PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes von Yu, Nancy Y., Wagner, James R., Laird, Matthew R., Melli, Gabor, Rey, Sébastien, Lo, Raymond, Dao, Phuong, Sahinalp, S. Cenk, Ester, Martin, Foster, Leonard J., Brinkman, Fiona S. L.

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Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data von Malikic, Salem, Jahn, Katharina, Kuipers, Jack, Sahinalp, S. Cenk, Beerenwinkel, Niko

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SCALCE: boosting sequence compression algorithms using locally consistent encoding von HACH, Faraz, NUMANAGIC, Ibrahim, ALKAN, Can, CENK SAHINALP, S

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Clonality inference in multiple tumor samples using phylogeny von Malikic, Salem, McPherson, Andrew W, Donmez, Nilgun, Sahinalp, Cenk S

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Sketching algorithms for genomic data analysis and querying in a secure enclave von Kockan, Can, Zhu, Kaiyuan, Dokmai, Natnatee, Karpov, Nikolai, Kulekci, M. Oguzhan, Woodruff, David P., Sahinalp, S. Cenk

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lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data von Haghshenas, Ehsan, Sahinalp, S Cenk, Hach, Faraz

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Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes von Hormozdiari, Fereydoun, Alkan, Can, Eichler, Evan E, Sahinalp, S Cenk

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CoLoRMap: Correcting Long Reads by Mapping short reads von Haghshenas, Ehsan, Hach, Faraz, Sahinalp, S Cenk, Chauve, Cedric

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Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes von Numanagić, Ibrahim, Malikić, Salem, Ford, Michael, Qin, Xiang, Toji, Lorraine, Radovich, Milan, Skaar, Todd C., Pratt, Victoria M., Berger, Bonnie, Scherer, Steve, Sahinalp, S. Cenk

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mrsFAST: a cache-oblivious algorithm for short-read mapping von Hach, Faraz, Hormozdiari, Fereydoun, Alkan, Can, Hormozdiari, Farhad, Birol, Inanc, Eichler, Evan E, Sahinalp, S Cenk

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Personalized copy number and segmental duplication maps using next-generation sequencing von Alkan, Can, Kidd, Jeffrey M, Marques-Bonet, Tomas, Aksay, Gozde, Antonacci, Francesca, Hormozdiari, Fereydoun, Kitzman, Jacob O, Baker, Carl, Malig, Maika, Mutlu, Onur, Sahinalp, S Cenk, Gibbs, Richard A, Eichler, Evan E

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HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology von Shrestha, Raunak, Hodzic, Ermin, Sauerwald, Thomas, Dao, Phuong, Wang, Kendric, Yeung, Jake, Anderson, Shawn, Vandin, Fabio, Haffari, Gholamreza, Collins, Colin C, Sahinalp, S Cenk

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Biomolecular network motif counting and discovery by color coding von Alon, Noga, Dao, Phuong, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Sahinalp, S. Cenk

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An efficient genotyper and star-allele caller for pharmacogenomics von Hari, Ananth, Zhou, Qinghui, Gonzaludo, Nina, Harting, John, Scott, Stuart A, Qin, Xiang, Scherer, Steve, Sahinalp, S Cenk, Numanagić, Ibrahim

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PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data von Malikic, Salem, Mehrabadi, Farid Rashidi, Ciccolella, Simone, Rahman, Md Khaledur, Ricketts, Camir, Haghshenas, Ehsan, Seidman, Daniel, Hach, Faraz, Hajirasouliha, Iman, Sahinalp, S Cenk

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Comparison of high-throughput sequencing data compression tools von Numanagić, Ibrahim, Bonfield, James K, Hach, Faraz, Voges, Jan, Ostermann, Jörn, Alberti, Claudio, Mattavelli, Marco, Sahinalp, S Cenk

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Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa von Morin, Ryan D, Aksay, Gozde, Dolgosheina, Elena, Ebhardt, H Alexander, Magrini, Vincent, Mardis, Elaine R, Sahinalp, S Cenk, Unrau, Peter J

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

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Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery von Hormozdiari, Fereydoun, Hajirasouliha, Iman, Dao, Phuong, Hach, Faraz, Yorukoglu, Deniz, Alkan, Can, Eichler, Evan E., Sahinalp, S. Cenk

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Tumor origin detection with tissue-specific miRNA and DNA methylation markers von Tang, Wei, Wan, Shixiang, Yang, Zhen, Teschendorff, Andrew E, Zou, Quan

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