The RNA Newton polytope and learnability of energy parameters

por Forouzmand, Elmirasadat, Chitsaz, Hamidreza
Publicado 2013

Enhancing Extraction of Drug-Drug Interaction from Literature Using Neutral Candidates, Negation, and Clause Dependency

por Bokharaeian, Behrouz, Diaz, Alberto, Chitsaz, Hamidreza
Publicado 2016

A partition function algorithm for interacting nucleic acid strands

por Chitsaz, Hamidreza, Salari, Raheleh, Sahinalp, S. Cenk, Backofen, Rolf
Publicado 2009

SEQuel: improving the accuracy of genome assemblies

por Ronen, Roy, Boucher, Christina, Chitsaz, Hamidreza, Pevzner, Pavel
Publicado 2012

HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly

por Shariat, Basir, Movahedi, Narjes Sadat, Chitsaz, Hamidreza, Boucher, Christina
Publicado 2014

DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome

por Azarkhalili, Behrooz, Saberi, Ali, Chitsaz, Hamidreza, Sharifi-Zarchi, Ali
Publicado 2019

Efficient Synergistic Single-Cell Genome Assembly

por Movahedi, Narjes S., Embree, Mallory, Nagarajan, Harish, Zengler, Karsten, Chitsaz, Hamidreza
Publicado 2016

SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature

por Bokharaeian, Behrouz, Diaz, Alberto, Taghizadeh, Nasrin, Chitsaz, Hamidreza, Chavoshinejad, Ramyar
Publicado 2017

ARYANA: Aligning Reads by Yet Another Approach

por Gholami, Milad, Arbabi, Aryan, Sharifi-Zarchi, Ali, Chitsaz, Hamidreza, Sadeghi, Mehdi
Publicado 2014

Genomewide Analysis of Clp1 Function in Transcription in Budding Yeast

por Al-Husini, Nadra, Sharifi, Ali, Mousavi, Seyed Ahmad, Chitsaz, Hamidreza, Ansari, Athar
Publicado 2017

Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks

por Abdolhosseini, Farzad, Azarkhalili, Behrooz, Maazallahi, Abbas, Kamal, Aryan, Motahari, Seyed Abolfazl, Sharifi-Zarchi, Ali, Chitsaz, Hamidreza
Publicado 2019

Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase

por Karamzadeh, Razieh, Karimi-Jafari, Mohammad Hossein, Sharifi-Zarchi, Ali, Chitsaz, Hamidreza, Salekdeh, Ghasem Hosseini, Moosavi-Movahedi, Ali Akbar
Publicado 2017

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...

por Moradi, Sharif, Kamal, Aryan, Aboulkheyr Es, Hamidreza, Farhadi, Farnoosh, Ebrahimi, Marzieh, Chitsaz, Hamidreza, Sharifi-Zarchi, Ali, Baharvand, Hossein
Publicado 2022

Increased robustness of early embryogenesis through collective decision-making by key transcription factors

por Sharifi-Zarchi, Ali, Totonchi, Mehdi, Khaloughi, Keynoush, Karamzadeh, Razieh, Araúzo-Bravo, Marcos J., Baharvand, Hossein, Tusserkani, Ruzbeh, Pezeshk, Hamid, Chitsaz, Hamidreza, Sadeghi, Mehdi
Publicado 2015

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism

por 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.
Publicado 2017

Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians

por 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
Publicado 2018

De novo assembly of bacterial genomes from single cells

por 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., Lasken, Roger S.
Publicado 2011

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

por Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich D, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J Graham, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, Korf, Ian F
Publicado 2013