Search filters

List of works by Bonnie Berger

"Local rules" theory applied to polyomavirus polymorphic capsid assemblies

scientific article published in March 2000

2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner

scientific article published on 30 June 2017

2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner

scientific article published on 26 June 2017

2017 ISCB Innovator Award: Aviv Regev

2017 ISCB Innovator Award: Aviv Regev

scientific article

2017 ISCB Overton Prize awarded to Christoph Bock

scientific article published on 30 June 2017

2017 ISCB Overton Prize: Christoph Bock

scientific article published on 26 June 2017

2017 Outstanding Contributions to ISCB Award: Fran Lewitter

scientific article published on 30 June 2017

2017 Outstanding Contributions to ISCB Award: Fran Lewitter

scientific article published on 26 June 2017

A Python-based programming language for high-performance computational genomics

scientific article published on 19 July 2021

A computational framework for boosting confidence in high-throughput protein-protein interaction datasets

scientific article

A dictionary based approach for gene annotation

article

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

scientific article published on August 21, 2012

A global sampling approach to designing and reengineering RNA secondary structures

scientific article

A method for probing the mutational landscape of amyloid structure.

scientific article published on July 2011

A parameterized algorithm for protein structure alignment.

scientific article

A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood

scientific article

A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways

scientific article

A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis

scientific article

A tree-decomposition approach to protein structure prediction.

scientific article published in January 2005

ARACHNE: a whole-genome shotgun assembler

scientific article

Algorithms for protein structural motif recognition

scientific article published in January 1995

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

scientific article published on 26 February 2018

Allergic inflammatory memory in human respiratory epithelial progenitor cells

scientific article published in Nature

An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values

scientific article published on March 2016

An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

scientific article

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

scientific article

An iterative method for improved protein structural motif recognition

scientific article published in January 1997

An iterative method for improved protein structural motif recognition

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

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

scientific article

Ancient west Eurasian ancestry in southern and eastern Africa

scientific article published on 03 February 2014

Assessing statistical significance in causal graphs

scientific article published on 20 February 2012

Assessment of Chemical Mixtures and Groundwater Effects on Daphnia magna Transcriptomics ⬇️

scientific article published on August 5, 2011

Automated real time constant-specificity surveillance for disease outbreaks

scientific article

BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis

scientific article

Building quantitative prediction models for tissue residue of two explosives compounds in earthworms from microarray gene expression data

scientific article

CHAINTWEAK: SAMPLING FROM THE NEIGHBOURHOOD OF A PROTEIN CONFORMATION

Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

scientific article

Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads

scientific article published on 24 February 2020

Compact Integration of Multi-Network Topology for Functional Analysis of Genes

scientific article

Comprehensive dissection of PDGF-PDGFR signaling pathways in PDGFR genetically defined cells

scientific article

Compressive genomics

scientific article

Compressive genomics for protein databases

scientific article

Compressive mapping for next-generation sequencing

scientific article published on April 2016

Computational Biology in the 21st Century: Scaling with Compressive Algorithms

scientific article published on August 2016

Computational analysis of noncoding RNAs

scientific article

Computational solutions for omics data

scientific article

Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3'UTRs

scientific article

Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals

scientific article (publication date: November 2015)

CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models

scientific article published on 8 February 2018

Density-equalizing Euclidean minimum spanning trees for the detection of all disease cluster shapes

scholarly article

Development of simulation tools for virus shell assembly. Final report

article

Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks

article by Hyunghoon Cho et al published April 2015 in Lecture Notes in Computer Science

Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data

scientific article

Efficient Algorithms for Probing the RNA Mutation Landscape

scientific article

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

scientific article

Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers

scientific article published on 29 December 2015

Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models ⬇️

scientific article published on September 29, 2011

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.

scientific article published on 6 May 2019

Efficient moment-based inference of admixture parameters and sources of gene flow

scientific article published on 24 May 2013

Emerging technologies towards enhancing privacy in genomic data sharing

scientific article published on 02 July 2019

Enabling Privacy-Preserving GWASs in Heterogeneous Human Populations

scientific article published on 20 July 2016

Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks

scientific article published on 19 December 2017

Entropy-scaling search of massive biological data ⬇️

scientific article

Exercise makes you feel good, but does feeling good make you exercise?: an examination of obese dieters

scientific article published in December 2007

Explicitly disentangling image content from translation and rotation with spatial-VAE ⬇️

scientific article published in January 2019

Exploiting ontology graph for predicting sparsely annotated gene function

scientific article

Fast and accurate algorithms for protein side-chain packing

scholarly article by Jinbo Xu & Bonnie Berger published 1 July 2006 in Journal of the ACM

