Publications¶

American Journal of Human Genetics2024

Genome-based newborn screening for severe childhood genetic diseases has high positive predictive value and sensitivity in a NICU pilot trial

Kingsmore SF, Wright M, Olsen L, Schultz B, Protopsaltis L, Averbuj D, Blincow E, Carroll J, Caylor S, Defay T, Ellsworth K, Feigenbaum A, Gover M, Guidugli L, Hansen C, Van Der Kraan L, Kunard CM, Kwon H, Madhavrao L, Leipzig J, Liang Y, Mardach R, Mowrey WR, Nguyen H, Niemi AK, Oh D, Saad M, Scharer G, Schleit J, Mehtalia SS, Sanford E, Smith LD, Willis MJ, Wigby K, Reimers R

Large prospective clinical trials are underway or planned that examine the clinical utility and cost effectiveness of genome-based newborn screening (gNBS).

American Journal of Human Genetics2024

Prequalification of genome-based newborn screening for severe childhood genetic diseases through federated training based on purifying hyperselection

Kingsmore SF, Wright M, Smith LD, Liang Y, Mowrey WR, Protopsaltis L, Bainbridge M, Baker M, Batalov S, Blincow E, Cao B, Caylor S, Chambers C, Ellsworth K, Feigenbaum A, Frise E, Guidugli L, Hall KP, Hansen C, Kiel M, Van Der Kraan L, Krilow C, Kwon H, Madhavrao L, Lefebvre S, Leipzig J, Mardach R, Moore B, Oh D, Olsen L, Ontiveros E, Owen MJ, Reimers R, Scharer G, Schleit J, Shelnutt S, Mehtalia SS, Oriol A, Sanford E, Schwartz S, Wigby K, Willis MJ, Yandell M, Kunard CM, Defay T

Genome-sequence-based newborn screening (gNBS) has substantial potential to improve outcomes in hundreds of severe childhood genetic disorders (SCGDs).

Methods in Ecology and Evolution2022

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

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

Drexel University2021

Tests of Robustness in Peer Review

Leipzig, J

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

Patterns2021

The role of metadata in reproducible computational research

Leipzig J, Nüst D, Hoyt CT, Ram K, Greenberg J

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

Research Conference on Metadata and Semantics Research2020

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

Best Research Paper, MTSR 2020

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

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

Cancer Genetics2019

A comparison of survival analysis methods for cancer gene expression RNA-Sequencing data

Raman P, Zimmerman S, Rathi KS, de Torrenté L, Sarmady M, Wu C, Leipzig J, Taylor DM, Tozeren A, Mar JC

Identifying genetic biomarkers of patient survival remains a major goal of large-scale cancer profiling studies.

Cell Metabolism2019

Mitochondrial DNA Variation Dictates Expressivity and Progression of Nuclear DNA Mutations Causing Cardiomyopathy

McManus MJ, Picard M, Chen HW, De Haas HJ, Potluri P, Leipzig J, Towheed A, Angelin A, Sengupta P, Morrow RM, Kauffman BA, Vermulst M, Narula J, Wallace DC

Nuclear-encoded mutations causing metabolic and degenerative diseases have highly variable expressivity.

Reference Module in Life Sciences, Elsevier2018

Computational Pipelines and Workflows in Bioinformatics

Leipzig, J

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

Briefings in Bioinformatics2017

A review of bioinformatic pipeline frameworks

ISI Top 1% Highly Cited

Leipzig J

This paper provides a comprehensive review of bioinformatic pipeline frameworks.

JAMA Psychiatry2017

Association Between Mitochondrial DNA Haplogroup Variation and Autism Spectrum Disorders

Chalkia D, Singh LN, Leipzig J, Lvova M, Derbeneva O, Lakatos A, Hadley D, Hakonarson H, Wallace DC

Autism spectrum disorders (ASD) are characterized by impairments in social interaction, communication, and repetitive or restrictive behavior.

