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Novel computational frameworks for driver gene identification and evolutionary informed genomics analysis in melanoma and prostate cancer
(2022-01-20)
We performed harmonized molecular and clinical analysis on 1,048 melanoma whole-exomes and discovered markedly different global genomic properties among genomic subtypes (BRAF, (N)RAS, NF1, Triple Wild-Type), subtype-specific ...
Integration of common and rare genetic variation across complex traits and neuropsychiatric disorders
(2022-09-08)
Research into the genetic basis of human disease has progressed rapidly over the past 20 years. Genome-wide association studies have identified thousands of links between common variants and phenotypic outcomes. More ...
Transposable Elements in Health and Disease
(2021-11-16)
Transposable elements are DNA sequences that can move within the genome. They play a pivotal role in genomic variability in humans and can cause diseases. Their repetitive nature requires specific computational algorithms ...
Development and validation of computational models for efficient design of biological sequences
(2022-01-10)
There is a huge surge of interest in designing a wide variety of proteins to use as molecular research tools and biotherapeutics - promising to revolutionize our capacity to design what we need at will. This is particularly ...
Risk Prediction and Calibration with Weak Supervision using the Electronic Health Record
(2021-01-05)
Electronic health records (EHRs) promise unprecedented opportunities for in silico clinical and translational discovery ranging from disease risk prediction to survival analysis. However, the scarcity of reliable labels ...
Mesoscopic physiological interactions in the human brain reveal small-world properties and associations with behavior
(2021-04-29)
Cognition depends on rapid and robust communication between neural circuits spanning different brain areas. Here we investigated the mesoscopic network of cortico-cortical interactions in the human brain in an extensive ...
Longitudinal Evolutionary Dynamics of HIV Escape from Broadly Neutralizing Antibodies
(2021-03-05)
We conducted experimental in vivo evolution of HIV to understand how the virus mutates to resist broadly neutralizing antibodies (bNAbs). In the first part, we longitudinally sequenced HIV escape from bNAbs in humanized ...
Characterization of the functions and therapeutic potential of deubiquitinating enzymes in oncology
(2021-09-02)
DUBs are dysregulated in cancer and other diseases, but there is much that is unknown about the specific substrates and pathways that individual DUBs regulate and their clinical utility remains incompletely explored. In ...
Learning Inductive Representations of Biomedical Data
(2020-09-15)
Representation learning with neural networks has catalyzed rapid progress in biomedical pattern recognition. This progress, however, has generally been limited to domains where data are abundant, richly structured, and ...
Integrating large-scale genomics data to improve variant interpretation in coding and non-coding regions
(2021-05-06)
Large-scale human population genomic studies have significantly accelerated our understanding of genetic contributions of rare and common diseases; approaches include genome wide association studies (GWAS) utilizing single ...