Hamidreza Chitsaz

According to our database, Hamidreza Chitsaz authored at least 30 papers between 2009 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2025

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., December, 2025

2021

BPPart: RNA-RNA Interaction Partition Function in the Absence of Entropy.

Ali Ebrahimpour Boroojeny, Sanjay V. Rajopadhye, Hamidreza Chitsaz

Proceedings of the 21st International Workshop on Algorithms in Bioinformatics, 2021

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

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

Proximal Stochastic AUC Maximization.

Majdi Khalid, Hamidreza Chitsaz, Indrakshi Ray

Proceedings of the 2020 International Joint Conference on Neural Networks, 2020

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

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

GTED: Graph Traversal Edit Distance.

Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz

Proceedings of the Research in Computational Molecular Biology, 2018

Scalable Nonlinear AUC Maximization Methods.

Majdi Khalid, Indrakshi Ray, Hamidreza Chitsaz

Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2018

2017

AUC Maximization with K-hyperplane.

Majdi Khalid, Indrakshi Ray, Hamidreza Chitsaz

CoRR, 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

Principal Variety Analysis.

Reza Iraji, Hamidreza Chitsaz

Proceedings of the 1st Annual Conference on Robot Learning, CoRL 2017, Mountain View, 2017

2016

Proceedings of the 1st International Workshop on Robot Learning and Planning (RLP 2016).

Nancy M. Amato, Charles Anderson, Gregory S. Chirikjian, Hamidreza Chitsaz, Vishnu R. Desaraju, Chinwe Ekenna, Kris K. Hauser, Geoffrey A. Hollinger, Reza Iraji, Minwoo Lee, Qianli Ma, Seth McCammon, Nathan Michael, Shawna L. Thomas, Diane Uwacu, Yan Yan

CoRR, 2016

Confidence-Weighted Bipartite Ranking.

Majdi Khalid, Indrakshi Ray, Hamidreza Chitsaz

Proceedings of the Advanced Data Mining and Applications - 12th International Conference, 2016

2015

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

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

CoRR, 2014

NuRA: Numerical Roadmap Algorithm.

Reza Iraji, Hamidreza Chitsaz

CoRR, 2014

ARYANA: Aligning Reads by Yet Another Approach.

Milad Gholami, Aryan Arbabi, Ali Sharifi-Zarchi, Hamidreza Chitsaz, Mehdi Sadeghi

BMC Bioinform., 2014

Exact Learning of RNA Energy Parameters from Structure.

Hamidreza Chitsaz, Mohammad Aminisharifabad

Proceedings of the Research in Computational Molecular Biology, 2014

NUROA: A numerical roadmap algorithm.

Reza Iraji, Hamidreza Chitsaz

Proceedings of the 53rd IEEE Conference on Decision and Control, 2014

2013

An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids.

Hamidreza Chitsaz, Elmirasadat Forouzmand, Gholamreza Haffari

J. Comput. Biol., 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

Distilled single-cell genome sequencing and <i>de novo</i> assembly for sparse microbial communities.

Zeinab Taghavi, Narjes S. Movahedi, Sorin Draghici, Hamidreza Chitsaz

Bioinform., 2013

The RNA Newton polytope and learnability of energy parameters.

Elmirasadat Forouzmand, Hamidreza Chitsaz

Bioinform., 2013

On Time-optimal Trajectories for a Car-like Robot with One Trailer.

Hamidreza Chitsaz

Proceedings of the SIAM Conference on Control and its Applications, 2013

2012

SEQuel: improving the accuracy of genome assemblies.

Roy Ronen, Christina Boucher, Hamidreza Chitsaz, Pavel A. Pevzner

Bioinform., 2012

De novo co-assembly of bacterial genomes from multiple single cells.

Narjes S. Movahedi, Elmirasadat Forouzmand, Hamidreza Chitsaz

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2010

Session Introduction.

Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009

A partition function algorithm for interacting nucleic acid strands.

Hamidreza Chitsaz, Raheleh Salari, Süleyman Cenk Sahinalp, Rolf Backofen

Bioinform., 2009

biRNA: Fast RNA-RNA Binding Sites Prediction.

Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp

Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009