Publications

Chang, H., Ashlock, D.A., Graether, S.P. & Keller, S.M. (2024). Anchor Clustering for million-scale immune repertoire sequencing data. BMC Bioinformatics 25(1):42.

Olenick, C.E., Jordan, H. & Fallah, M. (2024). Identifying a distractor produces object-based inhibition in an allocentric reference frame for saccade planning. Scientific Reports 14:17534.

May, J.A., Feng, Z. & Adamowicz, S.J. (2023). A real data-driven simulation strategy to select an imputation method for mixed-type trait data. PLoS Computational Biology, 19(3): e1010154.

Riley, A.C., Ashlock, D.A. & Graether, S.P. (2023). The difficulty of aligning intrinsically disordered protein sequences as assessed by conservation and phylogeny. PLOS One 18(7):e0288388.

Rudar, J., Golding, G.B., Kremer, S.C. & Hajibabaei, M. (2023). Decision Tree Ensembles Utilizing Multivariate Splits Are Effective at Investigating Beta Diversity in Medically Relevant 16S Amplicon Sequencing Data. Microbiology Spectrum e02065-22.

Rudar, J., Porter, T.M., Wright, M., Golding, G.B. & Hajibabaei, M. (2022). LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data. BMC Bioinformatics 23, 110.

May, J.A., Feng, Z., Orton, M.G. & Adamowicz, S.J. (2020). The Effects of Ecological Traits on the Rate of Molecular Evolution in Ray-Finned Fishes: A Multivariable Approach. Journal of Molecular Evolution, 88: 689–702.

Riley, A.C., Ashlock, D.A. & Graether, S.P. (2019). Evolution of the modular, disordered stress proteins known as dehydrins. PLoS One. 14(2):e0211813.

Moore, C. & Meng, B. (2019). Prediction of the molecular boundary and functionality of novel viral AlkB domains using homology modelling and principal component analysis. Journal of General Virology. 10.1099/jgv.0.001237. 

Rajna, A., Gibling, H., Sarr, O., Matravadia, S., Holloway, G.P. & Mutch, D.M. (2018). Alpha-linolenic acid and linoleic acid differentially regulate the skeletal muscle secretome of obese Zucker rats. Physiological genomics, 50 8, 580-589.

Ekrem, T. & Stur, E. Orton, M. & Adamowicz, S. (2018). DNA barcode data reveal biogeographic trends in Arctic non-biting midges. Genome. 61. 10.1139/gen-2018-0100. 

Orton, M.G., May, J.A., Ly, W., Lee, D.J. & Adamowicz, S.J. (2018). Is molecular evolution faster in the tropics? Heredity, 1-12.

Malik, A.A., Veltri, M., Boddington, K.F., Singh, K.K. & Graether, S.P. (2017). Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants. Front Plant Sci. 8:709.

Linquist, S.S., Gregory, T.R., Elliott, T.A., Saylor, B., Kremer, S.C. & Cottenie, K. (2016). Yes! There are resilient generalizations (or "laws") in ecology. The Quarterly review of biology, 91 2, 119-31.

Phillips, J.R., Gwiazdowski, R.A., Ashlock, D.A. & Hanner, R. (2015). An exploration of sufficient sampling effort to describe intraspecific DNA barcode haplotype diversity: examples from the ray-finned fishes (Chordata: Actinopterygii). DNA Barcodes, 3: 66-73.

Coneva, V., Simopoulos, C., Casaretto, J.A., El-kereamy, A., Guevara, D.R., Cohn, J., Zhu, T., Guo, L., Alexander, D.C., Bi, Y.-M., McNicholas, P.D. & Rothstein, S.J. (2014). Metabolic and co-expression network-based analyses associated with nitrate response in rice. BMC Genomics 15, 1056.

Makhmoudova, A., Williams, D., Brewer, D., Massey, S., Patterson, J., Silva, A., Vassall, K.A., Liu, F., Subedi, S., Harauz, G., Siu, K.W., Tetlow, I.J. & Emes, M.J. (2014). Identification of multiple phosphorylation sites on maize endosperm starch branching enzyme IIb, a key enzyme in amylopectin biosynthesis. J Biol Chem. 289(13):9233-46.

Chiu, D. & Manjunath, R. (2014). Discovering functional patterns from pattern signatures of p53 protein sequence association structure. Neurocomputing, 145 (2014), 62-67.

Badoud, F., Lam, K.P., DiBattista, A., Perreault, M., Zulyniak, M.A., Cattrysse, B., Stephenson, S., Britz-McKibbin, P., & Mutch, D.M. (2014). Serum and adipose tissue amino acid homeostasis in the metabolically healthy obese. J Proteome Res. 13(7):3455-66

Ralston, J.C., Badoud, F., Cattrysse, B., McNicholas, P.D., & Mutch, D.M. (2014). Inhibition of stearoyl-CoA desaturase-1 in differentiating 3T3-L1 preadipocytes upregulates elongase 6 and downregulates genes affecting triacylglycerol synthesis. Int J Obes (Lond). 38(11):1449-56.

Saylor, B., Elliott, T.A., Linquist, S.S., Kremer, S.C., Gregory, T.R. & Cottenie, K. (2013). A novel application of ecological analyses to assess transposable element distributions in the genome of the domestic cow, Bos taurus. Genome, 56 9, 521-33.

Linquist, S., Saylor, B., Cottenie, K., Elliott, T.A., Kremer, S.C. & Ryan Gregory, T. (2013). Distinguishing ecological from evolutionary approaches to transposable elements. Biol Rev, 88: 573-584.

Bessonov, K. & Chiu, D. (2013). Functional analysis of NSF1 in wine yeast using interconnected correlation clustering and molecular analyses. PLoS ONE, 8 (10), 1-15.

Vassall, K.A., Bessonov, K., De Avila, M., Polverini, E. & Harauz, G. (2013). The effects of threonine phosphorylation on the stability and dynamics of the central molecular switch region of 18.5-kDa myelin basic protein. PLoS One. 8(7):e68175.

Wilson, S.A.F., Wong, M.H.T., Stryjecki, C., De Boer, A., Lui, E.M.K. & Mutch, D.M. (2013). Unraveling the adipocyte inflammomodulatory pathways activated by North American ginseng. International Journal of Obesity. 37(3):350-6.

Wong, M.H.T., Holst, C., Astrup, A., Handjieva-Darlenska, T., Jebb, S.A., Kafatos, A., Kunesova, M., Larsen, T.M., Martinez, J.A., Pfeiffer, A.F.H., van Baak, M.A., Saris, W.H.M., McNicholas, P.D. & Mutch, D.M., on behalf of DiOGenes. (2012). Caloric Restriction Induces Changes in Insulin and Body Weight Measurements That Are Inversely Associated with Subsequent Weight Regain. PLoS One 7(8):e42858.

Ma, E.Y., Cameron, C.J. & Kremer, S.C. (2010). Classifying and scoring of molecules with the NGN: new datasets, significance tests, and generalization. BMC Bioinformatics. 11 (Suppl 8):S4.