P. Greenside

发表

Learning Important Features Through Propagating Activation Differences pdf

Avanti Shrikumar, Anshul Kundaje, Peyton Greenside, 2017, ICML.

Not Just a Black Box: Learning Important Features Through Propagating Activation Differences pdf

Anna Shcherbina, Avanti Shrikumar, Anshul Kundaje, 2016, ArXiv.

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles

Angela N. Brooks, Jacob K. Asiedu, Joshua A. Bittker, 2017, Cell.

Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution

Howard Y. Chang, Jason D. Buenrostro, A. Kundaje, 2016, Nature Genetics.

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

Judith B. Zaugg, Alicia R. Martin, Fabian Grubert, 2015, Cell.

Effective Surrogate Models for Protein Design with Bayesian Optimization

A. G. Wilson, Phillip M. Maffettone, P. Greenside, 2021 .

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

Nicholas A. Sinnott-Armstrong, Howard Y. Chang, Viviana I. Risca, 2017, Nature Methods.

Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds

A. Butte, D. Hadley, Bin Chen, 2015, CPT: pharmacometrics & systems pharmacology.

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

Howard Y. Chang, Ansuman T. Satpathy, Ryan A. Flynn, 2017, Nature Genetics.

Supplementary Information for Impact of regulatory variation across human iPSCs and differentiated cells

Anshul Kundaje, Samantha M Thomas, Yoav Gilad, 2017 .

Discovery of common and rare genetic risk variants for colorectal cancer

Mathieu Lemire, Steven Gallinger, Michael Wainberg, 2018, Nature Genetics.

Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data

Mathieu Lemire, Steven Gallinger, Anshul Kundaje, 2017, PloS one.

Discovering epistatic feature interactions from neural network models of regulatory DNA sequences

Tyler C. Shimko, A. Kundaje, P. Greenside, 2018, bioRxiv.

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays

Avanti Shrikumar, Anshul Kundaje, Peyton Greenside, 2018, bioRxiv.

Landscape of cohesin-mediated chromatin loops in the human genome

Judith B. Zaugg, Fabian Grubert, Michael P. Snyder, 2020, Nature.

Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin.

A. Kundaje, J. Sage, N. Jahchan, 2018, Cancer discovery.

Omni-ATAC-seq: Improved ATAC-seq protocol

Nicholas A. Sinnott-Armstrong, Howard Y. Chang, Viviana I. Risca, 2017 .

Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders

Wesley J. Maddox, Phillip M. Maffettone, P. Greenside, 2022, ICML.

Molecular definition of a metastatic lung cancer state reveals a targetable CD109–Janus kinase–Stat axis

A. Kundaje, Dian Yang, P. Greenside, 2017, Nature Medicine.

An Arntl2-Driven Secretome Enables Lung Adenocarcinoma Metastatic Self-Sufficiency.

A. Kundaje, P. Greenside, A. Connolly, 2016, Cancer cell.

Discovering epistatic feature interactions from neural network models of regulatory DNA sequences

Anshul Kundaje, Tyler C. Shimko, Peyton Greenside, 2018, bioRxiv.

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements

Michael P Snyder, Michael Wainberg, Anshul Kundaje, 2019, Nature Communications.

Identification and mitigation of pervasive off-target activity in CRISPR-Cas9 screens for essential non-coding elements

Michael Wainberg, Anshul Kundaje, Oana Ursu, 2019, bioRxiv.

Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map

Ted Natoli, Aravind Subramanian, David Wadden, 2017, bioRxiv.

Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements

Trieu Nguyen, Anshul Kundaje, Howard Y. Chang, 2017, bioRxiv.

PyBoost: A parallelized Python implementation of 2D boosting with hierarchies

Jessica K. Chang, A. Kundaje, N. Hussami, 2017, bioRxiv.

Reverse-complement parameter sharing improves deep learning models for genomics

Avanti Shrikumar, Anshul Kundaje, Peyton Greenside, 2017, bioRxiv.

CrowdVariant: a crowdsourcing approach to classify copy number variants

Ryan Poplin, Justin M. Zook, Mark A. DePristo, 2016, bioRxiv.

Inverse Protein Folding Using Deep Bayesian Optimization

Phillip M. Maffettone, P. Greenside, Yimeng Zeng, 2023, ArXiv.

Discovery of common and rare genetic risk variants for colorectal cancer

Stephanie A. Bien, Aung Ko Win, Sarah C. Nelson, 2018, Nature Genetics.

Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures

Anshul Kundaje, Peyton Greenside, Maureen Hillenmeyer, 2018, PSB.