Han Fang

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

The paper uses long-read sequencing to analyze structural variations in the SK-BR-3 breast cancer cell line, revealing complex rearrangements and novel gene fusions.

Accurate detection of complex structural variations using single molecule sequencing

The paper introduces open-source tools for detecting structural variations using long-read sequencing, achieving high sensitivity and precision in complex regions and identifying novel variants in human genomes.

Scikit-ribo: Accurate estimation and robust modeling of translation dynamics at codon resolution

Scikit-ribo provides accurate A-site prediction and translation efficiency estimation from Riboseq and RNAseq data, correcting biases and improving TE estimation for over 2000 genes in S. cerevisiae.

HadoopCNV: A Dynamic Programming Imputation Algorithm To Detect Copy Number Variants From Sequencing Data

HadoopCNV detects copy number variants from WGS data using dynamic programming and allelic depth, outperforming existing tools in accuracy and scalability.

GenomeScope: Fast reference-free genome profiling from short reads

GenomeScope estimates genome size, heterozygosity, and repeat content from short reads to aid in genome analysis parameter selection.

Indel variant analysis of short-read sequencing data with Scalpel

This paper introduces Scalpel, an open-source tool for accurate indel detection from short-read sequencing data, and demonstrates its application in various analysis modes.

A variant in TAF1 is associated with a new syndrome with severe intellectual disability and characteristic dysmorphic features

The paper identifies a maternally inherited TAF1 variant in two brothers with severe intellectual disability and distinctive facial features, linking it to a new syndrome.

Whole genome analysis of an extended pedigree with Prader–Willi Syndrome, hereditary hemochromatosis, and dysautonomia-like symptoms

This paper reports whole genome sequencing of a family with PWS, HH, and dysautonomia-like symptoms, identifying genetic variants and highlighting the importance of standardized phenotypic and genomic data.

Genome Wide Variant Analysis of Simplex Autism Families with an Integrative Clinical-Bioinformatics Pipeline

This study uses an integrative clinical-bioinformatics pipeline to analyze genome-wide variants in simplex autism families, identifying candidate variants associated with ASD.

Reducing INDEL calling errors in whole-genome and exome sequencing data

This study identifies sources of INDEL calling errors in sequencing data and shows that whole-genome sequencing (WGS) outperforms whole-exome sequencing (WES) in accuracy and sensitivity for detecting INDELs.

Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly

Scalpel detects de novo and transmitted INDELs in exome data with high specificity and sensitivity, outperforming existing tools in challenging repeat regions and identifying new autism-related genes.