biRNA: Fast RNA-RNA Binding Sites Prediction. - Hamidreza Chitsaz; Rolf Backofen; Süleyman Cenk Sahinalp (WABI, 2009)

A partition function algorithm for interacting nucleic acid strands. - Hamidreza Chitsaz; Raheleh Salari; Süleyman Cenk Sahinalp; Rolf Backofen (Bioinform., 2009)

Session Introduction. - Rolf Backofen; Hamidreza Chitsaz; Ivo L. Hofacker; Süleyman Cenk Sahinalp; Peter F. Stadler (Pacific Symposium on Biocomputing, 2010)

De novo co-assembly of bacterial genomes from multiple single cells. - Narjes S. Movahedi; Elmirasadat Forouzmand; Hamidreza Chitsaz (BIBM, 2012)

SEQuel: improving the accuracy of genome assemblies. - Roy Ronen; Christina Boucher 001; Hamidreza Chitsaz; Pavel A. Pevzner (Bioinform., 2012)

On Time-optimal Trajectories for a Car-like Robot with One Trailer. - Hamidreza Chitsaz (SIAM Conf. on Control and its Applications, 2013)

The RNA Newton polytope and learnability of energy parameters. - Elmirasadat Forouzmand; Hamidreza Chitsaz (Bioinform., 2013)

Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities. - Zeinab Taghavi; Narjes S. Movahedi; Sorin Draghici; Hamidreza Chitsaz (Bioinform., 2013)

Distilled Single Cell Genome Sequencing and De Novo Assembly for Sparse Microbial Communities - Zeinab Taghavi; Narjes S. Movahedi; Sorin Draghici; Hamidreza Chitsaz (CoRR, 2013)

An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids. - Hamidreza Chitsaz; Elmirasadat Forouzmand; Gholamreza Haffari (J. Comput. Biol., 2013)

NUROA: A numerical roadmap algorithm. - Reza Iraji; Hamidreza Chitsaz (CDC, 2014)

ARYANA: Aligning Reads by Yet Another Approach. - Milad Gholami; Aryan Arbabi; Ali Sharifi-Zarchi; Hamidreza Chitsaz; Mehdi Sadeghi (BMC Bioinform., 2014)

NuRA: Numerical Roadmap Algorithm. - Reza Iraji; Hamidreza Chitsaz (CoRR, 2014)

HyDA-Vista: Towards Optimal Guided Selection of k-mer Size for Sequence Assembly. - Seyed Basir Shariat Razavi; Narjes Sadat Movahedi Tabrizi; Hamidreza Chitsaz; Christina Boucher 001 (CoRR, 2014)

Increased robustness of early embryogenesis through collective decision-making by key transcription factors. - Ali Sharifi-Zarchi; Mehdi Totonchi; Keynoush Khaloughi; Razieh Karamzadeh; Marcos J. Araúzo-Bravo; Hossein Baharvand; Ruzbeh Tusserkani; Hamid Pezeshk; Hamidreza Chitsaz; Mehdi Sadeghi (BMC Syst. Biol., 2015)

Exact Learning of RNA Energy Parameters From Structure. - Hamidreza Chitsaz; Mohammad Aminisharifabad (J. Comput. Biol., 2015)

Confidence-Weighted Bipartite Ranking. - Majdi Khalid; Indrakshi Ray; Hamidreza Chitsaz (ADMA, 2016)

Proceedings of the 1st International Workshop on Robot Learning and Planning (RLP 2016). - Nancy M. Amato; Charles Anderson 001; Gregory S. Chirikjian; Hamidreza Chitsaz; Vishnu R. Desaraju; Chinwe Ekenna; Kris K. Hauser; Geoffrey A. Hollinger; Reza Iraji; Minwoo Lee 001; Qianli Ma 002; Seth McCammon; et al. (CoRR, 2016)

Principal Variety Analysis. - Reza Iraji; Hamidreza Chitsaz (CoRL, 2017)

SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature. - Behrouz Bokharaeian; Alberto Díaz Esteban; Nasrin Taghizadeh; Hamidreza Chitsaz; Ramyar Chavoshinejad (J. Biomed. Semant., 2017)

AUC Maximization with K-hyperplane. - Majdi Khalid; Indrakshi Ray; Hamidreza Chitsaz (CoRR, 2017)

Scalable Nonlinear AUC Maximization Methods. - Majdi Khalid; Indrakshi Ray; Hamidreza Chitsaz (ECML/PKDD (2), 2018)

GTED: Graph Traversal Edit Distance. - Ali Ebrahimpour Boroojeny; Akash Shrestha; Ali Sharifi-Zarchi; Suzanne Renick Gallagher; Süleyman Cenk Sahinalp; Hamidreza Chitsaz (RECOMB, 2018)

Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks. - Farzad Abdolhosseini; Behrooz Azarkhalili; Abbas Maazallahi; Aryan Kamal; Seyed Abolfazl Motahari; Ali Sharifi-Zarchi; Hamidreza Chitsaz (CoRR, 2018)

Inferring Molecular Pathology and micro-RNA Transcriptome from mRNA Profiles of Cancer Biopsies through Deep Multi-Task Learning. - Behrooz Azarkhalili; Ali Saberi; Hamidreza Chitsaz; Ali Sharifi-Zarchi (CoRR, 2018)

Proximal Stochastic AUC Maximization. - Majdi Khalid; Hamidreza Chitsaz; Indrakshi Ray (IJCNN, 2020)

Graph Traversal Edit Distance and Extensions. - Ali Ebrahimpour Boroojeny; Akash Shrestha; Ali Sharifi-Zarchi; Suzanne Renick Gallagher; Süleyman Cenk Sahinalp; Hamidreza Chitsaz (J. Comput. Biol., 2020)

PyGTED: Python Application for Computing Graph Traversal Edit Distance. - Ali Ebrahimpour Boroojeny; Akash Shrestha; Ali Sharifi-Zarchi; Suzanne Renick Gallagher; Süleyman Cenk Sahinalp; Hamidreza Chitsaz (J. Comput. Biol., 2020)

BPPart: RNA-RNA Interaction Partition Function in the Absence of Entropy. - Ali Ebrahimpour Boroojeny; Sanjay V. Rajopadhye; Hamidreza Chitsaz (WABI, 2021)

Aryana-bs: context-aware alignment of bisulfite-sequencing reads. - Hassan Nikaein; Ali Sharifi-Zarchi; Afsoon Afzal; Saeedeh Ezzati; Farzane Rasti; Hamidreza Chitsaz; Kunde Ramamoorthy Govindarajan (BMC Bioinform., 2025)