Personalized copy number and segmental duplication maps using next-generation sequencing
Can Alkan, Jeffrey M. Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O. Kitzman, Carl Baker, Maika Malig, Onur Mutlu, S. Cenk Sahinalp, Richard A. Gibbs, Evan E. Eichler.
Nature Genetics,Oct, 41(10):1061-1067, 2009.

Towards improved assessment of functional similarity in large-scale screens: an indel study.
Alexander Schönhuth , Raheleh Salari, Fereydoun Hormozdiari, Artem Cherkasov, and S. Cenk Sahinalp.
Journal of Computational Biology 2009, to appear.

Quantifying systemic evolutionary changes by color coding confidence-sored PPI networks
Phuong Dao, Alexander Schönhuth, Fereydoun. Hormozdiari, Iman Hajirasouliha, S. Cenk Sahinalp, Martin Ester.
WABI'09 (The 9th Workshop on Algorithms in Bioinformatics), 2009

Fast RNA-RNA interaction prediction.
Raheleh Salari, Rolf Backofen, and S. Cenk Sahinalp.
WABI'09 (The 9th Workshop on Algorithms in Bioinformatics), 2009.
Also in Journal of Algorithm for Molecular Biology 2009. to appear.

biRNA: Fast RNA-RNA Binding Sites Prediction
Hamidreza Chitsaz, Rolf Backofen, S. Cenk Sahinalp
WABI'09 (The 9th Workshop on Algorithms in Bioinformatics), 2009.

Improved Small Molecule Activity Determination via Centroid Nearest Neighbors Classification
Phuong Dao, Farhad Hormozdiari, Hossein Jowhari, Kendall Byler, Artem Cherkasov, S.Cenk Sahinalp
CSB'09 (The 8th Annual Conference on Computational Systems Bioinformatics), 2009.

smyRNA: A novel ab initio ncRNA gene finder
Raheleh Salari, Cagri Aksay, Emre Karakoc, Peter Unrau, Iman Hajirasouliha, and S. Cenk Sahinalp
PLoS ONE 4(5): e5433. doi:10.1371/journal.pone.0005433, 2009.

A Partition Function Algorithm for Interacting Nucleic Acid Strands
Hamidreza Chitsaz, Raheleh Salari, S. Cenk Sahinalp, Rolf Backofen
17th Annual International Conference Intelligent Systems for Molecular Biology. (ISMB/ECCB 2009), Stockholm, Sweden.
Also: Bioinformatics 25(12):i365-i373; doi:10.1093/bioinformatics/btp212

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes
Fereydoun Hormozdiari, Can Alkan, Evan Eichler and S.Cenk Sahinalp.
Genome Research, Jul, 19(7):1270-8, 2009.
Also, International Conference on Research in Computational Molecular Biology (RECOMB 2009).

Dense graphlet statistics of protein interaction networks and random networks
Receb Colak, Fereydoun Hormozdiari, Flavia Moser, Alexander Schönhuth, Jeremy Holman, Martin Ester and S.Cenk Sahinalp.
Pacific Symposium on Biocomputing (PSB 2009).

Edit distance under block operations
S. Cenk Sahinalp.
Encyclopedia of Algorithms (Ming Yang Kao, ed.), Springer (2008).

The effect of insertion and deletions (indels) on wirings in protein interaction networks: a large scale study
Fereydoun Hormozdiari, Michael Hsing, Raheleh Salari, Alexander Schönhuth, S.Cenk Sahinalp and Artem Cherkasov.
RECOMB satellite conference on Systems Biology (2008).
Also: Journal of Computational Biology, February 1, 2009, 16(2): 159-167. doi:10.1089/cmb.2008.03TT.

The relation between indel length and functional divergence: a formal study
Raheleh Salari, Alexander Schönhuth, Fereydoun Hormozdiari, Artem Cherkasov and S. Cenk Sahinalp.
8th Workshop on Algorithms in Bioinformatics (WABI 2008), Universität Karlsruhe, Germany.

Biomolecular Network Motif Counting and Discovery by Color Coding
Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Cenk Sahinalp.
16th Annual International Conference Intelligent Systems for Molecular Biology. (ISMB 2008), Toronto, Canada.
Also: Bioinformatics 2008 24: i241-i249; doi:10.1093/bioinformatics/btn163

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies
Iman Hajirasouliha, Fereydoun Hormozdiari, Cenk Sahinalp, Inanc Birol.
16th Annual International Conference Intelligent Systems for Molecular Biology. (ISMB 2008), Toronto, Canada.
Also: Bioinformatics 2008 24: i32-i40; doi:10.1093/bioinformatics/btn173

Conifers have a unique small RNA silencing signature
Dolgosheina EV, Morin RD, Aksay G, Sahinalp SC, Magrini V, Mardis ER, Mattsson J, Unrau PJ.
RNA 2008 Jun 19.

