|Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity|
KM Turner, V Deshpande, D Beyter, T Koga, J Rusert, C Lee, B Li, ...
Nature 543 (7643), 122-125, 2017
|Cerulean: A hybrid assembly using high throughput short and long reads|
V Deshpande, EDK Fung, S Pham, V Bafna
International workshop on algorithms in bioinformatics, 349-363, 2013
|Exploring the landscape of focal amplifications in cancer using AmpliconArchitect|
V Deshpande, J Luebeck, NPD Nguyen, M Bakhtiari, KM Turner, ...
Nature communications 10 (1), 1-14, 2019
|ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions|
E Dolzhenko, V Deshpande, F Schlesinger, P Krusche, R Petrovski, ...
Bioinformatics 35 (22), 4754-4756, 2019
|ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer|
ND Nguyen, V Deshpande, J Luebeck, PS Mischel, V Bafna
Nucleic acids research 46 (7), 3309-3325, 2018
|Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers|
H Kim, NP Nguyen, K Turner, S Wu, AD Gujar, J Luebeck, J Liu, ...
Nature Genetics, 1-7, 2020
|EcSeg: semantic segmentation of metaphase images containing extrachromosomal DNA|
U Rajkumar, K Turner, J Luebeck, V Deshpande, M Chandraker, ...
iScience 21, 428-435, 2019
|AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications|
J Luebeck, C Coruh, SR Dehkordi, JT Lange, KM Turner, V Deshpande, ...
Nature Communications 11 (1), 1-14, 2020
|Methods of diagnosing and treating cancer targeting extrachromosomal dna|
P Mischel, P Mali, V Bafna, K Turner, V Deshpande, D Beyter
US Patent App. 15/989,100, 2018
|Computational methods to study genomic structure and structural variation|
UC San Diego, 2017