2026
GenCore: Genomic distance estimation using Locally Consistent Parsing

bioRxiv, 2026.01. 10.698768, 2026

2025
Wakhan: reconstruction of chromosome-scale copy number profiles of tumor genomes with long-read sequencing

medRxiv, 2025.12. 11.25342098, 2025

72. Long-read sequencing of mouse melanoma subclones reveals multifaceted and parallel tumor progression

Cancer Genetics 298, S32-S33, 2025

71. Improved tumor profiling and diagnosis via long-read variant detection toolkit

Cancer Genetics 298, S32, 2025

Secure phasing of private genomes in a trusted execution environment with TX-Phase

Genome Research 35 (12), 2626-2636, 2025

LCPan: efficient variation graph construction using Locally Consistent Parsing

arXiv preprint arXiv:2511.12205, 2025

Genotyping using high throughput sequencing data

US Patent App. 19/272,343, 2025

MAP2K1 and MAP2K2 genes alterations in hairy cell leukemia and hairy cell leukemia variant.

Blood 146, 3532, 2025

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories

bioRxiv, 2025

Genotyping of selected germline adaptive immune system loci using short-read sequencing data

Genome Research 35 (9), 2076-2086, 2025

Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer

Bioinformatics 41 (Supplement_1), i150–i159, 2025

A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data

International Conference on Research in Computational Molecular Biology, 409-413, 2025

TX-Phase: Secure Phasing of Private Genomes in a Trusted Execution Environment

International Conference on Research in Computational Molecular Biology, 325-329, 2025

Non-V600E BRAF mutations and treatment for hairy cell leukemia

Blood 145 (17), 1957-1961, 2025

Elucidating developmental methylation programs and cell type compositions in glioblastoma using combinatorial optimization

Cancer Research 85 (8_Supplement_1), 2494-2494, 2025

Severus: A tool for detecting and characterizing complex structural variants in cancer using long-read sequencing

Cancer Research 85 (8_Supplement_1), 2848-2848, 2025

Nanopore sequencing of single-cell derived sublines provides insights into melanoma heterogeneity and evolution

Cancer Research 85 (8_Supplement_1), 7497-7497, 2025

Integrating structural variants and single nucleotide variants to uncover evolutionary trajectories in melanoma

Cancer Research 85 (8_Supplement_1), 3898-3898, 2025

Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing

Nature Biotechnology, 1-11, 2025

Learning-augmented sketching offers improved performance for privacy preserving and secure GWAS

iScience 28 (3), 2025

Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones

Cell Systems 16 (1), 2025

Improved Algorithms for Bi-Partition Function Computation

25th International Conference on Algorithms for Bioinformatics (WABI 2025 …, 2025

Characterization of MAIT cells in glioblastoma reveals a potential immunosuppressive role through a MAIT-neutrophil axis

Neuro-Oncology Advances 7 (1), vdaf173, 2025

2024
Geny: a genotyping tool for allelic decomposition of killer cell immunoglobulin-like receptor genes

Frontiers in Immunology 15, 1494995, 2024

Non-V600E BRAF Gene Alterations in Hairy Cell Leukemia

Blood 144, 1586, 2024

Biologically-informed killer cell immunoglobulin-like receptor gene annotation tool

Bioinformatics 40 (11), btae622, 2024

Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes

Science advances 10 (27), eadj7402, 2024

How has the AI boom impacted algorithmic biology?

Cell Systems 15 (6), 483-487, 2024

Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History

International Conference on Research in Computational Molecular Biology, 438-443, 2024

Balanced molecular feature selection unveils universally tumor-lineage informative methylation sites in colorectal cancer

Cancer Research 84 (6_Supplement), 1615-1615, 2024

Structural variant dynamics in melanoma: Unraveling tumor heterogeneity and evolution

Cancer Research 84 (6_Supplement), 6924-6924, 2024

Melanoma clonal subline analysis reveals genetic factors driving intra-tumor heterogeneity

