Bonnie Berger
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American mathematician and computer scientist
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Bonnie Bergermathematics Degrees
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Applied Mathematics
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Computer Science Mathematics
Bonnie Berger's Degrees
- PhD Mathematics Princeton University
- Bachelors Mathematics University of California, Berkeley
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Why Is Bonnie Berger Influential?
(Suggest an Edit or Addition)According to Wikipedia, Bonnie Anne Berger is an American mathematician and computer scientist, who works as the Simons professor of mathematics and professor of electrical engineering and computer science at the Massachusetts Institute of Technology. Her research interests are in algorithms, bioinformatics and computational molecular biology.
Bonnie Berger's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- 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) (1833)
- Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE (2010) (1211)
- Efficient Bayesian mixed model analysis increases association power in large cohorts (2014) (1114)
- Ancient human genomes suggest three ancestral populations for present-day Europeans (2013) (1082)
- MultiCoil: A program for predicting two‐and three‐stranded coiled coils (1997) (771)
- ARACHNE: a whole-genome shotgun assembler. (2002) (686)
- Predicting coiled coils by use of pairwise residue correlations. (1995) (660)
- Global alignment of multiple protein interaction networks with application to functional orthology detection (2008) (619)
- An integrative approach to ortholog prediction for disease-focused and other functional studies (2011) (525)
- Protein Folding in the Hydrophobic-Hydrophilic(HP) Model is NP-Complete (1998) (480)
- Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders (2015) (431)
- Herpesviral Protein Networks and Their Interaction with the Human Proteome (2006) (427)
- Paircoil2: improved prediction of coiled coils from sequence (2006) (422)
- Human and mouse gene structure: comparative analysis and application to exon prediction (2000) (412)
- IsoRankN: spectral methods for global alignment of multiple protein networks (2009) (411)
- Efficient integration of heterogeneous single-cell transcriptomes using Scanorama (2019) (380)
- Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium (2012) (377)
- A Quantitative Chaperone Interaction Network Reveals the Architecture of Cellular Protein Homeostasis Pathways (2014) (345)
- Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology (2007) (328)
- Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs (2018) (312)
- Computational solutions for omics data (2013) (303)
- The genetic prehistory of southern Africa (2012) (276)
- Allergic inflammatory memory in human respiratory epithelial progenitor cells (2018) (270)
- Genetic evidence for recent population mixture in India. (2013) (252)
- Ancient west Eurasian ancestry in southern and eastern Africa (2013) (246)
- Matt: Local Flexibility Aids Protein Multiple Structure Alignment (2008) (222)
- Learning protein sequence embeddings using information from structure (2019) (218)
- Pertactin beta-helix folding mechanism suggests common themes for the secretion and folding of autotransporter proteins. (2006) (208)
- Topaz-Denoise: general deep denoising models for cryoEM and cryoET (2019) (202)
- Local rule-based theory of virus shell assembly. (1994) (201)
- CryoDRGN: Reconstruction of heterogeneous cryo-EM structures using neural networks (2021) (187)
- Compact Integration of Multi-Network Topology for Functional Analysis of Genes. (2016) (169)
- Local rules simulation of the kinetics of virus capsid self-assembly. (1998) (167)
- Large-scale identification of genetic design strategies using local search (2009) (160)
- Opposing effects of glutamine and asparagine govern prion formation by intrinsically disordered proteins. (2011) (159)
- Reconstructing Austronesian population history in Island Southeast Asia (2014) (158)
- LearnCoil-VMF: computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins1 (1999) (153)
- Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3′UTRs (2010) (153)
- Structural freedom, topological disorder, and the irradiation-induced amorphization of ceramic structures (1996) (141)
- Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs (2019) (138)
- Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs. (2011) (136)
- Secure genome-wide association analysis using multiparty computation (2018) (133)
- Efficient NC algorithms for set cover with applications to learning and geometry (1989) (127)
- Structured States of Disordered Proteins from Genomic Sequences (2016) (123)
- betawrap: Successful prediction of parallel β-helices from primary sequence reveals an association with many microbial pathogens (2001) (121)
- Learning the language of viral evolution and escape (2020) (120)
- IsoBase: a database of functionally related proteins across PPI networks (2010) (114)
- Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery (2004) (113)
- Struct2Net: a web service to predict protein–protein interactions using a structure-based approach (2010) (111)
- Efficient Moment-Based Inference of Admixture Parameters and Sources of Gene Flow (2012) (110)
- Comprehensive Dissection of PDGF-PDGFR Signaling Pathways in PDGFR Genetically Defined Cells (2008) (109)
- Compressive genomics (2012) (107)
- Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete (1998) (106)
- Simulating (logcn)-wise independence in NC (1991) (105)
- Learning the protein language: Evolution, structure, and function. (2021) (104)
- Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways. (2017) (104)
- Approximation alogorithms for the maximum acyclic subgraph problem (1990) (100)
- Near-Linear Time Construction of Sparse Neighborhood Covers (1999) (100)
- MSARI: multiple sequence alignments for statistical detection of RNA secondary structure. (2004) (98)
- Proteomic and Functional Genomic Landscape of Receptor Tyrosine Kinase and Ras to Extracellular Signal–Regulated Kinase Signaling (2011) (97)
- Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks (2017) (95)
- Fast and accurate algorithms for protein side-chain packing (2006) (87)
- BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis (2009) (86)
- Exploiting ontology graph for predicting sparsely annotated gene function (2015) (85)
- Global Alignment of Multiple Protein Interaction Networks (2007) (82)
- Local topology of silica networks (1998) (79)
- Computational learning reveals coiled coil-like motifs in histidine kinase linker domains (1998) (79)
- Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks (2015) (76)
- Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach (2014) (76)
- Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape (2019) (75)
- Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone (2011) (74)
- High-resolution de novo structure prediction from primary sequence (2022) (74)
- HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data (2014) (73)
- Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals (2015) (70)
- Predicting the mutational drivers of future SARS-CoV-2 variants of concern (2021) (69)
- Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design. (2020) (68)
- Reconstructing continuous distributions of 3D protein structure from cryo-EM images (2019) (66)
- Enabling Privacy Preserving GWAS in Heterogeneous Human Populations (2016) (65)
- Fast Distributed Network Decompositions and Covers (1996) (64)
- Identification of protein complexes by integrating multiple alignment of protein interaction networks (2017) (64)
- A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers (2012) (62)
- Revealing the spatial distribution of a disease while preserving privacy (2008) (62)
- Visualization of clustered protocadherin neuronal self-recognition complexes (2019) (61)
- Optimizing a global alignment of protein interaction networks (2013) (61)
- Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction (2005) (61)
- A method for probing the mutational landscape of amyloid structure (2011) (60)
- iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. (2010) (59)
- Near-linear cost sequential and distributed constructions of sparse neighborhood covers (1993) (58)
- Realizing privacy preserving genome-wide association studies (2016) (58)
- Reconstructing Roma History from Genome-Wide Data (2012) (57)
- Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes (2018) (56)
- Quality score compression improves genotyping accuracy (2015) (56)
- RCK: accurate and efficient inference of sequence- and structure-based protein–RNA binding models from RNAcompete data (2016) (56)
