Bonnie Berger

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 37

Top Topics

Genome Wide Association

Top Venues

Nature biotechnology

Nature protocols

Nature communications

This page only lists publications with an associated author ORCID identifier.

Publications

Brian L Hie, Soochi Kim, Thomas A Rando, Bryan Bryson, Bonnie Berger
Scanorama: integrating large and diverse single-cell transcriptomic datasets. Nature protocols (2024)
Brian L Hie, Soochi Kim, Thomas A Rando, Bryan Bryson, Bonnie Berger
Scanorama: integrating large and diverse single-cell transcriptomic datasets. Nature protocols 19 (8) (2024)
Brian L Hie, Soochi Kim, Thomas A Rando, Bryan Bryson, Bonnie Berger
Scanorama: integrating large and diverse single-cell transcriptomic datasets. Nature protocols 19 (8) (2024)
Brian L Hie, Soochi Kim, Thomas A Rando, Bryan Bryson, Bonnie Berger
Scanorama: integrating large and diverse single-cell transcriptomic datasets. Nature protocols 19 (8) (2024)
Brian L Hie, Soochi Kim, Thomas A Rando, Bryan Bryson, Bonnie Berger
Scanorama: integrating large and diverse single-cell transcriptomic datasets. Nature protocols (2024)
Samuel Sledzieski, Meghana Kshirsagar, Minkyung Baek, Bonnie Berger, Rahul Dodhia, Juan M Lavista Ferres
Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning. bioRxiv : the preprint server for biology (2023)
Simon Mendelsohn, David Froelicher, Denis Loginov, David Bernick, Bonnie Berger, Hyunghoon Cho
sfkit: a web-based toolkit for secure and federated genomic analysis. Nucleic acids research (2023)
Barış Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi
Efficient mapping of accurate long reads in minimizer space with mapquik. Genome research (2023)
Caylin G Winchell, Sarah K Nyquist, Michael C Chao, Pauline Maiello, Amy J Myers, Forrest Hopkins, Michael R Chase, Hannah Priyadarshini Gideon, Kush V Patel, Joshua D Bromley, Andrew W Simonson, Roisin Floyd-O'Sullivan, Marc H Wadsworth, Jacob M Rosenberg, Rockib Uddin, Travis Hughes, Ryan J Kelly, Josephine Griffo, Jaime Tomko, Edwin Klein, Bonnie Berger, Charles A Scanga, Joshua T Mattila, Sarah M Fortune, Alex K Shalek, Philana Ling Lin, Joanne L Flynn
CD8+ lymphocytes are critical for early control of tuberculosis in macaques. The Journal of experimental medicine 220 (12) (2023)
Shuvom Sadhuka, Daniel Fridman, Bonnie Berger, Hyunghoon Cho
Assessing transcriptomic reidentification risks using discriminative sequence models. Genome research (2023)
Ben Ewen-Campen, Haojiang Luan, Jun Xu, Rohit Singh, Neha Joshi, Tanuj Thakkar, Bonnie Berger, Benjamin H White, Norbert Perrimon
split-intein Gal4 provides intersectional genetic labeling that is fully repressible by Gal80. bioRxiv : the preprint server for biology (2023)
Benjamin DeMeo, Bonnie Berger
SCA: recovering single-cell heterogeneity through information-based dimensionality reduction. Genome biology 24 (1) (2023)
Bonnie Berger, Yun William Yu
Navigating bottlenecks and trade-offs in genomic data analysis. Nature reviews. Genetics (2022)
Daniel F Dwyer, José Ordovas-Montañes, Samuel J Allon, Kathleen M Buchheit, Marko Vukovic, Tahereh Derakhshan, Chunli Feng, Juying Lai, Travis K Hughes, Sarah K Nyquist, Matthew P Giannetti, Bonnie Berger, Neil Bhattacharyya, Rachel E Roditi, Howard R Katz, Martijn C Nawijn, Marijn Berg, Maarten van den Berge, Tanya M Laidlaw, Alex K Shalek, Nora A Barrett, Joshua A Boyce
Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation. Science immunology 6 (56) (2022)
Maxwell A Sherman, Adam U Yaari, Oliver Priebe, Felix Dietlein, Po-Ru Loh, Bonnie Berger
Genome-wide mapping of somatic mutation rates uncovers drivers of cancer. Nature biotechnology 40 (11) (2022)
Rohit Singh, Kapil Devkota, Samuel Sledzieski, Bonnie Berger, Lenore J Cowen
Topsy-Turvy: integrating a global view into sequence-based PPI prediction. Bioinformatics (Oxford, England) 38 (Suppl 1) (2022)