Cancer Research 84 (6_Supplement), 7407-7407, 2024

2023
Computational pharmacogenotype extraction from clinical next-generation sequencing

Frontiers in Oncology 13, 1199741, 2023

Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models

Genome Research, gr. 277608.122, 2023

Author Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

nature genetics 55 (6), 1076-1076, 2023

Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms

bioRxiv, 2023.04. 03.535074, 2023

Single-cell methylation sequencing data reveals succinct metastatic migration histories and tumor progression models

Cancer Research 83 (7_Supplement), 127-127, 2023

Author Correction: Pan-cancer analysis of whole genomes

Nature 614 (7948), E39-E39, 2023

Author Correction: The evolutionary history of 2,658 cancers

Nature 614 (7948), E42-E42, 2023

The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

Nature 614 (7948), E42-E42, 2023

An efficient genotyper and star-allele caller for pharmacogenomics

Genome Research, 2023

2022
Pathway and network analysis of more than 2500 whole cancer genomes (vol 11, 729, 2020)

NATURE COMMUNICATIONS 13 (1), 2022

Big data in basic and translational cancer research

Nature Reviews Cancer 22 (11), 625-639, 2022

ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data

Cell systems 13 (10), 808-816. e5, 2022

Fast intratumor heterogeneity inference from single-cell sequencing data

Nature computational science 2 (9), 577-583, 2022

Analytical validation of a computational method for pharmacogenetic genotyping from clinical whole exome sequencing

The Journal of Molecular Diagnostics 24 (6), 576-585, 2022

Immunotyper-sr: A novel computational approach for genotyping immunoglobulin heavy chain variable genes using short read data

International conference on research in computational molecular biology, 382-384, 2022

CYP2C8, CYP2C9, and CYP2C19 characterization using next-generation sequencing and haplotype analysis: a GeT-RM collaborative project

The Journal of Molecular Diagnostics 24 (4), 337-350, 2022

eP373: Analytical validation of a computational method for pharmacogenetic genotyping from clinical exome sequencing

Genetics in Medicine 24 (3), S234-S235, 2022

Strain Level Microbial Detection and Quantification with Applications to Single Cell Metagenomics

Nature Communications 13 (1), 1-13, 2022

2021
Privacy-preserving genotype imputation in a trusted execution environment

Cell systems 12 (10), 983-993. e7, 2021

Studying the history of tumor evolution from single-cell sequencing data by exploring the space of binary matrices

Journal of Computational Biology 28 (9), 857-879, 2021

Trisicell: Scalable Tumor Phylogeny Reconstruction and Validation Reveals Developmental Origin and Therapeutic Impact of Intratumoral Heterogeneity.

CANCER RESEARCH 81 (13), 2021

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

Cell 184 (8), 2239-2254. e39, 2021

Profiles of expressed mutations in single cells reveal subclonal expansion patterns and therapeutic impact of intratumor heterogeneity

bioRxiv, 2021.03. 26.437185, 2021

ANALYTICAL VALIDATION OF A COMPUTATIONAL METHOD, ALDY, FOR PHARMACOGENOMICS GENOTYPING FROM CLINICAL WHOLE EXOME SEQUENCING.

CLINICAL PHARMACOLOGY & THERAPEUTICS 109, S26-S26, 2021

Emerging topics in cancer evolution

PACIFIC SYMPOSIUM ON BIOCOMPUTING 2022, 397-401, 2021

Proteogenomic analysis unveils the HLA class I-presented immunopeptidome in melanoma and EGFR-mutant lung adenocarcinoma

Molecular & Cellular Proteomics 20, 100136, 2021

2020
Tumor phylogeny topology inference via deep learning

Iscience 23 (11), 2020

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Nature communications 11 (1), 4748, 2020

Sex differences in oncogenic mutational processes

Nature Publishing Group UK, 2020

Identification of conserved evolutionary trajectories in tumors

Bioinformatics 36 (Supplement_1), i427-i435, 2020

PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem

Bioinformatics 36 (Supplement_1), i169-i176, 2020

Genotyping using high throughput sequencing data

US Patent App. 16/615,089, 2020

Clonal evolution and heterogeneity of osimertinib acquired resistance mechanisms in EGFR mutant lung cancer

Cell reports medicine 1 (1), 2020

Genotyping and Copy Number Analysis of Immunoglobin Heavy Chain Variable Genes Using Long Reads