- A tree-decomposition approach to protein structure prediction (2005) (55)
- Computational analysis of noncoding RNAs (2012) (55)
- Explicitly disentangling image content from translation and rotation with spatial-VAE (2019) (54)
- Entropy-scaling search of massive biological data (2015) (54)
- Computational Methods for Single-Cell RNA Sequencing (2020) (53)
- Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes (2015) (53)
- Compressive genomics for protein databases (2013) (53)
- Local Optimization for Global Alignment of Protein Interaction Networks (2010) (52)
- A Parameterized Algorithm for Protein Structure Alignment (2006) (52)
- The fourth moment method (1991) (50)
- Improving the Power of GWAS and Avoiding Confounding from Population Stratification with PC-Select (2014) (50)
- Predicting the Beta-Helix Fold from Protein Sequence Data (2002) (49)
- "Local rules" theory applied to polyomavirus polymorphic capsid assemblies. (2000) (47)
- Realizing private and practical pharmacological collaboration (2018) (47)
- An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models (2014) (46)
- A computational framework for boosting confidence in high-throughput protein-protein interaction datasets (2012) (46)
- Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption (2021) (46)
- Reconstructing a three-dimensional model with arbitrary errors (1996) (45)
- Efficient Algorithms for Probing the RNA Mutation Landscape (2008) (44)
- An iterative method for improved protein structural motif recognition (1997) (44)
- Fast genotyping of known SNPs through approximate k-mer matching (2016) (44)
- Computational biology in the 21st century (2016) (44)
- Large-Margin Classification in Hyperbolic Space (2018) (44)
- Making sense out of massive data by going beyond differential expression (2012) (43)
- Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation (2021) (42)
- Structures of radial spokes and associated complexes important for ciliary motility (2020) (42)
- Compressive mapping for next-generation sequencing (2016) (42)
- Assessing Single-Cell Transcriptomic Variability through Density-Preserving Data Visualization (2020) (42)
- Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities (2016) (41)
- Structure-based prediction reveals capping motifs that inhibit β-helix aggregation (2011) (41)
- Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks. (2018) (40)
- Emerging technologies towards enhancing privacy in genomic data sharing (2019) (40)
- Predicting transmembrane β‐barrels and interstrand residue interactions from sequence (2006) (40)
- Fast characterization of segmental duplications in genome assemblies (2018) (39)
- BETASCAN: Probable beta-amyloids Identified by Pairwise Probabilistic Analysis (2009) (39)
- Density-equalizing Euclidean minimum spanning trees for the detection of all disease cluster shapes (2007) (39)
- Structure-based whole-genome realignment reveals many novel noncoding RNAs (2012) (39)
- A global sampling approach to designing and reengineering RNA secondary structures (2012) (38)
- Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control (2022) (37)
- Reconstructing Causal Biological Networks through Active Learning (2016) (34)
- transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels (2006) (34)
- MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis (2012) (33)
- Algorithms for Protein Structural Motif Recognition (1995) (33)
- Tight Bounds for the Maximum Acyclic Subgraph Problem (1997) (32)
- D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions. (2021) (32)
- Fold recognition and accurate sequence–structure alignment of sequences directing β‐sheet proteins (2006) (31)
- A better performance guarantee for approximate graph coloring (1990) (31)
- Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system (2010) (31)
- Assessment of chemical mixtures and groundwater effects on Daphnia magna transcriptomics. (2012) (31)
- Reconstructing a three-dimensional model with arbitrary errors (1999) (31)
- Low-Diameter Graph Decomposition Is in NC (1992) (31)
- A Practical Platform for Blood Biomarker Study by Using Global Gene Expression Profiling of Peripheral Whole Blood (2009) (30)
- Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen. (2010) (30)
- Trilogy: discovery of sequence-structure patterns across diverse proteins (2002) (30)
- Inverting the Viterbi algorithm: an abstract framework for structure design (2008) (29)
