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Dynamic kernel matching for non-conforming data: A case study of T cell receptor datasets

PloS one, 2023-03, Vol.18 (3), p.e0265313-e0265313

2023

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Fecal microbiota transplant rescues mice from human pathogen mediated sepsis by restoring systemic immunity

Nature communications, 2020-05, Vol.11 (1), p.2354-2354, Article 2354

2020

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TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors

Frontiers in immunology, 2021-03, Vol.12, p.640725-640725

2021

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Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis

BMC bioinformatics, 2017-09, Vol.18 (1), p.401-401, Article 401

2017

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Human genomes as email attachments

Bioinformatics, 2009-01, Vol.25 (2), p.274-275

2009

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Biophysicochemical motifs in T cell receptor sequences as a potential biomarker for high-grade serous ovarian carcinoma

PloS one, 2020-03, Vol.15 (3), p.e0229569-e0229569

2020

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Towards anatomic scale agent-based modeling with a massively parallel spatially explicit general-purpose model of enteric tissue (SEGMEnT_HPC)

PloS one, 2015-03, Vol.10 (3), p.e0122192-e0122192

2015

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Intestinal anastomotic injury alters spatially defined microbiome composition and function

Microbiome, 2014-09, Vol.2 (1), p.35-35, Article 35

2014

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Data structures and compression algorithms for high-throughput sequencing technologies

BMC bioinformatics, 2010-10, Vol.11 (1), p.514-514, Article 514

2010

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Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data

Frontiers in immunology, 2017-11, Vol.8, p.1418-1418

2017

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Comparative genetics of Enterococcus faecalis intestinal tissue isolates before and after surgery in a rat model of colon anastomosis

PloS one, 2020-04, Vol.15 (4), p.e0232165-e0232165

2020

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Investigation of inflammation and tissue patterning in the gut using a Spatially Explicit General-purpose Model of Enteric Tissue (SEGMEnT)

PLoS computational biology, 2014-03, Vol.10 (3), p.e1003507-e1003507

2014

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AIRR Community Standardized Representations for Annotated Immune Repertoires

Frontiers in immunology, 2018-09, Vol.9, p.2206-2206

2018

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VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements

Frontiers in immunology, 2018-05, Vol.9, p.976-976

2018

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Astrocytic stress response is induced by exposure to astrocyte-binding antibodies expressed by plasmablasts from pediatric patients with acute transverse myelitis

Journal of neuroinflammation, 2024-06, Vol.21 (1), p.161-16, Article 161

2024

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Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent

BMC systems biology, 2010-07, Vol.4 (1), p.99-99, Article 99

2010

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T Cell Receptor Repertoires Acquired via Routine Pap Testing May Help Refine Cervical Cancer and Precancer Risk Estimates

Frontiers in immunology, 2021-04, Vol.12, p.624230-624230

2021

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VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data

BMC bioinformatics, 2017-10, Vol.18 (1), p.448-448, Article 448

2017

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Incorporating existing network information into gene network inference

PloS one, 2009-08, Vol.4 (8), p.e6799-e6799

2009

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Patterns of mesenchymal condensation in a multiscale, discrete stochastic model

PLoS computational biology, 2007-04, Vol.3 (4), p.e76-e76

2007

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The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons

Frontiers in big data, 2020-06, Vol.3, p.22-22

2020

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An automated homology-based approach for identifying transposable elements

BMC bioinformatics, 2011-05, Vol.12 (1), p.130-130, Article 130

2011

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Integration of TGF-β- and EGFR-based signaling pathways using an agent-based model of epithelial restitution

Wound repair and regeneration, 2012-11, Vol.20 (6), p.862-863

2012

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Biophysicochemical Motifs in T-cell Receptor Sequences Distinguish Repertoires from Tumor-Infiltrating Lymphocyte and Adjacent Healthy Tissue

Cancer research (Chicago, Ill.), 2019-04, Vol.79 (7), p.1671-1680

2019

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Immune Repertoire Analysis on High-Performance Computing Using VDJServer V1: A Method by the AIRR Community

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2453, p.439

2022

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Dynamic kernel matching for non-conforming data: A case study of T cell receptor datasets

Fecal microbiota transplant rescues mice from human pathogen mediated sepsis by restoring systemic immunity

TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors

Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis

Human genomes as email attachments

Biophysicochemical motifs in T cell receptor sequences as a potential biomarker for high-grade serous ovarian carcinoma

Towards anatomic scale agent-based modeling with a massively parallel spatially explicit general-purpose model of enteric tissue (SEGMEnT_HPC)

Intestinal anastomotic injury alters spatially defined microbiome composition and function

Data structures and compression algorithms for high-throughput sequencing technologies

Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data

Comparative genetics of Enterococcus faecalis intestinal tissue isolates before and after surgery in a rat model of colon anastomosis

Investigation of inflammation and tissue patterning in the gut using a Spatially Explicit General-purpose Model of Enteric Tissue (SEGMEnT)

AIRR Community Standardized Representations for Annotated Immune Repertoires

VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements

Astrocytic stress response is induced by exposure to astrocyte-binding antibodies expressed by plasmablasts from pediatric patients with acute transverse myelitis

Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent

T Cell Receptor Repertoires Acquired via Routine Pap Testing May Help Refine Cervical Cancer and Precancer Risk Estimates

VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data

Incorporating existing network information into gene network inference

Patterns of mesenchymal condensation in a multiscale, discrete stochastic model

The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons

An automated homology-based approach for identifying transposable elements

Integration of TGF-β- and EGFR-based signaling pathways using an agent-based model of epithelial restitution

Biophysicochemical Motifs in T-cell Receptor Sequences Distinguish Repertoires from Tumor-Infiltrating Lymphocyte and Adjacent Healthy Tissue

Immune Repertoire Analysis on High-Performance Computing Using VDJServer V1: A Method by the AIRR Community

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