Iscience 23 (3), 100883, 2020

PyGTED: Python application for computing graph traversal edit distance

Journal of Computational Biology 27 (3), 436-439, 2020

Sketching algorithms for genomic data analysis and querying in a secure enclave

Nature Methods 17 (3), 295-301, 2020

Graph traversal edit distance and extensions

Journal of Computational Biology 27 (3), 317-329, 2020

Pan-cancer analysis of whole genomes

Nature 578 (7793), 82-93, 2020

The evolutionary history of 2,658 cancers

Nature 578 (7793), 122-128, 2020

Combined burden and functional impact tests for cancer driver discovery using DriverPower

Nature communications 11 (1), 734, 2020

Pathway and network analysis of more than 2500 whole cancer genomes

Nature communications 11 (1), 729, 2020

2019
PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data

Genome research 29 (11), 1860-1877, 2019

A multi-labeled tree dissimilarity measure for comparing “clonal trees” of tumor progression

Algorithms for Molecular Biology 14 (1), 17, 2019

Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data

Nature communications 10 (1), 1-12, 2019

Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA

Nucleic acids research 47 (7), e38-e38, 2019

Combinatorial detection of conserved alteration patterns for identifying cancer subnetworks

GigaScience 8 (4), giz024, 2019

The proteogenomic landscape of curable prostate cancer

Cancer Cell 35 (3), 414-427. e6, 2019

BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma

Genome medicine 11 (1), 8, 2019

Widespread and functional RNA circularization in localized prostate cancer

Cell 176 (4), 831-843. e22, 2019

Genomic Data Compression

Encyclopedia of Big Data Technologies, 783-783, 2019

Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave

RECOMB, Research in Computational Molecular Biology 23, 302-304, 2019

lordFAST: sensitive and fast alignment search tool for long noisy read sequencing data

Bioinformatics 35 (1), 20-27, 2019

2018
MechRNA: prediction of lncRNA mechanisms from RNA–RNA and RNA–protein interactions

Bioinformatics 34 (18), 3101-3110, 2018

Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data

IEEE Transactions on Knowledge and Data Engineering 30 (7), 1352-1365, 2018

Preface: Selected Articles from RECOMB 2017

Journal of Computational Biology 25 (7), 623-623, 2018

The evolutionary history of 2,658 cancers

Cancer Research 78 (13_Supplement), 218-218, 2018

Pervasive intra-tumour heterogeneity and subclonal selection across cancer types

Cancer Research 78 (13_Supplement), 3000-3000, 2018

Analysis of the androgen receptor–regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression

Nature genetics 50 (6), 814-824, 2018

The long noncoding RNA landscape of neuroendocrine prostate cancer and its clinical implications

Gigascience 7 (6), giy050, 2018

Computational identification of micro-structural variations and their proteogenomic consequences in cancer

Bioinformatics 34 (10), 1672-1681, 2018

Portraits of genetic intra-tumour heterogeneity and subclonal selection across cancer types

BioRxiv, 312041, 2018

GTED: Graph Traversal Edit Distance

RECOMB: International Conference on Research in Computational Molecular …, 2018

Stromal gene expression is predictive for metastatic primary prostate cancer

European urology 73 (4), 524-532, 2018

BAP1 Loss Predicts Therapeutic Vulnerability in Malignant Peritoneal Mesothelioma

Integrated Multi-omics Molecular Subtyping Predicts Therapeutic Vulnerability in Malignant Peritoneal Mesothelioma

bioRxiv, 243477, 2018

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

Nature communications 9 (1), 828, 2018

Optimal compressed representation of high throughput sequence data via light assembly

Nature communications 9 (1), 566, 2018

Genomic Data Compression

Encyclopedia of Big Data Technologies, 1-5, 2018

PCAWG Evolution, Heterogeneity Working Group, and PCAWG network

The evolutionary history of 2, 161562, 2018

Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data

RECOMB: Research in Computational Molecular Biology 22, 269-270, 2018

Protecting genomic data privacy with probabilistic modeling

BIOCOMPUTING 2019: Proceedings of the Pacific Symposium, 403-414, 2018

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