- Large mosaic copy number variations confer autism risk (2020) (29)
- Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization (2022) (29)
- Optimal contact map alignment of protein–protein interfaces (2008) (28)
- A self-organizing neural net chip (1988) (28)
- Sequencing a genome by walking with clone-end sequences: a mathematical analysis. (1999) (28)
- RNAiCut: automated detection of significant genes from functional genomic screens (2009) (28)
- Panoramic stitching of heterogeneous single-cell transcriptomic data (2018) (28)
- Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer. (2021) (27)
- Predicting and Annotating Catalytic Residues: An Information Theoretic Approach (2007) (26)
- Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification (2014) (26)
- SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone (2012) (26)
- Levenshtein Distance, Sequence Comparison and Biological Database Search (2020) (25)
- Automated real time constant-specificity surveillance for disease outbreaks (2007) (25)
- Metagenomic binning through low-density hashing (2017) (25)
- CryoDRGN2: Ab initio neural reconstruction of 3D protein structures from real cryo-EM images (2021) (25)
- Two variance component model improves genetic prediction in family data sets (2015) (25)
- Active learning for sampling in time-series experiments with application to gene expression analysis (2005) (24)
- Fast network decomposition (1992) (24)
- STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions (2011) (23)
- Simulating (log/sup c/n)-wise independence in NC (1989) (23)
- Nearly optimal algorithms and bounds for multilayer channel routing (1995) (22)
- A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets (2020) (22)
- Density-Preserving Data Visualization Unveils Dynamic Patterns of Single-Cell Transcriptomic Variability (2020) (22)
- Local rule mechanism for selecting icosahedral shell geometry (2000) (21)
- trilogy: Discovery of sequence–structure patterns across diverse proteins (2002) (21)
- Sequence-based prediction of protein-protein interactions: a structure-aware interpretable deep learning model (2021) (20)
- A dictionary based approach for gene annotation (1999) (19)
- RNAmutants: a web server to explore the mutational landscape of RNA secondary structures (2009) (18)
- An engineered protein-phosphorylation toggle network with implications for endogenous network discovery (2021) (18)
- Topological modeling of cascade amorphization in network structures using local rules (1998) (18)
- Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities (2021) (17)
- Statistical Binning for Barcoded Reads Improves Downstream Analyses (2018) (17)
- Modeling ensembles of transmembrane beta-barrel proteins. (2008) (17)
- Building quantitative prediction models for tissue residue of two explosives compounds in earthworms from microarray gene expression data. (2012) (16)
- Local Rule Switching Mechanism for Viral Shell Geometry (1995) (16)
- Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species (2003) (16)
- Privacy-preserving biomedical database queries with optimal privacy-utility trade-offs (2020) (15)
- An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values (2016) (15)
- ChainTweak: Sampling from the Neighbourhood of a Protein Conformation (2004) (15)
- Assessing statistical significance in causal graphs (2012) (15)
- CryoDRGN: Reconstruction of heterogeneous structures from cryo-electron micrographs using neural networks (2020) (15)
- On the Mathematics of Virus Shell Assembly (1995) (14)
- Genetic Determinants of Phosphate Response in Drosophila (2013) (14)
- Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils (2004) (14)
- One Size Doesn't Fit All: Measuring Individual Privacy in Aggregate Genomic Data (2015) (14)
- Modeling ensembles of transmembrane β‐barrel proteins (2008) (14)
- Local Rules Modeling of Nucleation-Limited Virus Capsid Assembly MIT-LCS-TM-584 (1998) (14)
- Hopper: a mathematically optimal algorithm for sketching biological data (2019) (14)
- Reconstruction of phyletic trees by global alignment of multiple metabolic networks (2013) (13)
- Phenotype Prediction Using Regularized Regression on Genetic Data in the DREAM5 Systems Genetics B Challenge (2011) (13)
- Methods in comparative genomics: genome correspondence, gene identification and motif discovery (2003) (13)
- Reconstructing continuously heterogeneous structures from single particle cryo-EM with deep generative models (2019) (13)
