Research overview
My research aims to address biological questions through computational and statistical methods with emphasis on analyses of high-throughput genomics and genetics data. As a graduate student, the focus of my research was on the computational analysis of promoter regions to study gene regulation. I developed a paired-hidden markov model approach to predict transcription factor binding sites conserved between pairs of promoter sequences while simultaneously aligning them. In my postdoctoral work, I developed a computational approach for the identification of condition-specific subtypes of transcription factor binding sites. Through these studies I gained experience in the analyses of large-scale genomic sequence as well as functional data. Thereafter, I studied allele-specific expression of a pathogenic fungus under multiple conditions using RNA-seq data. More recently, I have analyzed data from a number of high-throughput experiments including ChIP-seq, whole exome/genome sequencing, bulk and single-cell RNA-seq data, to name a few. For instance, through the analysis of whole exome sequencing as well as a multi-factorial RNA-seq dataset, I contributed to research addressing the pathogenicity of a severe congenital heart disease in humans. In another ongoing study, I am involved in the development of methods for the analysis of single-cell RNA-seq data profiling human primary cardiomyocytes.
[to be updated ..]
Publications
scds: Computational
annotation of doublets in single-cell RNA sequencing data. AS
Bais and D Kostka. Bioinformatics 2019 Sept 10 [link]
Enhancing acute kidney injury regeneration by promoting cellular
dedifferentiation in zebrafish.
LB Skvarca, HI Han, EB Espiritu,
MA Missinato, ER Rochon, MD McDaniels, AS Bais, BL Roman, JS
Waxman, SC Watkins, AJ Davidson, M Tsang, NA Hukriede. Disease Models
& Mechanisms 2019 March. [link]
The Lhx1-Ldb1 complex interacts with Furry to regulate microRNA
expression during pronephric kidney development.
EB Espiritu,
AE Crunk, AS Bais , D Hochbaum, AS Cervino, YL Phua, MB
Butterworth, T Goto, J Ho, NA Hukriede, MC Cirio.
Scientific Reports 2018 Oct 30;8(1):16029. [link]
Airway ciliary dysfunction and respiratory symptoms in patients
with transposition of the great arteries.
M Zahid, AS Bais, X Tian, W Devine, DM Lee, C Yau, D
Sonnenberg, L Beerman, O Khalifa, CW Lo. PLoS One. 2018
Feb; 13(2):e0191605. [link]
The complex genetics of hypoplastic left heart syndrome.
X Liu, H Yagi, S Saeed, AS Bais, [29 authors], CW
Lo. Nature Genetics, 2017 Jul;49(7):1152-1159. [link]
Novel modeling of combinatorial miRNA targeting identifies SNP with
potential role in bone density.
C Coronnello, R Hartmaier, A Arora, L Huleihei, KV Pandit, AS Bais, M
Butterworth, N Kaminski, GD Stormo, S Oesterreich, PV Benos. PLoS
Computational Biology, 2012 8(12): e1002830. [link]
Finding subtypes of transcription factor motif pairs with distinct
regulatory roles.
AS Bais, N Kaminski and PV Benos. Nucleic Acids Research, 2011
April:39(11):e76. [link]
High Throughput Determination of TGFβ1/SMAD3 Targets in A549 Lung
Epithelial Cells.
Y Zhang, D Handley, T Kaplan, H Yu, AS Bais, T Richards, KV Pandit, Q
Zeng, PV Benos, N Friedman, O Eickelberg, N Kaminski. PLoS One. 2011
May; 6(5):e20319. [link]
In silico identification of a core regulatory network of OCT4 in
human embryonic stem cells using an integrated approach.
L Chavez, AS Bais, M Vingron, H Lehrach, J Adjaye, R
Herwig. BMC Genomics. 2009 Jul;15(10):314. [link]
Incorporating evolution of binding sites into annotated
alignments.
AS Bais, S Grossmann and M Vingron.
Journal of Biosciences. 2007 Aug; 32(5):841-850. (Proceedings of
International Conference on Bioinformatics, 2006). [link]
Simultaneous alignment and annotation of cis-regulatory
regions.
