Zobrazeno 1 - 10
of 280
pro vyhledávání: '"Vineet, Bafna"'
Autor:
Miin S Lin, Se-Young Jo, Jens Luebeck, Howard Y Chang, Sihan Wu, Paul S Mischel, Vineet Bafna
Publikováno v:
eLife, Vol 12 (2024)
Extrachromosomal DNA is a common cause of oncogene amplification in cancer. The non-chromosomal inheritance of ecDNA enables tumors to rapidly evolve, contributing to treatment resistance and poor outcome for patients. The transcriptional context in
Externí odkaz:
https://doaj.org/article/046c3f6729814f22a71b2d46f9439236
Autor:
Helyaneh Ziaei Jam, Yang Li, Ross DeVito, Nima Mousavi, Nichole Ma, Ibra Lujumba, Yagoub Adam, Mikhail Maksimov, Bonnie Huang, Egor Dolzhenko, Yunjiang Qiu, Fredrick Elishama Kakembo, Habi Joseph, Blessing Onyido, Jumoke Adeyemi, Mehrdad Bakhtiari, Jonghun Park, Sara Javadzadeh, Daudi Jjingo, Ezekiel Adebiyi, Vineet Bafna, Melissa Gymrek
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-15 (2023)
Abstract Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from
Externí odkaz:
https://doaj.org/article/fc3ce6b9d4d04929afdde67a60974243
Publikováno v:
iScience, Vol 25, Iss 8, Pp 104785- (2022)
Summary: The human genome contains more than one million tandem repeats (TRs), DNA sequences containing multiple approximate copies of a motif repeated contiguously. TRs account for significant genetic variation, with 50 + diseases attributed to chan
Externí odkaz:
https://doaj.org/article/494fcfc348e444b4abcd30216fff212e
Autor:
Mehrdad Bakhtiari, Jonghun Park, Yuan-Chun Ding, Sharona Shleizer-Burko, Susan L. Neuhausen, Bjarni V. Halldórsson, Kári Stefánsson, Melissa Gymrek, Vineet Bafna
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)
Variable number tandem repeats (VNTRs) are implicated in human diseases yet have been difficult to analyse computationally. Here, the authors describe a neural network method, adVNTR-NN, that allows rapid and accurate genotyping of VNTRs from large w
Externí odkaz:
https://doaj.org/article/c0620434d6a14d2c97241fa0db512255
Autor:
Arya Iranmehr, Tsering Stobdan, Dan Zhou, Huiwen Zhao, Sergey Kryazhimskiy, Vineet Bafna, Gabriel G. Haddad
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-10 (2021)
The genomic details of adaptation to extreme environments remain challenging to characterize. Using new methods to analyze flies experimentally evolved to survive extreme O2 conditions, the authors find a surprising level of synchronicity in selectiv
Externí odkaz:
https://doaj.org/article/2f35837d18f748b5835fa3f201891620
Autor:
Jens Luebeck, Ceyda Coruh, Siavash R. Dehkordi, Joshua T. Lange, Kristen M. Turner, Viraj Deshpande, Dave A. Pai, Chao Zhang, Utkrisht Rajkumar, Julie A. Law, Paul S. Mischel, Vineet Bafna
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020)
Focal copy number amplifications (fCNAs), which drive cancer pathogenicity, arise by a number of mechanisms and can be challenging to call. Here the authors present AmpliconReconstructor for precise and scalable fCNA reconstruction using optical mapp
Externí odkaz:
https://doaj.org/article/f072105319bb4cc08d37a2a5027abc98
Autor:
Tomoyuki Koga, Isaac A. Chaim, Jorge A. Benitez, Sebastian Markmiller, Alison D. Parisian, Robert F. Hevner, Kristen M. Turner, Florian M. Hessenauer, Matteo D’Antonio, Nam-phuong D. Nguyen, Shahram Saberi, Jianhui Ma, Shunichiro Miki, Antonia D. Boyer, John Ravits, Kelly A. Frazer, Vineet Bafna, Clark C. Chen, Paul S. Mischel, Gene W. Yeo, Frank B. Furnari
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020)
The dearth of glioblastoma model systems that accurately recapitulate the disease remains a challenge. Here, the authors develop cancer avatars using genetically engineered human induced pluripotent cells.
Externí odkaz:
https://doaj.org/article/129339bec1d846d6beb84462802c2cb9
Autor:
Nikhil Shri Sahajpal, Chi-Yu Jill Lai, Alex Hastie, Ashis K. Mondal, Siavash Raeisi Dehkordi, Caspar I. van der Made, Olivier Fedrigo, Farooq Al-Ajli, Sawan Jalnapurkar, Marta Byrska-Bishop, Rashmi Kanagal-Shamanna, Brynn Levy, Maximilian Schieck, Thomas Illig, Silviu-Alin Bacanu, Janet S. Chou, Adrienne G. Randolph, Amyn M. Rojiani, Michael C. Zody, Catherine A. Brownstein, Alan H. Beggs, Vineet Bafna, Erich D. Jarvis, Alexander Hoischen, Alka Chaubey, Ravindra Kolhe
Publikováno v:
iScience, Vol 25, Iss 2, Pp 103760- (2022)
Summary: Impressive global efforts have identified both rare and common gene variants associated with severe COVID-19 using sequencing technologies. However, these studies lack the sensitivity to accurately detect several classes of variants, especia
Externí odkaz:
https://doaj.org/article/6522ade0da724f48b8c81dc340d11287
Autor:
Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 11, p e1009449 (2021)
The cost of sequencing the genome is dropping at a much faster rate compared to assembling and finishing the genome. The use of lightly sampled genomes (genome-skims) could be transformative for genomic ecology, and results using k-mers have shown th
Externí odkaz:
https://doaj.org/article/1b2807756750402fbe091bd2503aa6e9
Autor:
Utkrisht Rajkumar, Kristen Turner, Jens Luebeck, Viraj Deshpande, Manmohan Chandraker, Paul Mischel, Vineet Bafna
Publikováno v:
iScience, Vol 21, Iss , Pp 428-435 (2019)
Summary: Oncogene amplification is one of the most common drivers of genetic events in cancer, potently promoting tumor development, growth, and progression. The recent discovery that oncogene amplification commonly occurs on extrachromosomal DNA, dr
Externí odkaz:
https://doaj.org/article/26302513220d48faaf6a83ae092393c6