- Seq: A High-Performance Language for Bioinformatics (2019) (12)
- LTHREADER: Prediction of extracellular ligand–receptor interactions in cytokines using localized threading (2008) (12)
- Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads (2020) (12)
- RIGIDITY CONSTRAINTS IN AMORPHIZATION OF SINGLY- AND MULTIPLY-POLYTOPIC STRUCTURES (2002) (12)
- Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments (2006) (12)
- Multimodal profiling of lung granulomas reveals cellular correlates of tuberculosis control (2021) (11)
- Protecting Genomic Data Privacy with Probabilistic Modeling (2018) (11)
- Graph algorithms for biological systems analysis (2008) (11)
- Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data (2015) (11)
- ISCB’s initial reaction to New England Journal of Medicine editorial on data sharing (2016) (11)
- HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data (2015) (11)
- A dictionary-based approach for gene annotation. (1999) (11)
- Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets (2020) (11)
- Genome-wide mapping of somatic mutation rates uncovers drivers of cancer (2022) (10)
- Developmental Dynamics of RNA Translation in the Human Brain (2021) (10)
- Exploring generative atomic models in cryo-EM reconstruction (2021) (10)
- Latent variable model for aligning barcoded short-reads improves downstream analyses (2017) (10)
- ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing (2016) (10)
- Inference of Admixture Parameters in Human Populations Using Weighted Linkage Disequilibrium (2012) (9)
- Domino tiling, gene recognition, and mice (1999) (9)
- Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control (2020) (9)
- Finding RNA structure in the unstructured RBPome (2018) (8)
- Reply to “Do genome-scale models need exact solvers or clearer standards?” (2015) (8)
- High-Resolution Modeling of Cellular Signaling Networks (2008) (8)
- Complexity results and algorithms for {<,≤,=}-constrained scheduling (1991) (8)
- Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning (2016) (7)
- Recent Developments in Computational Gene Recognition (1998) (7)
- The modENCODE Consortium modENCODE Drosophila Identification of Functional Elements and Regulatory Circuits (2011) (7)
- Uncovering structural ensembles from single particle cryo-EM data using cryoDRGN (2022) (7)
- TOPAZ: A Positive-Unlabeled Convolutional Neural Network CryoEM Particle Picker that can Pick Any Size and Shape Particle (2019) (7)
- A Python-based programming language for high-performance computational genomics (2021) (7)
- Local Rule Simulations of Capsid Assembly (2005) (7)
- Sequence biases in CLIP experimental data are incorporated in protein RNA-binding models (2016) (7)
- Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models (2011) (7)
- Extracting information from biological networks (2010) (6)
- Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation (2019) (6)
- Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers (2015) (6)
- Enabling Privacy-Preservi ng GWASs in Heterogeneous Human Populations Graphical Abstract Highlights (2016) (6)
- Predicting the β-helix fold from protein sequence data (2001) (6)
- Improved algorithms for protein motif recognition (1995) (6)
- Cellular and transcriptional diversity over the course of human lactation (2021) (6)
- HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells (2021) (6)
- Rna: algorithms, evolution and design (2011) (5)
- Fast Network Decomposition (Extended Abstract). (1992) (5)
- Effects of the human-animal bond on individuals: pet ownership and psychological status (1984) (5)
- Schema: A general framework for integrating heterogeneous single-cell modalities (2019) (5)
- Topsy-Turvy: integrating a global view into sequence-based PPI prediction (2022) (5)
- iTreePack: Protein Complex Side-Chain Packing by Dual Decomposition (2015) (5)
- ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus (2015) (5)
- Supplementary Information for: The genetic prehistory of southern Africa (2012) (5)
- Granger causal inference on DAGs identifies genomic loci regulating transcription (2022) (4)
- Simultaneous Alignment and Folding of Protein Sequences (2009) (4)
- Modeling Collision Cascade Structure of SiO 2 , Si 3 N 4 and SiC using Local Topological Approaches (1997) (4)
- Coexpression enables multi-study cellular trajectories of development and disease (2019) (4)