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa
Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC, Unrau PJ.
Genome Res. 2008 Apr;18(4):571-84.

Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis
Zhu, H.; Tropsha, A.; Fourches, D.; Varnek, A.; Papa, E.; Gramatica, P.; O¨berg, T.; Dao, P.; Cherkasov, A.; Tetko, I. V.
J. Chem. Inf. Model; (Article); 2008; 48(4); 766-784. DOI:10.1021/ci700443v

Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data
Alkan C, Ventura M, Archidiacono N, Rocchi M, Sahinalp SC, Eichler EE.
PLoS Comput Biol. 2007 Sep;3(9):1807-18.

Novel Approaches for Small Biomolecule Classification and Structural Similarity Search
Emre Karakoc, Artem Cherkasov, S. Cenk Sahinalp.
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
Fereydoun Hormozdiari , Petra Berenbrink, Natasa Przulj, S. Cenk Sahinalp.
PLoS Computational Biology 3(7). July 2007:e118.doi:10.1371/journal.pcbi.0030118

taveRNA: a web suite for RNA algorithms and applications
Cagri Aksay, Raheleh Salari, Emre Karakoc, Can Alkan, S. Cenk Sahinalp.
Nucleic Acids Research , Web Server Issue, 2007

The intelligence in developing systems for molecular biology
S. Cenk Sahinalp.
Genome Biology, 8:301, 2007

Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites
Emre Karakoc, S. Cenk Sahinalp, Artem Cherkasov.
Pacific Symposium on Biocomputing, 12:133-144, 2007

Relationship between insertion/deletion (indel) frequency of proteins and essentiality
Simon K Chan, Michael Hsing, Fereydoun Hormozdiari and Artem Cherkasov.
BMC Bioinformatics, 8:277, 2007

Not All Scale Free Networks are Born Equal: the Role of the Seed Graph in PPI Network Emulation
Fereydoun Hormozdiari, Petra Berenbrink, Natasa Przulj, S. Cenk Sahinalp.
RECOMB Satellite Conference on Systems Biology, San Diego, CA, USA (2006).

Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds
Emre Karakoc, S. Cenk Sahinalp, Artem Cherkasov.
Journal of Chemical Information and Modelling, 2006 July 28 Issue.

Distance Based Algorithms for Small Biomolecule Classification and Structural Similarity Search
Emre Karakoc, Artem Cherkasov, S. Cenk Sahinalp.
ISMB'06, 14th Annual International conference on Intelligent Systems for Molecular Biology, Fortaleza, Brazil (2006). Also: Bioinformatics 22(14): e243-51, Jul 2006.

The Degree Distribution of the Generalized Duplication Model
G. Bebek, P. Berenbrink, C. Cooper, T. Friedetzky, J. H. Nadeau, S. C. Sahinalp.
Theoretical Computer Science, Volume 369, Issues 1-3, 15 December 2006, Pages 239-249.

RNA Secondary Structure Prediction via Energy Density Minimization
C. Alkan, E. Karakoc, C. Sahinalp, P. Unrau, A. Ebhardt, K. Zhang, J. Buhler.
RECOMB'06 Research in Computational Molecular Biology, Venice, Italy 2006.

String Embeddings and Edit Distance Approximations
Tugkan Batu, Funda Ergun, S. Cenk Sahinalp.
SODA'06, ACM-SIAM Symposium on Discrete Algorithms, Miami, Fl 2006.

RNA-RNA Interaction Prediction and Antisense RNA Target Search
C. Alkan, E. Karakoc, J. Nadeau, C. Sahinalp, K. Zhang.
Journal of Computational Biology, March 2006, Vol.13,No.2:267-283 2006.

Topological properties of proteome networks
G. Bebek, P. Berenbrink, C. Cooper, T. Friedetzky, J. Nadeau, S. Cenk Sahinalp.
RECOMB Satellite Conference on Systems Biology, LNBI 4023, San Diego, CA, USA 2005.

Approximate String Comparisions via Locally Consistent Parsing
Tugkan Batu, S. Cenk Sahinalp.
DLT'05, Symposium on Developments in Language Theory, (invited paper) Palermo, Italy 2005.

Manipulating Multiple Sequence Alignments via MaM and WebMaM
Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, S. Cenk Sahinalp.
Nucleic Acids Research 33, Web Server Issue, W295-8 (2005).