PNAS2017

Mitochondrial energy deficiency leads to hyperproliferation of skeletal muscle mitochondria and enhanced insulin sensitivity

Morrow RM, Picard M, Derbeneva O, Leipzig J, McManus MJ, Gouspillou G, Barbat-Artigas S, Dos Santos C, Hepple RT, Murdock DG, Wallace DC

Diabetes is associated with impaired glucose metabolism in the presence of excess insulin.

PLoS Computational Biology2017

Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP

Sonney S, Leipzig J, Lott MT, Zhang S, Procaccio V, Wallace DC, Sondheimer N

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

Human Mutation2016

MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease

Shen L, Diroma MA, Gonzalez M, Navarro-Gomez D, Leipzig J, Lott MT, van Oven M, Wallace DC, Muraresku CC, Zolkipli-Cunningham Z, Chinnery PF, Attimonelli M, Zuchner S, Falk MJ, Gai X

MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants.

PLoS One2015

Peripheral Blood Mitochondrial DNA as a Biomarker of Cerebral Mitochondrial Dysfunction following Traumatic Brain Injury in a Porcine Model

Kilbaugh TJ, Lvova M, Karlsson M, Zhang Z, Leipzig J, Wallace DC, Margulies SS

Traumatic brain injury (TBI) has been shown to activate the peripheral innate immune system and systemic inflammatory response, possibly through the central release of damage associated molecular patterns (DAMPs).

Bioinformatics2015

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

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

Molecular Genetics and Metabolism2015

Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities

Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen AP, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, et al

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

Circulation Research2014

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 JT, Bick AG, Ito K, Homsy J, Rodriguez-Murillo L, Fromer M, Mazaika E, Vardarajan B, Italia M, Leipzig J, DePalma SR, Golhar R, Sanders SJ, Yamrom B, Ronemus M, Iossifov I, Willsey AJ, State MW, Kaltman JR, White PS, Shen Y, Warburton D, Brueckner M, Seidman C, Goldmuntz E, Gelb BD, Lifton R, Seidman J, Hakonarson H, Chung WK

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

Nature2013

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

Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, Romano-Adesman A, Bjornson RD, Breitbart RE, Brown KK, Carriero NJ, Cheung YH, Deanfield J, DePalma S, Fakhro KA, Glessner J, Hakonarson H, Italia MJ, Kaltman JR, Kaski J, Kim R, Kline JK, Lee T, Leipzig J, Lopez A, Mane SM, Mitchell LE, Newburger JW, Parfenov M, Pe'er I, Porter G, Roberts AE, Sachidanandam R, Sanders SJ, Seiden HS, State MW, Subramanian S, Tikhonova IR, Wang W, Warburton D, White PS, Williams IA, Zhao H, Seidman JG, Brueckner M, Chung WK, Gelb BD, Goldmuntz E, Seidman CE, Lifton RP

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

BMC Bioinformatics2013

Efficient digest of high-throughput sequencing data in a reproducible report

Zhang Z, Leipzig J, Sasson A, Yu AM, Perin JC, Xie HM, Sarmady M, Warren PV, White PS

High-throughput sequencing (HTS) technologies are spearheading the accelerated development of biomedical research.

arXiv2013

Work Issues in Software Engineering

J Leipzig

Current Protocols in Bioinformatics2013

mtDNA Variation and Analysis Using Mitomap and Mitomaster

Lott MT, Leipzig JN, Derbeneva O, Xie HM, Chalkia D, Sarmady M, Procaccio V, Wallace DC

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

Gene Regulation and Systems Biology2012

A next-generation sequencing approach to study the transcriptomic changes during the differentiation of physarum at the single-cell level

Barrantes I, Leipzig J, Marwan W

Physarum polycephalum is a unicellular eukaryote belonging to the amoebozoa group of organisms.

Gene2011

Genome-wide analysis of interferon regulatory factor I binding in primary human monocytes

Shi L, Perin JC, Leipzig J, Zhang Z, Sullivan KE

IRF1 is a transcription factor that participates in interferon signaling.

