Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes.

Aydin B, Kakumanu A, Rossillo M, Moreno-Estellés M, Garipler G, Ringstad N, Flames N, Mahony S, Mazzoni EO. 2019. Nature Neuroscience.

Deconvolving sequence features that discriminate between overlapping regulatory annotations.

Kakumanu A, Velasco S, Mazzoni EO and Mahony S. 2017. PLoS Comput Biol.

A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells

Velasco S1, Ibrahim MM1, Kakumanu A1, Garipler G, Aydin B, Al-Sayegh MA, Hirsekorn A, Abdul-Rahman F, Ohler U, Mahony M and Mazzoni E. 2016. Cell Stem Cell. [1 Co-first author]

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, Lee D, Kaestner KH and Zaret KS. 2016. Molecular Cell.

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H and Gifford DK. 2014. PLoS Comput Biol.

Metabolic and transcriptional reprogramming in developing soybean (Glycine max) embryos

Collakova E, Aghamirzale D, Fang Y, Klumas C, Tabataba F, Kakumanu A, Myers E, Heath LS and Grene R. 2013. Metabolites.

Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq

Kakumanu A, Ambavaram MMR, Klumas C, Krishnan A, Batlang U, Myers E, Grene R and Pereira A. 2012. Plant Physiology.