Alireza Hadj Khodabakhshi
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Explore the profile of Alireza Hadj Khodabakhshi including associated specialties, affiliations and a list of published articles.
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9
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6552
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Recent Articles
1.
Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi A, Tanaseichuk O, et al.
Nat Commun
. 2019 Apr;
10(1):1523.
PMID: 30944313
A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of a...
2.
Khodabakhshi A, Fejes A, Birol I, Jones S
BMC Bioinformatics
. 2013 May;
14:167.
PMID: 23714400
Background: In the past decade, bioinformatics tools have matured enough to reliably perform sophisticated primary data analysis on Next Generation Sequencing (NGS) data, such as mapping, assemblies and variant calling,...
3.
Morin R, Mungall K, Pleasance E, Mungall A, Goya R, Huff R, et al.
Blood
. 2013 May;
122(7):1256-65.
PMID: 23699601
Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome...
4.
Khodabakhshi A, Morin R, Fejes A, Mungall A, Mungall K, Bolger-Munro M, et al.
Oncotarget
. 2012 Nov;
3(11):1308-19.
PMID: 23131835
Somatic hypermutation (SHM) in the variable region of immunoglobulin genes (IGV) naturally occurs in a narrow window of B cell development to provide high-affinity antibodies. However, SHM can also aberrantly...
5.
Bashashati A, Johnson N, Khodabakhshi A, Whiteside M, Zare H, Scott D, et al.
Am J Clin Pathol
. 2012 Apr;
137(5):805-14.
PMID: 22523221
Despite advances in the understanding of diffuse large B-cell lymphoma (DLBCL) biology, only the clinically based International Prognostic Index (IPI) is used routinely for risk stratification at diagnosis. To find...
6.
Fejes A, Khodabakhshi A, Birol I, Jones S
Bioinformatics
. 2011 Mar;
27(8):1155-6.
PMID: 21367872
Motivation: Current public variation databases are based upon collaboratively pooling data into a single database with a single interface available to the public. This gives little control to the collaborator...
7.
Hahne F, Khodabakhshi A, Bashashati A, Wong C, Gascoyne R, Weng A, et al.
Cytometry A
. 2009 Nov;
77(2):121-31.
PMID: 19899135
Between-sample variation in high-throughput flow cytometry data poses a significant challenge for analysis of large-scale data sets, such as those derived from multicenter clinical trials. It is often hard to...
8.
Khodabakhshi A, Manuch J, Rafiey A, Gupta A
J Comput Biol
. 2009 Jun;
16(6):769-802.
PMID: 19522663
The inverse protein folding problem is that of designing an amino acid sequence which has a prescribed native protein fold. This problem arises in drug design where a particular structure...
9.
Khodabakhshi A, Manuch J, Rafiey A, Gupta A
J Comput Biol
. 2008 Dec;
16(1):19-30.
PMID: 19072580
The inverse protein folding problem is that of designing an amino acid sequence which folds into a prescribed conformation/structure. This problem arises in drug design where a particular structure is...