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Article: WITHDRAWN: The effect of ischemia on expression quantitative trait loci (eQTL) in human myocardium and insights into myocardial injury etiology.

Yazdani, Azam / Tiwari, Sameeksha / Heydarpour, Mahyar

Research square

2024

Abstract: 26 February, 2024. Research Square has withdrawn this preprint as it was submitted and made public without the full consent of all the authors and without the full consent of the principle investigator of the registered clinical trial. Therefore, this ... ...

Abstract	26 February, 2024. Research Square has withdrawn this preprint as it was submitted and made public without the full consent of all the authors and without the full consent of the principle investigator of the registered clinical trial. Therefore, this work should not be cited as a reference.
Language	English
Publishing date	2024-02-26
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3967889/v2
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Article: From classical mendelian randomization to causal networks for systematic integration of multi-omics.

Yazdani, Azam / Yazdani, Akram / Mendez-Giraldez, Raul / Samiei, Ahmad / Kosorok, Michael R / Schaid, Daniel J

Frontiers in genetics

2022 Volume 13, Page(s) 990486

Abstract: The number of studies with information at multiple biological levels of granularity, such as genomics, proteomics, and metabolomics, is increasing each year, and a biomedical questaion is how to systematically integrate these data to discover new ... ...

Abstract	The number of studies with information at multiple biological levels of granularity, such as genomics, proteomics, and metabolomics, is increasing each year, and a biomedical questaion is how to systematically integrate these data to discover new biological mechanisms that have the potential to elucidate the processes of health and disease. Causal frameworks, such as Mendelian randomization (MR), provide a foundation to begin integrating data for new biological discoveries. Despite the growing number of MR applications in a wide variety of biomedical studies, there are few approaches for the systematic analysis of omic data. The large number and diverse types of molecular components involved in complex diseases interact through complex networks, and classical MR approaches targeting individual components do not consider the underlying relationships. In contrast, causal network models established in the principles of MR offer significant improvements to the classical MR framework for understanding omic data. Integration of these mostly distinct branches of statistics is a recent development, and we here review the current progress. To set the stage for causal network models, we review some recent progress in the classical MR framework. We then explain how to transition from the classical MR framework to causal networks. We discuss the identification of causal networks and evaluate the underlying assumptions. We also introduce some tests for sensitivity analysis and stability assessment of causal networks. We then review practical details to perform real data analysis and identify causal networks and highlight some of the utility of causal networks. The utilities with validated novel findings reveal the full potential of causal networks as a systems approach that will become necessary to integrate large-scale omic data.
Language	English
Publishing date	2022-09-15
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.990486
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Article ; Online: Serologic and Molecular Evidence of Widespread Infection of Avian Hepatitis E Virus in Poultry Farms of Iran.

Razmyar, Jamshid / Abbasi, Mina / Mirsalimi, Seyed Mehdi / Baghkheirati, Amir Asghari / Ahmadian, Gholamreza / Yazdani, Azam

Avian diseases

2022 Volume 65, Issue 4, Page(s) 572–577

Abstract: Hepatitis-splenomegaly syndrome is caused by avian hepatitis E virus (aHEV), a nonenveloped, single-stranded RNA virus. The economic importance of this disease in the poultry industry is due to the decline in egg production (10%-40%) and the rise in ... ...

Abstract	Hepatitis-splenomegaly syndrome is caused by avian hepatitis E virus (aHEV), a nonenveloped, single-stranded RNA virus. The economic importance of this disease in the poultry industry is due to the decline in egg production (10%-40%) and the rise in mortality (1%-4%). In the present study, 1540 serum samples from 33 broiler breeder flocks were analyzed by an enzyme-linked immunosorbent assay for the presence of an anti-aHEV antibody. In addition, a diagnostic nested reverse transcriptase-PCR was done on all farm samples. In the serologic study, 66.7% (22/33) of the flocks and 28.5% (439/1540) of the chickens were positive. The molecular study showed that three farms were positive, and PCR products were observed for the conserved regions of the aHEV
MeSH term(s)	Animals ; Chickens ; Farms ; Hepatitis, Viral, Animal/diagnosis ; Hepatitis, Viral, Animal/epidemiology ; Hepevirus/genetics ; Iran/epidemiology ; Poultry ; Poultry Diseases/pathology
Language	English
Publishing date	2022-01-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	40871-2
ISSN	1938-4351 ; 0005-2086
ISSN (online)	1938-4351
ISSN	0005-2086
DOI	10.1637/aviandiseases-D-21-00077
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Book ; Thesis: Analytic comparison of pearl and rubin causal frameworks

Yazdani, Azam

2013

Author's details	von: Azam Yazdani
Keywords	Kausalanalyse ; Induktive Statistik ; Theorie
Language	English
Size	211 Bl., Ill., graph. Darst., 29,5 cm
Document type	Book ; Thesis
Thesis / German Habilitation thesis	Univ., Diss.--Jena, 2013
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Article: Serologic and Molecular Evidence of Widespread Infection of Avian Hepatitis E Virus in Poultry Farms of Iran

Razmyar, Jamshid / Abbasi, Mina / Mirsalimi, Seyed Mehdi / Baghkheirati, Amir Asghari / Ahmadian, Gholamreza / Yazdani, Azam

Avian diseases. 2021 Nov. 12, v. 65, no. 4

2021

Abstract	Hepatitis-splenomegaly syndrome is caused by avian hepatitis E virus (aHEV), a nonenveloped, single-stranded RNA virus. The economic importance of this disease in the poultry industry is due to the decline in egg production (10%–40%) and the rise in mortality (1%–4%). In the present study, 1540 serum samples from 33 broiler breeder flocks were analyzed by an enzyme-linked immunosorbent assay for the presence of an anti-aHEV antibody. In addition, a diagnostic nested reverse transcriptase-PCR was done on all farm samples. In the serologic study, 66.7% (22/33) of the flocks and 28.5% (439/1540) of the chickens were positive. The molecular study showed that three farms were positive, and PCR products were observed for the conserved regions of the aHEV helicase and capsid virus genes as 386 bp and 242 bp, respectively. It should be noted that clinical and pathologic symptoms including decreased egg production, enlarged livers and spleens, and a slight rise in mortality rate were observed in eight farms. To our knowledge, this is the first documented study on the aHEV identification and its antibody detection in broiler breeder farms in Iran.
Keywords	Orthohepevirus B ; antibodies ; antibody detection ; blood serum ; broiler breeders ; capsid ; egg production ; enzyme-linked immunosorbent assay ; farms ; mortality ; poultry industry ; reverse transcriptase polymerase chain reaction ; serological surveys ; viruses ; Iran
Language	English
Dates of publication	2021-1112
Size	p. 572-577.
Publishing place	American Association of Avian Pathologists Inc
Document type	Article
ZDB-ID	40871-2
ISSN	1938-4351 ; 0005-2086
ISSN (online)	1938-4351
ISSN	0005-2086
DOI	10.1637/aviandiseases-D-21-00077
Database	NAL-Catalogue (AGRICOLA)

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Article: Gene expression biomarkers differentiate overall survival of colorectal cancer upon targeted therapies.

Yazdani, Akram / Yazdani, Azam / Mendez-Giraldez, Raul / Pillonetto, Gianluigi / Samiei, Esmat / Hadi, Reza / Lenz, Heinz-Josef / Venook, Alan / Samiei, Ahmad / Nixon, Andrew / Lucci, Joseph / Kopetz, Scott / Bertagnolli, Monica / Perou, Charles / Innocenti, Federico

Research square

2024

Abstract: While monoclonal antibody-based targeted therapies have substantially improved progression-free survival in cancer patients, the variability in individual responses poses a significant challenge in patient care. Therefore, identifying cancer subtypes and ...

