Publications
	2022 Sharif Moradi, Aryan Kamal, Hamidreza Aboulkheyr Es, Farnoosh Farhadi, Marzieh Ebrahimi, Hamidreza Chitsaz, Ali Sharifi-Zarchi, Hossein Baharvand. Pan-cancer analysis of microRNA expression profiles highlights microRNAs enriched in normal body cells as effective suppressors of multiple tumor types: A study based on TCGA database, PLoS One, 2022 2021 Ali Ebrahimpour Boroojeny, Sanjay Rajopadhye, Hamidreza Chitsaz. BPPart: RNA-RNA Interaction Partition Function in the Absence of Entropy, WABI, 2021 2020 Majdi Khalid, Hamidreza Chitsaz, Indrakshi Ray. Proximal Stochastic AUC Maximization, International Joint Conference on Neural Networks (IJCNN), 2020 Ali Ebrahimpour Boroojeny, Sanjay Rajopadhye, Hamidreza Chitsaz. BPPart and BPMax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model, arXiv:1904.01235, 2020 Ali Ebrahimpour Boroojeny, Hamidreza Chitsaz. SARS-CoV-2 orthologs of pathogenesis-involved small viral RNAs of SARS-CoV, arXiv:2007.05859, 2020 Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, S. Cenk Sahinalp, Hamidreza Chitsaz. PyGTED: Python Application for Computing Graph Traversal Edit Distance, Journal of Computational Biology, 2020 Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, S. Cenk Sahinalp, Hamidreza Chitsaz. Graph Traversal Edit Distance and Extensions, Journal of Computational Biology, 2020 2019 Behrooz Azarkhalili, Ali Saberi, Hamidreza Chitsaz, Ali Sharifi-Zarchi. DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome, Scientific Reports 9, Article number: 16526, 2019 Dilyara A Murtazina, J Alejandro Arreguin-Arevalo, Jeremy D Cantlon, Ali Ebrahimpour Boroojeny, Akash Shrestha, Jennifer A Hicks, Christianne Magee, Kelly Kirkley, Kenneth Jones, Terry M Nett, Hamidreza Chitsaz, Colin M Clay. Enrichment of ovine gonadotropes via adenovirus gene targeting enhances assessment of transcriptional changes in response to estradiol-17β, Biology of Reproduction, ioz166, August 2019 Majdi Khalid, Indrakshi Ray, Hamidreza Chitsaz. Scalable Nonlinear AUC Maximization Methods, Machine Learning and Knowledge Discovery in Databases, Lecture Notes in Computer Science book series (LNCS, volume 11052), 2019 Farzad Abdolhosseini, Behrooz Azarkhalili, Abbas Maazallahi, Aryan Kamal, Seyed Abolfazl Motahari, Ali Sharifi-Zarchi, Hamidreza Chitsaz. Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks, Scientific Reports 9, Article number: 2342, 2019 2018 Yang An, Akane Kawaguchi, Chen Zhao, Atsushi Toyoda, Ali Sharifi-Zarchi, Seyed Ahmad Mousavi, Reza Bagherzadeh, Takeshi Inoue, Hajime Ogino, Asao Fujiyama, Hamidreza Chitsaz, Hossein Baharvand, Kiyokazu Agata. Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians, Zoological Letters 4:24, August 2018 Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Gallagher, S. Cenk Sahinalp, Hamidreza Chitsaz. GTED: Graph Traversal Edit Distance, Lecture Notes in Computer Science Volume 10812, pp 37-53 Also, 22nd Annual International Conference on Research in Computational Molecular Biology (RECOMB), Paris, France, April 2018 2017 Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan