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Krithika Bhuvaneshwar

Bio: Krithika Bhuvaneshwar is an academic researcher from Georgetown University Medical Center. The author has contributed to research in topics: Computer science & Segmentation. The author has an hindex of 11, co-authored 36 publications receiving 440 citations. Previous affiliations of Krithika Bhuvaneshwar include Georgetown University & University of Washington.

Papers
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Journal ArticleDOI
TL;DR: The Rembrandt brain cancer dataset includes 671 patients collected from 14 contributing institutions from 2004–2006 and would provide researchers with a unique opportunity to conduct integrative analysis of gene expression and copy number changes in patients alongside clinical outcomes (overall survival) using this large brain cancer study.
Abstract: The Rembrandt brain cancer dataset includes 671 patients collected from 14 contributing institutions from 2004-2006. It is accessible for conducting clinical translational research using the open access Georgetown Database of Cancer (G-DOC) platform. In addition, the raw and processed genomics and transcriptomics data have also been made available via the public NCBI GEO repository as a super series GSE108476. Such combined datasets would provide researchers with a unique opportunity to conduct integrative analysis of gene expression and copy number changes in patients alongside clinical outcomes (overall survival) using this large brain cancer study.

101 citations

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TL;DR: The data suggest that loss of SPTBN1 activates Wnt signaling, which promotes acquisition of stem cell‐like features, and ultimately contributes to malignant tumor progression.

81 citations

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TL;DR: The Georgetown Database of Cancer (G-DOC) as discussed by the authors is a Web platform that enables basic and clinical research by integrating patient characteristics and clinical outcome data with a variety of high-throughput research data in a unified environment.

64 citations

Journal ArticleDOI
TL;DR: It is found that overexpression of CCAT2 in colon cells promotes CIN and carcinogenesis, by stabilizing and inducing expression of BOP1 an activator of AURKB, which regulates chromosomal segregation.

63 citations

Journal ArticleDOI
TL;DR: This paper presented the largest FL study to date, involving data from 71 sites across 6 continents, to generate an automatic tumor boundary detector for the rare disease of glioblastoma, reporting the largest such dataset in the literature.
Abstract: Abstract Although machine learning (ML) has shown promise across disciplines, out-of-sample generalizability is concerning. This is currently addressed by sharing multi-site data, but such centralization is challenging/infeasible to scale due to various limitations. Federated ML (FL) provides an alternative paradigm for accurate and generalizable ML, by only sharing numerical model updates. Here we present the largest FL study to-date, involving data from 71 sites across 6 continents, to generate an automatic tumor boundary detector for the rare disease of glioblastoma, reporting the largest such dataset in the literature ( n = 6, 314). We demonstrate a 33% delineation improvement for the surgically targetable tumor, and 23% for the complete tumor extent, over a publicly trained model. We anticipate our study to: 1) enable more healthcare studies informed by large diverse data, ensuring meaningful results for rare diseases and underrepresented populations, 2) facilitate further analyses for glioblastoma by releasing our consensus model, and 3) demonstrate the FL effectiveness at such scale and task-complexity as a paradigm shift for multi-site collaborations, alleviating the need for data-sharing.

51 citations


Cited by
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01 Jan 2013
TL;DR: In this article, the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs) was described, including several novel mutated genes as well as complex rearrangements of signature receptors, including EGFR and PDGFRA.
Abstract: We describe the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutated genes as well as complex rearrangements of signature receptors, including EGFR and PDGFRA. TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation. Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself. These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer.

