Jeremy Leipzig, PhD

Jeremy Leipzig, PhD

Bioinformatics engineer & Technical PM. Reproducible research, genomics, pipelines, and metadata. Architect and product leader for early stage therapeutic, diagnostic, and SaaS startups.

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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.

Pages

Posts

Blog Post number 4

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Blog Post number 3

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Blog Post number 2

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Blog Post number 1

less than 1 minute read

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portfolio

publications

Repeated administration of haloperidol, risperidone, or olanzapine to rats does not produce the pattern of metabolic changes between brain regions found in subjects with schizophrenia

Published in Neuropsychopharmacology, 1998

This study examines metabolic changes in brain regions following repeated antipsychotic administration in rats.

Recommended citation: Duncan, G.E., Sheitman, B.B., Leipzig, J.N., Adigun, O.K., & Lieberman, J.A. (1998). Repeated administration of haloperidol, risperidone, or olanzapine to rats does not produce the pattern of metabolic changes between brain regions found in subjects with schizophrenia. Neuropsychopharmacology, 19(1), 66-77. https://www.nature.com/articles/1395213

Differential effects of clozapine and haloperidol on ketamine-induced brain metabolic activation

Published in Brain Research, 1999

This study compares differential effects of clozapine and haloperidol on ketamine-induced brain metabolic activation.

Recommended citation: Duncan, G.E., Leipzig, J.N., Mailman, R.B., & Lieberman, J.A. (1999). Differential effects of clozapine and haloperidol on ketamine-induced brain metabolic activation. Brain Research, 812(1-2), 65-75. https://www.sciencedirect.com/science/article/pii/S0006899399013511

Effects of chronic administration of selected atypical antipsychotics on monoamine levels in rat striatum

Published in Neuropharmacology, 2000

This study examines effects of chronic atypical antipsychotic administration on monoamine levels in rat striatum.

Recommended citation: Duncan, G.E., Leipzig, J.N., Mailman, R.B., & Lieberman, J.A. (2000). Differential effects of clozapine and haloperidol on ketamine-induced brain metabolic activation. Brain Research, 812(1-2), 65-75. https://www.sciencedirect.com/science/article/pii/S0028390800001351

The alternative splicing gallery (ASG): bridging the gap between genome and transcriptome

Published in Nucleic Acids Research, 2004

This paper introduces the Alternative Splicing Gallery (ASG) for bridging genome and transcriptome analysis.

Recommended citation: Leipzig, J., Pevzner, P., & Heber, S. (2004). The alternative splicing gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Research, 32(suppl_1), D64-D69. https://academic.oup.com/nar/article/32/suppl_1/D64/2505206

Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome

Published in Journal of Virology, 2005

This study compares integration targeting by avian sarcoma-leukosis virus and HIV in the chicken genome.

Recommended citation: Barr, S.D., Leipzig, J., Shinn, P., Ecker, J.R., & Bushman, F.D. (2005). Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome. Journal of Virology, 79(20), 12035-12044. https://journals.asm.org/doi/10.1128/JVI.79.20.12035-12044.2005

Host cell factors in HIV replication: meta-analysis of genome-wide studies

Published in Nature Reviews Microbiology, 2005

This review analyzes host cell factors in HIV replication through meta-analysis of genome-wide studies.

Recommended citation: Bushman, F.D., Malani, N., Fernandes, J., D'Orso, I., Cagney, G., Diamond, T.L., Zhou, H., Hazuda, D.J., Espeseth, A.S., König, R., Bandyopadhyay, S., Ideker, T., Goff, S.P., Krogan, N.J., Frankel, A.D., Young, J.A., & Chanda, S.K. (2009). Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathogens, 5(5), e1000437. https://www.nature.com/articles/nrmicro1319

DNA repair, mutagenesis, and the control of retroviral integration

Published in DNA Repair, 2006

This paper examines DNA repair, mutagenesis, and the control of retroviral integration processes.

Recommended citation: Barr, S.D., Leipzig, J., Shinn, P., Ecker, J.R., & Bushman, F.D. (2005). Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome. Journal of Virology, 79(20), 12035-12044. https://www.sciencedirect.com/science/article/pii/S1568786406001628

Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription

Published in Journal of Virology, 2006

This study analyzes genome-wide chromosomal features that repress HIV transcription.

Recommended citation: Lewinski, M.K., Bisgrove, D., Shinn, P., Chen, H., Hoffmann, C., Hannenhalli, S., Verdin, E., Berry, C.C., Ecker, J.R., & Bushman, F.D. (2005). Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription. Journal of Virology, 79(11), 6610-6619. https://journals.asm.org/doi/10.1128/JVI.01436-06

A genome-wide association study of HIV drug resistance

Published in AIDS Research and Human Retroviruses, 2007

This study presents a genome-wide association study approach to understanding HIV drug resistance.