Optimal Spaced Seeds for Faster Approximate String Matching
M. Farach-Colton, G. Landau, S. Cenk Sahinalp, D. Tsur.
ICALP'05, Lisbon, Portugal (2005).

RNA-RNA Interaction Prediction and Antisense RNA Target Search
Can Alkan, Emre Karakoç, Joe Nadeau, S. Cenk Sahinalp, Kaizhong Zhang.
RECOMB'05, Research in Computational Molecular Biology, pp. 152-171, Cambridge, Ma. 2005.

The structure and evolution of centromeric transition regions within the human genome
She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W, Schwartz S, Eichler EE.
Nature, 2004 Aug 19;430(7002):857-64, (2004).

Hardness of string similarity search and other indexing problems
S. Cenk Sahinalp, Andrey Utis.
ICALP'04, Turku, Finland, (2004).

A New Sequence Comparison Method for Repeated Segment Identification
S. Cenk Sahinalp, E. Eichler, P. Goldberg, P. Berenbrink, T. Friedetzky, F. Ergün
Journal of Bioinformatics and Computational Biology, (2004).

The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis
C. Alkan, J. Bailey, E. Eichler, S.C. Sahinalp, E. Tüzün
Journal of Computational Biology , Oct 2004, Vol. 11, No. 5: 933-944 (2004).

Novel approaches to Biomolecular Sequence Indexing
E. Karakoç, M. Ozsoyoglu, S. Cenk Sahinalp, M. Tasan, X. Zhang.
IEEE Data Engineering Bulletin, special issue on biological sequences, pp 37-44 (2004).

Sublinear methods for detecting periodic trends in data streams
F. Ergun, S. Muthukrishnan, S. Cenk Sahinalp.
LATIN'04, Buenos Aires, Argentina (2004).

An Improved Algorithm for Sequence Comparison with Block Reversals
S. Muthukrishnan, S. Cenk Sahinalp.
Theoretical Computer Science -invited paper (2004).

Distance Based Indexing for Sequence Proximity Search
M. Tasan, J. Macker, M. Ozsoyoglu, S. Cenk Sahinalp.
ICDE'03, IEEE Data Engineering Conference, Banglore, India (2003).

Comparing Sequences with Segment Rearrangements
F. Ergün, S. Muthukrishnan, S. Cenk Sahinalp.
FSTTCS'03, Bombay, India (2003).

Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
G. Liu, S. Zhao, J. Bailey, S.C. Sahinalp, C. Alkan, E. Tüzün, E. Green, E. Eichler.
Genome Research (2003).

An algorithmic analysis of the role of unequal crossover in alpha satellite DNA evolution
C. Alkan, J. Bailey, E. Eichler, S.C. Sahinalp, E. Tüzün.
GIW'02, Genome Informatics Conference, 13, pp 93-102 (2002).

A New Sequence Comparison Method for Repeated Segment Identification
S. Cenk Sahinalp, E. Eichler, P. Goldberg, P. Berenbrink, T. Friedetzky, F. Ergün
CPM'02, Symposium on Combinatorial Pattern Matching, Fukuoka, Japan (2002).

Simple and Practical Sequence Nearest Neighbors Under Block Edit Operations
S. Muthukrishnan, S. Cenk Sahinalp.
CPM'02, Symposium on Combinatorial Pattern Matching, Fukuoka, Japan (2002).

An Improved Algorithm for Sequence Comparison with Block Reversals
S. Muthukrishnan, S. Cenk Sahinalp.
LATIN'02, Cancun, Mexico, (2002).

Dictionary Based Data Compression
N. Rajpoot, S. Cenk Sahinalp.
Handbook of Lossless Data Compression, K. Sayood (ed.), Academic Press, (2002).

MaM: Multiple Alignment Manipulator
C. Alkan, E. Tüzün, E. Eichler, J. Bailey, S.C. Sahinalp
RECOMB'02, Research in Computational Biology, (poster), Washington DC (2002).

Divergent Origins and Concerted Expansion of Two Segmental Duplications on Chromosome 16
E. Eichler, M.E. Johnson, C. Alkan, E. Tüzün, S.C. Sahinalp, L.Viggiano, M.Rocchi
Journal of Heredity 92, pp 462-468 (2001).

Complexity of Gene Placement
L. A. Goldberg, P.Goldberg, P.Pevzner, M. Paterson, S.C. Sahinalp, and Z. Sweedyk
Journal of Algorithms, 40 pp 1-19 (2001).