2,616 citations

Journal ArticleDOI
TL;DR: The current status of TCGA Research Network structure, purpose, and achievements are discussed, to provide publicly available datasets to help improve diagnostic methods, treatment standards, and finally to prevent cancer.
Abstract: The Cancer Genome Atlas (TCGA) is a public funded project that aims to catalogue and discover major cancer-causing genomic alterations to create a comprehensive "atlas" of cancer genomic profiles. So far, TCGA researchers have analysed large cohorts of over 30 human tumours through large-scale genome sequencing and integrated multi-dimensional analyses. Studies of individual cancer types, as well as comprehensive pan-cancer analyses have extended current knowledge of tumorigenesis. A major goal of the project was to provide publicly available datasets to help improve diagnostic methods, treatment standards, and finally to prevent cancer. This review discusses the current status of TCGA Research Network structure, purpose, and achievements.

2,530 citations

01 Mar 2017
TL;DR: Recent advances in understanding of mTOR function, regulation, and importance in mammalian physiology are reviewed and how the mTOR-signaling network contributes to human disease is highlighted.
Abstract: The mechanistic target of rapamycin (mTOR) coordinates eukaryotic cell growth and metabolism with environmental inputs, including nutrients and growth factors. Extensive research over the past two decades has established a central role for mTOR in regulating many fundamental cell processes, from protein synthesis to autophagy, and deregulated mTOR signaling is implicated in the progression of cancer and diabetes, as well as the aging process. Here, we review recent advances in our understanding of mTOR function, regulation, and importance in mammalian physiology. We also highlight how the mTOR signaling network contributes to human disease and discuss the current and future prospects for therapeutically targeting mTOR in the clinic.

2,014 citations

Journal ArticleDOI
TL;DR: Results indicate that cir-ITCH may have an inhibitory effect on ESCC by regulating the Wnt pathway.
Abstract: // Fang Li 1,* , Liyuan Zhang 2,* , Wei Li 1 , Jieqiong Deng 1 , Jian Zheng 1 , Mingxing An 1 , Jiachun Lu 3 and Yifeng Zhou 1 1 Department of Genetics, Medical College of Soochow University, Suzhou, China 2 Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China 3 The Institute for Chemical Carcinogenesis, The State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou, China * These authors contributed equally to this work Correspondence to: Yifeng Zhou, email: // Keywords : Cir-ITCH, ESCC, Wnt/β-catenin pathway Received : December 01, 2014 Accepted : January 20, 2015 Published : February 28, 2015 Abstract Circular RNAs with exonic sequences represent a special form of non-coding RNAs, discovered by analyzing a handful of transcribed genes. It has been observed that circular RNAs function as microRNA sponges. In the present study, we investigated whether the expression of circular RNAs is altered during the development of esophageal squamous cell carcinoma (ESCC). Using a TaqMan-based reverse transcriptase polymerase chain reaction assay, the relationship between cir-ITCH and ESCC was analyzed in a total of 684 ESCC and paired adjacent non-tumor tissue samples from eastern and southern China. We found that cir-ITCH expression was usually low in ESCC compared to the peritumoral tissue. The functional relevance of cir-ITCH was further examined by biochemical assays. As sponge of miR-7, miR-17, and miR-214, cir-ITCH might increase the level of ITCH . ITCH hyper expression promotes ubiquitination and degradation of phosphorylated Dvl2, thereby inhibiting the Wnt/β-catenin pathway. These results indicate that cir-ITCH may have an inhibitory effect on ESCC by regulating the Wnt pathway.

605 citations

Book
01 Jan 2016
TL;DR: It’s time to dust off the gloves and get ready for the cold weather.
Abstract: 1 インフラを構築する(AWSにおけるインフラ;VPCを構成する;VPCとオンプレミス環境とを接続する) 2 ファイルオブジェクトを保存・共有・公開する(オブジェクトストレージS3の機能;ファイルストレージとして利用する;Webサーバーを構築する;信頼性とコストのバランスをとりたい) 3 アプリケーションサーバーを構築する(Amazon EC2とAWS Lambda;スケーラビリティーを高める;サーバーレスでプログラムを動かす;データベースサービスを活用する) 4 AWSシステムを管理する(リソース監視と異常検知・通報;耐障害性を高める仕組みとバックアップ&リカバリー;構成管理)

350 citations