Fast characterization of segmental duplications in genome assemblies

scholarly article by Ibrahim Numanagic published in September 2018

Fast genotyping of known SNPs through approximate k-mer matching

scientific article

Finding RNA structure in the unstructured RBPome

scientific article published on 20 February 2018

Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins

scientific article published in June 2006

GLOBAL ALIGNMENT OF MULTIPLE PROTEIN INTERACTION NETWORKS

Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks

scientific article published on 20 June 2018

Generalizable visualization of mega-scale single-cell data

Genetic determinants of phosphate response in Drosophila

scientific article

Genetic evidence for recent population mixture in India

scientific article

Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways

scientific article

Genomics in 2011: challenges and opportunities

scientific article published on 28 December 2011

Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape

scientific article published on 05 June 2019

Global alignment of multiple protein interaction networks

scientific article published in January 2008

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

scholarly article

HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data

article published in 2015

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data

scientific article published on 27 March 2014

Herpesviral protein networks and their interaction with the human proteome

scientific article published on 8 December 2005

HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications.

scientific article published in February 2018

Hopper: a mathematically optimal algorithm for sketching biological data

scientific article published on 01 July 2020

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus

scientific article (publication date: 29 January 2015)

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus

scientific article

ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing

scientific article

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing

scientific article published on 24 March 2016

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing

scientific article

ISMB 2012 Proceedings Papers Committee. July 15 to July 19, 2012, Long Beach, CA, USA. Editorial

scientific article published on June 2012

Identification of protein complexes by integrating multiple alignment of protein interaction networks

scientific article published on 27 January 2017

Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

scientific article published on 16 September 2020

Improving the power of GWAS and avoiding confounding from population stratification with PC-Select

scientific article

Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen

scientific article

Inferring admixture histories of human populations using linkage disequilibrium

scientific article published on 14 February 2013

Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection

scientific article published on 23 March 2020

Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities

scientific article

IsoBase: a database of functionally related proteins across PPI networks

scientific article

IsoRankN: spectral methods for global alignment of multiple protein networks

scientific article published on June 2009

Joker de Bruijn: Covering k-Mers Using Joker Characters

article

Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters

scientific article published on 01 May 2017

Kpax3: Bayesian bi-clustering of large sequence datasets

scientific article published on 7 February 2018

LOCAL OPTIMIZATION FOR GLOBAL ALIGNMENT OF PROTEIN INTERACTION NETWORKS

LTHREADER: PREDICTION OF LIGAND-RECEPTOR INTERACTIONS USING LOCALIZED THREADING

LTHREADER: prediction of extracellular ligand-receptor interactions in cytokines using localized threading

scientific article published on 20 December 2007

LTHREADER: prediction of ligand-receptor interactions using localized threading

scientific article published in January 2007

Large-Margin Classification in Hyperbolic Space

scientific article published on 01 April 2019

Large-scale identification of genetic design strategies using local search

scientific article published on 18 August 2009

Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses

LearnCoil-VMF: computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins

article

Learning Mutational Semantics ⬇️

Levenshtein Distance, Sequence Comparison and Biological Database Search

scientific article published on 21 May 2020

Local optimization for global alignment of protein interaction networks

scientific article published in January 2010

Local rules simulation of the kinetics of virus capsid self-assembly

scientific article

Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning

MSARI: multiple sequence alignments for statistical detection of RNA secondary structure

scientific article

Making sense out of massive data by going beyond differential expression ⬇️

scientific article published on March 23, 2012

Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system

scientific article

Matt: local flexibility aids protein multiple structure alignment.

scientific article

Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner

scientific article

Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev

scientific article published in July 2017

Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock

scientific article

Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter

scientific article

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus

scientific article published on 2 February 2015

Meta-analysis of C. elegans single-cell developmental data reveals multi-frequency oscillation in gene activation

scientific article published on 20 December 2019

MetaMerge: scaling up genome-scale metabolic reconstructions, with application to Mycobacterium tuberculosis

scientific article (publication date: 31 January 2012)

Metabolic Network Analysis Demystified

Metagenomic binning through low-density hashing.

scientific article published in January 2019

Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery

scientific article published in January 2004

Modeling Amorphization of Tetrahedral Structures Using Local Approaches

Modeling ensembles of transmembrane beta-barrel proteins

scientific article published in May 2008

MultiCoil: a program for predicting two- and three-stranded coiled coils

scientific article (publication date: June 1997)

Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone.

