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 ..]


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


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.


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.