A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC
Gopalan, Vishaka, Singh, Arashdeep, Rashidi Mehrabadi, Farid, Wang, Li, Ruppin, Eytan, Arda, H Efsun, Hannenhalli, Sridhar
Published in Cancer research (Chicago, Ill.) (01.08.2021)
Published in Cancer research (Chicago, Ill.) (01.08.2021)
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Journal Article
Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
Liu, Yuelin, Li, Xuan Cindy, Rashidi Mehrabadi, Farid, Schäffer, Alejandro A, Pratt, Drew, Crawford, David R, Malikić, Salem, Molloy, Erin K, Gopalan, Vishaka, Mount, Stephen M, Ruppin, Eytan, Aldape, Kenneth D, Sahinalp, S Cenk
Published in Genome research (01.07.2023)
Published in Genome research (01.07.2023)
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Journal Article
PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem
Sadeqi Azer, Erfan, Rashidi Mehrabadi, Farid, Malikić, Salem, Li, Xuan Cindy, Bartok, Osnat, Litchfield, Kevin, Levy, Ronen, Samuels, Yardena, Schäffer, Alejandro A, Gertz, E Michael, Day, Chi-Ping, Pérez-Guijarro, Eva, Marie, Kerrie, Lee, Maxwell P, Merlino, Glenn, Ergun, Funda, Sahinalp, S Cenk
Published in Bioinformatics (Oxford, England) (01.07.2020)
Published in Bioinformatics (Oxford, England) (01.07.2020)
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Journal Article
Fast intratumor heterogeneity inference from single-cell sequencing data
Kızılkale, Can, Rashidi Mehrabadi, Farid, Sadeqi Azer, Erfan, Pérez-Guijarro, Eva, Marie, Kerrie L, Lee, Maxwell P, Day, Chi-Ping, Merlino, Glenn, Ergün, Funda, Buluç, Aydın, Sahinalp, S Cenk, Malikić, Salem
Published in Nature Computational Science (01.09.2022)
Published in Nature Computational Science (01.09.2022)
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Journal Article
PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
Malikic, Salem, Mehrabadi, Farid Rashidi, Ciccolella, Simone, Rahman, Md Khaledur, Ricketts, Camir, Haghshenas, Ehsan, Seidman, Daniel, Hach, Faraz, Hajirasouliha, Iman, Sahinalp, S Cenk
Published in Genome research (01.11.2019)
Published in Genome research (01.11.2019)
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Journal Article
Studying the History of Tumor Evolution from Single-Cell Sequencing Data by Exploring the Space of Binary Matrices
Malikić, Salem, Mehrabadi, Farid Rashidi, Azer, Erfan Sadeqi, Ebrahimabadi, Mohammad Haghir, Sahinalp, Suleyman Cenk
Published in Journal of computational biology (01.09.2021)
Published in Journal of computational biology (01.09.2021)
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Journal Article
Abstract LB019: Trisicell: Scalable Tumor Phylogeny Reconstruction and Validation Reveals Developmental Origin and Therapeutic Impact of Intratumoral Heterogeneity
Mehrabadi, Farid Rashidi, Malikić, Salem, Marie, Kerrie L., Pérez-Guijarro, Eva, Azer, Erfan Sadeqi, Yang, Howard H., Kızılkale, Can, Gruen, Charli, Liu, Huaitian, Marcelus, Christina, Buluç, Aydın, Ergün, Funda, Lee, Maxwell P., Merlino, Glenn, Day, Chi-Ping, Sahinalp, S. Cenk
Published in Cancer research (Chicago, Ill.) (01.07.2021)
Published in Cancer research (Chicago, Ill.) (01.07.2021)
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Journal Article
A study on prediction of user's tendency toward purchases in websites based on behavior models
Gohari Boroujerdi, Emad, Mehri, Soroush, Sadeghi Garmaroudi, Saeed, Pezeshki, Mohammad, Rashidi Mehrabadi, Farid, Malakouti, SeyyedSalim, Khadivi, Shahram
Published in 2014 6th Conference on Information and Knowledge Technology (IKT) (01.05.2014)
Published in 2014 6th Conference on Information and Knowledge Technology (IKT) (01.05.2014)
