Berger, Bonnie

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

Ziegler, C. G. K., Allon, S. J., Nyquist, S. K., Mbano, I. M., Miao, V. N., Tzouanas, C. N., Cao, Y., Yousif, A. S., Bals, J., Hauser, B. M., et al. (2020) · Cell

SARS-CoV-2 and COVID-19 ResearchCOVID-19 Clinical Research Studies

Cited by 2,284

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

Loh, P.-R., Tucker, G., Bulik-Sullivan, B. K., Vilhjálmsson, B. J., Finucane, H. K., Salem, R. M., Chasman, D. I., Ridker, P. M., Neale, B. M., Berger, B., et al. (2015) · Nature Genetics

Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and Animals

Cited by 1,507

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

Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature

Forensic and Genetic ResearchGenetic diversity and population structure

Cited by 1,357

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

Wolf, E., Kim, P. S., & Berger, B. (1997) · Protein Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 720

Widespread macromolecular interaction perturbations in human genetic disorders

Sahni, N., Yi, S., Taipale, M., Fuxman Bass, J. I., Coulombe-Huntington, J., Yang, F., Peng, J., Weile, J., Karras, G. I., Wang, Y., et al. (2015) · Cell

Genomics and Rare DiseasesBioinformatics and Genomic Networks

Cited by 594

Learning the protein language: Evolution, structure, and function

Bepler, T., & Berger, B. (2021) · Cell Systems

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 483

Inferring admixture histories of human populations using linkage disequilibrium

Loh, P.-R., Lipson, M., Patterson, N., Moorjani, P., Pickrell, J. K., Reich, D., & Berger, B. (2013) · Genetics

Forensic and Genetic ResearchGenetic diversity and population structure

Cited by 466

Paircoil2: improved prediction of coiled coils from sequence.

McDonnell, A. V., Jiang, T., Keating, A. E., & Berger, B. (2006) · Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 424

High-resolution de novo structure prediction from primary sequence

Wu, R., Ding, F., Wang, R., Shen, R., Zhang, X., Luo, S., Su, C., Wu, Z., Xie, Q., Berger, B., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 392

Learning the language of viral evolution and escape

Hie, B., Zhong, E. D., Berger, B., & Bryson, B. (2021) · Science

vaccines and immunoinformatics approachesEvolution and Genetic Dynamics

Cited by 361

Genetic Evidence for Recent Population Mixture in India

Moorjani, P., Thangaraj, K., Patterson, N., Lipson, M., Loh, P.-R., Govindaraj, P., Berger, B., Reich, D., & Singh, L. (2013) · The American Journal of Human Genetics

Forensic and Genetic ResearchGenetic diversity and population structure

Cited by 350

Ancient west Eurasian ancestry in southern and eastern Africa

Pickrell, J. K., Patterson, N., Loh, P.-R., Lipson, M., Berger, B., Stoneking, M., Pakendorf, B., & Reich, D. (2014) · Proceedings of the National Academy of Sciences

Forensic and Genetic ResearchGenetic diversity and population structure

Cited by 300

Compact integration of multi-network topology for functional analysis of genes

Cho, H., Berger, B., & Peng, J. (2016) · Cell Systems

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 241

Learning protein sequence embeddings using information from structure

Bepler, T., & Berger, B. (2019) · arXiv

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 219

Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization

Shan, S., Luo, S., Yang, Z., Hong, J., Su, Y., Ding, F., Fu, L., Li, C., Chen, P., Ma, J., et al. (2022) · Proceedings of the National Academy of Sciences

SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approaches

Cited by 157

Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design

Hie, B., Bryson, B. D., & Berger, B. (2020) · Cell Systems

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 154

Comprehensive Dissection of PDGF-PDGFR Signaling Pathways in PDGFR Genetically Defined Cells

Wu, E., Palmer, N., Tian, Z., Moseman, A. P., Galdzicki, M., Wang, X., Berger, B., Zhang, H., & Kohane, I. S. (2008) · PLoS ONE

Fibroblast Growth Factor ResearchLiver physiology and pathology

Cited by 118

Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks

Liu, Y., Palmedo, P., Ye, Q., Berger, B., & Peng, J. (2018) · Cell Systems

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 114

Visualization of clustered protocadherin neuronal self-recognition complexes

Brasch, J., Goodman, K. M., Noble, A. J., Rapp, M., Mannepalli, S., Bahna, F., Dandey, V. P., Bepler, T., Berger, B., Maniatis, T., et al. (2019) · Nature

Axon Guidance and Neuronal SignalingNeuroscience and Neuropharmacology Research

Cited by 99

Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone

Trigg, J., Gutwin, K., Keating, A. E., & Berger, B. (2011) · PLoS One

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 91

Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning

Sledzieski, S., Kshirsagar, M., Baek, M., Berger, B., Dodhia, R., & Ferres, J. L. (2023) · Proceedings of the National Academy of Sciences

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 86

A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers

Palmer, N. P., Schmid, P. R., Berger, B., & Kohane, I. S. (2012) · Genome Biology

Cancer Cells and MetastasisPluripotent Stem Cells Research

Cited by 86

Democratizing protein language models with parameter-efficient fine-tuning

Sledzieski, S., Kshirsagar, M., Baek, M., Dodhia, R., Lavista Ferres, J., & Berger, B. (2024) · Proceedings of the National Academy of Sciences

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 86

Genome-wide mapping of somatic mutation rates uncovers drivers of cancer

Sherman, M. A., Yaari, A. U., Priebe, O., Dietlein, F., Loh, P.-R., & Berger, B. (2022) · Nature Biotechnology

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 80