Peyton Greenside
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View article: Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences
Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences Open
To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only ty…
View article: Generative Humanization for Therapeutic Antibodies
Generative Humanization for Therapeutic Antibodies Open
Antibody therapies have been employed to address some of today's most challenging diseases, but must meet many criteria during drug development before reaching a patient. Humanization is a sequence optimization strategy that addresses one …
View article: Inverse Protein Folding Using Deep Bayesian Optimization
Inverse Protein Folding Using Deep Bayesian Optimization Open
Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem a…
View article: Supplementary_table_S3 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Supplementary_table_S3 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
table_S3_differential_genes
View article: Data from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Data from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
The extent to which early events shape tumor evolution is largely uncharacterized, even though a better understanding of these early events may help identify key vulnerabilities in advanced tumors. Here, using genetically defined mouse mod…
View article: Supplementary_table_S2 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Supplementary_table_S2 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
table_S2_housekeeping_genes
View article: Supplementary_table_S4 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Supplementary_table_S4 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
table_S4_gene_ontology_combined
View article: Supplementary_table_S4 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Supplementary_table_S4 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
table_S4_gene_ontology_combined
View article: Supplementary_table_S2 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Supplementary_table_S2 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
table_S2_housekeeping_genes
View article: Data from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Data from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
The extent to which early events shape tumor evolution is largely uncharacterized, even though a better understanding of these early events may help identify key vulnerabilities in advanced tumors. Here, using genetically defined mouse mod…
View article: Supplementary_table_S5 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Supplementary_table_S5 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
table_S5_ATACseq_sample_summary
View article: Supplementary Figure S1-S17 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Supplementary Figure S1-S17 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
All supplementary figures (S1-S17)
View article: Supplementary_table_S1 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Supplementary_table_S1 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
table_S1_SCLC_cre model_pathology
View article: Supplementary Figure S1-S17 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Supplementary Figure S1-S17 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
All supplementary figures (S1-S17)
View article: Supplementary_table_S1 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Supplementary_table_S1 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
table_S1_SCLC_cre model_pathology
View article: Supplementary_table_S3 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Supplementary_table_S3 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
table_S3_differential_genes
View article: Supplementary_table_S5 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Supplementary_table_S5 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
table_S5_ATACseq_sample_summary
View article: Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders
Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders Open
Bayesian optimization (BayesOpt) is a gold standard for query-efficient continuous optimization. However, its adoption for drug design has been hindered by the discrete, high-dimensional nature of the decision variables. We develop a new a…
View article: Landscape of cohesin-mediated chromatin loops in the human genome
Landscape of cohesin-mediated chromatin loops in the human genome Open
Physical interactions between distal regulatory elements have a key role in regulating gene expression, but the extent to which these interactions vary between cell types and contribute to cell-type-specific gene expression remains unclear…
View article: A Hierarchical Approach to Scaling Batch Active Search Over Structured\n Data
A Hierarchical Approach to Scaling Batch Active Search Over Structured\n Data Open
Active search is the process of identifying high-value data points in a large\nand often high-dimensional parameter space that can be expensive to evaluate.\nTraditional active search techniques like Bayesian optimization trade off\nexplor…
View article: A Hierarchical Approach to Scaling Batch Active Search Over Structured Data
A Hierarchical Approach to Scaling Batch Active Search Over Structured Data Open
Active search is the process of identifying high-value data points in a large and often high-dimensional parameter space that can be expensive to evaluate. Traditional active search techniques like Bayesian optimization trade off explorati…
View article: LD matrices for 1000 genomes phase 1 files for EUR and YRI
LD matrices for 1000 genomes phase 1 files for EUR and YRI Open
Pairwise LD values >=0.8 are stored for SNPs from the Phase1 1000 Genomes panel Format: chr_snp1 start_snp1 end_snp1 rsid_snp1 chr_snp2 start_snp2 end_snp2 rsid_snp2 r^2 (D' provided in some files) EUR_hap.txt from Pouya Kheradpour (Kellis…
View article: LD matrices for 1000 genomes phase 1 files for EUR and YRI
LD matrices for 1000 genomes phase 1 files for EUR and YRI Open
Pairwise LD values >=0.8 are stored for SNPs from the Phase1 1000 Genomes panel Format: chr_snp1 start_snp1 end_snp1 rsid_snp1 chr_snp2 start_snp2 end_snp2 rsid_snp2 r^2 (D' provided in some files) EUR_hap.txt from Pouya Kheradpour (Kellis…
View article: Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays
Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays Open
The relationship between noncoding DNA sequence and gene expression is not well-understood. Massively parallel reporter assays (MPRAs), which quantify the regulatory activity of large libraries of DNA sequences in parallel, are a powerful …
View article: Identification and mitigation of pervasive off-target activity in CRISPR-Cas9 screens for essential non-coding elements
Identification and mitigation of pervasive off-target activity in CRISPR-Cas9 screens for essential non-coding elements Open
Pooled CRISPR-Cas9 screens have recently emerged as a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, w…
View article: CrowdVariant: a crowdsourcing approach to classify copy number variants
CrowdVariant: a crowdsourcing approach to classify copy number variants Open
Copy number variants (CNVs) are an important type of genetic variation that play a causal role in many diseases. The ability to identify high quality CNVs is of substantial clinical relevance. However, CNVs are notoriously difficult to ide…
View article: Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin Open
The extent to which early events shape tumor evolution is largely uncharacterized, even though a better understanding of these early events may help identify key vulnerabilities in advanced tumors. Here, using genetically defined mouse mod…