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J. Listgarten · SciRah

Researcher profile · Semantic Scholar

J. Listgarten

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J. Listgarten — researcher profile on SciRah

h-index: 38
Works: 87
Citations: 11K

Most-cited papers

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
John G Doench, N. Fusi, M. Sullender, M. Hegde +9 more
2016Nature Biotechnology4,198 citations Open access
Semantic Scholar
FaST linear mixed models for genome-wide association studies
Christoph Lippert, J. Listgarten, Ying Liu, C. Kadie +2 more
2011Nature Methods1,204 citations
Semantic Scholar
Rethinking drug design in the artificial intelligence era
P. Schneider, W. Walters, A. Plowright, Norman Sieroka +14 more
2019Nature reviews. Drug discovery766 citations
Semantic Scholar
Improved linear mixed models for genome-wide association studies
J. Listgarten, Christoph Lippert, C. Kadie, R. Davidson +2 more
2012Nature Methods404 citations Open access
Semantic Scholar
Statistical and Computational Methods for Comparative Proteomic Profiling Using Liquid Chromatography-Tandem Mass Spectrometry
J. Listgarten, A. Emili
2005Molecular & Cellular Proteomics319 citations Open access
Semantic Scholar
Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs
J. Listgarten, Michael Weinstein, B. Kleinstiver, Alexander Sousa +7 more
2018Nature Biomedical Engineering314 citations Open access
Semantic Scholar
Orthologous CRISPR-Cas9 enzymes for Combinatorial Genetic Screens
Fadi J. Najm, Christine Strand, K. Donovan, M. Hegde +11 more
2017Nature Biotechnology259 citations Open access
Semantic Scholar
Conditioning by adaptive sampling for robust design
David H. Brookes, Hahnbeom Park, J. Listgarten
2019International Conference on Machine Learning245 citations
Semantic Scholar
Learning protein fitness models from evolutionary and assay-labeled data
Chloe Hsu, Hunter M. Nisonoff, Clara Fannjiang, J. Listgarten
2022Nature Biotechnology224 citations
Semantic Scholar
Epigenome-wide association studies without the need for cell-type composition
J. Zou, Christoph Lippert, D. Heckerman, M. Aryee +1 more
2014Nature Methods223 citations
Semantic Scholar
Predictive Models for Breast Cancer Susceptibility from Multiple Single Nucleotide Polymorphisms
J. Listgarten, S. Damaraju, B. Poulin, Lillian M. Cook +6 more
2004Clinical Cancer Research187 citations
Semantic Scholar
Additive Contribution of HLA Class I Alleles in the Immune Control of HIV-1 Infection
A. Leslie, P. Matthews, J. Listgarten, J. Carlson +7 more
2010Journal of Virology182 citations Open access
Semantic Scholar
Gaussian Process Prior Variational Autoencoders
F. Casale, Adrian V. Dalca, Luca Saglietti, J. Listgarten +1 more
2018Neural Information Processing Systems176 citations
Semantic Scholar
A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control
I. Bartha, J. Carlson, C. Brumme, Paul J. McLaren +25 more
2013eLife176 citations Open access
Semantic Scholar
Correction for hidden confounders in the genetic analysis of gene expression
J. Listgarten, C. Kadie, E. Schadt, D. Heckerman
2010Proceedings of the National Academy of Sciences of the United States of America167 citations Open access
Semantic Scholar
Multiple Alignment of Continuous Time Series
J. Listgarten, Radford M. Neal, S. Roweis, A. Emili
2004Neural Information Processing Systems156 citations
Semantic Scholar
Widespread Impact of HLA Restriction on Immune Control and Escape Pathways of HIV-1
J. Carlson, J. Listgarten, Nico Pfeifer, Vincent Y. F. Tan +8 more
2012Journal of Virology140 citations Open access
Semantic Scholar
Extensive HLA class I allele promiscuity among viral CTL epitopes
N. Frahm, K. Yusim, T. Suscovich, S. Adams +25 more
2007European Journal of Immunology133 citations Open access
Semantic Scholar
Lymphovascular Invasion Is Associated With Poor Survival in Gastric Cancer: An Application of Gene-Expression and Tissue Array Techniques
Bryan J. Dicken, K. Graham, S. Hamilton, S. Andrews +6 more
2006Annals of Surgery130 citations Open access
Semantic Scholar
Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1
J. Carlson, C. Brumme, E. Martin, J. Listgarten +17 more
2012Journal of Virology121 citations Open access
Semantic Scholar
let-7 miRNAs Can Act through Notch to Regulate Human Gliogenesis
Michaela Patterson, X. Gaeta, K. Loo, M. Edwards +8 more
2014Stem Cell Reports102 citations Open access
Semantic Scholar
Conformal prediction under feedback covariate shift for biomolecular design
Clara Fannjiang, Stephen Bates, Anastasios Nikolas Angelopoulos, J. Listgarten +1 more
2022Proceedings of the National Academy of Sciences of the United States of America97 citations Open access
Semantic Scholar
Autofocused oracles for model-based design
Clara Fannjiang, J. Listgarten
2020Neural Information Processing Systems90 citations
Semantic Scholar
Difference detection in LC-MS data for protein biomarker discovery
J. Listgarten, Radford M. Neal, S. Roweis, Peter Wong +1 more
2007Bioinform.90 citations Open access
Semantic Scholar
A powerful and efficient set test for genetic markers that handles confounders
J. Listgarten, Christoph Lippert, E. Kang, Jing Xiang +2 more
2012Bioinform.81 citations Open access
Semantic Scholar
Design by adaptive sampling
David H. Brookes, J. Listgarten
2018arXiv.org79 citations
Semantic Scholar
Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction
D. Heckerman, C. Kadie, J. Listgarten
2006Annual International Conference on Research in Computational Molecular Biology79 citations Open access
Semantic Scholar
FaST-LMM-Select for addressing confounding from spatial structure and rare variants
J. Listgarten, Christoph Lippert, D. Heckerman
2013Nature Genetics78 citations
Semantic Scholar
An Exhaustive Epistatic SNP Association Analysis on Expanded Wellcome Trust Data
Christoph Lippert, J. Listgarten, R. Davidson, S. Baxter +3 more
2013Scientific Reports77 citations Open access
Semantic Scholar
Optimal trade-off control in machine learning–based library design, with application to adeno-associated virus (AAV) for gene therapy
Danqing Zhu, David H. Brookes, A. Busia, A. Carneiro +11 more
2021bioRxiv75 citations Open access
Semantic Scholar
Further Improvements to Linear Mixed Models for Genome-Wide Association Studies
Christian Widmer, Christoph Lippert, Omer Weissbrod, N. Fusi +4 more
2014Scientific Reports71 citations Open access
Semantic Scholar
Statistical Resolution of Ambiguous HLA Typing Data
J. Listgarten, Z. Brumme, C. Kadie, Xiao-Jiang Gao +4 more
2008PLoS Comput. Biol.63 citations Open access
Semantic Scholar
HLA-A*7401–Mediated Control of HIV Viremia Is Independent of Its Linkage Disequilibrium with HLA-B*5703
P. Matthews, E. Adland, J. Listgarten, A. Leslie +24 more
2011Journal of Immunology61 citations Open access
Semantic Scholar
The benefits of selecting phenotype-specific variants for applications of mixed models in genomics
Christoph Lippert, G. Quon, E. Kang, C. Kadie +2 more
2013Scientific Reports57 citations Open access
Semantic Scholar
On the sparsity of fitness functions and implications for learning
David H. Brookes, Amirali Aghazadeh, J. Listgarten
2021Proceedings of the National Academy of Sciences of the United States of America55 citations Open access
Semantic Scholar
Epistatic Net allows the sparse spectral regularization of deep neural networks for inferring fitness functions
Amirali Aghazadeh, Hunter M. Nisonoff, Orhan Ocal, David H. Brookes +4 more
2021Nature Communications54 citations Open access
Semantic Scholar
Patterns of methylation heritability in a genome-wide analysis of four brain regions
G. Quon, Christoph Lippert, D. Heckerman, J. Listgarten
2013Nucleic Acids Research52 citations Open access
Semantic Scholar
Greater power and computational efficiency for kernel-based association testing of sets of genetic variants
Christoph Lippert, Jing Xiang, D. Horta, Christian Widmer +3 more
2014Bioinform.42 citations Open access
Semantic Scholar
In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency
N. Fusi, I. Smith, John G Doench, J. Listgarten
2015bioRxiv36 citations Open access
Semantic Scholar
Evidence that dysregulated DNA mismatch repair characterizes human nonmelanoma skin cancer
L. C. Young, J. Listgarten, M. Trotter, S. Andrew +1 more
2007British Journal of Dermatology31 citations
Semantic Scholar
Co-Operative Additive Effects between HLA Alleles in Control of HIV-1
P. Matthews, J. Listgarten, J. Carlson, R. Payne +14 more
2012PLoS ONE30 citations Open access
Semantic Scholar
Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.
J. Dudley, J. Listgarten, O. Stegle, S. Brenner +1 more
2014Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing29 citations Open access
Semantic Scholar
Combining evolutionary and assay-labelled data for protein fitness prediction
Chloe Hsu, Hunter M. Nisonoff, Clara Fannjiang, J. Listgarten
2021bioRxiv28 citations Open access
Semantic Scholar
Determining the Number of Non-Spurious Arcs in a Learned DAG Model: Investigation of a Bayesian and a Frequentist Approach
J. Listgarten, D. Heckerman
2007Conference on Uncertainty in Artificial Intelligence27 citations
Semantic Scholar
Practical proteomic biomarker discovery: taking a step back to leap forward.
J. Listgarten, A. Emili
2005Drug Discovery Today26 citations
Semantic Scholar
A view of estimation of distribution algorithms through the lens of expectation-maximization
David H. Brookes, A. Busia, Clara Fannjiang, Kevin P. Murphy +1 more
2019GECCO Companion24 citations Open access
Semantic Scholar
Analysis of sibling time series data: Alignment and difference detection
J. Listgarten
200720 citations
Semantic Scholar
Bayesian Detection of Infrequent Differences in Sets of Time Series with Shared Structure
J. Listgarten, Radford M. Neal, S. Roweis, Rachel Puckrin +1 more
2006Neural Information Processing Systems19 citations
Semantic Scholar
Is novelty predictable?
Clara Fannjiang, J. Listgarten
2023Cold Spring Harbor Perspectives in Biology18 citations Open access
Semantic Scholar
Rare HLA Drive Additional HIV Evolution Compared to More Frequent Alleles
Christine M. Rousseau, D. Lockhart, J. Listgarten, Stephen N. Maley +12 more
2009AIDS Research and Human Retroviruses13 citations Open access
Semantic Scholar

Frequent co-authors

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D. Heckerman×21
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Christoph Lippert×10
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N. Fusi×7
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Clara Fannjiang

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David H. Brookes×6

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