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Computational Genomics Summer Institute CGSI
Приєднався 3 чер 2016
Ben Raphael | Models and Methods for Spatial Transcriptomics | CGSI 2023
Related papers:
Related papers: C Ma*, U Chitra*, S Zhang, BJ Raphael (2022). Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics. Cell Systems 13 (10), 786-797. e13
Alignment and integration of spatial transcriptomics data (2022). R Zeira, M Land, A Strzalkowski, BJ Raphael. Nature Methods 19 (5), 567-575
X Liu, R Zeira, B Raphael. (2023) PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data. bioRxiv 10.1101/2023.01.08.523162
Related papers: C Ma*, U Chitra*, S Zhang, BJ Raphael (2022). Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics. Cell Systems 13 (10), 786-797. e13
Alignment and integration of spatial transcriptomics data (2022). R Zeira, M Land, A Strzalkowski, BJ Raphael. Nature Methods 19 (5), 567-575
X Liu, R Zeira, B Raphael. (2023) PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data. bioRxiv 10.1101/2023.01.08.523162
Переглядів: 548
Відео
Ben Raphael | Evolutionary Models for Cancer and Lineage Tracing | CGSI 2023
Переглядів 2735 місяців тому
Related Papers: P Sashittal, H Zhang, CA Iacobuzio-Donahue, BJ Raphael. (2023) ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model. bioRxiv doi.org/10.1101/2023.01.05.522408 P Sashittal, H Schmidt, MM Chan, BJ Raphael. (2022) Startle: a star homoplasy approach for CRISPR-Cas9 lineage tracing. bioRxiv doi.org/10.1101/2022.12.18.520935
Shalmali Josh | Observational Causal Inference for Improving and Auditing ML for Healthcare | CGSI23
Переглядів 1318 місяців тому
Related papers: 1. Zhang, H., Singh, H., Ghassemi, M., & Joshi, S. (2022). " Why did the Model Fail?": Attributing Model Performance Changes to Distribution Shifts. arXiv preprint arXiv:2210.10769. 2. Joshi S, Zhang J, & Bareinboim E (2023). Towards Safe Policy Learning under Partial Identifiability: A Causal Approach 3. Singh, H., Joshi, S., Doshi-Velez, F., & Lakkaraju, H. (2022, July). Towar...
James Zou | Leveraging Medical Twitter to Build a Visual language AI Model for Pathology | CGSI 2023
Переглядів 2708 місяців тому
Related papers: Wu, Z., Trevino, A. E., Wu, E., Swanson, K., Kim, H. J., D’Angio, H. B., ... & Zou, J. (2022). Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering, 1-14. Wu, E., Trevino, A. E., Wu, Z., Swanson, K., Kim, H. J., D’Angio, H. B., ... & Zou, J. (2023). 7-UP: generating in silico COD...
Kris Sankaran | Selective Inference for Computational Genomics | CGSI 2023
Переглядів 1689 місяців тому
Related Papers: Dai, C., Lin, B., Xing, X., & Liu, J.S. (2020). False Discovery Rate Control via Data Splitting. Journal of the American Statistical Association. Fannjiang, C., Bates, S., Angelopoulos, A.N., Listgarten, J., & Jordan, M.I. (2022). Conformal prediction under feedback covariate shift for biomolecular design. Proceedings of the National Academy of Sciences of the United States of A...
Layla Oesper | Tumor Evolution: Methods for Comparing, Summarizing and Visualizing Clonal Trees | 23
Переглядів 1409 місяців тому
Related papers: Guang, Z., Smith-Erb, M., & Oesper, L. (2023). A weighted distance-based approach for deriving consensus tumor evolutionary trees. ISMB/ECCB (to appear). Nguyen, Q., & Oesper, L. (2022, December). An Approach to Relax the Infinite Sites Assumption in Tumor Phylogeny Distance Measures. In 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 3862-3863)....
Mohammed El Kebir | Inferring Parsimonious Migration Histories for Metastatic Cancers | CGSI 2023
Переглядів 899 місяців тому
Related papers: El-Kebir, Mohammed, Gryte Satas, and Benjamin J. Raphael. “Inferring Parsimonious Migration Histories for Metastatic Cancers.” Nature Genetics 50, no. 5 (May 2018): 718-26. doi.org/10.1038/s41588-018-0106-z El-Kebir, Mohammed. “Parsimonious Migration History Problem: Complexity and Algorithms.” Application/pdf, 2018, 14 pages. doi.org/10.4230/LIPICS.WABI.2018.24 Sashittal, Palas...
