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TreeCluster: Clustering biological sequences using phylogenetic trees

PloS one, 2019-08, Vol.14 (8), p.e0221068-e0221068

2019

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ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes

Bioinformatics, 2021-05, Vol.37 (5), p.714-716

2021

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The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

Science (American Association for the Advancement of Science), 2022-08, Vol.377 (6609), p.960-966

2022

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Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks

PLoS computational biology, 2019-07, Vol.15 (7), p.e1007007-e1007007

2019

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The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction

Scientific reports, 2022-03, Vol.12 (1), p.5077-5077, Article 5077

2022

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ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data

Bioinformatics (Oxford, England), 2023-05, Vol.39 (5)

2023

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An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology

Viruses, 2022-04, Vol.14 (4), p.774

2022

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Ten simple rules for attending your first conference

PLoS computational biology, 2021-07, Vol.17 (7), p.e1009133-e1009133

2021

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SEPIA: simulation-based evaluation of prioritization algorithms

BMC medical informatics and decision making, 2021-06, Vol.21 (1), p.1-177, Article 177

2021

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ViralWasm: a client-side user-friendly web application suite for viral genomics

Bioinformatics (Oxford, England), 2024-01, Vol.40 (1)

2024

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A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition

Systematic biology, 2018-05, Vol.67 (3), p.475-489

2018

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Timing the SARS-CoV-2 index case in Hubei province

Science (American Association for the Advancement of Science), 2021-04, Vol.372 (6540), p.412-417

2021

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Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases

mSystems, 2022-04, Vol.7 (2), p.e0137821-e0137821

2022

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Accelerating open modification spectral library searching on tensor core in high-dimensional space

Bioinformatics (Oxford, England), 2023-07, Vol.39 (7)

2023

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HyperSpec: Ultrafast Mass Spectra Clustering in Hyperdimensional Space

Journal of proteome research, 2023-06, Vol.22 (6), p.1639-1648

2023

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HIV Care Prioritization Using Phylogenetic Branch Length

Journal of acquired immune deficiency syndromes (1999), 2021-04, Vol.86 (5), p.626-637

2021

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GenieHD: efficient DNA pattern matching accelerator using hyperdimensional computing

Proceedings of the 23rd Conference on Design, Automation and Test in Europe, 2020, p.115-120

2020

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HyperGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors

Bioinformatics (Oxford, England), 2024-07, Vol.40 (7)

2024

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FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences

Bioinformatics (Oxford, England), 2019-06, Vol.35 (11), p.1852-1861

2019

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Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce

The New England journal of medicine, 2021-09, Vol.385 (14), p.1330-1332

2021

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DRAM-Based Acceleration of Open Modification Search in Hyperdimensional Space

IEEE transactions on computer-aided design of integrated circuits and systems, 2024-09, Vol.43 (9), p.2592-2605

2024

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RAPIDx: High-performance ReRAM Processing in-Memory Accelerator for Sequence Alignment

IEEE transactions on computer-aided design of integrated circuits and systems, 2023-10, Vol.42 (10), p.1-1

2023

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Accelerators for Classical Molecular Dynamics Simulations of Biomolecules

Journal of chemical theory and computation, 2022-07, Vol.18 (7), p.4047-4069

2022

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Leveraging social networks for identification of people with HIV who are virally unsuppressed

AIDS (London), 2024-02, Vol.38 (2), p.245-254

2024

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SpecHD: Hyperdimensional Computing Framework for FPGA-Based Mass Spectrometry Clustering

2024 Design, Automation & Test in Europe Conference & Exhibition (DATE), 2024, p.1-6

2024

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TreeCluster: Clustering biological sequences using phylogenetic trees

ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes

The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks

The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction

ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data

An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology

Ten simple rules for attending your first conference

SEPIA: simulation-based evaluation of prioritization algorithms

ViralWasm: a client-side user-friendly web application suite for viral genomics

A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition

Timing the SARS-CoV-2 index case in Hubei province

Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases

Accelerating open modification spectral library searching on tensor core in high-dimensional space

HyperSpec: Ultrafast Mass Spectra Clustering in Hyperdimensional Space

HIV Care Prioritization Using Phylogenetic Branch Length

GenieHD: efficient DNA pattern matching accelerator using hyperdimensional computing

HyperGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences

Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce

DRAM-Based Acceleration of Open Modification Search in Hyperdimensional Space

RAPIDx: High-performance ReRAM Processing in-Memory Accelerator for Sequence Alignment

Accelerators for Classical Molecular Dynamics Simulations of Biomolecules

Leveraging social networks for identification of people with HIV who are virally unsuppressed

SpecHD: Hyperdimensional Computing Framework for FPGA-Based Mass Spectrometry Clustering

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