Zobrazeno 1 - 10
of 65
pro vyhledávání: '"Arif Harmanci"'
Publikováno v:
PLoS Computational Biology, Vol 20, Iss 7, p e1012142 (2024)
Increasing genetic and phenotypic data size is critical for understanding the genetic determinants of diseases. Evidently, establishing practical means for collaboration and data sharing among institutions is a fundamental methodological barrier for
Externí odkaz:
https://doaj.org/article/dad99edfdd764ecdba189c97ff815314
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-38 (2023)
Abstract Growing regulatory requirements set barriers around genetic data sharing and collaborations. Moreover, existing privacy-aware paradigms are challenging to deploy in collaborative settings. We present COLLAGENE, a tool base for building secur
Externí odkaz:
https://doaj.org/article/33badbe60a244f409759a4ed3ac93fd4
Publikováno v:
iScience, Vol 26, Iss 8, Pp 107227- (2023)
Summary: Federated association testing is a powerful approach to conduct large-scale association studies where sites share intermediate statistics through a central server. There are, however, several standing challenges. Confounding factors like pop
Externí odkaz:
https://doaj.org/article/e81ee8ccce654b0f8f7d6deea3dd4719
Publikováno v:
BMC Genomics, Vol 23, Iss 1, Pp 1-21 (2022)
Abstract Background RNA-sequencing has become a standard tool for analyzing gene activity in bulk samples and at the single-cell level. By increasing sample sizes and cell counts, this technique can uncover substantial information about cellular tran
Externí odkaz:
https://doaj.org/article/aca0b8965f2d45be89e32f7c7f0f38cb
Publikováno v:
BMC Bioinformatics, Vol 23, Iss 1, Pp 1-39 (2022)
Abstract Background Sequencing of thousands of samples provides genetic variants with allele frequencies spanning a very large spectrum and gives invaluable insight into genetic determinants of diseases. Protecting the genetic privacy of participants
Externí odkaz:
https://doaj.org/article/1a1ee615b58b47c59f3fa9c03752042a
Autor:
Shavali Shaik, Shinji Maegawa, Amanda R Haltom, Feng Wang, Xue Xiao, Tara Dobson, Ajay Sharma, Yanwen Yang, Jyothishmathi Swaminathan, Vikas Kundra, Xiao Nan Li, Keri Schadler, Arif Harmanci, Lin Xu, Vidya Gopalakrishnan
Publikováno v:
Molecular Oncology, Vol 15, Iss 5, Pp 1486-1506 (2021)
Expression of the RE1‐silencing transcription factor (REST), a master regulator of neurogenesis, is elevated in medulloblastoma (MB) tumors. A cell‐intrinsic function for REST in MB tumorigenesis is known. However, a role for REST in the regulati
Externí odkaz:
https://doaj.org/article/2fd985365fb74e1ca2c9a58c50c1a78b
Autor:
Jyothishmathi Swaminathan, Shinji Maegawa, Shavali Shaik, Ajay Sharma, Javiera Bravo-Alegria, Lei Guo, Lin Xu, Arif Harmanci, Vidya Gopalakrishnan
Publikováno v:
Frontiers in Oncology, Vol 12 (2022)
The RE1 Silencing Transcription Factor (REST) is a major regulator of neurogenesis and brain development. Medulloblastoma (MB) is a pediatric brain cancer characterized by a blockade of neuronal specification. REST gene expression is aberrantly eleva
Externí odkaz:
https://doaj.org/article/adbcf35e4afc4f71ab1fa836a5a1653c
Autor:
Xiaotong Li, Sushant Kumar, Arif Harmanci, Shantao Li, Robert R. Kitchen, Yan Zhang, Vikram B. Wali, Sangeetha M. Reddy, Wendy A. Woodward, James M. Reuben, Joel Rozowsky, Christos Hatzis, Naoto T. Ueno, Savitri Krishnamurthy, Lajos Pusztai, Mark Gerstein
Publikováno v:
Genome Medicine, Vol 13, Iss 1, Pp 1-14 (2021)
Abstract Background Inflammatory breast cancer (IBC) has a highly invasive and metastatic phenotype. However, little is known about its genetic drivers. To address this, we report the largest cohort of whole-genome sequencing (WGS) of IBC cases. Meth
Externí odkaz:
https://doaj.org/article/1add699a6a154a93abe43aacbd318851
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-21 (2020)
Abstract There is a lack of approaches for identifying pathogenic genomic structural variants (SVs) although they play a crucial role in many diseases. We present a mechanism-agnostic machine learning-based workflow, called SVFX, to assign pathogenic
Externí odkaz:
https://doaj.org/article/a9468e81821c487c88ac4046ec58d328
Autor:
Tsung-Ting Kuo, Xiaoqian Jiang, Haixu Tang, XiaoFeng Wang, Tyler Bath, Diyue Bu, Lei Wang, Arif Harmanci, Shaojie Zhang, Degui Zhi, Heidi J. Sofia, Lucila Ohno-Machado
Publikováno v:
BMC Medical Genomics, Vol 13, Iss S7, Pp 1-12 (2020)
Externí odkaz:
https://doaj.org/article/505aba2a40dc4a7e9ca7913bcfb3ac9b