Ma Laboratory - Computational Genomics

Learning Genome Structure and Function

SCHOOL OF COMPUTER SCIENCE | CARNEGIE MELLON UNIVERSITY

TFBS Evo

This model traces the evolution of lineage-specific transcription factor binding sites without relying on detailed base-by-base cross-species alignments.
[Yokoyama et al., PLOS Computational Biology, 2014]

DawnRank

DawnRank directly prioritizes altered genes on a single patient level which would allow us to discover potential personalized driver mutations.
[Hou and Ma, Genome Medicine, 2014]

NCIS

NCIS (network-assisted co-clustering for the identification of cancer subtypes) combines molecular interaction network into co-clustering.
[Liu et al., BMC Bioinformatics, 2014]

PSAR-Align

PSAR-Align is a multiple sequence realignment tool that can refine a given multiple sequence alignment based on suboptimal alignments.
[Kim and Ma, Bioinformatics, 2013]

RACA

RACA (reference-assisted chromosome assembly) is a novel algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments.
[Kim et al., PNAS, 2013]

TrueSight

TrueSight utilizes a machine-learning approach to precisely map RNA-seq reads to splice junctions, combining read mapping quality and coding potential of genomic sequences into a unified model.
[Li et al., Nucleic Acids Research, 2012]

TIGER

TIGER is a novel de novo genome assembly framework that adapts to available computing resources by iteratively decomposing the assembly problem into sub-problems.
[Wu et al., BMC Bioinformatics, 2012]

PSAR

PSAR is a probabilistic sampling-based alignment reliability score to assess the uncertainty of multiple sequence alignment. It generates suboptimal alignments based on pair-HMM.
[Kim and Ma, Nucleic Acids Research, 2011]

FusionHunter

FusionHunter reliably identifies fusion transcripts in cancer transcriptome based on paired-end RNA-seq. It detects fusion junctions in base-level resolution.
[Li et al., Bioinformatics, 2011]

InferCARs

Given a set of related genomes, InferCARs reconstructs the chromosomal architecture of their most recent common ancestor. It also provides lineage-specific genomic breakpoint information.
[Ma et al., Genome Research, 2006]

DupCar

DupCar reconstructs the ancestral genomic orders with duplications from a set of related genomes (source code available upon request).
[Ma et al., Journal of Computational Biology, 2008]

Infinite Sites Model

The program solves the problem of recovering the history of a set of genomes that are related to an unseen common ancestor genome by operations of speciation, deletion, insertion, duplication, and rearrangement (source code available upon request).
[Ma et al., PNAS, 2008]