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Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data

Nature methods, 2022-03, Vol.19 (3), p.316

2022

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RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

Bioinformatics, 2016-06, Vol.32 (12), p.i192-i200

2016

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Alignment and mapping methodology influence transcript abundance estimation

Genome Biology, 2020-09, Vol.21 (1), p.239-239, Article 239

2020

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Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses

Nature communications, 2023-02, Vol.14 (1), p.663-663, Article 663

2023

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Single-cell analysis of immune and stroma cell remodeling in clear cell renal cell carcinoma primary tumors and bone metastatic lesions

Genome medicine, 2024-01, Vol.16 (1), p.1-21, Article 1

2024

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Quark enables semi-reference-based compression of RNA-seq data

Bioinformatics (Oxford, England), 2017-11, Vol.33 (21), p.3380-3386

2017

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A space and time-efficient index for the compacted colored de Bruijn graph

Bioinformatics, 2018-07, Vol.34 (13), p.i169-i177

2018

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Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level

Bioinformatics, 2019-07, Vol.35 (14), p.i136-i144

2019

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A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification

Bioinformatics (Oxford, England), 2020-07, Vol.36 (Supplement_1), p.i292-i299

2020

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Best practices for single-cell analysis across modalities

Nature reviews. Genetics, 2023-08, Vol.24 (8), p.550

2023

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A count-based model for delineating cell–cell interactions in spatial transcriptomics data

Bioinformatics (Oxford, England), 2024-06, Vol.40 (Supplement_1), p.i481-i489

2024

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Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets

Bioinformatics (Oxford, England), 2022-05, Vol.38 (10), p.2773-2780

2022

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Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets

Bioinformatics, 2022-05, Vol.38 (10), p.2773-2780

2022

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Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes

Nature biotechnology, 2023-03, Vol.41 (3), p.417-426

2023

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Voronoi game on graphs

Theoretical computer science, 2015, Vol.562, p.270-282

2015

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Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data

Bioinformatics (Oxford, England), 2020-07, Vol.36 (Supplement_1), p.i102-i110

2020

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Compression of quantification uncertainty for scRNA-seq counts

Bioinformatics, 2021-07, Vol.37 (12), p.1699-1707

2021

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Computational Approaches for Improving the Accuracy and Efficiency of RNA-Seq Analysis

Sarkar, Hirak

2020

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Epigenetic regulation during cancer transitions across 11 tumour types

Nature (London), 2023-11, Vol.623 (7986), p.432-441

2023

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Abstract 1678: Single-cell landscape of the TH-MYCN neuroblastoma mouse model

Cancer research (Chicago, Ill.), 2022-06, Vol.82 (12_Supplement), p.1678-1678

2022

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A comparative study of ELF and VLF noise characteristics of nor’wester at a low latitude tropical station

SN applied sciences, 2019-02, Vol.1 (2), p.154, Article 154

2019

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Abstract 2510: An atlas of single-cell and spatial transcriptomics reveals alterations that correlate with human prostate cancer progression

Cancer research (Chicago, Ill.), 2022-06, Vol.82 (12_Supplement), p.2510-2510

2022

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Implementation of the system II transit point data for investigating the reduction of the rotational speed of the planet Jupiter

SN applied sciences, 2019, Vol.1 (1), p.115, Article 115

2019

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Abstract 631: Single-cell analysis of immune and stroma cell remodeling in renal cell carcinoma primary tumors and bone metastatic lesions

Cancer research (Chicago, Ill.), 2023-04, Vol.83 (7_Supplement), p.631-631

2023

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Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

Alignment and mapping methodology influence transcript abundance estimation

Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses

Single-cell analysis of immune and stroma cell remodeling in clear cell renal cell carcinoma primary tumors and bone metastatic lesions

Quark enables semi-reference-based compression of RNA-seq data

A space and time-efficient index for the compacted colored de Bruijn graph

Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level

A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification

Best practices for single-cell analysis across modalities

A count-based model for delineating cell–cell interactions in spatial transcriptomics data

Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets

Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets

Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes

Voronoi game on graphs

Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data

Compression of quantification uncertainty for scRNA-seq counts

Computational Approaches for Improving the Accuracy and Efficiency of RNA-Seq Analysis

Epigenetic regulation during cancer transitions across 11 tumour types

Abstract 1678: Single-cell landscape of the TH-MYCN neuroblastoma mouse model

A comparative study of ELF and VLF noise characteristics of nor’wester at a low latitude tropical station

Abstract 2510: An atlas of single-cell and spatial transcriptomics reveals alterations that correlate with human prostate cancer progression

Implementation of the system II transit point data for investigating the reduction of the rotational speed of the planet Jupiter

Abstract 631: Single-cell analysis of immune and stroma cell remodeling in renal cell carcinoma primary tumors and bone metastatic lesions

Single-cell analyses of metastatic bone marrow in human neuroblastoma reveals microenvironmental remodeling and metastatic signature

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