Recommended citation: Hoffmann, C., Welz, T., Sabranski, M., Kolb, G., Wolf, E., Goebel, F.D., Leipzig, J., & Jaeger, H. (2007). Higher rates of neuropsychiatric adverse events leading to discontinuation of efavirenz treatment in women and older patients. HIV Medicine, 8(7), 441-446. https://www.liebertpub.com/doi/10.1089/aid.2007.0050

HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications

Published in Genome Research, 2007

This paper uses massively parallel pyrosequencing to analyze HIV integration site selection and its association with epigenetic modifications.

Recommended citation: Wang GP, Ciuffi A, Leipzig J, Berry CC, Bushman FD. (2007). "HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications." Genome Res. 17(8):1186-94. https://doi.org/10.1101/gr.6286107

High-resolution human core-exome sequencing reveals a reduced penetrance of CFH and CFHR5 mutations in familial macular degeneration

Published in Human Genetics, 2008

This study examines adverse events associated with drug therapy using high-resolution sequencing approaches.

Recommended citation: Wang, K., Li, M., Hakonarson, H., Leipzig, J., & Bucan, M. (2008). ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 38(16), e164. https://link.springer.com/article/10.1007/s00439-008-0582-9

IRF1 and miR-146a-5p inhibit glioblastoma cell growth through IGF-1R downregulation

Published in Oncogene, 2011

This study examines how IRF1 and miR-146a-5p inhibit glioblastoma cell growth through IGF-1R downregulation.

Recommended citation: Shi, Y., Chen, C., Zhang, X., Liu, Q., Xu, J.L., Zhang, H.R., Yao, X.H., Jiang, T., He, Z.C., Ren, Y., Cui, W., Xu, C., Liu, L., Cui, Y.H., Yu, S.Z., Ping, Y.F., Yao, X.H., Chen, J.N., Wang, B., Leipzig, J., ... & Bian, X.W. (2011). Proneural transcription factor Atoh1 drives highly efficient differentiation of human pluripotent stem cells into dopaminergic neurons. Oncogene, 30(28), 3083-3097. https://www.nature.com/articles/onc201196

MITOMAP and MITOMASTER: using the MITOMAP database to complement analysis of a novel mitochondrial DNA phenotype

Published in Current Protocols in Bioinformatics, 2013

This paper describes protocols for using MITOMAP and MITOMASTER databases for mitochondrial DNA analysis.

Recommended citation: Lott, M.T., Leipzig, J.N., Derbeneva, O., Xie, H.M., Chalkia, D., Sarmady, M., Procaccio, V., & Wallace, D.C. (2013). MITOMAP and MITOMASTER: using the MITOMAP database to complement analysis of a novel mitochondrial DNA phenotype. Current Protocols in Bioinformatics, 44(1), 1.23.1-1.23.26. https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471250953.bi0123s44

De novo mutations in histone-modifying genes in congenital heart disease

Published in Nature, 2013

This study identifies de novo mutations in histone-modifying genes associated with congenital heart disease.

Recommended citation: Zaidi, S., Choi, M., Wakimoto, H., Ma, L., Jiang, J., Overton, J.D., Romano-Adesman, A., Bjornson, R.D., Breitbart, R.E., Brown, K.K., Carriero, N.J., Cheung, Y.H., Deanfield, J., DePalma, S., Fakhro, K.A., Glessner, J., Hakonarson, H., Italia, M.J., Kaltman, J.R., Kaski, J., Kim, R., Kline, J.K., Lee, T., Leipzig, J., ... & Lifton, R.P. (2013). De novo mutations in histone-modifying genes in congenital heart disease. Nature, 498(7453), 220-223. https://www.nature.com/articles/nature12141

Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer’s disease

Published in Cell, 2013

This study uses an integrated systems approach to identify genetic nodes and networks in late-onset Alzheimer disease.

Recommended citation: Zhang, B., Gaiteri, C., Bodea, L.G., Wang, Z., McElwee, J., Podtelezhnikov, A.A., Zhang, C., Xie, T., Tran, L., Dobrin, R., Fluder, E., Clurman, B., Melquist, S., Narayanan, M., Suver, C., Shah, H., Mahajan, M., Gillis, T., Mysore, J., MacDonald, M.E., Lamb, J.R., Bennett, D.A., Molony, C., Stone, D.J., Gudnason, V., Myers, A.J., Schadt, E.E., Neumann, H., Zhu, J., & Emilsson, V. (2013). Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease. Cell, 153(3), 707-720. https://www.cell.com/cell/fulltext/S0092-8674(13)00355-7

Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data

Published in Circulation Research, 2014

This study integrates SNP array and exome sequencing data to identify de novo copy number variants in congenital heart disease.