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Conference Proceeding
Abstract 127: Single-cell methylation sequencing data reveals succinct metastatic migration histories and tumor progression models
Li, Xuan C., Liu, Yuelin, Mehrabadi, Farid Rashidi, Schäffer, Alejandro A., Pratt, Drew, Crawford, David R., Malikić, Salem, Molloy, Erin K., Gopalan, Vishaka, Mount, Stephen M., Ruppin, Eytan, Aldape, Kenneth, Sahinalp, S. Cenk
Published in Cancer research (Chicago, Ill.) (04.04.2023)
Published in Cancer research (Chicago, Ill.) (04.04.2023)
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Journal Article
PhISCS - A Combinatorial Approach for Sub-perfect Tumor Phylogeny Reconstruction via Integrative use of Single Cell and Bulk Sequencing Data
Salem Malikic, Ciccolella, Simone, Farid Rashidi Mehrabadi, Ricketts, Camir, Rahman, Md Khaledur, Haghshenas, Ehsan, Seidman, Daniel, Hach, Faraz, Hajirasouliha, Iman, Sahinalp, S Cenk
Published in bioRxiv (25.07.2018)
Published in bioRxiv (25.07.2018)
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Paper
Stochastic modelling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones
Hirsch, M G, Pal, Soumitra, Mehrabadi, Farid Rashidi, Malikic, Salem, Gruen, Charli, Sassano, Antonella, Pérez-Guijarro, Eva, Merlino, Glenn, Sahinalp, Cenk, Molloy, Erin K, Day, Chi-Ping, Przytycka, Teresa M
Published in bioRxiv : the preprint server for biology (20.04.2024)
Published in bioRxiv : the preprint server for biology (20.04.2024)
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Journal Article
Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms
Gruen, Charli, Yang, Howard H, Sassano, Antonella, Wu, Emily, Gopalan, Vishaka, Marie, Kerrie L, Castro, Andrea, Mehrabadi, Farid Rashidi, Wu, Chih Hao, Church, Isabella, Needle, Gabriel A, Smith, Cari, Chin, Sung, Ebersole, Jessica, Marcelus, Christina, Fon, Anyen, Liu, Huaitian, Malikic, Salem, Sahinalp, Cenk, Carter, Hanna, Hannenhalli, Sridhar, Day, Chi-Ping, Lee, Maxwell P, Merlino, Glenn, Pérez-Guijarro, Eva
Published in bioRxiv : the preprint server for biology (05.04.2023)
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Published in bioRxiv : the preprint server for biology (05.04.2023)
Journal Article
Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
Liu, Yuelin, Li, Xuan C, Farid Rashidi Mehrabadi, Schäffer, Alejandro A, Pratt, Drew, Crawford, David R, Salem Malikić, Molloy, Erin, Gopalan, Vishaka, Mount, Steve M, Ruppin, Eytan, Aldape, Kenneth, Sahinalp, S Cenk
Published in bioRxiv (12.01.2023)
Published in bioRxiv (12.01.2023)
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Paper
Profiles of expressed mutations in single cells reveal patterns of tumor evolution and therapeutic impact of intratumor heterogeneity
Farid Rashidi Mehrabadi, Marie, Kerrie L, Perez-Guijarro, Eva, Salem Malikic, Erfan Sadeqi Azer, Yang, Howard H, Kizilkale, Can, Gruen, Charli, Liu, Huaitian, Kelly, Michael C, Marcelus, Christina, Burkett, Sandra, Aydin Buluc, Ergun, Funda, Lee, Maxwell P, Merlino, Glenn, Day, Chi-Ping, Sahinalp, S Cenk
Published in bioRxiv (28.03.2021)
Published in bioRxiv (28.03.2021)
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Paper
PhISCS-BnB: A Fast Branch and Bound Algorithm for the Perfect Tumor Phylogeny Reconstruction Problem
Erfan Sadeqi Azer, Farid Rashidi Mehrabadi, Xuan Cindy Li, Salem Malikic, Schaffer, Alejandro A, Gertz, E Michael, Day, Chi-Ping, Perez-Guijarro, Eva, Marie, Kerrie, Lee, Maxwell P, Merlino, Glenn, Ergun, Funda, Sahinalp, S Cenk
Published in bioRxiv (12.02.2020)
Published in bioRxiv (12.02.2020)
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Paper