Papers |

SCALLOPS: a scalable, integrated computational framework for Optical Pooled Screens

Tue, 16 Jun 2026 00:00:00 +0000

The Hippo Pathway Is Dysregulated in Cancer-Associated Fibroblasts in Anti–PD-L1–Resistant Cancer

Mon, 01 Jun 2026 00:00:00 +0000

Linking live-cell behavior to transcriptional responses across perturbations using dynamic caging

Fri, 08 May 2026 00:00:00 +0000

Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells

Wed, 14 Oct 2020 00:00:00 +0000

Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq

Mon, 27 Jul 2020 00:00:00 +0000

A Single-Cell and Single-Nucleus RNA-Seq Toolbox for Fresh and Frozen Human Tumors

Mon, 11 May 2020 00:00:00 +0000

Thousands of Novel Unannotated Proteins Expand the MHC I Immunopeptidome in Cancer

Mon, 11 May 2020 00:00:00 +0000

Linking Indirect Effects of Cytomegalovirus in Transplantation to Modulation of Monocyte Innate Immune Function

Wed, 22 Apr 2020 00:00:00 +0000

Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes

Fri, 17 Apr 2020 00:00:00 +0000

Accuracy Assessment of Fusion Transcript Detection via Read-Mapping and De Novo Fusion Transcript Assembly-based Methods

Mon, 21 Oct 2019 00:00:00 +0000

Decoding Human Fetal Liver Haematopoiesis

Wed, 09 Oct 2019 00:00:00 +0000

Nuclei Multiplexing with Barcoded Antibodies for Single-Nucleus Genomics

Tue, 02 Jul 2019 00:00:00 +0000

An example preprint / working paper

Sun, 07 Apr 2019 00:00:00 +0000

This work is driven by the results in my on LLMs.

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PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays

Wed, 24 May 2017 00:00:00 +0000

STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq

Fri, 24 Mar 2017 00:00:00 +0000

Metrics for Rapid Quality Control in RNA Structure Probing Experiments

Thu, 01 Dec 2016 00:00:00 +0000

Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping

Tue, 20 Oct 2015 00:00:00 +0000

An example journal article

Tue, 01 Sep 2015 00:00:00 +0000

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Evaluation of de novo Transcriptome Assemblies from RNA-Seq Data

Sun, 21 Dec 2014 00:00:00 +0000

De novo Transcript Sequence Reconstruction from RNA-seq using the Trinity Platform for Reference Generation and Analysis

Thu, 11 Jul 2013 00:00:00 +0000

An example conference paper

Mon, 01 Jul 2013 00:00:00 +0000

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RSEM: Accurate Transcript Quantification from RNA-Seq Data with or without a Reference Genome

Thu, 04 Aug 2011 00:00:00 +0000

Discoevering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

Thu, 14 Jul 2011 00:00:00 +0000

RNA-Seq Gene Expression Estimation with Read Mapping Uncertainty

Mon, 15 Feb 2010 00:00:00 +0000