- On the Structure of the Scaffolding Core of Bacteriophage T4 (1999) (4)
- Metric learning enables synthesis of heterogeneous single-cell modalities (2020) (4)
- Msari (2004) (4)
- Voices of biotech (2016) (4)
- Modeling of Topologically-Disordered Tetrahedral Network Structures using Local Rules (1997) (4)
- A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis (2013) (4)
- Learning Mutational Semantics (2020) (3)
- Neural Data Visualization for Scalable and Generalizable Single Cell Analysis (2018) (3)
- Modeling Amorphization of Tetrahedral Structures Using Local Approaches (1996) (3)
- Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology (2010) (3)
- Learning with uncertainty for biological discovery and design (2020) (3)
- C. Elegans Exhibits Coordinated Oscillation in Gene Expression During Development (2018) (2)
- Sparse estimation for structural variability (2010) (2)
- Deciphering the species-level structure of topologically associating domains (2021) (2)
- C. elegans exhibits coordinated oscillation in gene activation in single-cell developmental data (2018) (2)
- Phylogenetic reconciliation reveals extensive ancestral recombination in Sarbecoviruses and the SARS-CoV-2 lineage (2021) (2)
- Multi-resolution modeling of a discrete stochastic process identifies causes of cancer (2021) (2)
- Algorithmic advances take advantage of the structure of massive biological data landscape (2016) (2)
- Assessing statistical significance in causal graphs (2012) (2)
- Conformational landscape of the yeast SAGA complex as revealed by cryo-EM (2022) (2)
- Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities (2016) (2)
- 2017 Outstanding Contributions to ISCB Award: Fran Lewitter (2017) (2)
- Recovering Single-cell Heterogeneity Through Information-based Dimensionality Reduction (2021) (2)
- Near-Linear Cost Sequential and Distributed Constructions of SparseNeighborhood CoversBaruch Awerbuch (1993) (1)
- A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers (2012) (1)
- A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models (2018) (1)
- Intrinsic instability of the dysbiotic microbiome revealed through dynamical systems inference at scale (2021) (1)
- Local-rules based topological modeling of tetrahedral ceramic network structures (1998) (1)
- Enriching and Characterizing T Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products. (2022) (1)
- Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis) (2022) (1)
- Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection (2020) (1)
- Supplementary information for: Ancient west Eurasian ancestry in southern and eastern Africa (2014) (1)
- Minimizer-space de Bruijn graphs (2021) (1)
- A Python-based optimization framework for high-performance genomics (2020) (1)
- Efficient Design of Compact Unstructured RNA Libraries (2016) (1)
- Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading (2006) (1)
- ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus (2015) (1)
- Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities (2021) (1)
- Towards a topological description of poorly-crystalline networks (1999) (1)
- Genomics in 2011: challenges and opportunities (2011) (1)
- Scheduling with Concurrency-Based Constraints (1995) (1)
- Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing (2023) (1)
- Efficient Algorithms to Explore the RNA Mutational Landscape (2012) (1)
- A computational framework for boosting confidence in high-throughput protein-protein interaction datasets (2012) (1)
- ISMB 2012 Proceedings Papers Committee. July 15 to July 19, 2012, Long Beach, CA, USA. Editorial. (2012) (0)
- ISMB 2010 Organization (2010) (0)
- 2008 Reviewers List (2009) (0)
- D-SCRIPT: Structure-aware deep learning for protein interaction prediction (2020) (0)
- Neural network particle picking and denoising in cryoEM with Topaz (2020) (0)
- Codon: A Compiler for High-Performance Pythonic Applications and DSLs (2023) (0)
- Scalable and Privacy-Preserving Federated Principal Component Analysis (2023) (0)
- Contrasting drugs from decoys (2022) (0)
- MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis (2012) (0)
- Sequre: a high-performance framework for rapid development of secure bioinformatics pipelines (2022) (0)
- Computational, statistical and graph-theoretical methods for disease mapping and cluster detection (2007) (0)
- regions of mammalian mRNAs Unusually effective microRNA targeting within repeat-rich coding Material Supplemental (2011) (0)
- 2017 ISCB Innovator Award: Aviv Regev (2017) (0)
- Accurate detection of arbitrarily-shaped spatial disease clusters (2007) (0)
- Strain Tracking with Uncertainty Quantification (2023) (0)
- Sis for Approximate Mst Clustering by Deleting from the Claim 6. with Probability 2 at Least 19 20 the following Holds for Every Y 2 P : If the Algorithm Computes ~ (0)
- Causally-guided Regularization of Graph Attention Improves Generalizability (2022) (0)
- Learning the Language of Antibody Hypervariability (2023) (0)
- Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens. (2023) (0)
- Because residues a xed distance in sequence exhibit these correlations in coiled coils (2004) (0)
- Visualization of clustered protocadherin neuronal self-recognition complexes (2019) (0)
- Optimal transport analysis of single-cell transcriptomics directs hypotheses 1 prioritization and validation (2022) (0)
- Learning the Drug-Target Interaction Lexicon (2022) (0)
- Efficient minimizer orders for large values of k using minimum decycling sets (2023) (0)
- Advances in heterogeneous reconstruction with cryoDRGN (2021) (0)
- Finding RNA structure in the unstructured RBPome (2018) (0)
- An econometric lens resolves cell-state parallax (2023) (0)
- Bayesian information sharing enhances detection of regulatory associations in rare cell types (2021) (0)
- Unraveling causal gene regulation from the RNA velocity graph using Velorama (2023) (0)
- Prioritizing transcription factor perturbations from single-cell transcriptomics (2023) (0)
- Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis) (2022) (0)
- Learning the mutational landscape of the cancer genome (2021) (0)
- Secure and Federated Genome-Wide Association Studies for Biobank-Scale Datasets (2022) (0)
- Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads (2020) (0)
- Carnelian: alignment-free functional binning and abundance estimation of metagenomic reads (2018) (0)
- Efficient integration of heterogeneous single-cell transcriptomes using Scanorama (2019) (0)
- Author Correction: Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption (2021) (0)
- Metabolic Network Analysis Demystified (2011) (0)
- Secure and federated linear mixed model association tests (2022) (0)
- Allergic inflammatory memory in human respiratory epithelial progenitor cells (2018) (0)
- A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis (2013) (0)
- CryoDRGN: a tool for reconstructing highly heterogeneous structural ensembles from cryo-electron micrographs (2020) (0)
- Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes (2018) (0)
- EigenFold: Generative Protein Structure Prediction with Diffusion Models (2023) (0)
- virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2 (2022) (0)
- Joker de Bruijn: Covering k-Mers Using Joker Characters (2018) (0)
- HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control (2022) (0)
- Assessing transcriptomic re-identification risks using discriminative sequence models (2023) (0)
- Reconstruction of phyletic trees by global alignment of multiple metabolic networks (2013) (0)
- CryoDRGN2: Ab Initio Neural Reconstruction of Dynamic Protein Complexes (2022) (0)
- mapquik: Efficient low-divergence mapping of long reads in minimizer space (2022) (0)
- HIV-specific CD8+ T-cells in tonsils express exhaustive TRM-like signatures (2021) (0)
- Mathematical methods for protein structural motif recognition (2001) (0)
- 2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner (2017) (0)
- Analysis of antiviral therapy in 241 cases with corona virus disease 2019 in Guangzhou (2020) (0)
- Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter (2017) (0)
- Enabling IMaC purification of low abundance recombinant proteins from E . coli lysates (2009) (0)
- 2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner (2017) (0)
- Graphs, matrices, and populations: linear algebraic techniques in theoretical computer science and population genetics (2013) (0)
- 2017 ISCB Overton Prize: Christoph Bock (2017) (0)
- Ras to Extracellular Signal-Regulated Kinase Signaling Proteomic and Functional Genomic Landscape of Receptor Tyrosine (2011) (0)
- Whole-organism integrative expressome for caenorhabditis elegans enables in silico study of developmental regulation (2011) (0)
- Novel Perspectives on Protein Structure Prediction (2010) (0)
- Scalpel: Information-based Dimensionality Reduction for Rare Cell Type Discovery (2021) (0)
- Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock (2017) (0)
- 7 Coping with Apparent Shortcomings 6.2 Other Known Distributed Cover-construction Algorithms 6.1 an Improved Distributed Version of the Gv Algorithm 6 a Distributed Version of Algorithm Gv 5 Synchronizer (0)
- A Multi-Threaded Simulator for the Kinetics of Virus Shell Assembly (2008) (0)
- Supplement for ” Enabling Privacy Preserving GWAS in Heterogenous Human Populations ” (2015) (0)
- Structure-based algorithms for protein-protein interaction prediction (2012) (0)
- Methods for building genomic networks and uses thereof (2018) (0)
- SemanticDx: a prototype to facilitate use of biostatistics at the point-of-care. (2008) (0)
- morphological data from a combinatorial RNAi screen Inference of RhoGAP / GTPase regulation using single-cell Material (2010) (0)
- interactions in cytokines using localized threading LTHREADER : Prediction of extracellular ligand receptor (0)
- GM-CSF differentiation of human monocytes stabilizes macrophage state via oxidative signaling (2020) (0)
- OP-CBIO170043 1681..1688 (2017) (0)
- Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner (2017) (0)
- Single-cell RNA-sequencing (scRNA-seq) studies now profile millions of transcriptomes (2020) (0)
- Algorithms for genomics and genetics: compression-accelerated search and admixture analysis (2013) (0)
- The genetic prehistory of southern Africa The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters (2012) (0)
- 1 Supplement : iWRAP : An interface threading approach for protein-protein interaction prediction (2010) (0)
- 2017 Outstanding Contributions to ISCB Award: Fran Lewitter (2017) (0)
- Bonnie Berger non-coding RNAs Structure-based whole genome realignment reveals many novel Material (2012) (0)
- Development of simulation tools for virus shell assembly. Final report (2001) (0)
- Sequencing a genome by walking with clone-end sequences (abstract): a mathematical analysis (2000) (0)
- Preface: 14th International Conference on Research in Computational Molecular Biology (RECOMB 2010) (2011) (0)
- Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping. (2017) (0)
- Protecting Genomic Data Privacy with Probabilistic Modeling (2019) (0)
- Research in Computational Molecular Biology, 14th Annual International Conference, RECOMB 2010, Lisbon, Portugal, April 25-28, 2010. Proceedings (2010) (0)
- Section 16. Applications Recent Developments in Computational Gene Recognition (1998) (0)
- Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters (2017) (0)
- 3D PROTEIN STRUCTURE FROM CRYO-EM IMAGES (0)
- Generalizable Visualization of Mega-Scale Single-Cell Data (2018) (0)
- Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev (2017) (0)
- noncoding RNAs Structure-based whole-genome realignment reveals many novel (2013) (0)
- split-intein Gal4 provides intersectional genetic labeling that is fully repressible by Gal80 (2023) (0)
- 2017 ISCB Innovator Award: Aviv Regev (2017) (0)
- Principles of Systems Biology, No. 31. (2018) (0)
- Geometric Sketching of Single-Cell Data Preserves Transcriptional Structure (2019) (0)
- Computational analysis of noncoding RNAs Citation (2012) (0)
- Localized methods for protein interaction prediction (2008) (0)
- CryoDRGN: Deep Generative Models for Reconstructing Heterogeneous 3D Structures from Cryo-electron Micrographs (2020) (0)
- 2017 ISCB Overton Prize awarded to Christoph Bock (2017) (0)
- Genes, Regulation, Evolution (2003) (0)
- Structures of radial spokes and associated complexes important for ciliary motility (2020) (0)
- Strahlentherapie spinaler Metastasen (2016) (0)
- The mathematics of virus shell assembly. Progress report 1995--1996 (1996) (0)
- Compact Integration of Mu lti-Network Topology for Functional Analysis of Genes Graphical Abstract Highlights (0)
- ISCB’s initial reaction to New England Journal of Medicine editorial on data sharing (2016) (0)
- Supplementary Information for Compressive genomics allows computational analysis to keep pace with genomic data (2012) (0)
- Coexpression uncovers a unified single-cell transcriptomic landscape (2019) (0)
- Navigating bottlenecks and trade-offs in genomic data analysis (2022) (0)
- ISMB/ECCB 2013 Proceedings Papers Committee (2013) (0)
- ISMB 2016 Proceedings Papers Committee (2016) (0)
- Editorial (2012) (0)
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