+------------------------------------------------------------------------------+
|                                                                              |
|                                 PUBLICATIONS                                 |
|                                                                              |
+------------------------------------------------------------------------------+

2026
________________________________________________________________________________

Arya Kaul, Fernando Rossine, Karel Brinda, and Michael Baym. 2026. "Novel
genes arise from genomic deletions across the bacterial tree of life." bioRxiv 
doi: 10.64898/2026.01.05.697752


2025
________________________________________________________________________________

Arya Kaul, Célia Souque, Mische Holland, and Michael Baym. 2025. "Genomic
resistance in historical clinical isolates increased in frequency and mobility
after the age of antibiotics." Microbial Genomics doi: 10.1099/mgen.0.001474

2020
________________________________________________________________________________

Kaul, Arya, Sourya Bhattacharyya, and Ferhat Ay. 2020. “Identifying
Statistically Significant Chromatin Contacts from Hi-C Data with FitHiC2.”
Nature Protocols 15(3):991–1012. doi: 10.1038/s41596-019-0273-0.  


2019
________________________________________________________________________________

Fong, Samson H., Daniel E. Carlin, Kivilcim Ozturk, 2018 UCSD Network Biology
Class and Trey Ideker. 2019. “Strategies for Network GWAS Evaluated Using 
Classroom Crowd Science (Vol 8, Pg 275, 2019).” Cell Systems 9(4):414–414. 
doi: 10.1016/j.cels.2019.09.001.  

Yardimci, Galip Gurkan, Hakan Ozadam, Michael E. G. Sauria, Oana Ursu, Koon-Kiu
Yan, Tao Yang, Abhijit Chakraborty, Arya Kaul, Bryan R. Lajoie, Fan Song, Ye
Zhan, Ferhat Ay, Mark Gerstein, Anshul Kundaje, Qunhua Li, James Taylor, Feng
Yue, Job Dekker, and William S. Noble. 2019. “Measuring the Reproducibility and
Quality of Hi-C Data.” Genome Biology 20:57. doi: 10.1186/s13059-019-1658-7.


2016
________________________________________________________________________________

Mitton, B., H. D. Chae, K. Hsu, R. Dutta, G. Aldana-Masangkay, R. Ferrari, K.
Davis, B. C. Tiu, A. Kaul, N.  Lacayo, G. Dahl, F. Xie, B. X. Li, M. R. Breese,
E. M. Landaw, G. Nolan, M.  Pellegrini, S. Romanov, X. Xiao, and K. M. Sakamoto.
2016. “Small Molecule Inhibition of CAMP Response Element Binding Protein in
Human Acute Myeloid Leukemia Cells.” Leukemia 30(12):2302–11. doi:
10.1038/leu.2016.139.  


2015
________________________________________________________________________________

Dutta, Ritika, Bruce Tiu, Arya Kaul, Bryan Mitton, and Kathleen M. Sakamoto.
2015. “CREB Increases Chemotherapy Resistance through Regulation of the DNA
Damage Repair Pathway in AML Cells.” Blood 126(23).  


________________________________________________________________________________

Arya Kaul (C) now - forever