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OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement

PLoS computational biology, 2018-07, Vol.14 (7), p.e1006223-e1006223

2018

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Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

PLoS computational biology, 2018-06, Vol.14 (6), p.e1006245-e1006245

2018

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Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline

PLoS computational biology, 2016-09, Vol.12 (9), p.e1005112-e1005112

2016

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BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods

PLoS computational biology, 2017-03, Vol.13 (3), p.e1005209-e1005209

2017

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Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes

Nature communications, 2021-08, Vol.12 (1), p.4676-4676, Article 4676

2021

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Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2

Science (American Association for the Advancement of Science), 2020-12, Vol.370 (6523), p.1479-1484

2020

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The SARS-CoV-2 Exerts a Distinctive Strategy for Interacting with the ACE2 Human Receptor

Viruses, 2020-04, Vol.12 (5), p.497

2020

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Exploring the potential of structure-based deep learning approaches for T cell receptor design

PLoS computational biology, 2024-09, Vol.20 (9), p.e1012489

2024

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Dissecting peripheral protein-membrane interfaces

PLoS computational biology, 2022-12, Vol.18 (12), p.e1010346

2022

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NanoNet: Rapid and accurate end-to-end nanobody modeling by deep learning

Frontiers in immunology, 2022-08, Vol.13, p.958584

2022

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The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement

PLoS computational biology, 2023-11, Vol.19 (11), p.e1011248-e1011248

2023

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Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

Biophysical journal, 2013-08, Vol.105 (4), p.962-974

2013

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Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution

PLoS computational biology, 2023-08, Vol.19 (8), p.e1011090-e1011090

2023

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BIPS—A code base for designing and coding of a Phage ImmunoPrecipitation Oligo Library

PLoS computational biology, 2022-11, Vol.18 (11), p.e1010663-e1010663

2022

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Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies

PLoS biology, 2012-01, Vol.10 (1), p.e1001244-e1001244

2012

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EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos

PLoS computational biology, 2018-04, Vol.14 (4), p.e1006128-e1006128

2018

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An open source tool for automatic spatiotemporal assessment of calcium transients and local 'signal-close-to-noise' activity in calcium imaging data

PLoS computational biology, 2018-03, Vol.14 (3), p.e1006054-e1006054

2018

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fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks

PLoS computational biology, 2017-11, Vol.13 (11), p.e1005838-e1005838

2017

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Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex

eLife, 2016-10, Vol.5

2016

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Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2

Proceedings of the National Academy of Sciences - PNAS, 2021-08, Vol.118 (34), p.1

2021

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HaSAPPy: A tool for candidate identification in pooled forward genetic screens of haploid mammalian cells

PLoS computational biology, 2018-01, Vol.14 (1), p.e1005950

2018

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Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1

Proceedings of the National Academy of Sciences - PNAS, 2017-02, Vol.114 (7), p.1560-1565

2017

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Cryo-EM structures of engineered active bc 1-cbb 3 type CIII2CIV super-complexes and electronic communication between the complexes

Nature communications, 2021-12, Vol.12 (1), p.1-14

2021

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Modeling Protein Conformational Changes with SAXS Profiles

Biophysical journal, 2018-02, Vol.114 (3), p.66a-66a

Schneidman, Dina

2018

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Polypolish: Short-read polishing of long-read bacterial genome assemblies

PLoS computational biology, 2022-01, Vol.18 (1), p.e1009802-e1009802

2022

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OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline

BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods

Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes

Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2

The SARS-CoV-2 Exerts a Distinctive Strategy for Interacting with the ACE2 Human Receptor

Exploring the potential of structure-based deep learning approaches for T cell receptor design

Dissecting peripheral protein-membrane interfaces

NanoNet: Rapid and accurate end-to-end nanobody modeling by deep learning

The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution

BIPS—A code base for designing and coding of a Phage ImmunoPrecipitation Oligo Library

Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies

EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos

An open source tool for automatic spatiotemporal assessment of calcium transients and local 'signal-close-to-noise' activity in calcium imaging data

fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks

Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex

Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2

HaSAPPy: A tool for candidate identification in pooled forward genetic screens of haploid mammalian cells

Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1

Cryo-EM structures of engineered active bc 1-cbb 3 type CIII2CIV super-complexes and electronic communication between the complexes

Modeling Protein Conformational Changes with SAXS Profiles

Polypolish: Short-read polishing of long-read bacterial genome assemblies

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