Hamidreza Chitsaz

36 papers B 3C 3Misc 2Journal 24Unranked 4
YearRankTypeTitle / Venue / Authors
2025 J jnl
Aryana-bs: context-aware alignment of bisulfite-sequencing reads.
BMC Bioinform.
Hassan Nikaein, Ali Sharifi-Zarchi, Afsoon Afzal, Saeedeh Ezzati, Farzane Rasti, Hamidreza Chitsaz, Kunde Ramamoorthy Govindarajan
2021 C conf
BPPart: RNA-RNA Interaction Partition Function in the Absence of Entropy.
WABI
Ali Ebrahimpour Boroojeny, Sanjay V. Rajopadhye, Hamidreza Chitsaz
2020 J jnl
Graph Traversal Edit Distance and Extensions.
J. Comput. Biol.
Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz
2020 B conf
Proximal Stochastic AUC Maximization.
IJCNN
Majdi Khalid, Hamidreza Chitsaz, Indrakshi Ray
2020 J jnl
PyGTED: Python Application for Computing Graph Traversal Edit Distance.
J. Comput. Biol.
Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz
2018 J jnl
Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks.
CoRR
Farzad Abdolhosseini, Behrooz Azarkhalili, Abbas Maazallahi, Aryan Kamal, Seyed Abolfazl Motahari, Ali Sharifi-Zarchi, Hamidreza Chitsaz
2018 B conf
GTED: Graph Traversal Edit Distance.
RECOMB
Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz
2018 J jnl
Inferring Molecular Pathology and micro-RNA Transcriptome from mRNA Profiles of Cancer Biopsies through Deep Multi-Task Learning.
CoRR
Behrooz Azarkhalili, Ali Saberi, Hamidreza Chitsaz, Ali Sharifi-Zarchi
2018 — conf
Scalable Nonlinear AUC Maximization Methods.
ECML/PKDD (2)
Majdi Khalid, Indrakshi Ray, Hamidreza Chitsaz
2017 J jnl
AUC Maximization with K-hyperplane.
CoRR
Majdi Khalid, Indrakshi Ray, Hamidreza Chitsaz
2017 Misc conf
Principal Variety Analysis.
CoRL
Reza Iraji, Hamidreza Chitsaz
2017 J jnl
SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature.
J. Biomed. Semant.
Behrouz Bokharaeian, Alberto Díaz Esteban, Nasrin Taghizadeh, Hamidreza Chitsaz, Ramyar Chavoshinejad
2016 C conf
Confidence-Weighted Bipartite Ranking.
ADMA
Majdi Khalid, Indrakshi Ray, Hamidreza Chitsaz
2016 J jnl
Confidence-Weighted Bipartite Ranking.
CoRR
Majdi Khalid, Indrakshi Ray, Hamidreza Chitsaz
2016 J jnl
Proceedings of the 1st International Workshop on Robot Learning and Planning (RLP 2016).
CoRR
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
2015 J jnl
Exact Learning of RNA Energy Parameters From Structure.
J. Comput. Biol.
Hamidreza Chitsaz, Mohammad Aminisharifabad
2015 J jnl
Increased robustness of early embryogenesis through collective decision-making by key transcription factors.
BMC Syst. Biol.
Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkani, Hamid Pezeshk, Hamidreza Chitsaz, Mehdi Sadeghi
2014 J jnl
ARYANA: Aligning Reads by Yet Another Approach.
BMC Bioinform.
Milad Gholami, Aryan Arbabi, Ali Sharifi-Zarchi, Hamidreza Chitsaz, Mehdi Sadeghi
2014 B conf
Exact Learning of RNA Energy Parameters from Structure.
RECOMB
Hamidreza Chitsaz, Mohammad Aminisharifabad
2014 J jnl
HyDA-Vista: Towards Optimal Guided Selection of k-mer Size for Sequence Assembly.
CoRR
Seyed Basir Shariat Razavi, Narjes Sadat Movahedi Tabrizi, Hamidreza Chitsaz, Christina Boucher
2014 — conf
NUROA: A numerical roadmap algorithm.
CDC
Reza Iraji, Hamidreza Chitsaz
2014 J jnl
NuRA: Numerical Roadmap Algorithm.
CoRR
Reza Iraji, Hamidreza Chitsaz
2013 J jnl
An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids
CoRR
Hamidreza Chitsaz, Elmirasadat Forouzmand, Gholamreza Haffari
2013 J jnl
An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids.
J. Comput. Biol.
Hamidreza Chitsaz, Elmirasadat Forouzmand, Gholamreza Haffari
2013 J jnl
Distilled Single Cell Genome Sequencing and De Novo Assembly for Sparse Microbial Communities
CoRR
Zeinab Taghavi, Narjes S. Movahedi, Sorin Draghici, Hamidreza Chitsaz
2013 J jnl
Distilled single-cell genome sequencing and
Bioinform.
Zeinab Taghavi, Narjes S. Movahedi, Sorin Draghici, Hamidreza Chitsaz
2013 J jnl
Exact Learning of RNA Energy Parameters From Structure.
CoRR
Hamidreza Chitsaz, Mohammad Aminisharifabad
2013 J jnl
On Time-optimal Trajectories for a Car-like Robot with One Trailer
CoRR
Hamidreza Chitsaz
2013 — conf
On Time-optimal Trajectories for a Car-like Robot with One Trailer.
SIAM Conf. on Control and its Applications
Hamidreza Chitsaz
2013 J jnl
The RNA Newton Polytope and Learnability of Energy Parameters
CoRR
Elmirasadat Forouzmand, Hamidreza Chitsaz
2013 J jnl
The RNA Newton polytope and learnability of energy parameters.
Bioinform.
Elmirasadat Forouzmand, Hamidreza Chitsaz
2012 — conf
De novo co-assembly of bacterial genomes from multiple single cells.
BIBM
Narjes S. Movahedi, Elmirasadat Forouzmand, Hamidreza Chitsaz
2012 J jnl
SEQuel: improving the accuracy of genome assemblies.
Bioinform.
Roy Ronen, Christina Boucher, Hamidreza Chitsaz, Pavel A. Pevzner
2010 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler
2009 J jnl
A partition function algorithm for interacting nucleic acid strands.
Bioinform.
Hamidreza Chitsaz, Raheleh Salari, Süleyman Cenk Sahinalp, Rolf Backofen
2009 C conf
biRNA: Fast RNA-RNA Binding Sites Prediction.
WABI
Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp