Postdoc In Statistical Genetics / Sequencing Data Analysis - Lal Research Group

Cleveland Clinic

Cleveland, OH

Job posting number: #7076244 (Ref:4a16276e)

Posted: March 23, 2021

Application Deadline: Open Until Filled

Job Description

The Lal research group focuses on translational genetic research and bioinformatics. Research interests involve developing a comprehensive understanding of how alterations in the genome contribute to disease.


The lab pursues questions such as, “Why did the patient develop this disease?” “Will the patient respond to this medication?” “Can we predict the disease prognosis?” “What is the underlying mechanism?” We have published ~90 publications in the last six years, several in prestigious journals such as PNAS, Nature Genetics, Lancet Neurology, Annals of Neurology, Bioinformatics, Genome Medicine, Nuclei Acid Research, and Brain. A full list of recent studies can be found in PubMed: https://pubmed.ncbi.nlm.nih.gov/?term=Dennis+lal&show_snippets=off&sort=date&size=100 .

 

The candidate will be integrated within the Genomic Medicine Institute of the Cleveland Clinic to perform translational genetics research. The position will be at the Lerner Research Institute of the Cleveland Clinic. The team is closely collaborating with other data scientists, neuroscientists as well as epileptologists, and clinical researchers from related fields. Besides local collaborations, the team will interact on a daily to weekly basis with the Lal research groups at the Broad Institute of MIT and Harvard and the Cologne Center for Genomics in Germany.

 

Specifically, we are looking for a new member interested in leading projects analyzing large-scale genomic data from internal cohorts and international consortia. Our team has extensive experience in genomics, bioinformatics, data science, software engineering, neuroscience and protein structural biology. The candidate would support and lead ongoing projects. We screen thousands of patients and controls using WES, WGS, or SNP arrays to identify genes and genetic risk factors associated with neurological disorders.

 

REQUIREMENTS:

--Extensive experience with next-gen genome analysis software for variant calling and interpretation (e.g. GATK, VCF/BCFtools, IGV, PLINK, Annovar, SNPeff, Promethease, other online and open-source software) and bioinformatics databases (e.g. gnomAD, NCBI, Ensembl, dbSNP, COSMIC, ClinVar, UniProt etc).

--Extensive experience in working on HPCs or cloud

--Advanced programming skills in one and basic skills in a second of the following coding languages: Python, R, Bash, Perl, Java, or C++

--Self-starter, highly motivated

--At least one published first-author publication (preprint or PubMed).

 

WHAT WE OFFER:

--The chance to have a real impact on the advancement of science and medicine. We work closely with clinicians, family foundations, and industry -partners.

--We offer great mentoring and support in career development. Previous postdocs were successful in acquiring faculty and industry job positions of their choice.

--You will learn a lot from other members of the team who are working on a wide range of projects. Members of our team have a diverse background including genomics, biology, bioinformatics, software development, structural biology, and we interact daily with neuroscientists, pediatric neurologists, epileptologists, computational chemists, gene therapy scientists, statisticians, and pathologists.

--Opportunities to participate in training workshops and present results at national and international meetings.

--A good working environment in a fun team.

  

CONTACT:

 

Dr. Dennis Lal; lald@ccf.org

  

Selected studies from the team:

 

Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants.

Iqbal S, Pérez-Palma E, Jespersen JB, May P, Hoksza D, Heyne HO, Ahmed SS, Rifat ZT, Rahman MS, Lage K, Palotie A, Cottrell JR, Wagner FF, Daly MJ, Campbell AJ, Lal D.Proc Natl Acad Sci U S A. 2020 Nov 10;117(45):28201-28211. doi: 10.1073/pnas.2002660117. Epub 2020 Oct 26

 

MISCAST: MIssense variant to protein StruCture Analysis web SuiTe.

Iqbal S, Hoksza D, Pérez-Palma E, May P, Jespersen JB, Ahmed SS, Rifat ZT, Heyne HO, Rahman MS, Cottrell JR, Wagner FF, Daly MJ, Campbell AJ, Lal D.Nucleic Acids Res. 2020 Jul 2;48(W1):W132-W139. doi: 10.1093/nar/gkaa361.

 

A catalogue of new incidence estimates of monogenic neurodevelopmental disorders caused by de novo variants.

López-Rivera JA, Pérez-Palma E, Symonds J, Lindy AS, McKnight DA, Leu C, Zuberi S, Brunklaus A, Møller RS, Lal D.Brain. 2020 Apr 1;143(4):1099-1105. doi: 10.1093/brain/awaa051.

 

Identification of pathogenic variant enriched regions across genes and gene families.

Pérez-Palma E, May P, Iqbal S, Niestroj LM, Du J, Heyne HO, Castrillon JA, O'Donnell-Luria A, Nürnberg P, Palotie A, Daly M, Lal D.Genome Res. 2020 Jan;30(1):62-71. doi: 10.1101/gr.252601.119. Epub 2019 Dec 23.

 

Epilepsy subtype-specific copy number burden observed in a genome-wide study of 17 458 subjects.

Niestroj LM, Perez-Palma E, Howrigan DP, Zhou Y, Cheng F, Saarentaus E, Nürnberg P, Stevelink R, Daly MJ, Palotie A, Lal D; Epi25 Collaborative.

Brain. 2020 Jul 1;143(7):2106-2118. doi: 10.1093/brain/awaa171.

 

Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database.

Pérez-Palma E, Gramm M, Nürnberg P, May P, Lal D.

Nucleic Acids Res. 2019 Jul 2;47(W1):W99-W105. doi: 10.1093/nar/gkz411.

 

Polygenic burden in focal and generalized epilepsies.

Leu C, Stevelink R, Smith AW, Goleva SB, Kanai M, Ferguson L, Campbell C, Kamatani Y, Okada Y, Sisodiya SM, Cavalleri GL, Koeleman BPC, Lerche H, Jehi L, Davis LK, Najm IM, Palotie A, Daly MJ, Busch RM; Epi25 Consortium, Lal D.

Brain. 2019 Nov 1;142(11):3473-3481. doi: 10.1093/brain/awz292.

 

De novo variants in neurodevelopmental disorders with epilepsy.

Heyne HO, Singh T, Stamberger H, Abou Jamra R, Caglayan H, Craiu D, De Jonghe P, Guerrini R, Helbig KL, Koeleman BPC, Kosmicki JA, Linnankivi T, May P, Muhle H, Møller RS, Neubauer BA, Palotie A, Pendziwiat M, Striano P, Tang S, Wu S; EuroEPINOMICS RES Consortium, Poduri A, Weber YG, Weckhuysen S, Sisodiya SM, Daly MJ, Helbig I, Lal D, Lemke JR.

Nat Genet. 2018 Jul;50(7):1048-1053. doi: 10.1038/s41588-018-0143-7. Epub 2018 Jun 25.

PMID: 29942082




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