Na Cai | Polygenic Means To Test And Refine Depression Disease Models | CGSI 2023
Переглядів 1119 місяців тому
Related papers: 1. Dahl, A., Thompson, M., An, U., Krebs, M., Appadurai, V., Border, R., Bacanu, S.-A., Werge, T., Flint, J., Schork, A. J., Sankararaman, S., Kendler, K., & Cai, N. (2022). Phenotype integration improves power and preserves specificity in biobank-based genetic studies of MDD. In bioRxiv. doi.org/10.1101/2022.08.15.503980 2. Huang, L., Tang, S., Rietkerk, J., Appadurai, V., Kreb...
Nicholas Mancuso | Computationally Scalable Approaches for Characterizing Genetic Architectures in..
Переглядів 1349 місяців тому
Nicholas Mancuso | Computationally Scalable Approaches for Characterizing Genetic Architectures in Diverse Ancestries | CGSI 2023 Related papers: Lu, Zeyun, et al. "Multi-ancestry fine-mapping improves precision to identify causal genes in transcriptome-wide association studies." The American Journal of Human Genetics 109.8 (2022): 1388-1404. Wang, Gao, et al. "A simple new approach to variable...
Steven Gazal | The Functional Architectures of Human Diseases and Complex Traits From Polygenic...
Переглядів 1419 місяців тому
Steven Gazal | The Functional Architectures of Human Diseases and Complex Traits: From Polygenicity to Variant Function | CGSI 2023 Related papers: Sullivan*, Meadows*, Gazal* et al. 2023 Science Gazal et al. 2022 Nat Genet Jagadeesh*, Dey* et al. 2022 Nat Genet
Vasilis Ntranos | Genome wide Prediction of Disease Variants with a Deep Protein Language Model | 23
Переглядів 1739 місяців тому
Related papers: [1] Rives, A., Meier, J., Sercu, T., Goyal, S., Lin, Z., Liu, J., ... & Fergus, R. (2021). Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. Proceedings of the National Academy of Sciences, 118(15), e2016239118. [2] Frazer, J., Notin, P., Dias, M., Gomez, A., Min, J. K., Brock, K., ... & Marks, D. S. (2021). Disease var...
Iman Hajirasouliha | Applications of Deep Learning in Digital Pathology and Embryology | CGSI 2023
Переглядів 1249 місяців тому
Related papers: 1) A non-invasive artificial intelligence approach for the prediction of human blastocyst ploidy: a retrospective model development and validation study. Barnes J, Brendel M, Gao VR, Rajendran S, Kim J, Li Q, Malmsten JE, Sierra JT, Zisimopoulos P, Sigaras A, Khosravi P, Meseguer M, Zhan Q, Rosenwaks Z, Elemento O, Zaninovic N, Hajirasouliha I. Lancet Digit Health. 2023 Jan;5(1)...
Jeffrey Chiang | Strategies for Integrating Deep Learning with Current Biomedical Research | CGSI 23
Переглядів 1419 місяців тому
Related papers: Rakocz, N., Chiang, J. N., Nittala, M. G., Corradetti, G., Tiosano, L., Velaga, S., Thompson, M., Hill, B. L., Sankararaman, S., Haines, J. L., Pericak-Vance, M. A., Stambolian, D., Sadda, S. R., & Halperin, E. (2021). Automated identification of clinical features from sparsely annotated 3-dimensional medical imaging. Npj Digital Medicine, 4(1), Article 1. doi.org/10.1038/s41746...
Nancy Cox | Confounding sneaks into biobanks in myriad ways… | CGSI 2023
Переглядів 949 місяців тому
Related papers: Okbay, A., et al. (2022). Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals. Nat Genet 54: 437-49. Yengo, L., et al. (2022). A saturated map of common genetic variants associated with human height. Nature 610: 704-712. Berg, J. J., et al. (2019) Reduced signal for polygenic adaptation of heig...