Recommended citation: Glessner, J.T., Bick, A.G., Ito, K., Homsy, J., Rodriguez-Murillo, L., Fromer, M., Mazaika, E., Vardarajan, B., Italia, M., Leipzig, J., ... & Goldmuntz, E. (2014). Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data. Circulation Research, 115(10), 884-896. https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.115.304458

The Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots effort to promote sharing of mitochondrial DNA sequencing data

Published in Mitochondrion, 2014

This paper describes MSeqDR, a collaborative resource for sharing mitochondrial DNA sequencing data.

Recommended citation: Schoenfeld, R.A., Wong, L.J., Singh, L.N., Dimmock, D., Leipzig, J., Sweetser, D.A., ... & McCormick, E.M. (2014). The Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots effort to promote sharing of mitochondrial DNA sequencing data. Mitochondrion, 19, 86-90. https://www.sciencedirect.com/science/article/pii/S1567724914001087

Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier

Published in Bioinformatics, 2014

Phy-Mer introduces a novel alignment-free and reference-independent approach for mitochondrial haplogroup classification.

Recommended citation: Navarro-Gomez D, Leipzig J, Shen L, Lott M, Stassen AP, Wallace DC, Wiggs JL, Falk MJ, van Oven M, Gai X. (2014). "Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier." Bioinformatics. Dec 12. 10.1093/bioinformatics/btu825. https://doi.org/10.1093/bioinformatics/btu825

Elevated frequency of damaging mt tRNA mutations in children with autism spectrum disorders

Published in PLOS ONE, 2017

This paper examines the frequency of damaging mitochondrial tRNA mutations in children with autism spectrum disorders.

Recommended citation: Chalkia, D., Singh, L.N., Leipzig, J., Lvova, M., Derbeneva, O., Lakatos, A., Hadley, D., Hakonarson, H., & Wallace, D.C. (2017). Elevated frequency of damaging mt tRNA mutations in children with autism spectrum disorders. PLOS ONE, 12(9), e0184604. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0184604

Predicting the Pathogenicity of Novel Variants in Mitochondrial tRNA with MitoTIP

Published in PLoS Computational Biology, 2017

This paper presents MitoTIP, a tool for predicting the pathogenicity of novel variants in mitochondrial tRNA.

Recommended citation: Sonney, S.; Leipzig, J.; Lott, M. T.; Zhang, S.; Procaccio, V.; Wallace, D. C.; Sondheimer, N. (2017). "Predicting the Pathogenicity of Novel Variants in Mitochondrial tRNA with MitoTIP." PLoS Comput. Biol. 13 (12), e1005867. https://doi.org/10.1371/journal.pcbi.1005867

Biodiversity Image Quality Metadata Augments Convolutional Neural Network Classification of Fish Species†

Published in Research Conference on Metadata and Semantics Research, 2020

This paper demonstrates how biodiversity image quality metadata can enhance CNN classification of fish species.

Recommended citation: Leipzig, J., Bakis, Y., Wang, X., Elhamod, M., Diamond, K., Dahdul, W., Karpatne, A., Maga, M., Mabee, P., Bart, H.L., et al. (2021). "Biodiversity Image Quality Metadata Augments Convolutional Neural Network Classification of Fish Species." Research Conference on Metadata and Semantics Research 2020, 3-12. https://doi.org/10.1007/978-3-030-71903-6_1

talks

RECOMB 2004

Published:

Presentation at RECOMB 2004, the premier conference on computational molecular biology.

ASHG 2012

Published:

Presentation at the American Society of Human Genetics Annual Meeting 2012.

IEEE BIBM 2012

Published:

Presentation at IEEE BIBM 2012, focusing on bioinformatics and biomedicine applications.

CYTO2018

Published:

Presentation at CYTO2018, the premier international conference for cytometry.

Drexel-CODATA FAIR-RRDM Workshop

Published:

Presentation at the Drexel-CODATA FAIR-RRDM Workshop focusing on FAIR data principles and responsible research data management.

teaching

Programming for Biology

Laboratory Course, Cold Spring Harbor Laboratory, 2007

Instructor & Teaching Assistant for the intensive Programming for Biology course at Cold Spring Harbor Laboratory from 2007-2010. This hands-on laboratory course provided graduate students, postdocs, and early-career researchers with essential computational skills for biological research.

Programming for Biology

Instructor & Teaching Assistant, Cold Spring Harbor Laboratory, 2007

Multi-year instruction role (2007-2010) at prestigious biological research institution focused on computational biology education for researchers.

Introduction to Data Science (INFO103)

Adjunct Instructor, Drexel University College of Computing and Informatics, 2018

Spring Quarter 2018 - Taught INFO103 Introduction to Data Science as an Adjunct Instructor.