Toward Turbo Decoding of RNA Secondary Structure. - Arif Ozgun Harmanci; Gaurav Sharma 001; David H. Mathews (ICASSP (1), 2007)

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. - Arif Ozgun Harmanci; Gaurav Sharma 001; David H. Mathews (BMC Bioinform., 2007)

Probabilistic structural alignment of RNA sequences. - Arif Ozgun Harmanci; Gaurav Sharma 001; David H. Mathews (ICASSP, 2008)

Joint stochastic sampling for RNA secondary structure prediction. - Arif Ozgun Harmanci; Gaurav Sharma 001; David H. Mathews (GENSiPS, 2009)

Iterative estimation of structures of multiple RNA homologs: Turbofold. - Gaurav Sharma 001; Arif Ozgun Harmanci; David H. Mathews (ICASSP, 2011)

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences. - Arif Ozgun Harmanci; Gaurav Sharma 001; David H. Mathews (BMC Bioinform., 2011)

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. - Lukas Habegger; Suganthi Balasubramanian; David Z. Chen; Ekta Khurana; Andrea Sboner; Arif Ozgun Harmanci; Joel S. Rozowsky; Declan Clarke; Michael Snyder 001; Mark Gerstein (Bioinform., 2012)

Session Introduction. - Gamze Gürsoy; Arif Ozgun Harmanci; Haixu Tang; Erman Ayday; Steven E. Brenner (PSB, 2019)

Detecting and Annotating Rare Variants. - Jieming Chen; Akdes Serin Harmanci; Arif Ozgun Harmanci (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements. - Arif Ozgun Harmanci; Akdes Serin Harmanci; Jyothishmathi Swaminathan; Vidya Gopalakrishnan (Bioinform., 2020)

SCOR: A secure international informatics infrastructure to investigate COVID-19. - 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 016; Assaf Gottlieb; Arif Ozgun Harmanci; et al. (J. Am. Medical Informatics Assoc., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - 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; et al. (Nat., 2020)

SVAT: Secure outsourcing of variant annotation and genotype aggregation. - Miran Kim; Su Wang; Xiaoqian Jiang; Arif Ozgun Harmanci (BMC Bioinform., 2022)

Evaluation of vicinity-based hidden Markov models for genotype imputation. - Su Wang; Miran Kim; Xiaoqian Jiang; Arif Ozgun Harmanci (BMC Bioinform., 2022)

The evolving privacy and security concerns for genomic data analysis and sharing as observed from the iDASH competition. - Tsung-Ting Kuo; Xiaoqian Jiang; Haixu Tang; XiaoFeng Wang 001; Arif Ozgun Harmanci; Miran Kim; Kai W. Post; Diyue Bu; Tyler Bath; Jihoon Kim 001; Weijie Liu 004; Hongbo Chen; et al. (J. Am. Medical Informatics Assoc., 2022)

Privacy-aware estimation of relatedness in admixed populations. - Su Wang; Miran Kim; Wentao Li; Xiaoqian Jiang; Han Chen; Arif Ozgun Harmanci (Briefings Bioinform., 2022)

FedGMMAT: Federated generalized linear mixed model association tests. - Wentao Li; Han Chen; Xiaoqian Jiang; Arif Ozgun Harmanci (PLoS Comput. Biol., 2024)

FSLearning: An Efficient Federated Split Learning Framework for Privacy-Preserving Disease Prediction. - Bin Li; Xiaoqian Jiang; Yu-Chun Hsu; Arif Ozgun Harmanci; Hongchang Gao; Xinghua Shi (AIME (1), 2025)