AS Bais, S Grossmann and M Vingron. Bioinformatics, 2007 Jan;
23(2):e44-9. (Proceedings of European Conference of Computational
Biology, 2006). [link]
Other contributions
Abstracts/Posters
A Rare MEGF8 Variant is Involved in the Genetic Risk for
Transposition of the Great Arteries. AM Bellaing, K Williams, S
Li, AS Bais, CB Young and CW
Lo. Circulation. 2018;138:A16615. [link]
Characterization of Neurodevelopmental Defects Associated With a
Mouse Model of Hypoplastic Left Heart Syndrome. GC Gabriel, N
Salamacha, WT Reynolds, T Tan, X Liu, H Yagi, AS Bais, A
Panigrahy, D Simon, Y Wu and CW Lo. Circulation. 2018;138:A16609. [link]
Dominant Mouse Mutagenesis Screen Unveils a Complex Genetic
Architecture for Congenital Heart Disease. M Wang, T Tan, S
Hildebrand, AS Bais, S Ho, Y Wang, D
Sonnenberg, M Kukkillaya, C Radomile, L Meyer, W Devine, L Reinholdt,
B Beutler, Y Wu, and C Lo. Circulation. 2018;138:A16596. [link]
Identification of a Novel Sarcomeric TPM1 Variant in Familial
Atrial Septal Defect.
P Teekakirikul, W Zhu, X Xu, AM Smith, C Wang, G Gabriel, D
Sonnenberg, AM Bellaing, MX Wang, H Gou, YL Wu, A Bais, O
Khalifa, M Zahid, H Zhao, SM Ware, B Feingold, and CW
Lo. Circulation. 2018;138:A15276. [link]
Identification of a Novel TPM1 Mutation in Congenital
Atrial Septal Defect With Autosomal Dominant Inheritance.
P Teekakirikul, W Zhu, MX Wang, AM Smith, H Gou, AS Bais, O
Khalifa, M Zahid, SM Ware, B Feingold and CW
Lo. Circulation. 2017;136:A15941. [link]
Transcriptional Profiling of Single Human Heart Cells Reveals
Subtypes of Ventricular Cardiomyocytes.
A Bais, N Ammanamanchi, J Spaethling, S Choudhury, H Liu, M
Khaladkar, JD Mich-Basso, SA Fisher, J Kim, J Eberwine, D Kostka and B
Kühn. Poster at AHA 2016. Circulation. 2016;134:A16650. [link]
The response of male and female placental transcriptomes to
phthalate exposure.
JJ Adibi, Y Zhao, MK Lee, V Zhan, R Gerona, AS Bais. Abstract
at “DoHAD, the Environment and Sexual Dimorphism Workshop”, 2015.
Etiology of Hypoplastic Left Heart Syndrome: insights from analysis of
mutant mouse models. X Liu, S Zaed, Z Chen, G Gabriel, K
Peterson, AS Bais, D Kostka, S Murray, G Porter Jr, C
Lo. Abstract at “Weinstein Cardiovascular Development
Conference”, 2015.
Lectures/Talks
Genomics, proteomics and metabolomics. Guest Lecture for 1st year
Dental Students at School of Dental Medicine, University of
Pittsburgh, Oct. 2018.
A transcriptional map of human cardiomyocyte differentiation at the
single cell level. A Bais, N Ammanamanchi, J
Spaethling, S Choudhury, H Liu, M Khaladkar, JD Mich-Basso, SA Fisher,
J Kim, J Eberwine, D Kostka and B Kühn. Talk at AHA Fellows Research
Day, 2017.
Introduction to RNA-seq analysis with an example in R.
Presented workshop at Health Science Library System, 2014,
University of Pittsburgh.
Next-generation sequencing: applications and statistical
challenges. Seminar at University of Pittsburgh, 2013.
Using RNA-Seq data to explore allele-specific expression in Candida
albicans. Talk at DCB Retreat 2011, University of California
Berkeley.
Review work
Scientific Reports, Nucleic Acids Research, Bioinformatics, BMC Bioinformatics, BMC Evolutionary Biology, Genome Biology, Genome Research.