Viraj B Deshpande
Title
Cited by
Cited by
Year
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
3122017
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 52 (9), 891-897, 2020
682020
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
672019
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
57*2013
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
562019
ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer
NPD Nguyen, V Deshpande, J Luebeck, PS Mischel, V Bafna
Nucleic acids research 46 (7), 3309-3325, 2018
282018
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
152020
EcSeg: semantic segmentation of metaphase images containing extrachromosomal DNA
U Rajkumar, K Turner, J Luebeck, V Deshpande, M Chandraker, ...
Iscience 21, 428-435, 2019
82019
Whole genome sequencing for diagnosis of neurological repeat expansion disorders
K Ibanez, J Polke, T Hagelstrom, E Dolzhenko, D Pasko, E Thomas, ...
bioRxiv, 2020
42020
Methods of diagnosing and treating cancer targeting extrachromosomal DNA
P Mischel, P Mali, V Bafna, K Turner, V Deshpande, D Beyter
US Patent 11,193,164, 2021
2021
Rapid Detection of Gene Fusions
Viraj Deshpande, Johann Felix Wilhelm Schlesinger, Sean Truong, John Cooper ...
WO Patent US20210193254A1, 2021
2021
REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats
E Dolzhenko, B Weisburd, K Ibanez, ISR Babu, MF Bennett, KJ Billingsley, ...
bioRxiv, 2021
2021
Computational methods to study genomic structure and structural variation
VB Deshpande
UC San Diego, 2017
2017
Cancer diagnostics
PE Kearney, KC Fang, XJ Li, C Hayward, K Sugaya, V Manjusha, ...
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Articles 1–14