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Author Details

Bonnie Berger
Massachusetts Institute of Technology
1994
227
57
Emma Lundberg (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36376590Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN.Nat Protoc2023
37626411SCA: recovering single-cell heterogeneity through information-based dimensionality reduction.Genome Biol2023
37558282Efficient minimizer orders for large values of <i>k</i> using minimum decycling sets.Genome Res2023
37541758Assessing transcriptomic reidentification risks using discriminative sequence models.Genome Res2023
36993523split-intein Gal4 provides intersectional genetic labeling that is fully repressible by Gal80.bioRxiv2023
37289807Contrastive learning in protein language space predicts interactions between drugs and protein targets.Proc Natl Acad Sci U S A2023
37246709sfkit: a web-based toolkit for secure and federated genomic analysis.Nucleic Acids Res2023
37276389split-intein Gal4 provides intersectional genetic labeling that is repressible by Gal80.Proc Natl Acad Sci U S A2023
37399256Efficient mapping of accurate long reads in minimizer space with mapquik.Genome Res2023
37064532EigenFold: Generative Protein Structure Prediction with Diffusion Models.ArXiv2023
37028419Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens.Mol Cell2023
36476810Navigating bottlenecks and trade-offs in genomic data analysis.Nat Rev Genet2023
36747646Strain Tracking with Uncertainty Quantification.bioRxiv2023
36631897Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing.Genome Biol2023
36125448virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.J Comput Biol2023
35238654Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization.Proc Natl Acad Sci U S A2022
35377806Cellular and transcriptional diversity over the course of human lactation.Proc Natl Acad Sci U S A2022
35726091Genome-wide mapping of somatic mutation rates uncovers drivers of cancer.Nat Biotechnol2022
35853968Conformational landscape of the yeast SAGA complex as revealed by cryo-EM.Sci Rep2022
35758793Topsy-Turvy: integrating a global view into sequence-based PPI prediction.Bioinformatics2022
35483355Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control.Immunity2022
36330531HIV specific CD8<sup>+</sup> T<sub>RM</sub>-like cells in tonsils express exhaustive signatures in the absence of natural HIV control.Front Immunol2022
35958356Sequre: a high-performance framework for rapid development of secure bioinformatics pipelines.IEEE Int Symp Parallel Distrib Process Workshops Phd Forum2022
36087201Enriching and Characterizing T Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products.Methods Mol Biol2022
35014856Predicting the mutational drivers of future SARS-CoV-2 variants of concern.Sci Transl Med2022
33318703Structures of radial spokes and associated complexes important for ciliary motility.Nat Struct Mol Biol2021
33542510CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks.Nat Methods2021
33637594Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation.Sci Immunol2021
34764286Author Correction: Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption.Nat Commun2021
34525345Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.Cell Syst2021
34635645Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption.Nat Commun2021
34536380D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions.Cell Syst2021
34252956Bayesian information sharing enhances detection of regulatory associations in rare cell types.Bioinformatics2021
34252054HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells.JCI Insight2021
33941239Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities.Genome Biol2021
34210851An engineered protein-phosphorylation toggle network with implications for endogenous network discovery.Science2021
34282326A Python-based programming language for high-performance computational genomics.Nat Biotechnol2021
34257466Levenshtein Distance, Sequence Comparison and Biological Database Search.IEEE Trans Inf Theory2021
34139171Learning the protein language: Evolution, structure, and function.Cell Syst2021
33462509Assessing single-cell transcriptomic variability through density-preserving data visualization.Nat Biotechnol2021
33432194Large mosaic copy number variations confer autism risk.Nat Neurosci2021
33446556Learning the language of viral evolution and escape.Science2021
32359425Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs.Cell Syst2020
31860066Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation.Bioinformatics2020
32093762Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads.Genome Biol2020
33060581Topaz-Denoise: general deep denoising models for cryoEM and cryoET.Nat Commun2020
33065027Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design.Cell Syst2020
32938926Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets.Nat Commun2020
30963078Protecting Genomic Data Privacy with Probabilistic Modeling.Pac Symp Biocomput2019
35775031Seq: A High-Performance Language for Bioinformatics.Proc ACM Program Lang2019
  • 1 - 50 of 227

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Collaborators

Jian Peng
University of Illinois
Co-authored papers 22
Hyunghoon Cho
Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Stanford University, Yale University
Co-authored papers 21
Lenore J Cowen
Tufts University, 177 College Avenue
Co-authored papers 13
Norbert Perrimon
Co-authored papers 11
Nick Patterson
Harvard University
Co-authored papers 11
Ibrahim Numanagi??
University of Victoria
Co-authored papers 9
David Reich
Co-authored papers 9
Alex K Shalek
Institute for Medical Engineering & Science, Massachusetts Institute of Technology
Co-authored papers 8
Jinbo Xu
Toyota Technological Institute at Chicago
Co-authored papers 8
Ariya Shajii
Massachusetts Institute of Technology
Co-authored papers 7
Bryan D Bryson
Massachusetts Institute of Technology, USA The Ragon Institute of MGH
Co-authored papers 7
Brian Hie
Stanford University
Co-authored papers 7
Susan Lindquist
Whitehead Institute for Biomedical Research
Co-authored papers 7
Isaac S Kohane
Harvard Medical School
Co-authored papers 6
Sean K Simmons
Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard
Co-authored papers 6
Jadwiga Bienkowska
Pfizer Global Research and Development La Jolla
Co-authored papers 6
Nathan Palmer
Harvard Medical School
Co-authored papers 6
Eric S Lander
Vanderbilt-Ingram Cancer Center, Vanderbilt University
Co-authored papers 5
Aviv Regev
Broad Institute of MIT and Harvard
Co-authored papers 5
Manolis Kellis
Massachusetts Institute of Technology
Co-authored papers 4
Serafim Batzoglou
Co-authored papers 4
Jill P Mesirov
University of California San Diego
Co-authored papers 3
Alfonso Valencia
Josep Carreras Leukaemia Research Institute (IJC)
Co-authored papers 3
Kenneth D Mandl
Boston Children's Hospital
Co-authored papers 3
Jose Ordovas-Montanes
Co-authored papers 3
Alkes L Price
Broad Institute of MIT and Harvard
Co-authored papers 3
Yanhui Hu
Co-authored papers 3
Ryan Kim
Inc. (formerly Macrogen USA)
Co-authored papers 3
Lawrence Shapiro
Zuckerman Mind Brain Behaviour Institute
Co-authored papers 3
Terry Gaasterland
Scripps Institution of Oceanography, University of California San Diego
Co-authored papers 3
Release 1.2