Taft, Hans Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand, Marcos J. Arauzo-Bravo. DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism, BMC Genomics 18:964, 2017 Reza Iraji, Hamidreza Chitsaz. Principal Variety Analysis, Proceedings of Machine Learning Research 78:97-108 Also, Annual Conference on Robot Learning (CoRL), 2017 Nadra Alhusini, Ali Sharifi-Zarchi, Seyed Mousavi, Hamidreza Chitsaz, Athar Ansari. Genomewide Analysis of Clp1 Function in Transcription in Budding Yeast, Scientific Reports 7, Article number: 6894, 2017 Razieh Karamzadeh, Mohammad Hossein Karimi-Jafari, Ali Sharifi-Zarchi, Hamidreza Chitsaz, Ghasem Hosseini Salekdeh, Ali Akbar Moosavi-Movahedi. Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Protein Disulfide Isomerase, Scientific Reports 7, Article number: 3666, 2017 Behrouz Bokharaeian, Alberto Diaz, Nasrin Taghizadeh, Hamidreza Chitsaz, Ramyar Chavoshinejad. SNPPhenA: A Corpus for Extracting Ranked Associations of Single-nucleotide Polymorphisms and Phenotypes from Literature, Journal of Biomedical Semantics 8:14, April 2017 2016 Majdi Khalid, Indrakshi Ray, Hamidreza Chitsaz. Confidence-Weighted Bipartite Ranking, International Conference on Advanced Data Mining and Applications (ADMA), 2016 Behrouz Bokharaeian, Alberto Diaz, Hamidreza Chitsaz. Enhancing Extraction of Drug-Drug Interaction from Literature Using Neutral Candidates, Negation, and Clause Dependency, PLOS One 11(10): e0163480, 2016 Narjes S. Movahedi, Mallory Embree, Harish Nagarajan, Karsten Zengler, Hamidreza Chitsaz. Efficient synergistic single-cell genome assembly, Frontiers in Bioengineering and Biotechnology 4(42), 2016 2015 Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkani, Hamid Pezeshk, Hamidreza Chitsaz, Mehdi Sadeghi. Increased Robustness of Early Embryogenesis through Collective Decision-Making by Key Transcription Factors, BMC Systems Biology 9:23, June 2015 Hamidreza Chitsaz, Mohammad Aminisharifabad. Exact Learning of RNA Energy Parameters from Structure, Journal of Computational Biology 22(6): 463 - 473, June 2015 2014 Seyed Basir Shariat Razavi, Narjes Sadat Movahedi Tabrizi, Hamidreza Chitsaz, Christina Boucher. HyDA-Vista: Towards Optimal Guided Selection of k-mer Size for Sequence Assembly, BMC Genomics 15(Suppl 10):S9 Also, 25th GIW / ISCB-Asia (arXiv:1408.5592 [cs.CE]), December 2014 Reza Iraji, Hamidreza Chitsaz. NUROA: A Numerical Roadmap Algorithm, Proceedings of the 53rd IEEE Conference on Decision and Control (CDC), pp 5359 - 5366 (arXiv:1403.5384 [cs.RO]), December 2014 Milad Gholami, Aryan Arbabi, Ali Sharifi-Zarchi, Hamidreza Chitsaz, Mehdi Sadeghi. ARYANA: Aligning Reads by Yet Another Approach, BMC Bioinformatics 15(Suppl 9):S12 Also RECOMB-SEQ: Fourth Annual RECOMB Satelite Workshop on Massively Parallel Sequencing, Pittsburgh, PA, March 31st - April 1st, 2014 Hamidreza Chitsaz, Mohammad Aminisharifabad. Exact Learning of RNA Energy Parameters from Structure, Lecture Notes in Computer Science Volume 8394, pp 56-68 Also, 18th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Pittsburgh, PA (arXiv:1310.4223 [q-bio.BM]), April 2014 2013 Mallory Embree, Harish Nagarajan, Narjes Movahedi, Hamidreza Chitsaz, Karsten Zengler. Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community, The ISME Journal, Nature Publishing Group, Oct 2013 Jeffrey S. McLean, Mary-Jane Lombardo, Jonathan H. Badger, Anna Edlund, Mark Novotny, Joyclyn Yee-Greenbaum, Nikolay Vyahhi, Adam P. Hall, Youngik Yang, Christopher L. Dupont, Michael G. Ziegler, Hamidreza Chitsaz, Andrew E. Allen, Shibu Yooseph, Glenn Tesler, Pavel A. Pevzner, Robert M. Friedman, Kenneth H. Nealson, J. Craig Venter, Roger S. Lasken. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum, Proceedings of the National Academy of Sciences (PNAS), Vol. 110, No. 26, pp E2390 - E2399, June 2013 Zeinab Taghavi, Narjes S. Movahedi, Sorin Draghici, Hamidreza Chitsaz. Distilled Single-Cell Genome Sequencing and De Novo Assembly for Sparse Microbial Communities, Bioinformatics 29 (19): 2395-2401; (doi: 10.1093/bioinformatics/btt420) (arXiv:1305.0062 [q-bio.GN]), Oct 2013 Hamidreza Chitsaz. On Time-optimal Trajectories for a Car-like Robot with One Trailer, SIAM Control and its Applications CT13 (arXiv:1301.6662 [math.OC]), July 2013 Elmirasadat Forouzmand, Hamidreza Chitsaz. The RNA Newton Polytope and Learnability of Energy Parameters, Bioinformatics 29(13): i300-i307 (doi:10.1093/bioinformatics/btt226) Also, 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB) 2013, Berlin, Germany (arXiv:1301.1608 [q-bio.BM]), July 2013 Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, İnanç Birol, Sébastien Boisvert, Jarrod A. Chapman, Guillaume Chapuis, Rayan Chikhi, Hamidreza Chitsaz, Wen-Chi Chou, Jacques Corbeil, Cristian Del Fabbro, T. Roderick Docking, Richard Durbin, Dent Earl, Scott Emrich, Pavel Fedotov, Nuno A. Fonseca, Ganeshkumar Ganapathy, Richard A. Gibbs, Sante Gnerre, Élénie Godzaridis, Steve Goldstein, Matthias Haimel, Giles Hall, David Haussler, Joseph B. Hiatt, Isaac Y. Ho, Jason Howard, Martin Hunt, Shaun D. Jackman, David B Jaffe, Erich Jarvis, Huaiyang Jiang, Sergey Kazakov, Paul J. Kersey, Jacob O. Kitzman, James R. Knight, Sergey Koren, Tak-Wah Lam, Dominique Lavenier, François Laviolette, Yingrui Li, Zhenyu Li, Binghang Liu, Yue Liu, Ruibang Luo, Iain MacCallum, Matthew D MacManes, Nicolas Maillet, Sergey Melnikov, Bruno Miguel Vieira, Delphine Naquin, Zemin Ning, Thomas D. Otto, Benedict Paten, Octávio S. Paulo, Adam M. Phillippy, Francisco Pina-Martins, Michael Place, Dariusz Przybylski, Xiang Qin, Carson Qu, Filipe J Ribeiro, Stephen Richards, Daniel S. Rokhsar, J. Graham Ruby, Simone Scalabrin, Michael C. Schatz, David C. Schwartz, Alexey Sergushichev, Ted Sharpe, Timothy I. Shaw, Jay Shendure, Yujian Shi, Jared T. Simpson, Henry Song, Fedor Tsarev, Francesco Vezzi, Riccardo Vicedomini, Jun Wang, Kim C. Worley, Shuangye Yin, Siu-Ming Yiu, Jianying Yuan, Guojie Zhang, Hao Zhang, Shiguo Zhou, Ian F. Korf. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, GigaScience 2:10 (arXiv:1301.5406 [q-bio.GN]), Aug 2013 Hamidreza Chitsaz, Elmirasadat Forouzmand, Gholamreza Haffari. An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids, Journal of Computational Biology 20(7): 486-494; (doi:10.1089/cmb.2013.0003) (arXiv:1301.1590 [q-bio.BM]), July 2013 2012 Narjes S. Movahedi, Elmirasadat Forouzmand, Hamidreza Chitsaz. De Novo Co-assembly of Bacterial Genomes from Multiple Single Cells, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp 561-565, 2012 *Roy Ronen, *Christina Boucher, Hamidreza Chitsaz, Pavel A. Pevzner. SEQuel: Improving the Accuracy of Genome Assemblies, Bioinformatics 28(12): i188-i196; (doi:10.1093/bioinformatics/bts219) Also, 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) 2012, Long Beach, CA *joint first authors 2011 Hamidreza Chitsaz, Joyclyn L. Yee-Greenbaum, Glenn Tesler, Mary-Jane Lombardo, Christopher L. Dupont, Jonathan H. Badger, Mark Novotny, Douglas B. Rusch, Louise J. Fraser, Niall A. Gormley, Ole Schulz-Trieglaff, Geoffrey P. Smith, Dirk J. Evers, Pavel A. Pevzner, Roger S. Lasken. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets, Nature Biotechnology, Vol. 29, No. 10, pp 915 - 921, October 2011 (doi:10.1038/nbt.1966) 2010 R. Backofen, H. Chitsaz, I. Hofacker, S. C. Sahinalp, and P. F. Stadler. Computational studies of non-coding RNAs, Pacific Symposium on Biocomputing (PSB), 2010 Tutorial Hamidreza Chitsaz. Prediction of RNA-RNA interaction structure by centroids in the Boltzmann ensemble, arXiv:1002.1736v1 [q-bio.BM], Feb 2010 2009 Hamidreza Chitsaz, Rolf Backofen, S. Cenk Sahinalp. biRNA: Fast RNA-RNA Binding Sites Prediction, Proceedings of the 9th Workshop on Algorithms in Bioinformatics (WABI), 2009 Supplementary material Hamidreza Chitsaz, Raheleh Salari, S. Cenk Sahinalp, Rolf Backofen. A Partition Function Algorithm for Interacting Nucleic Acid Strands, Bioinformatics 25(12): i365-i373; (doi:10.1093/bioinformatics/btp212) Also, 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB) 2009, Stockholm, Sweden Hamidreza Chitsaz, Steven M. LaValle, Devin J. Balkcom, Matthew T. Mason. Minimum Wheel-Rotation Paths for Differential-Drive Mobile Robots , International Journal of Robotics Research 28(1): 66-80, 2009 2008 Hamidreza Chitsaz, Steven M. LaValle, Jason M. O'Kane. Exact Pareto-Optimal Coordination of Two Translating Polygonal Robots on a Cyclic Roadmap, Proceedings of 20th Canadian Conference on Computational Geometry (CCCG), 2008 Andrei Furtuna, Devin J. Balkcom, Hamidreza Chitsaz, Paritosh Kavathekar. Generalizing the Dubins and Reeds-Shepp cars: fastest paths for bounded-velocity mobile robots, Proceedings of IEEE Conference on Robotics and Automation (ICRA), 2008 Hamidreza Chitsaz. Geodesic Problems for Mobile Robots, PhD Thesis, Department of Computer Science, University of Illinois at Urbana-Champaign (UIUC), 2008 2007 Hamidreza Chitsaz and Steven M. LaValle. Time-optimal Paths for a Dubins Airplane, Proceedings of IEEE Conference on Decision and Control (CDC), 2007 Hamidreza Chitsaz and Steven M. LaValle. Minimum Wheel-Rotation Paths for Differential-Drive Mobile Robots Among Piecewise Smooth Obstacles, Proceedings of IEEE Conference on Robotics and Automation (ICRA), 2007 2006 Hamidreza Chitsaz, Steven M. LaValle, Devin J. Balkcom, Matthew T. Mason. An Explicit Characterization of Minimum Wheel-Rotation