M Cyrus Maher, István Bartha, Steven Weaver, Julia di Iulio, Elena Ferri, Leah B Soriaga, Florian A Lempp, Brian L Hie, Bryan D Bryson, Bonnie Berger, David L Robertson, Gyorgy Snell, Davide Corti, Herbert W Virgin, Sergei L Kosakovsky Pond, Amalio Telenti
Predicting the mutational drivers of future SARS-CoV-2 variants of concern. Science translational medicine 14 (633) (2022)
Deepak Mishra, Tristan Bepler, Brian Teague, Bonnie Berger, James R Broach, Ron Weiss
An engineered protein-phosphorylation toggle network with implications for endogenous network discovery. Science (New York, N.Y.) 373 (6550) (2021)
Ellen D Zhong, Tristan Bepler, Bonnie Berger, Joseph H Davis
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nature methods 18 (2) (2021)
Alexander P Wu, Jian Peng, Bonnie Berger, Hyunghoon Cho
Bayesian information sharing enhances detection of regulatory associations in rare cell types. Bioinformatics (Oxford, England) 37 (Suppl_1) (2021)
Ariya Shajii, Ibrahim Numanagić, Alexander T Leighton, Haley Greenyer, Saman Amarasinghe, Bonnie Berger
A Python-based programming language for high-performance computational genomics. Nature biotechnology 39 (9) (2021)
Ashwin Narayan, Bonnie Berger, Hyunghoon Cho
Assessing single-cell transcriptomic variability through density-preserving data visualization. Nature biotechnology 39 (6) (2021)
Brian L Hie, Ellen D Zhong, Bonnie Berger, Bryan D Bryson
Learning the language of viral evolution and escape. Science (New York, N.Y.) 371 (6526) (2021)
Bonnie Berger, Michael S Waterman, Yun William Yu
Levenshtein Distance, Sequence Comparison and Biological Database Search. IEEE transactions on information theory 67 (6) (2020)
Tristan Bepler, Kotaro Kelley, Alex J Noble, Bonnie Berger
Topaz-Denoise: general deep denoising models for cryoEM and cryoET. Nature communications 11 (1) (2020)
Emily Berger, Deniz Yorukoglu, Lillian Zhang, Sarah K Nyquist, Alex K Shalek, Manolis Kellis, Ibrahim Numanagić, Bonnie Berger
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets. Nature communications 11 (1) (2020)
Barış Ekim, Bonnie Berger, Yaron Orenstein
A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ) 12074 (2020)
Barış Ekim, Bonnie Berger, Yaron Orenstein
A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ) 12074 (2020)
Miao Gui, Meisheng Ma, Erica Sze-Tu, Xiangli Wang, Fujiet Koh, Ellen D Zhong, Bonnie Berger, Joseph H Davis, Susan K Dutcher, Rui Zhang, Alan Brown
Structures of radial spokes and associated complexes important for ciliary motility. Nature structural & molecular biology 28 (1) (2020)
Sumaiya Nazeen, Yun William Yu, Bonnie Berger
Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads. Genome biology 21 (1) (2020)
Barış Ekim, Bonnie Berger, Yaron Orenstein
A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ) 12074 (2020)
Bonnie Berger, Hyunghoon Cho
Emerging technologies towards enhancing privacy in genomic data sharing. Genome biology 20 (1) (2019)
Tristan Bepler, Andrew Morin, Micah Rapp, Julia Brasch, Lawrence Shapiro, Alex J Noble, Bonnie Berger
Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nature methods 16 (11) (2019)
Brian L Hie, Bryan D Bryson, Bonnie Berger
Efficient integration of heterogeneous single-cell transcriptomes using Scanorama. Nature biotechnology 37 (6) (2019)
Ibrahim Numanagić, Salem Malikić, Michael Ford, Xiang Qin, Lorraine Toji, Milan Radovich, Todd C Skaar, Victoria M Pratt, Bonnie Berger, Steve Scherer, S Cenk Sahinalp
Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes. Nature communications 9 (1) (2018)
Hyunghoon Cho, David J Wu, Bonnie Berger
Secure genome-wide association analysis using multiparty computation. Nature biotechnology 36 (6) (2018)
Brian L Hie, Hyunghoon Cho, Bonnie Berger
Realizing private and practical pharmacological collaboration. Science (New York, N.Y.) 362 (6412) (2018)