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Arif Ozgun Harmanci

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2020 – today

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2024
[j11]
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  - journals/ploscb/LiCJH24
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Wentao Li, Han Chen, Xiaoqian Jiang, Arif Ozgun Harmanci:
FedGMMAT: Federated generalized linear mixed model association tests. PLoS Comput. Biol. 20(7): 1012142 (2024)
2022
[j10]
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Su Wang, Miran Kim, Wentao Li, Xiaoqian Jiang, Han Chen, Arif Ozgun Harmanci:
Privacy-aware estimation of relatedness in admixed populations. Briefings Bioinform. 23(6) (2022)
[j9]
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Su Wang, Miran Kim, Xiaoqian Jiang, Arif Ozgun Harmanci:
Evaluation of vicinity-based hidden Markov models for genotype imputation. BMC Bioinform. 23(1): 356 (2022)
[j8]
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Miran Kim, Su Wang, Xiaoqian Jiang, Arif Ozgun Harmanci:
SVAT: Secure outsourcing of variant annotation and genotype aggregation. BMC Bioinform. 23(1): 409 (2022)
[j7]
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Tsung-Ting Kuo, Xiaoqian Jiang, Haixu Tang, XiaoFeng Wang, Arif Ozgun Harmanci, Miran Kim, Kai W. Post, Diyue Bu, Tyler Bath, Jihoon Kim, Weijie Liu, Hongbo Chen, Lucila Ohno-Machado:
The evolving privacy and security concerns for genomic data analysis and sharing as observed from the iDASH competition. J. Am. Medical Informatics Assoc. 29(12): 2182-2190 (2022)
2020
[j6]
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  - journals/bioinformatics/HarmanciHSG20
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Arif Ozgun Harmanci, Akdes Serin Harmanci, Jyothishmathi Swaminathan, Vidya Gopalakrishnan:
EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements. Bioinform. 36(4): 1014-1021 (2020)
[j5]
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  - journals/jamia/RaisaroMTBBMBWB20
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Jean Louis Raisaro, Francesco Marino, Juan Ramón Troncoso-Pastoriza, Raphaelle Beau-Lejdstrom, Riccardo Bellazzi, Robert Murphy, Elmer V. Bernstam, Henry Wang, Mauro Bucalo, Yong Chen, Assaf Gottlieb, Arif Ozgun Harmanci, Miran Kim, Yejin Kim, Jeffrey G. Klann, Catherine Klersy, Bradley A. Malin, Marie Méan, Fabian Prasser, Luigia Scudeller, Ali Torkamani, Julien Vaucher, Mamta Puppala, Stephen T. C. Wong, Milana Frenkel-Morgenstern, Hua Xu, Baba Maiyaki Musa, Abdulrazaq G. Habib, Trevor Cohen, Adam B. Wilcox, Hamisu M. Salihu, Heidi Sofia, Xiaoqian Jiang, Jean-Pierre Hubaux:
SCOR: A secure international informatics infrastructure to investigate COVID-19. J. Am. Medical Informatics Assoc. 27(11): 1721-1726 (2020)
[j4]
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  - journals/nature/RheinbayNAWSTHH20
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Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020)

2010 – 2019

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2019
[c5]
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  - conf/psb/GursoyHTAB19
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Gamze Gürsoy, Arif Ozgun Harmanci, Haixu Tang, Erman Ayday, Steven E. Brenner:
Session Introduction. PSB 2019: 386-390
[r1]
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Jieming Chen, Akdes Serin Harmanci, Arif Ozgun Harmanci:
Detecting and Annotating Rare Variants. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 388-399
2012
[j3]
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  - journals/bioinformatics/HabeggerBCKSHRCSG12
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Lukas Habegger, Suganthi Balasubramanian, David Z. Chen, Ekta Khurana, Andrea Sboner, Arif Ozgun Harmanci, Joel S. Rozowsky, Declan Clarke, Michael Snyder, Mark Gerstein:
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinform. 28(17): 2267-2269 (2012)
2011
[j2]
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  - journals/bmcbi/HarmanciSM11
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Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews:
TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences. BMC Bioinform. 12: 108 (2011)
[c4]
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  - conf/icassp/SharmaHM11
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Gaurav Sharma, Arif Ozgun Harmanci, David H. Mathews:
Iterative estimation of structures of multiple RNA homologs: Turbofold. ICASSP 2011: 529-532

2000 – 2009

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2009
[c3]
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  - conf/gensips/HarmanciSM09
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Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews:
Joint stochastic sampling for RNA secondary structure prediction. GENSiPS 2009: 1-4
2008
[c2]
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Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews:
Probabilistic structural alignment of RNA sequences. ICASSP 2008: 645-648
2007
[j1]
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Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews:
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinform. 8 (2007)
[c1]
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Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews:
Toward Turbo Decoding of RNA Secondary Structure. ICASSP (1) 2007: 365-368

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