Publications - Jeremy Leipzig, PhD

With an h-index of 30, my research spans computational biology, bioinformatics tool development, viral integration mechanisms, mitochondrial genomics, and modern AI applications to biological data. My work has been published in leading journals including Nature Medicine, Cell Metabolism, Genome Research, PLoS Computational Biology, and Bioinformatics.

Google Scholar Profile

40+ Total Publications

30 H-Index

4 First Author

(3 first author, 1 sole author, 1 book chapter, 1 book, 1 dissertation)

The role of metadata in reproducible computational research

Leipzig, J., Nüst, D., Hoyt, C.T., Ram, K., and Greenberg, J.

Cell Patterns, 2021

This paper discusses the critical role of metadata in ensuring reproducible computational research.

Paper

Hierarchy‐guided neural network for species classification

Elhamod, M., Diamond, K.M., Maga, A.M., Bakis, Y. Bart H.L, Mabee PM, Wasila Dahdul, W, Leipzig J., Greenberg, Avants B, Karpatne A.

Methods in Ecology and Evolution, 2021

This paper presents a hierarchy-guided neural network approach for species classification.

Paper

Tests of Robustness in Peer Review

Leipzig, J.

Drexel University, 2021

This dissertation examines the robustness of peer review systems and their effectiveness in ensuring research quality.

Dissertation

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

Leipzig, J., Bakis, Y., Wang, X., Elhamod, M., Diamond, K., Dahdul, W., Karpatne, A., Maga, M., Mabee, P., Bart, H.L., et al.

Research Conference on Metadata and Semantics Research, 2020

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

Paper

Computational Pipelines and Workflows in Bioinformatics

Leipzig, J.

Reference Module in Life Sciences, Elsevier, 2018

This book chapter provides a comprehensive overview of computational pipelines and workflows in bioinformatics.

Chapter

Predicting the Pathogenicity of Novel Variants in Mitochondrial tRNA with MitoTIP

Sonney, S.; Leipzig, J.; Lott, M. T.; Zhang, S.; Procaccio, V.; Wallace, D. C.; Sondheimer, N.

PLoS Computational Biology, 2017

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

Paper

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

Chalkia, D., Singh, L.N., Leipzig, J., Lvova, M., Derbeneva, O., Lakatos, A., Hadley, D., Hakonarson, H., & Wallace, D.C.

PLOS ONE, 2017

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

Paper

A review of bioinformatic pipeline frameworks*

Leipzig, J.

Briefings in Bioinformatics, 2017

This paper provides a comprehensive review of bioinformatic pipeline frameworks.

Paper

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

Navarro-Gomez D, Leipzig J, Shen L, Lott M, Stassen AP, Wallace DC, Wiggs JL, Falk MJ, van Oven M, Gai X.

Bioinformatics, 2014

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

Paper

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

Schoenfeld, R.A., Wong, L.J., Singh, L.N., Dimmock, D., Leipzig, J., Sweetser, D.A., ... & McCormick, E.M.

Mitochondrion, 2014

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

Paper

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

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.

Circulation Research, 2014

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

Paper

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

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.

Cell, 2013

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

Paper

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

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.

Nature, 2013

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

Paper

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

Lott, M.T., Leipzig, J.N., Derbeneva, O., Xie, H.M., Chalkia, D., Sarmady, M., Procaccio, V., & Wallace, D.C.

Current Protocols in Bioinformatics, 2013

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

Paper

Gene expression profiling of the plasmodium of Physarum polycephalum

Barrantes, I., Leipzig, J., Marwan, W., & Starostzik, C.

PLOS ONE, 2012

This study profiles gene expression in the plasmodium of Physarum polycephalum.

Paper

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

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.

Oncogene, 2011

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

Paper

Data Mashups in R

Leipzig J, Li Xiao-Yi.

O'Reilly Media, 2009

This book provides practical guidance for creating data mashups using the R statistical programming language.

Book

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

Wang, K., Li, M., Hakonarson, H., Leipzig, J., & Bucan, M.

Human Genetics, 2008

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

Paper

HTLV-1 integration site selection: involvement of chromosomal fragile sites

Meekings, K.N., Leipzig, J., Bushman, F.D., Brighton, P., & Leib, D.

Virology, 2008

This study examines HTLV-1 integration site selection and its involvement with chromosomal fragile sites.

Paper

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

Wang GP, Ciuffi A, Leipzig J, Berry CC, Bushman FD.

Genome Research, 2007

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

Paper

A genome-wide association study of HIV drug resistance

Hoffmann, C., Welz, T., Sabranski, M., Kolb, G., Wolf, E., Goebel, F.D., Leipzig, J., & Jaeger, H.

AIDS Research and Human Retroviruses, 2007

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

Paper

Selection of target sites for mobile DNA integration in the human genome

Berry C, Hannenhalli S, Leipzig J, Bushman FD.

PLoS Computational Biology, 2006

This paper investigates the selection mechanisms for target sites of mobile DNA integration in the human genome.

Paper

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

Lewinski, M.K., Bisgrove, D., Shinn, P., Chen, H., Hoffmann, C., Hannenhalli, S., Verdin, E., Berry, C.C., Ecker, J.R., & Bushman, F.D.

Journal of Virology, 2006

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

Paper

A role for LEDGF/p75 in targeting HIV DNA integration

Ciuffi, A., Llano, M., Poeschla, E., Hoffmann, C., Leipzig, J., Shinn, P., Ecker, J.R., & Bushman, F.D.

Nature Medicine, 2006

This study identifies a role for LEDGF/p75 protein in targeting HIV DNA integration.

Paper

DNA repair, mutagenesis, and the control of retroviral integration

Barr, S.D., Leipzig, J., Shinn, P., Ecker, J.R., & Bushman, F.D.

DNA Repair, 2006

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

Paper

A role for LEDGF/p75 in targeting HIV DNA integration

Ciuffi A, Llano M, Poeschla E, Hoffmann C, Leipzig J, Shinn P, Ecker J, Bushman F.

Nature Medicine, 2005

This paper identifies the role of LEDGF/p75 in targeting HIV DNA integration.

Paper

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

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.

Nature Reviews Microbiology, 2005

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

Paper

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

Barr, S.D., Leipzig, J., Shinn, P., Ecker, J.R., & Bushman, F.D.

Journal of Virology, 2005

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

Paper

The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome

Leipzig J, Pevzner P, Heber S.

Nucleic Acids Research, 2004

The Alternative Splicing Gallery (ASG) provides a tool for bridging the gap between genome and transcriptome analysis.

Paper

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

Leipzig, J., Pevzner, P., & Heber, S.

Nucleic Acids Research, 2004

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

Paper

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

Duncan, G.E., Leipzig, J.N., Mailman, R.B., & Lieberman, J.A.

Neuropharmacology, 2000

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

Paper

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

Duncan, G.E., Leipzig, J.N., Mailman, R.B., & Lieberman, J.A.

Brain Research, 1999

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

Paper

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

Duncan, G.E., Sheitman, B.B., Leipzig, J.N., Adigun, O.K., & Lieberman, J.A.

Neuropsychopharmacology, 1998

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

Paper

* ISI Highly Cited

† Best Research Paper: 14th International Conference on Metadata and Semantics Research