The intelligence in developing systems for molecular biology

by Sahinalp, S Cenk
Published 2007

Sparsification of RNA structure prediction including pseudoknots

by Möhl, Mathias, Salari, Raheleh, Will, Sebastian, Backofen, Rolf, Sahinalp, S Cenk
Published 2010

Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution

by Hormozdiari, Fereydoun, Berenbrink, Petra, Pržulj, Nataša, Sahinalp, S. Cenk
Published 2007

taveRNA: a web suite for RNA algorithms and applications

by Aksay, Cagri, Salari, Raheleh, Karakoc, Emre, Alkan, Can, Sahinalp, S. Cenk
Published 2007

Manipulating multiple sequence alignments via MaM and WebMaM

by Alkan, Can, Tüzün, Eray, Buard, Jerome, Lethiec, Franck, Eichler, Evan E., Bailey, Jeffrey A., Sahinalp, S. Cenk
Published 2005

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

by Yorukoglu, Deniz, Hach, Faraz, Swanson, Lucas, Collins, Colin C., Birol, Inanc, Sahinalp, S. Cenk
Published 2012

Optimally discriminative subnetwork markers predict response to chemotherapy

by Dao, Phuong, Wang, Kendric, Collins, Colin, Ester, Martin, Lapuk, Anna, Sahinalp, S. Cenk
Published 2011

Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data

by Alkan, Can, Ventura, Mario, Archidiacono, Nicoletta, Rocchi, Mariano, Sahinalp, S. Cenk, Eichler, Evan E
Published 2007

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

by Numanagić, Ibrahim, Malikić, Salem, Pratt, Victoria M., Skaar, Todd C., Flockhart, David A., Sahinalp, S. Cenk
Published 2015

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

by Hach, Faraz, Sarrafi, Iman, Hormozdiari, Farhad, Alkan, Can, Eichler, Evan E., Sahinalp, S. Cenk
Published 2014

Robustness of Massively Parallel Sequencing Platforms

by Kavak, Pınar, Yüksel, Bayram, Aksu, Soner, Kulekci, M. Oguzhan, Güngör, Tunga, Hach, Faraz, Şahinalp, S. Cenk, Alkan, Can, Sağıroğlu, Mahmut Şamil
Published 2015

PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension

by Feng Chen, Chenghong Wang, Wenrui Dai, Xiaoqian Jiang, Noman Mohammed, Md Momin Al Aziz, Md Nazmus Sadat, Cenk Sahinalp, Kristin Lauter, Shuang Wang
Published 2017-07-01

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

by Alkan, Can, Kavak, Pinar, Somel, Mehmet, Gokcumen, Omer, Ugurlu, Serkan, Saygi, Ceren, Dal, Elif, Bugra, Kuyas, Güngör, Tunga, Sahinalp, S Cenk, Özören, Nesrin, Bekpen, Cemalettin
Published 2014

ReMixT: clone-specific genomic structure estimation in cancer

by Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp, Sohrab P. Shah
Published 2017-07-01

Barnacle: Detecting and characterizing tandem duplications and fusions in transcriptome assemblies

by Swanson, L., Robertson, G., Mungall, K., Butterfield, Y., Chiu, R., Corbett, R., Docking, T., Hogge, D., Jackman, S., Moore, R., Mungall, A., Nip, K., Parker, J., Qian, J., Raymond, A., Sung, S., Tam, A., Thiessen, N., Varhol, Richard, Wang, S., Yorukoglu, D., Zhao, Y., Hoodless, P., Sahinalp, S., Karsan, A., Birol, I.
Published 2013

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

by McPherson, Andrew, Hormozdiari, Fereydoun, Zayed, Abdalnasser, Giuliany, Ryan, Ha, Gavin, Sun, Mark G. F., Griffith, Malachi, Heravi Moussavi, Alireza, Senz, Janine, Melnyk, Nataliya, Pacheco, Marina, Marra, Marco A., Hirst, Martin, Nielsen, Torsten O., Sahinalp, S. Cenk, Huntsman, David, Shah, Sohrab P.
Published 2011

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

by Swanson, Lucas, Robertson, Gordon, Mungall, Karen L, Butterfield, Yaron S, Chiu, Readman, Corbett, Richard D, Docking, T Roderick, Hogge, Donna, Jackman, Shaun D, Moore, Richard A, Mungall, Andrew J, Nip, Ka Ming, Parker, Jeremy DK, Qian, Jenny Qing, Raymond, Anthony, Sung, Sandy, Tam, Angela, Thiessen, Nina, Varhol, Richard, Wang, Sherry, Yorukoglu, Deniz, Zhao, YongJun, Hoodless, Pamela A, Sahinalp, S Cenk, Karsan, Aly, Birol, Inanc
Published 2013

The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression

by Niknafs, Yashar S., Han, Sumin, Ma, Teng, Speers, Corey, Zhang, Chao, Wilder-Romans, Kari, Iyer, Matthew K., Pitchiaya, Sethuramasundaram, Malik, Rohit, Hosono, Yasuyuki, Prensner, John R., Poliakov, Anton, Singhal, Udit, Xiao, Lanbo, Kregel, Steven, Siebenaler, Ronald F., Zhao, Shuang G., Uhl, Michael, Gawronski, Alexander, Hayes, Daniel F., Pierce, Lori J., Cao, Xuhong, Collins, Colin, Backofen, Rolf, Sahinalp, Cenk S., Rae, James M., Chinnaiyan, Arul M., Feng, Felix Y.
Published 2016