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 datab... von Moradi, Sharif, Kamal, Aryan, Aboulkheyr Es, Hamidreza, Farhadi, Farnoosh, Ebrahimi, Marzieh, Chitsaz, Hamidreza, Sharifi-Zarchi, Ali, Baharvand, Hossein

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Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community von Embree, Mallory, Nagarajan, Harish, Movahedi, Narjes, Chitsaz, Hamidreza, Zengler, Karsten

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DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism von Sharifi-Zarchi, Ali, Gerovska, Daniela, Adachi, Kenjiro, Totonchi, Mehdi, Pezeshk, Hamid, Taft, Ryan J, Schöler, Hans R, Chitsaz, Hamidreza, Sadeghi, Mehdi, Baharvand, Hossein, Araúzo-Bravo, Marcos J

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Optimization of hydrodynamic cavitation process of biodiesel production by response surface methodology von Chitsaz, Hamidreza, Omidkhah, Mohammadreza, Ghobadian, Barat, Ardjmand, Mehdi

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Enhancing Extraction of Drug-Drug Interaction from Literature Using Neutral Candidates, Negation, and Clause Dependency von Bokharaeian, Behrouz, Diaz, Alberto, Chitsaz, Hamidreza

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Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase von Karamzadeh, Razieh, Karimi-Jafari, Mohammad Hossein, Sharifi-Zarchi, Ali, Chitsaz, Hamidreza, Salekdeh, Ghasem Hosseini, Moosavi-Movahedi, Ali Akbar

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Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum von McLean, Jeffrey S, Lombardo, Mary-Jane, Badger, Jonathan H, Edlund, Anna, Novotny, Mark, Yee-Greenbaum, Joyclyn, Vyahhi, Nikolay, Hall, Adam P, Yang, Youngik, Dupont, Christopher L, Ziegler, Michael G, Chitsaz, Hamidreza, Allen, Andrew E, Yooseph, Shibu, Tesler, Glenn, Pevzner, Pavel A, Friedman, Robert M, Nealson, Kenneth H, Venter, J Craig, Lasken, Roger S

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Efficient de novo assembly of single-cell bacterial genomes from short-read data sets von Lasken, Roger S, Chitsaz, Hamidreza, Yee-Greenbaum, Joyclyn L, Tesler, Glenn, Lombardo, Mary-Jane, Dupont, Christopher L, Badger, Jonathan H, Novotny, Mark, Rusch, Douglas B, Fraser, Louise J, Gormley, Niall A, Schulz-Trieglaff, Ole, Smith, Geoffrey P, Evers, Dirk J, Pevzner, Pavel A

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

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A partition function algorithm for interacting nucleic acid strands von Chitsaz, Hamidreza, Salari, Raheleh, Sahinalp, S. Cenk, Backofen, Rolf

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SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature von Bokharaeian, Behrouz, Diaz, Alberto, Taghizadeh, Nasrin, Chitsaz, Hamidreza, Chavoshinejad, Ramyar

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Genomewide Analysis of Clp1 Function in Transcription in Budding Yeast von Al-Husini, Nadra, Sharifi, Ali, Mousavi, Seyed Ahmad, Chitsaz, Hamidreza, Ansari, Athar

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HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly von Shariat, Basir, Movahedi, Narjes Sadat, Chitsaz, Hamidreza, Boucher, Christina

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Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians von An, Yang, Kawaguchi, Akane, Zhao, Chen, Toyoda, Atsushi, Sharifi-Zarchi, Ali, Mousavi, Seyed Ahmad, Bagherzadeh, Reza, Inoue, Takeshi, Ogino, Hajime, Fujiyama, Asao, Chitsaz, Hamidreza, Baharvand, Hossein, Agata, Kiyokazu

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Minimum Wheel-Rotation Paths for Differential-Drive Mobile Robots von Chitsaz, Hamidreza, LaValle, Steven M., Balkcom, Devin J., Mason, Matthew T.

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DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome von Azarkhalili, Behrooz, Saberi, Ali, Chitsaz, Hamidreza, Sharifi-Zarchi, Ali

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Exact learning of RNA energy parameters from structure von Chitsaz, Hamidreza, Aminisharifabad, Mohammad

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SEQuel: improving the accuracy of genome assemblies von Ronen, Roy, Boucher, Christina, Chitsaz, Hamidreza, Pevzner, Pavel

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GTED: Graph Traversal Edit Distance von Boroojeny, Ali Ebrahimpour, Shrestha, Akash, Sharifi-Zarchi, Ali, Gallagher, Suzanne Renick, Sahinalp, S. Cenk, Chitsaz, Hamidreza

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The RNA Newton polytope and learnability of energy parameters von Forouzmand, Elmirasadat, Chitsaz, Hamidreza

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