O'Reilly Media2009

Data Mashups in R

Leipzig J, Li Xiao-Yi

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

Nucleic Acids Research2008

DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer

Wang GP, Garrigue A, Ciuffi A, Ronen K, Leipzig J, Berry C, Lagresle-Peyrou C, Benjelloun F, Hacein-Bey-Abina S, Fischer A, Cavazzana-Calvo M, Bushman FD

Gene transfer has been used to correct inherited immunodeficiencies, but in several patients integration of therapeutic retroviral vectors activated proto-oncogenes and caused leukemia.

PLoS Pathogens2008

HTLV-1 integration into transcriptionally active genomic regions is associated with proviral expression and with HAM/TSP

Meekings KN, Leipzig J, Bushman FD, Taylor GP, Bangham CR

Human T-lymphotropic virus type 1 (HTLV-1) causes leukaemia or chronic inflammatory disease in approximately 5% of infected hosts.

Nucleic Acids Research2007

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations

Hoffmann C, Minkah N, Leipzig J, Wang G, Arens MQ, Tebas P, Bushman FD

Treatment of HIV-infected individuals with antiretroviral agents selects for drug-resistant mutants, resulting in frequent treatment failures.

Genome Research2007

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

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

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

Molecular Therapy2006

HIV integration site selection: targeting in macrophages and the effects of different routes of viral entry

Barr SD, Ciuffi A, Leipzig J, Shinn P, Ecker JR, Bushman FD

We have studied the selection of HIV DNA integration sites in primary macrophages to investigate two questions.

Molecular Therapy2006

Integration site selection by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts

Ciuffi A, Mitchell RS, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman FD

DNA integration is a defining step in the retroviral life cycle and the basis of stable gene transfer in retrovirus-based gene therapy.

PLoS Pathogens2006

Retroviral DNA integration: viral and cellular determinants of target-site selection

Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, Crawford G, Collins F, Shinn P, Leipzig J, Hannenhalli S, Berry CC, Ecker JR, Bushman FD

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

PLoS Computational Biology2006

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

Berry C, Hannenhalli S, Leipzig J, Bushman FD

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

Nature Medicine2005

A role for LEDGF/p75 in targeting HIV DNA integration

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

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

Nature Reviews Microbiology2005

Genome-wide analysis of retroviral DNA integration

Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, Hannenhalli S, Hoffmann C

Retroviral vectors are often used to introduce therapeutic sequences into patients' cells.

Journal of Virology2005

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

Barr SD, Leipzig J, Shinn P, Ecker JR, Bushman FD

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

Nucleic Acids Research2004

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

Leipzig J, Pevzner P, Heber S

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

The Journal of Pharmacology and Experimental Therapeutics2000

Comparison of the effects of clozapine, risperidone, and olanzapine on ketamine-induced alterations in regional brain metabolism

Duncan GE, Miyamoto S, Leipzig JN, Lieberman JA

The ability of subanesthetic doses of N-methyl-D-aspartate (NMDA) antagonists to induce positive, negative, and cognitive schizophrenia-like symptoms suggests that reduced NMDA receptor function may contribute to the pathophysiology of schizophrenia.

Neuropsychopharmacology2000

Effects of ketamine, MK-801, and amphetamine on regional brain 2-deoxyglucose uptake in freely moving mice

Miyamoto S, Leipzig JN, Lieberman JA, Duncan GE

Although the pathophysiology of schizophrenia remains unclear, behavioral effects in humans induced by N-methyl-D-aspartate (NMDA) antagonists, such as ketamine, provide direction for formulating new pharmacologic models of the illness.

Brain Research1999

Comparison of brain metabolic activity patterns induced by ketamine, MK-801 and amphetamine in rats: support for NMDA receptor involvement in responses to subanesthetic dose of ketamine

Duncan GE, Miyamoto S, Leipzig JN, Lieberman JA

Subanesthetic doses of NMDA receptor antagonists induce positive, negative and cognitive schizophrenia-like symptoms in healthy humans and precipitate psychotic reactions in stabilized schizophrenic patients.

Brain Research1998

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

Duncan GE, Leipzig JN, Mailman RB, Lieberman JA

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