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Bonnie Berger

Bonnie Berger

D-Index & Metrics

Biology and Biochemistry

D-Index
89
Citations
38217
World Ranking
2512
National Ranking
1321

Research.com Recognitions

  • 2020 - Member of the National Academy of Sciences
  • 2019 - Fellow of the American Mathematical Society For contributions to computational biology, bioinformatics, algorithms and for mentoring.
  • 2016 - Fellow of the Indian National Academy of Engineering (INAE)
  • 2012 - Fellow of the American Academy of Arts and Sciences

Overview

Bonnie Berger is affiliated with MIT in the United States and has contributed extensively to the fields of Biochemistry, Genetics, and Molecular Biology. Their research spans multiple subfields, including Molecular Biology, Artificial Intelligence, Immunology, Genetics, and Infectious Diseases.

The scientist's work covers a broad range of main topics, such as:

  • Single-cell and spatial transcriptomics
  • Genomics and Phylogenetic Studies
  • Protein Structure and Dynamics
  • RNA and protein synthesis mechanisms
  • Machine Learning in Bioinformatics
  • Bioinformatics and Genomic Networks
  • Privacy-Preserving Technologies in Data

Bonnie Berger has published prolifically, with frequent appearances in venues including:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • arXiv (Cornell University)
  • Zenodo (CERN European Organization for Nuclear Research)
  • Cell Systems
  • Proceedings of the National Academy of Sciences

Recent notable papers include:

  • "SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues," 2020, Cell
  • "CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks," 2021, Nature Methods
  • "Topaz-Denoise: general deep denoising models for cryoEM and cryoET," 2020, Nature Communications
  • "Learning the protein language: Evolution, structure, and function," 2021, Cell Systems
  • "High-resolutionde novostructure prediction from primary sequence," 2022, bioRxiv (Cold Spring Harbor Laboratory)

Collaboration has been a significant element of Berger's career, with frequent co-authors including Rohit Singh, Samuel Sledzieski, Hyunghoon Cho, Sarah K. Nyquist, and Alex K. Shalek.

Awards and honors received by Berger include:

  • Member of the National Academy of Sciences, 2020
  • Fellow of the American Mathematical Society, 2019, for contributions to computational biology, bioinformatics, algorithms and mentoring
  • Fellow of the Indian National Academy of Engineering (INAE), 2016
  • Fellow of the American Academy of Arts and Sciences, 2012

Best Publications

  • SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.

    Carly G.K. Ziegler;Samuel J. Allon;Sarah K. Nyquist;Ian M. Mbano

  • Efficient Bayesian mixed-model analysis increases association power in large cohorts

    Po-Ru Loh;George Tucker;Brendan K Bulik-Sullivan;Bjarni J Vilhjálmsson;Bjarni J Vilhjálmsson

  • Ancient human genomes suggest three ancestral populations for present-day Europeans

    Iosif Lazaridis;Iosif Lazaridis;Nick Patterson;Alissa Mittnik;Gabriel Renaud

  • Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

    Sushmita Roy;Jason Ernst;Peter V. Kharchenko;Pouya Kheradpour

  • SARS-CoV-2 Receptor ACE2 is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Enriched in Specific Cell Subsets Across Tissues

    Carly Ziegler;Samuel J. Allon;Sarah K. Nyquist;Ian Mbano

  • Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs.

    Tristan Bepler;Andrew Morin;Micah Rapp;Julia Brasch

  • MultiCoil: A program for predicting two‐and three‐stranded coiled coils

    Ethan Wolf;Peter S. Kim;Bonnie Berger

  • Predicting coiled coils by use of pairwise residue correlations.

    Bonnie Berger;David B. Wilson;Ethan Wolf;Theodore Tonchev

  • Global alignment of multiple protein interaction networks with application to functional orthology detection.

    Rohit Singh;Jinbo Xu;Bonnie Berger

  • ARACHNE: A Whole-Genome Shotgun Assembler

    Serafim Batzoglou;David B. Jaffe;Ken Stanley;Jonathan Butler

  • An integrative approach to ortholog prediction for disease-focused and other functional studies

    Yanhui Hu;Ian Flockhart;Arunachalam Vinayagam;Clemens Bergwitz

  • Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.

    Brian Hie;Bryan Bryson;Bonnie Berger

  • Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete.

    Bonnie Berger;Tom Leighton

  • Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

    Nidhi Sahni;Song Yi;Mikko Taipale;Juan I. Fuxman Bass

  • Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction

    Serafim Batzoglou;Lior Pachter;Jill P. Mesirov;Bonnie Berger

  • Paircoil2: improved prediction of coiled coils from sequence

    A. V. Mcdonnell;T. Jiang;A. E. Keating;B. Berger

  • Herpesviral Protein Networks and Their Interaction with the Human Proteome

    Peter Uetz;Yu-An Dong;Yu-An Dong;Christine Zeretzke;Christine Zeretzke;Christine Atzler;Christine Atzler

  • Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium

    Po-Ru Loh;Mark Lipson;Nick Patterson;Priya Moorjani;Priya Moorjani

  • Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete

    Bonnie Berger;Tom Leighton

  • An integrative approach to ortholog prediction for disease-focused and other functional studies

    Yanhui Hu;Ian Flockhart;Arunachalam Vinayagam;Clemens Bergwitz

Frequent Co-Authors

Jian Peng
Jian Peng University of Illinois at Urbana-Champaign
David Reich
David Reich Harvard Medical School
Po-Ru Loh
Po-Ru Loh Harvard Medical School
Nick Patterson
Nick Patterson Harvard University
Norbert Perrimon
Norbert Perrimon Harvard University
George Tucker
George Tucker Google (United States)
Jinbo Xu
Jinbo Xu Toyota Technological Institute at Chicago
Isaac S. Kohane
Isaac S. Kohane Harvard University
Eric S. Lander
Eric S. Lander Broad Institute

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