Permutation editing and matching via embeddings
G. Cormode, S. Muthukrishnan, S. Cenk Sahinalp.
ICALP'01, Crete, Greece, (2001).

Biased Dictionaries with Fast Insert/ Deletes
F. Ergun, S. Cenk Sahinalp, J. Sharp, R. Sinha.
STOC'01, ACM Symposium on Theory of Computing, Crete, Greece, (2001).

A Dynamic Lookup Scheme for Bursty Access Patterns
F. Ergun, S. Mitra, S. Cenk Sahinalp, J. Sharp, R. Sinha.
IEEE INFOCOM'01, Anchorage, AK, (2001).

Biased Skip Lists for Highly Skewed Access Patterns
F. Ergun, S. Cenk Sahinalp, J. Sharp, R. Sinha.
ALENEX'01, Workshop on Algorithm Engineering and Experiments, Washington DC, (2001).

Implementation and Performance Evaluation of Flexible Parsing For Dynamic Dictionary Based Compression
Y. Matias, N. Rajpoot, S. Cenk Sahinalp.
ACM Journal of Experimental Algorithmics -invited paper (2001).

Approximate nearest neighbors and sequence comparison with block operations
S. Muthukrishnan, S. Cenk Sahinalp.
STOC'2000, ACM Symposium on Theory of Computing, Portland, OR,(2000).

Communication complexity of document exchange
Graham Cormode, Michael S. Paterson, S. Cenk Sahinalp, Uzi Vishkin.
SODA'2000, ACM-SIAM Symposium on Discrete Algorithms, San Francisco, CA (2000).

On the temporal HZY data compression scheme
Zeev Cohen, Yossi Matias, S. Muthukrishan, S. Cenk Sahinalp, Jacob Ziv.
SODA'2000, ACM-SIAM Symposium on Discrete Algorithms (short paper), San Francisco, CA (2000).

The Effect of Flexible Parsing for Lempel-Ziv Dictionary Compression
Yossi Matias, Nasir Rajpoot, S. Cenk Sahinalp.
DCC'99, IEEE Data Compression Conference, Snowbird, UT, (1999).

On the Optimality of Parsing for Dynamic Dictionary Compression
Yossi Matias, S. Cenk Sahinalp.
SODA'99, ACM-SIAM Symposium on Discrete Algorithms, (short paper) Baltimore, MD, (1999).

Complexity of Gene Placement
L. A. Goldberg, P.Goldberg, P.Pevzner, M. Paterson, S.C. Sahinalp, and Z. Sweedyk
SODA'99, ACM-SIAM Symposium on Discrete Algorithms, Baltimore, Md, (1999).

Compact Grid Layouts of Multi-Level Networks
S. Muthukrishnan, Michael S. Paterson, S. Cenk Sahinalp, Torsten Suel.
STOC'99, ACM Symposium on Theory of Computing, Atlanta, GA, (1999).

Area Efficient Layout of Bitonic Sorting Network
Shimon Even, S. Muthukrishnan, Michael S. Paterson, S. Cenk Sahinalp.
SPAA'98, ACM Symposium on Parallel Algorithms and Architectures, Puerto Vallerta, Mexico, (1998).

Implementation and Performance Evaluation of Flexible Parsing For Dynamic Dictionary Based Compression
Y. Matias, N. Rajpoot, S. Cenk Sahinalp.
WAE'98, Workshop on Algorithm Engineering, Saarbrucken, Germany, (1998).

Augmenting Suffix Trees with Applications
Yossi Matias, S. Muthukrishnan, S. Cenk Sahinalp, Jacob Ziv.
ESA'98, European Symposium on Algorithms, Venice, Italy, (1998).

Performance Evaluation of Approximate Priority Queues
Y. Matias, S. Cenk Sahinalp, N. E. Young.
DIMACS Implementation Challenge Workshop, Piscataway, NJ, (1996).

Efficient Approximate and Dynamic Matching of Patterns Using a Labeling Paradigm
S. Cenk Sahinalp, Uzi Vishkin.
FOCS'96, IEEE Symposium on Foundations of Computer Science, Burlington, VT, (1996).

Symmetry Breaking In Suffix Tree Construction
S. Cenk Sahinalp, Uzi Vishkin.
STOC'94, ACM Symposium on Theory of Computing, Montreal, QC Canada, (1994).

On a parallel-algorithms method for string matching problems
S. Cenk Sahinalp, Uzi Vishkin.
CIAC'94, Second Italian Conference on Algorithms and Complexity, Rome, Italy (invited paper, 1994).