODA 1999, 943-94

The Complexity of Gene Placement

Proc. of SODA 1999, 386-395

1998
Augmenting Suffix Trees with Applications

Proc. of ESA 1998, 67-78

Implementation and Experimental Evaluation of Flexible Parsing For Dynamic Dictionary Based Compression

Proc. of Algorithm Engineering

Layout of the Batcher Bitonic Sorter

Proc. of SPAA

1996
Performance Evaluation of Approximate Priority Queues

Presented at DIMACS Fifth Implementation Challenge, Priority Queues, Dictionaries, and Point Sets, Piscataway

Efficient Approximate and Dynamic Matching of Patterns Using a Labeling Paradigm

Proc. of FOCS

1994
Symmetry Breaking In Suffix Tree Construction

Proc. of STOC

On a parallel-algorithms method for string matching problems

Proc. of CIAC