Genion, an accurate tool to detect gene fusion from long transcriptomics reads von Karaoglanoglu, Fatih, Chauve, Cedric, Hach, Faraz

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An androgen receptor switch underlies lineage infidelity in treatment-resistant prostate cancer von Davies, Alastair, Nouruzi, Shaghayegh, Ganguli, Dwaipayan, Namekawa, Takeshi, Thaper, Daksh, Linder, Simon, Karaoğlanoğlu, Fatih, Omur, Meltem E., Kim, Soojin, Kobelev, Maxim, Kumar, Sahil, Sivak, Olena, Bostock, Chiara, Bishop, Jennifer, Hoogstraat, Marlous, Talal, Amina, Stelloo, Suzan, van der Poel, Henk, Bergman, Andries M., Ahmed, Musaddeque, Fazli, Ladan, Huang, Haojie, Tilley, Wayne, Goodrich, David, Feng, Felix Y., Gleave, Martin, He, Housheng Hansen, Hach, Faraz, Zwart, Wilbert, Beltran, Himisha, Selth, Luke, Zoubeidi, Amina

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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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Fast characterization of segmental duplications in genome assemblies von Numanagić, Ibrahim, Gökkaya, Alim S, Zhang, Lillian, Berger, Bonnie, Alkan, Can, Hach, Faraz

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

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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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HASLR: Fast Hybrid Assembly of Long Reads von Haghshenas, Ehsan, Asghari, Hossein, Stoye, Jens, Chauve, Cedric, Hach, Faraz

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Decoding the epigenetics and chromatin loop dynamics of androgen receptor-mediated transcription von Altıntaş, Umut Berkay, Seo, Ji-Heui, Giambartolomei, Claudia, Ozturan, Dogancan, Fortunato, Brad J., Nelson, Geoffrey M., Goldman, Seth R., Adelman, Karen, Hach, Faraz, Freedman, Matthew L., Lack, Nathan A.

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Fast characterization of segmental duplication structure in multiple genome assemblies von Išerić, Hamza, Alkan, Can, Hach, Faraz, Numanagić, Ibrahim

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Discovery and genotyping of novel sequence insertions in many sequenced individuals von Kavak, Pinar, Lin, Yen-Yi, Numanagic, Ibrahim, Asghari, Hossein, Güngör, Tunga, Alkan, Can, Hach, Faraz

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BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma von Shrestha, Raunak, Nabavi, Noushin, Lin, Yen-Yi, Mo, Fan, Anderson, Shawn, Volik, Stanislav, Adomat, Hans H, Lin, Dong, Xue, Hui, Dong, Xin, Shukin, Robert, Bell, Robert H, McConeghy, Brian, Haegert, Anne, Brahmbhatt, Sonal, Li, Estelle, Oo, Htoo Zarni, Hurtado-Coll, Antonio, Fazli, Ladan, Zhou, Joshua, McConnell, Yarrow, McCart, Andrea, Lowy, Andrew, Morin, Gregg B, Chen, Tianhui, Daugaard, Mads, Sahinalp, S Cenk, Hach, Faraz, Le Bihan, Stephane, Gleave, Martin E, Wang, Yuzhuo, Churg, Andrew, Collins, Colin C

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Functional mapping of androgen receptor enhancer activity von Huang, Chia-Chi Flora, Lingadahalli, Shreyas, Morova, Tunc, Ozturan, Dogancan, Hu, Eugene, Yu, Ivan Pak Lok, Linder, Simon, Hoogstraat, Marlous, Stelloo, Suzan, Sar, Funda, van der Poel, Henk, Altintas, Umut Berkay, Saffarzadeh, Mohammadali, Le Bihan, Stephane, McConeghy, Brian, Gokbayrak, Bengul, Feng, Felix Y., Gleave, Martin E., Bergman, Andries M., Collins, Colin, Hach, Faraz, Zwart, Wilbert, Emberly, Eldon, Lack, Nathan A.

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Identification of gene signature for treatment response to guide precision oncology in clear-cell renal cell carcinoma von D’Costa, Ninadh M., Cina, Davide, Shrestha, Raunak, Bell, Robert H., Lin, Yen-Yi, Asghari, Hossein, Monjaras-Avila, Cesar U., Kollmannsberger, Christian, Hach, Faraz, Chavez-Munoz, Claudia I., So, Alan I.

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Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments von Ebrahimi, Ghazal, Orabi, Baraa, Robinson, Meghan, Chauve, Cedric, Flannigan, Ryan, Hach, Faraz

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Alu repeat discovery and characterization within human genomes von Hormozdiari, Fereydoun, Alkan, Can, Ventura, Mario, Hajirasouliha, Iman, Malig, Maika, Hach, Faraz, Yorukoglu, Deniz, Dao, Phuong, Bakhshi, Marzieh, Sahinalp, S Cenk, Eichler, Evan E

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Mutational Analysis of Gene Fusions Predicts Novel MHC Class I-Restricted T-Cell Epitopes and Immune Signatures in a Subset of Prostate Cancer von Kalina, Jennifer L, Neilson, David S, Lin, Yen-Yi, Hamilton, Phineas T, Comber, Alexandra P, Loy, Emma M H, Sahinalp, S Cenk, Collins, Colin C, Hach, Faraz, Lum, Julian J

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Robustness of Massively Parallel Sequencing Platforms von Kavak, Pınar, Yüksel, Bayram, Aksu, Soner, Kulekci, M Oguzhan, Güngör, Tunga, Hach, Faraz, Şahinalp, S Cenk, Alkan, Can, Sağıroğlu, Mahmut Şamil

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Detecting high-scoring local alignments in pangenome graphs von Schulz, Tizian, Wittler, Roland, Rahmann, Sven, Hach, Faraz, Stoye, Jens

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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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