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Author Details

Vineet Bafna
University of California San Diego
1998
173
49
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36434258Variable number tandem repeats (VNTRs) as modifiers of breast cancer risk in carriers of BRCA1 185delAG.Eur J Hum Genet2023
36434258Variable number tandem repeats (VNTRs) as modifiers of breast cancer risk in carriers of BRCA1 185delAG.Eur J Hum Genet2023
37945900Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma.Nat Genet2023
37980879Multi-tissue proteogenomic analysis for mechanistic toxicology studies in non-model species.Environ Int2023
37872149A deep population reference panel of tandem repeat variation.Nat Commun2023
37155843Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity.Proc Natl Acad Sci U S A2023
36945429A deep population reference panel of tandem repeat variation.bioRxiv2023
37046089Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus.Nature2023
37425909Immortalization and transformation of primary cells mediated by engineered ecDNAs.bioRxiv2023
37168281TRviz: a Python library for decomposing and visualizing tandem repeat sequences.Bioinform Adv2023
37503111Coordinated inheritance of extrachromosomal DNA species in human cancer cells.bioRxiv2023
37501538Adverse events associated with Pegaspargase biosimilar in pediatric patients with acute lymphoblastic leukemia: A prospective single-center study.J Oncol Pharm Pract2023
37162993Transcriptional immune suppression and upregulation of double stranded DNA damage and repair repertoires in ecDNA-containing tumors.bioRxiv2023
37945900Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma.Nat Genet2023
37503111Coordinated inheritance of extrachromosomal DNA species in human cancer cells.bioRxiv2023
37501538Adverse events associated with Pegaspargase biosimilar in pediatric patients with acute lymphoblastic leukemia: A prospective single-center study.J Oncol Pharm Pract2023
37980879Multi-tissue proteogenomic analysis for mechanistic toxicology studies in non-model species.Environ Int2023
37872149A deep population reference panel of tandem repeat variation.Nat Commun2023
37425909Immortalization and transformation of primary cells mediated by engineered ecDNAs.bioRxiv2023
37155843Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity.Proc Natl Acad Sci U S A2023
37046089Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus.Nature2023
36945429A deep population reference panel of tandem repeat variation.bioRxiv2023
37168281TRviz: a Python library for decomposing and visualizing tandem repeat sequences.Bioinform Adv2023
37162993Transcriptional immune suppression and upregulation of double stranded DNA damage and repair repertoires in ecDNA-containing tumors.bioRxiv2023
34718575Heterozygous Tropomodulin 3 mice have improved lung vascularization after chronic hypoxia.Hum Mol Genet2022
35493723FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA.NAR Genom Bioinform2022
35999307Form follows function in cancer genomes.Nat Cancer2022
36265468Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling.Cell Syst2022
35672450ARID1B, a molecular suppressor of erythropoiesis, is essential for the prevention of Monge's disease.Exp Mol Med2022
35609926Extrachromosomal DNA in Cancer.Annu Rev Genomics Hum Genet2022
36123406The evolutionary dynamics of extrachromosomal DNA in human cancers.Nat Genet2022
35982790Detecting tandem repeat variants in coding regions using code-adVNTR.iScience2022
36255652Interferon-α/β-Receptor-2 Deficiency Leading to Multiple Infections, Hemophagocytic Lymphohistiocytosis, and Fatal Encephalopathy after MMR Vaccination.Indian J Pediatr2022
35036860Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19.iScience2022
34718575Heterozygous Tropomodulin 3 mice have improved lung vascularization after chronic hypoxia.Hum Mol Genet2022
35140399Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA.Nature2022
34752712Extrachromosomal DNA: An Emerging Hallmark in Human Cancer.Annu Rev Pathol2022
34930786Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications in Overcoming Targeted Therapy Dosage Challenges.Cancer Discov2022
35609926Extrachromosomal DNA in Cancer.Annu Rev Genomics Hum Genet2022
35672450ARID1B, a molecular suppressor of erythropoiesis, is essential for the prevention of Monge's disease.Exp Mol Med2022
35493723FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA.NAR Genom Bioinform2022
35999307Form follows function in cancer genomes.Nat Cancer2022
36265468Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling.Cell Syst2022
35982790Detecting tandem repeat variants in coding regions using code-adVNTR.iScience2022
36123406The evolutionary dynamics of extrachromosomal DNA in human cancers.Nat Genet2022
36255652Interferon-α/β-Receptor-2 Deficiency Leading to Multiple Infections, Hemophagocytic Lymphohistiocytosis, and Fatal Encephalopathy after MMR Vaccination.Indian J Pediatr2022
35036860Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19.iScience2022
35140399Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA.Nature2022
34930786Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications in Overcoming Targeted Therapy Dosage Challenges.Cancer Discov2022
34752712Extrachromosomal DNA: An Emerging Hallmark in Human Cancer.Annu Rev Pathol2022
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Collaborators

Paul S Mischel
Stanford University
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Jens Luebeck
University of California San Diego
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Vikas Bansal
University of California San Diego
Co-authored papers 15
Pavel A Pevzner
University of California
Co-authored papers 14
Gabriel G Haddad
university of california san diego
Co-authored papers 13
Dan Zhou
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Ali Bashir
Google Accelerated Science Team, Google Inc
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Kelly A Frazer
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Ali Akbari
Co-authored papers 8
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University of California San Diego
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Nitin Udpa
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Samuel H Payne
Brigham Young University
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The J. Craig Venter Institute
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Steven P Briggs
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Escola de Administracao de Empresas - FGV, Stanford University, University of California San Diego, University of Sao Paulo, Yale School of Medicine
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Shibu Yooseph
University of Central Florida
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Bing Ren
Center for Epigenomics, University of California San Diego
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Ewen F Kirkness
J. Craig Venter Institute
Co-authored papers 4
Frank B Furnari
University of California San Diego
Co-authored papers 4
Karin A Remington
The J. Craig Venter Institute.
Co-authored papers 4
Anton G Henssen
Co-authored papers 4
Pieter C Dorrestein
Co-authored papers 4
Banu Dost
university of california san diego
Co-authored papers 4
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