scientific article

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

scientific article

Novel Perspectives on Protein Structure Prediction

On the Structure of the Scaffolding Core of Bacteriophage T4 and Its Role in Head Length Determination ⬇️

scientific article published on January 1, 1998

One Size Doesn't Fit All: Measuring Individual Privacy in Aggregate Genomic Data

scientific article published on 20 July 2015

Opposing Effects of Glutamine and Asparagine Govern Prion Formation by Intrinsically Disordered Proteins ⬇️

scientific article published on July 8, 2011

Optimal contact map alignment of protein-protein interfaces

scientific article

Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping

scientific article

Optimizing a global alignment of protein interaction networks

scientific article published on 17 September 2013

PROBABILISTIC MODELING OF SYSTEMATIC ERRORS IN TWO-HYBRID EXPERIMENTS

Pertactin beta-helix folding mechanism suggests common themes for the secretion and folding of autotransporter proteins

scientific article

Phenotype prediction using regularized regression on genetic data in the DREAM5 Systems Genetics B Challenge

scientific article

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

scientific article published on 07 October 2019

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

Predicting and annotating catalytic residues: an information theoretic approach

scientific article published in October 2007

Predicting the beta-helix fold from protein sequence data

scientific article

Predicting the β-helix fold from protein sequence data

Predicting transmembrane beta-barrels and interstrand residue interactions from sequence

scientific article

Preface: 14th International Conference on Research in Computational Molecular Biology (RECOMB 2010) ⬇️

scientific article published on March 1, 2011

Principles of Systems Biology, No. 31

scientific article published on 01 August 2018

Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs

scientific article published on 28 April 2020

Probabilistic modeling of systematic errors in two-hybrid experiments.

scientific article published in January 2007

Protecting Genomic Data Privacy with Probabilistic Modeling

Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete ⬇️

scientific article published on January 1, 1998

Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling

scientific article

Quality score compression improves genotyping accuracy.

scientific article

RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.

scientific article

RNAiCut: automated detection of significant genes from functional genomic screens

scientific article published in July 2009

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures

scientific article published on 16 June 2009

Realizing privacy preserving genome-wide association studies

scientific article published on 14 January 2016

Realizing private and practical pharmacological collaboration

scientific article published in Science

Reconstructing Austronesian population history in Island Southeast Asia

article

Reconstructing Austronesian population history in Island Southeast Asia

scientific article

Reconstructing Causal Biological Networks through Active Learning

scientific article

Reconstructing Roma history from genome-wide data

scientific article

Reconstruction of phyletic trees by global alignment of multiple metabolic networks

scientific article

Reply to "Do genome-scale models need exact solvers or clearer standards?".

scientific article published on 14 October 2015

Revealing the spatial distribution of a disease while preserving privacy

scholarly article

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

scientific article published on 27 April 2020

SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone

scientific article

STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions

scientific article published on 17 November 2011

STRUCT2NET: INTEGRATING STRUCTURE INTO PROTEIN-PROTEIN INTERACTION PREDICTION

Secure genome-wide association analysis using multiparty computation

scientific article published on 07 May 2018

SemanticDx: a prototype to facilitate use of biostatistics at the point-of-care

scientific article

Sequencing a genome by walking with clone-end sequences (abstract)

Simultaneous alignment and folding of protein sequences

scientific article

Sparse Estimation for Structural Variability

Sparse estimation for structural variability ⬇️

scientific article published on April 19, 2011

Squeakr: an exact and approximate k-mer counting system

scientific article published in February 2018

Statistical Binning for Barcoded Reads Improves Downstream Analyses

scientific article published on 01 August 2018

Struct2Net: a web service to predict protein-protein interactions using a structure-based approach

scientific article

Struct2net: integrating structure into protein-protein interaction prediction.

scientific article published in January 2006

Structure-based prediction reveals capping motifs that inhibit β-helix aggregation

scientific article

Structure-based whole-genome realignment reveals many novel noncoding RNAs

scientific article (publication date: June 2013)

Structured States of Disordered Proteins from Genomic Sequences

scientific article published on September 2016

TRILOGY: Discovery of sequence-structure patterns across diverse proteins.

scientific article

The Fourth Moment Method

article by Bonnie Berger published August 1997 in SIAM Journal on Computing

The association between mood states and physical activity in postmenopausal, obese, sedentary women.

scientific article published in January 2006

The genetic prehistory of southern Africa

scientific article

Tight Bounds for the Maximum Acyclic Subgraph Problem

Topaz-Denoise: general deep denoising models for cryoEM and cryoET

scientific article published on 15 October 2020

Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification

scientific article published on 01 April 2014

Two-Variance-Component Model Improves Genetic Prediction in Family Datasets.

scientific article

Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs

scientific article

Visualization of clustered protocadherin neuronal self-recognition complexes

scientific article published on 10 April 2019

Voices of biotech

scientific article published on March 2016

Widespread macromolecular interaction perturbations in human genetic disorders

scientific journal article

Wrap-and-Pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils.

scientific article

diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data

scientific article

iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions

scientific article

transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels

scientific article

Paulina is supported by:

About Paulina

Help