Ziv Bar-Joseph

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 38

Top Venues

bioRxiv : the preprint server for biology

Genome research

PLoS computational biology

Bioinformatics (Oxford, England)

Carnegie Mellon University

Massachusetts Institute of Technology (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Carnegie Mellon University

United States

Professor :: SCS, Computational Biology and Machine Learning

Carnegie Mellon University

United States

Associate Prof. :: SCS, Computational Biology and Machine Learning

Carnegie Mellon University

United States

Assistant Prof. :: SCS, Computational Biology and Machine Learning

Education History

Massachusetts Institute of Technology

United States

PHD :: Computer Science

Hebrew University of Jerusalem

Israel

MSC :: Computer Science

Hebrew University of Jerusalem

Israel

BSC :: Computer Science, Mathematics

Publications

Sizhen Li, Saeed Moayedpour, Ruijiang Li, Michael Bailey, Saleh Riahi, Lorenzo Kogler-Anele, Milad Miladi, Jacob Miner, Fabien Pertuy, Dinghai Zheng, Jun Wang, Akshay Balsubramani, Khang Tran, Minnie Zacharia, Monica Wu, Xiaobo Gu, Ryan Clinton, Carla Asquith, Joseph Skaleski, Lianne Boeglin, Sudha Chivukula, Anusha Dias, Tod Strugnell, Fernando Ulloa Montoya, Vikram Agarwal, Ziv Bar-Joseph, Sven Jager
CodonBERT large language model for mRNA vaccines. Genome research 34 (7) (2024)
Sizhen Li, Saeed Moayedpour, Ruijiang Li, Michael Bailey, Saleh Riahi, Lorenzo Kogler-Anele, Milad Miladi, Jacob Miner, Fabien Pertuy, Dinghai Zheng, Jun Wang, Akshay Balsubramani, Khang Tran, Minnie Zacharia, Monica Wu, Xiaobo Gu, Ryan Clinton, Carla Asquith, Joseph Skaleski, Lianne Boeglin, Sudha Chivukula, Anusha Dias, Tod Strugnell, Fernando Ulloa Montoya, Vikram Agarwal, Ziv Bar-Joseph, Sven Jager
CodonBert large language model for mRNA vaccines. Genome research (2024)
Euxhen Hasanaj, Sachin Mathur, Ziv Bar-Joseph
Integrating patients in time series clinical transcriptomics data. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Haotian Teng, Marcus Stoiber, Ziv Bar-Joseph, Carl Kingsford
Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework. bioRxiv : the preprint server for biology (2024)
Sizhen Li, Saeed Moayedpour, Ruijiang Li, Michael Bailey, Saleh Riahi, Lorenzo Kogler-Anele, Milad Miladi, Jacob Miner, Fabien Pertuy, Dinghai Zheng, Jun Wang, Akshay Balsubramani, Khang Tran, Minnie Zacharia, Monica Wu, Xiaobo Gu, Ryan Clinton, Carla Asquith, Joseph Skaleski, Lianne Boeglin, Sudha Chivukula, Anusha Dias, Tod Strugnell, Fernando Ulloa Montoya, Vikram Agarwal, Ziv Bar-Joseph, Sven Jager
CodonBERT large language model for mRNA vaccines. Genome research 34 (7) (2024)
Sizhen Li, Saeed Moayedpour, Ruijiang Li, Michael Bailey, Saleh Riahi, Lorenzo Kogler-Anele, Milad Miladi, Jacob Miner, Fabien Pertuy, Dinghai Zheng, Jun Wang, Akshay Balsubramani, Khang Tran, Minnie Zacharia, Monica Wu, Xiaobo Gu, Ryan Clinton, Carla Asquith, Joseph Skaleski, Lianne Boeglin, Sudha Chivukula, Anusha Dias, Tod Strugnell, Fernando Ulloa Montoya, Vikram Agarwal, Ziv Bar-Joseph, Sven Jager
CodonBERT large language model for mRNA vaccines. Genome research (2024)
Haotian Teng, Marcus Stoiber, Ziv Bar-Joseph, Carl Kingsford
Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework. bioRxiv : the preprint server for biology (2024)
Euxhen Hasanaj, Sachin Mathur, Ziv Bar-Joseph
Integrating patients in time series clinical transcriptomics data. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Euxhen Hasanaj, Sachin Mathur, Ziv Bar-Joseph
Integrating patients in time series clinical transcriptomics data. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Hao Chen, Young Je Lee, Jose A Ovando, Lorena Rosas, Mauricio Rojas, Ana L Mora, Ziv Bar-Joseph, Jose Lugo-Martinez
scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics. bioRxiv : the preprint server for biology (2023)
Hao Chen, Dongshunyi Li, Ziv Bar-Joseph
SCS: cell segmentation for high-resolution spatial transcriptomics. bioRxiv : the preprint server for biology (2023)
Hao Chen, Young Je Lee, Jose A Ovando, Lorena Rosas, Mauricio Rojas, Ana L Mora, Ziv Bar-Joseph, Jose Lugo-Martinez
scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics. bioRxiv : the preprint server for biology (2023)
Hao Chen, Young Je Lee, Jose A Ovando, Lorena Rosas, Mauricio Rojas, Ana L Mora, Ziv Bar-Joseph, Jose Lugo-Martinez
scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics. bioRxiv : the preprint server for biology (2023)
Hao Chen, Young Je Lee, Jose A Ovando, Lorena Rosas, Mauricio Rojas, Ana L Mora, Ziv Bar-Joseph, Jose Lugo-Martinez
scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics. bioRxiv : the preprint server for biology (2023)
Hao Chen, Dongshunyi Li, Ziv Bar-Joseph
SCS: cell segmentation for high-resolution spatial transcriptomics. Nature methods (2023)
Qi Song, Matthew Ruffalo, Ziv Bar-Joseph
Using single cell atlas data to reconstruct regulatory networks. Nucleic acids research (2023)
Hao Chen, Young Je Lee, Jose A Ovando, Lorena Rosas, Mauricio Rojas, Ana L Mora, Ziv Bar-Joseph, Jose Lugo-Martinez
scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics. bioRxiv : the preprint server for biology (2023)
Dongshunyi Li, Jun Ding, Ziv Bar-Joseph
UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation. Journal of computational biology : a journal of computational molecular cell biology 29 (11) (2022)
Ye Yuan, Carlos Cosme, Taylor Sterling Adams, Jonas Christian Schupp, Koji Sakamoto, Nikos Xylourgidis, Matthew Ruffalo, Jiachen Li, Naftali Kaminski, Ziv Bar-Joseph
CINS: Cell Interaction Network inference from Single cell expression data. PLoS computational biology 18 (9) (2022)
Monica T Dayao, Maigan Brusko, Clive Wasserfall, Ziv Bar-Joseph
Membrane marker selection for segmenting single cell spatial proteomics data. Nature communications 13 (1) (2022)
Euxhen Hasanaj, Jingtao Wang, Arjun Sarathi, Jun Ding, Ziv Bar-Joseph
Interactive single-cell data analysis using Cellar. Nature communications 13 (1) (2022)
Jun Ding, Nadav Sharon, Ziv Bar-Joseph
Temporal modelling using single-cell transcriptomics. Nature reviews. Genetics 23 (6) (2022)
Qi Song, Jingtao Wang, Ziv Bar-Joseph
scSTEM: clustering pseudotime ordered single-cell data. Genome biology 23 (1) (2022)
Dongshunyi Li, Jun Ding, Ziv Bar-Joseph
Identifying signaling genes in spatial single-cell expression data. Bioinformatics (Oxford, England) 37 (7) (2021)
Daniel Ruiz-Perez, Jose Lugo-Martinez, Natalia Bourguignon, Kalai Mathee, Betiana Lerner, Ziv Bar-Joseph, Giri Narasimhan
Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data. mSystems 6 (2) (2021)
Hamim Zafar, Chieh Lin, Ziv Bar-Joseph
Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data. Nature communications 11 (1) (2020)
Amir Alavi, Ziv Bar-Joseph
Iterative point set registration for aligning scRNA-seq data. PLoS computational biology 16 (10) (2020)
Jun Ding, Jose Lugo-Martinez, Ye Yuan, Darrell N Kotton, Ziv Bar-Joseph
Reconstructing SARS-CoV-2 response signaling and regulatory networks. bioRxiv : the preprint server for biology (2020)
Ye Yuan, Ziv Bar-Joseph
GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data. Genome biology 21 (1) (2020)
Honghai Liu, Cheng-Hai Zhang, Niyatie Ammanamanchi, Sangita Suresh, Christopher Lewarchik, Krithika Rao, Gerrida M Uys, Lu Han, Maryline Abrial, Dean Yimlamai, Balakrishnan Ganapathy, Christelle Guillermier, Nathalie Chen, Mugdha Khaladkar, Jennifer Spaethling, James H Eberwine, Junhyong Kim, Stuart Walsh, Sangita Choudhury, Kathryn Little, Kimberly Francis, Mahesh Sharma, Melita Viegas, Abha S Bais, Dennis Kostka, Jun Ding, Ziv Bar-Joseph, Yijen L Wu, Vijay K Yechoor, Mousumi Moulik, Jennifer Johnson, Jacqueline G Weinberg, Miguel Reyes-Mugica, Matthew L Steinhauser, Bernhard Kühn
Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment. Science translational medicine 11 (513) (2020)
Mark Zander, Mathew G Lewsey, Natalie M Clark, Lingling Yin, Anna Bartlett, J Paola Saldierna Guzmán, Elizabeth C Hann, Amber E Langford, Bruce Jow, Aaron Wise, Joseph R Nery, Huaming Chen, Ziv Bar-Joseph, Justin W Walley, Roberto Solano, Joseph R Ecker
Integrated multi-omics framework of the plant response to jasmonic acid. Nature plants 6 (3) (2020)
Ye Yuan, Ziv Bar-Joseph
Deep learning for inferring gene relationships from single-cell expression data. Proceedings of the National Academy of Sciences of the United States of America (2019)
Matthew Ruffalo, Roby Thomas, Jian Chen, Adrian V Lee, Steffi Oesterreich, Ziv Bar-Joseph
Network-guided prediction of aromatase inhibitor response in breast cancer. PLoS computational biology 15 (2) (2019)
Sabrina Rashid, Zhicheng Long, Shashank Singh, Maryam Kohram, Harsh Vashistha, Saket Navlakha, Hanna Salman, Zoltán N Oltvai, Ziv Bar-Joseph
Adjustment in tumbling rates improves bacterial chemotaxis on obstacle-laden terrains. Proceedings of the National Academy of Sciences of the United States of America 116 (24) (2019)
Matthew Ruffalo, Ziv Bar-Joseph
Protein interaction disruption in cancer. BMC cancer 19 (1) (2019)
Mondira Ray, Matthew M Ruffalo, Ziv Bar-Joseph
Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer. Genes, chromosomes & cancer 58 (1) (2018)
Nicolas A Pabon, Yan Xia, Samuel K Estabrooks, Zhaofeng Ye, Amanda K Herbrand, Evelyn Süß, Ricardo M Biondi, Victoria A Assimon, Jason E Gestwicki, Jeffrey L Brodsky, Carlos Jaime Camacho, Ziv Bar-Joseph
Predicting protein targets for drug-like compounds using transcriptomics. PLoS computational biology 14 (12) (2018)
Michael Kleyman, Emre Sefer, Teodora Nicola, Celia Espinoza, Divya Chhabra, James S Hagood, Naftali Kaminski, Namasivayam Ambalavanan, Ziv Bar-Joseph
Selecting the most appropriate time points to profile in high-throughput studies. eLife 6 (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Ziv Bar-Joseph