Abstract	While monoclonal antibody-based targeted therapies have substantially improved progression-free survival in cancer patients, the variability in individual responses poses a significant challenge in patient care. Therefore, identifying cancer subtypes and their associated biomarkers is required for assigning effective treatment. In this study, we integrated genotype and pre-treatment tissue RNA-seq data and identified biomarkers causally associated with the overall survival (OS) of colorectal cancer (CRC) patients treated with either cetuximab or bevacizumab. We performed enrichment analysis for specific consensus molecular subtypes (CMS) of colorectal cancer and evaluated differential expression of identified genes using paired tumor and normal tissue from an external cohort. In addition, we replicated the causal effect of these genes on OS using validation cohort and assessed their association with the Cancer Genome Atlas Program data as an external cohort. One of the replicated findings was
Language	English
Publishing date	2024-03-11
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-4047331/v1
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Article ; Online: Triglycerides to high-density lipoprotein cholesterol ratio for diagnosing nonalcoholic fatty liver disease.

Catanzaro, Roberto / Selvaggio, Federica / Sciuto, Morena / Zanoli, Luca / Yazdani, Azam / He, Fang / Marotta, Francesco

Minerva gastroenterology

2021 Volume 68, Issue 3, Page(s) 261–268

Abstract: Background: Nonalcoholic Fatty Liver Disease (NAFLD) is a widespread disease in the western world. It can develop into more serious pathological conditions (i.e. liver cirrhosis). Therefore, it is important to diagnose it in order to prevent this ... ...

Abstract	Background: Nonalcoholic Fatty Liver Disease (NAFLD) is a widespread disease in the western world. It can develop into more serious pathological conditions (i.e. liver cirrhosis). Therefore, it is important to diagnose it in order to prevent this evolution. For diagnosis it is possible to use both imaging methods and biomarkers, such as the Triglycerides To High-Density Lipoprotein Cholesterol Ratio (TG/HDL-C). Aim of our study is to determine whether TG/HDL-C ratio is significantly associated with NAFLD and Metabolic Syndrome (MetS). Methods: We recruited 231 patients, 131 with and 100 without NAFLD. The Body Mass Index had been calculated and different laboratory parameters had been obtained. TG/HDL-C ratio was calculated for each. Results: In our sample HDL-C was not significantly reduced in NAFLD group (P=0.49), but higher TG and TG/HDL-C ratio were significantly associated with NAFLD: in both P<0.001. According to receiver operating characteristic curve, the best cut-off of TG/HDL-C in NAFLD population was 1.64 (area under the curve [AUC] 0.675 [95% CI 0.604-0.746], P<0.001). TG/HDL-C higher ratio was significantly associated with MetS (P<0.001). The best cut-off of TG/HDL-C in patients with MetS was 2.48 (AUC 0.871 [95% CI 0.808-0.935], P<0.001). Conclusions: We demonstrated that higher TG/HDL-C ratio is associated with NAFLD and MetS. Though nowadays TG/HDL-C ratio is not a criteria for NAFLD diagnosis, we believe that in the future it could be used as a reliable non-invasive marker in routine diagnostics of NAFLD.
MeSH term(s)	Biomarkers ; Body Mass Index ; Cholesterol, HDL ; Humans ; Metabolic Syndrome/diagnosis ; Non-alcoholic Fatty Liver Disease/diagnosis ; Non-alcoholic Fatty Liver Disease/epidemiology ; Triglycerides
Chemical Substances	Biomarkers ; Cholesterol, HDL ; Triglycerides
Language	English
Publishing date	2021-04-08
Publishing country	Italy
Document type	Journal Article
ZDB-ID	3062713-8
ISSN	2724-5365
ISSN (online)	2724-5365
DOI	10.23736/S2724-5985.21.02818-X
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Article ; Online: Comprehensive characterization of putative genetic influences on plasma metabolome in a pediatric cohort.

Lee, In-Hee / Smith, Matthew Ryan / Yazdani, Azam / Sandhu, Sumiti / Walker, Douglas I / Mandl, Kenneth D / Jones, Dean P / Kong, Sek Won

Human genomics

2022 Volume 16, Issue 1, Page(s) 67

Abstract: Background: The human exposome is composed of diverse metabolites and small chemical compounds originated from endogenous and exogenous sources, respectively. Genetic and environmental factors influence metabolite levels, while the extent of genetic ... ...