Lisa Bastarache | From Population to Person How to Help a Single, Actual Person with Data Science
Переглядів 1149 місяців тому
Related papers: Vesoulis ZA, Husain AN, Cole FS. Improving child health through Big Data and data science. Pediatr Res. 2023 Jan;93(2):342-349. doi: 10.1038/s41390-022-02264-9. Epub 2022 Aug 16. PMID: 35974162; PMCID: PMC9380977. Phenotypic convergence: a novel phenomenon in the diagnostic process of Mendelian genetic disorders RJ Tinker, J Peterson, L Bastarache medRxiv, 2023.01. 17.23284691 [...
Pengtao Xie | Training Highly Generalizable Biomedical Image Segmentation Models with Very Few Annot
Переглядів 1419 місяців тому
Pengtao Xie | Training Highly Generalizable Biomedical Image Segmentation Models with Very Few Annot
Rajesh Ranganath | Revisiting Out of Distribution Generalization | CGSI 2023
Переглядів 1729 місяців тому
Rajesh Ranganath | Revisiting Out of Distribution Generalization | CGSI 2023
Ron Shamir | Methods for Disease Analysis Using Multiomic Data | CGSI 2023
Переглядів 1269 місяців тому
Ron Shamir | Methods for Disease Analysis Using Multiomic Data | CGSI 2023
Rayan Chikhi | Living in the Future of Genomics | CGSI 2023
Переглядів 3309 місяців тому
Rayan Chikhi | Living in the Future of Genomics | CGSI 2023
Nancy Cox | Ways to Find Confounding in Biobanks | CGSI 2023
Переглядів 1109 місяців тому
Nancy Cox | Ways to Find Confounding in Biobanks | CGSI 2023
Francesco Paolo Casale | Computational Analysis of Liver Whole slide Images Empowers Genomic Analyse
Переглядів 939 місяців тому
Francesco Paolo Casale | Computational Analysis of Liver Whole slide Images Empowers Genomic Analyse
Christoph Lippert | Recent Advances in Normalizing Flows | CGSI 2023
Переглядів 2229 місяців тому
Christoph Lippert | Recent Advances in Normalizing Flows | CGSI 2023
Christoph Lippert | Performing GWAS of Images by Combining Deep Transfer Learning with Statistical T
Переглядів 749 місяців тому
Christoph Lippert | Performing GWAS of Images by Combining Deep Transfer Learning with Statistical T
Wei Li | Computational Biomedicine Epigenetics Liquid Biopsy and Alternative Polyadenylation Therap
Переглядів 959 місяців тому
Wei Li | Computational Biomedicine Epigenetics Liquid Biopsy and Alternative Polyadenylation Therap
Can Alkan | Characterization of Genomic Structural Variation Using Various Sequencing Technologies
Переглядів 879 місяців тому
Can Alkan | Characterization of Genomic Structural Variation Using Various Sequencing Technologies
Wenyi Wang | Statistical Methods for Cancer Risk Prediction Models | CGSI 2023
Переглядів 919 місяців тому
Wenyi Wang | Statistical Methods for Cancer Risk Prediction Models | CGSI 2023
Kenneth Lange | MM Principle of Optimization | CGSI 2023
Переглядів 4509 місяців тому
Kenneth Lange | MM Principle of Optimization | CGSI 2023
Tandy Warnow | Advances in Large scale Multiple Sequence Alignment | CGSI 2023
Переглядів 1209 місяців тому
Tandy Warnow | Advances in Large scale Multiple Sequence Alignment | CGSI 2023
Stefano Lonardi | How to “Squeeze” the Best Genome Assembly From Your HiFi Reads | CGSI 2023
Переглядів 3189 місяців тому
Stefano Lonardi | How to “Squeeze” the Best Genome Assembly From Your HiFi Reads | CGSI 2023
Or Zuk | Independence Tests and Dependence Measures, for Unbiased and Biased Samples | CGSI 2023
Переглядів 339 місяців тому
Or Zuk | Independence Tests and Dependence Measures, for Unbiased and Biased Samples | CGSI 2023
Amazing talk, would love to have a teacher like her ^^ so passionate and fun.
The presenter is so cool!
The Q&A of this should be fun! It's sad that it wasn't included in the video.