Show/Hide Menu
Hide/Show Apps
Logout
Türkçe
Türkçe
Search
Search
Login
Login
OpenMETU
OpenMETU
About
About
Open Science Policy
Open Science Policy
Open Access Guideline
Open Access Guideline
Postgraduate Thesis Guideline
Postgraduate Thesis Guideline
Communities & Collections
Communities & Collections
Help
Help
Frequently Asked Questions
Frequently Asked Questions
Guides
Guides
Thesis submission
Thesis submission
MS without thesis term project submission
MS without thesis term project submission
Publication submission with DOI
Publication submission with DOI
Publication submission
Publication submission
Supporting Information
Supporting Information
General Information
General Information
Copyright, Embargo and License
Copyright, Embargo and License
Contact us
Contact us
Subclonal reconstruction of tumors by using machine learning and population genetics
Date
2020-09-01
Author
Caravagna, Giulio
Heide, Timon
Williams, Marc J.
Zapata, Luis
Nichol, Daniel
Chkhaidze, Ketevan
Cross, William
Cresswell, George D.
Werner, Benjamin
Acar, Ahmet
Chesler, Louis
Barnes, Chris P.
Sanguinetti, Guido
Graham, Trevor A.
Sottoriva, Andrea
Metadata
Show full item record
This work is licensed under a
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License
.
Item Usage Stats
177
views
0
downloads
Cite This
MOBSTER is an approach for subclonal reconstruction of tumors from cancer genomics data on the basis of models that combine machine learning with evolutionary theory, thus leading to more accurate evolutionary histories of tumors.
URI
https://hdl.handle.net/11511/89494
Journal
NATURE GENETICS
DOI
https://doi.org/10.1038/s41588-020-0675-5
Collections
Department of Biology, Article
Suggestions
OpenMETU
Core
Pan-cancer clinical impact of latent drivers from double mutations
Yavuz, Bengi Ruken; Tsai, Chung-Jung; Nussinov, Ruth; Tuncbag, Nurcan (2023-12-01)
Here, we discover potential ‘latent driver’ mutations in cancer genomes. Latent drivers have low frequencies and minor observable translational potential. As such, to date they have escaped identification. Their discovery is important, since when paired in cis, latent driver mutations can drive cancer. Our comprehensive statistical analysis of the pan-cancer mutation profiles of ~60,000 tumor sequences from the TCGA and AACR-GENIE cohorts identifies significantly co-occurring potential latent drivers. We ob...
Bioreaction network flux analysis for human protein producing Bacillus subtilis based on genome-scale model
ÖZDAMAR, HASAN TUNÇER; Senturk, Birguel; YILMAZ, OĞUZ; KOCABAŞ, PINAR; Calik, Guezide; Çalık, Pınar (Elsevier BV, 2010-01-01)
To interpret the effect of human protein gene, e.g., human growth hormone gene hGH, on the intracellular bioreaction network of Bacillus subtilis, the intracellular reaction fluxes were calculated by solving the mass-balance-based genome-scale mathematical model, at pseudo-steady state by using bioreactor data. The bioreaction network consists of 1340 reactions including 990 metabolites. Reaction fluxes in B. subtilis carrying pMK4::pre(subC)::hGH (rBsHGH) and B. subtilis carrying merely pMK4 (rBsP) were ca...
The synthesis and characterization of thioglycolic acid and thiourea capped fluorescent zinc sulfide nanoparticles
Mertoğlu, Cemre; Volkan, Mürvet; Department of Chemistry (2021-6)
The changes in mitochondrial bioenergetics due to DNA mutations lead to an increase in the significance of mitochondria imaging of cancer cells. Since fluorescent imaging provides high resolution, sensitivity, and selectivity to many targets in living cells, fluorescent nanoparticles can be used as imaging probes. Zinc is one of the essential elements in cells used for cell growth, division, and apoptosis. Therefore, zinc sulfide semiconductor nanoparticles have been attracted attention due to its character...
Alternative Polyadenylation: Another Foe in Cancer
Erson Bensan, Ayşe Elif; Can, Tolga (2016-06-01)
Advancements in sequencing and transcriptome analysis methods have led to seminal discoveries that have begun to unravel the complexity of cancer. These studies are paving the way toward the development of improved diagnostics, prognostic predictions, and targeted treatment options. However, it is clear that pieces of the cancer puzzle are still missing. In an effort to have a more comprehensive understanding of the development and progression of cancer, we have come to appreciate the value of the noncoding...
Subsequence feature maps for protein function annotation
Saraç, Ömer Sinan; Atalay, Mehmet Volkan; Department of Computer Engineering (2008)
With the advances in sequencing technologies, the number of protein sequences with unknown function increases rapidly. Hence, computational methods for functional annotation of these protein sequences become of the upmost importance. In this thesis, we first defined a feature space mapping of protein primary sequences to fixed dimensional numerical vectors. This mapping, which is called the Subsequence Profile Map (SPMap), takes into account the models of the subsequences of protein sequences. The resulting...
Citation Formats
IEEE
ACM
APA
CHICAGO
MLA
BibTeX
G. Caravagna et al., “Subclonal reconstruction of tumors by using machine learning and population genetics,”
NATURE GENETICS
, pp. 898–919, 2020, Accessed: 00, 2021. [Online]. Available: https://hdl.handle.net/11511/89494.