Abstract	Background: The human exposome is composed of diverse metabolites and small chemical compounds originated from endogenous and exogenous sources, respectively. Genetic and environmental factors influence metabolite levels, while the extent of genetic contributions across metabolic pathways is not yet known. Untargeted profiling of human metabolome using high-resolution mass spectrometry (HRMS) combined with genome-wide genotyping allows comprehensive identification of genetically influenced metabolites. As such previous studies of adults discovered and replicated genotype-metabotype associations. However, these associations have not been characterized in children. Results: We conducted the largest genome by metabolome-wide association study to date of children (N = 441) using 619,688 common genetic variants and 14,342 features measured by HRMS. Narrow-sense heritability (h Conclusion: Comprehensive profiling of plasma metabolome across age groups combined with genome-wide genotyping revealed a wide range of genetic influence on diverse chemical species and metabolic pathways. The developmental trajectory of a biological system is shaped by gene-environment interaction especially in early life. Therefore, continuous efforts on generating metabolomics data in diverse human tissue types across age groups are required to understand gene-environment interaction toward healthy aging trajectories.
MeSH term(s)	Humans ; Child ; Metabolomics ; Genomics
Language	English
Publishing date	2022-12-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2147618-4
ISSN	1479-7364 ; 1479-7364
ISSN (online)	1479-7364
ISSN	1479-7364
DOI	10.1186/s40246-022-00440-w
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Article: Cutaneous xanthogranuloma associated with

Shokrpoor, Sara / Asghari Baghkheirati, Amir / Yazdani, Azam / Razmyar, Jamshid

Veterinary research forum : an international quarterly journal

2019 Volume 10, Issue 4, Page(s) 365–367

Abstract: Budgerigar is a common name for a colorful Australian native bird belonging to ... ...

Abstract	Budgerigar is a common name for a colorful Australian native bird belonging to the
Language	English
Publishing date	2019-12-15
Publishing country	Iran
Document type	Case Reports
ISSN	2008-8140
ISSN	2008-8140
DOI	10.30466/vrf.2019.102621.2445
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Article ; Online: Differential gene regulatory pattern in the human brain from schizophrenia using transcriptomic-causal network.

Yazdani, Akram / Mendez-Giraldez, Raul / Yazdani, Azam / Kosorok, Michael R / Roussos, Panos

BMC bioinformatics

2020 Volume 21, Issue 1, Page(s) 469

Abstract: Background: Common and complex traits are the consequence of the interaction and regulation of multiple genes simultaneously, therefore characterizing the interconnectivity of genes is essential to unravel the underlying biological networks. However, ... ...

Abstract	Background: Common and complex traits are the consequence of the interaction and regulation of multiple genes simultaneously, therefore characterizing the interconnectivity of genes is essential to unravel the underlying biological networks. However, the focus of many studies is on the differential expression of individual genes or on co-expression analysis. Methods: Going beyond analysis of one gene at a time, we systematically integrated transcriptomics, genotypes and Hi-C data to identify interconnectivities among individual genes as a causal network. We utilized different machine learning techniques to extract information from the network and identify differential regulatory pattern between cases and controls. We used data from the Allen Brain Atlas for replication. Results: Employing the integrative systems approach on the data from CommonMind Consortium showed that gene transcription is controlled by genetic variants proximal to the gene (cis-regulatory factors), and transcribed distal genes (trans-regulatory factors). We identified differential gene regulatory patterns in SCZ-cases versus controls and novel SCZ-associated genes that may play roles in the disorder since some of them are primary expressed in human brain. In addition, we observed genes known associated with SCZ are not likely (OR = 0.59) to have high impacts (degree > 3) on the network. Conclusions: Causal networks could reveal underlying patterns and the role of genes individually and as a group. Establishing principles that govern relationships between genes provides a mechanistic understanding of the dysregulated gene transcription patterns in SCZ and creates more efficient experimental designs for further studies. This information cannot be obtained by studying a single gene at the time.
MeSH term(s)	Brain/metabolism ; Computational Biology ; Gene Regulatory Networks ; Humans ; Schizophrenia/genetics ; Transcriptome
Language	English
Publishing date	2020-10-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-020-03753-6
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