Bioinformatics Software

Here is a list of bioinformatics software written by the Hammell Lab:


TEToolkit is a software package that utilizes both unambiguously (uniquely) and ambiguously (multi-) mapped reads to perform differential enrichment analyses from high throughput sequencing experiments.


BAMQC is a software package that performs quality control on alignment files from high throughput sequencing experiments and assesses their suitability for downstream analysis.

Transposon Control Systems in Animals

hammell-research2TDP-43 is an RNA-binding protein that is known to control proper splicing and translation of many RNA targets in neurons. Mutation of TDP-43 has been associated with a variety of neurdogenerative diseases including Amyotrophic Lateral Sclerosis (ALS), Fronto-Temporal Lobar Degeneration (FTLD), and Alzheimer’s Disease (AD). However, the normal function of TDP-43 in neuronal development and maintenance has not been fully characterized and few of its mRNA targets have been definitively associated with the neurodegenerative diseases that result from loss of TDP-43 function. In collaboration with the Dubnau lab at CSHL, my group has explored the novel hypothesis that TDP-43 normally plays a large and hitherto uncharacterized role in regulating the expression of transposable elements (TEs), mobile genetic elements whose unregulated expression leads to genetic instability as well as cellular toxicity. Members of my group have shown that TDP-43 binds widely to TE transcripts in mammals, and that TDP-43 binding to TEs is lost in human patients diagnosed with FTLD (Li et al., 2012), a disease characterized by TDP-43 proteinopathy. While these studies support a role for TDP-43 in regulating TE expression, our future goals are centered on defining a causal role for TDP-43 mediated regulation of TEs in neurodegenerative disease. One important element of this project will be the identification of how TDP-43 interacts with the small RNA regulators of TE expression known to be involved in controlling TE mobility.

Small RNA Pathways in Maize

hammell-research1The maize genome has remained relatively unexplored despite the importance of maize as one of the early genetic model organisms. Preliminary characterizations of the maize genome and transcriptome suggest that substantial differences exist, both between maize ecotypes as well as the well-characterized plant model Arabidopsis. Furthermore, these maize inbreds exhibit dramatic phenotypic differences in response to mutations in small RNA biogenesis factors, suggesting extensive evolution in both small RNA function and activity. In collaboration with the Timmermans lab at CSHL, my group has undertaken a project to characterize the dynamics of small RNA expression and activity in a variety of maize tissues and inbreds. The focus of this project is to determine the small RNA mediated regulatory circuits that give rise to inbred-specific phenotypic diversity both within the maize species and within the larger group of grasses. Our lab has developed novel algorithms for the identification of phased small RNAs, for microRNA gene identification, and for microRNA target interaction analysis. These algorithms are being applied to deep sequencing datasets of small RNAs and mRNAs isolated from developing maize tissues.