Paths for Differential-Drives, Proceedings of 12th IEEE International Conference on Methods and Models in Automation and Robotics (MMAR), 2006 Hamidreza Chitsaz, Steven M. LaValle, Devin J. Balkcom, Matthew T. Mason. Minimum Wheel-Rotation Paths for Differential-Drive Mobile Robots, Proceedings of IEEE Conference on Robotics and Automation (ICRA), 2006 2004 Hamidreza Chitsaz, Jason M. O'Kane, Steven M. LaValle. Exact Pareto-Optimal Coordination of Two Translating Polygonal Robots on an Acyclic Roadmap, Proceedings of IEEE Conference on Robotics and Automation (ICRA), 2004 [Slides] 2002 M. Jamzad, B. S. Sadjad, V. S. Mirrokni, M. Kazemi, H. Chitsaz, A. Heydarnoori, M. T. Hajiaghai, E. Chiniforooshan. A Fast Vision System for Middle Size Robots in RoboCup, Lecture Notes in Computer Science Vol. 2377, pp 71­-80, 2002 This paper was awarded the best Engineering Challenge Award in RoboCup 2001. Mansour Jamzad, Hamid Reza Chitsaz, Amirali Foroughnassirai, Reza Ghorbani, Moslem Kazemi, V. S. Mirrokni, B. S. Sadjad. Basic Requirements for a Teamwork in Middle Size RoboCup, RoboCup 2001: Lecture Notes in Computer Science Vol. 2377, pp 621-­626, 2002 Mohammad Taghi Manzuri, Hamid Reza Chitsaz, Reza Ghorbani, Pooya Karimian, Alireza Mirazi, Mehran Motamed, Roozbeh Mottaghi, Payam Sabzmeydani. Sharif CESR Small Size Robocup Team, RoboCup 2001: Lecture Notes in Computer Science Vol. 2377, pp 595­-598, 2002 Manuela M. Veloso, Tucker R. Balch, Peter Stone, Hiroaki Kitano, Fuminori Yamasaki, Ken Endo, Minoru Asada, Mansour Jamzad, B. S. Sadjad, V. S. Mirrokni, Moslem Kazemi, Hamid Reza Chitsaz, A. Heydarnoori, Mohammad Taghi Hajiaghayi, Ehsan Chiniforooshan. RoboCup­2001: The Fifth Robotic Soccer World Championships, AI Magazine Vol. 23(1), American Association for Artificial Intelligence, pp 55­-68, 2002 2001 Hamidreza Chitsaz. Design and Implementation of A Controller for Small Size Soccer Player Robot (in Farsi), BS Project, Computer Engineering Department, Sharif University of Tech, 2001 M. Jamzad, A. Foroughnassiraei, T. Hadjiaghai, V.S. Mirrokni, R. Ghorbani, A. Heydar Noori, M. Kazemi, H. Chitsaz, F. Mobasser, M. Ebraahimi Moghaddam, M. Gudarzi, N. Ghaffarzadegan. A Goalkeeper for Middle Size RoboCup, RoboCup­2000: Robot Soccer World Cup IV. Lecture notes in Artificial Intelligence, Vol. 2019, pp 583­-586, Springer, 2001 2000 M. Jamzad, A. Foroughnassiraei, E. Chiniforooshan, R. Ghorbani, M. Kazemi, H. Chitsaz, F. Mobasser, S.B. Sadjad. ARVAND: A Soccer Player Robot, AI Magazine, American Association for Artificial Intelligence, pp 47-­51, Fall 2000 M. Jamzad, A. Foroughnassiraei, E. Chiniforooshan, R. Ghorbani, M. Kazemi, H. Chitsaz, F. Mobasser, S.B. Sadjad. Middle Sized Soccer Robots: ARVAND, RoboCup­99: Robot Soccer World Cup III. Lecture notes in Artificial Intelligence, Vol. 1856, pp 61-­73, Springer, 2000 M. Jamzad, A. Foroughnassiraei, E. Chiniforooshan, R. Ghorbani, M. Kazemi, H. Chitsaz, F. Mobasser, S.B. Sadjad. Design and Construction of a Soccer Player Robot ARVAND, RoboCup­99: Robot Soccer World Cup III. Lecture notes in Artificial Intelligence, Vol. 1856, pp 745-­749, Springer, 2000