Publications

2023

NBSTRN Tools to Advance Newborn Screening Research and Support Newborn Screening Stakeholders.Chan K, Hu Z, Bush LW, Cope H, Holm IA, Kingsmore SF, Wilhelm K, Scharfe C, Brower A. Int J Neonatal Screen. 2023 Oct 30; 2023 Oct 30. PMID: 37987476.
Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs.Tayyab M, Barrett D, van Riel G, Liu S, Reinius B, Scharfe C, Griffin P, Steinmetz LM, Javanmard M, Pelechano V. Sci Adv. 2023 Sep 8; 2023 Sep 6. PMID: 37672583.
Contributions from medical geneticists in clinical trials of genetic therapies: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG).Peña LDM, Burrage LC, Enns GM, Esplin ED, Harding C, Mendell JR, Niu ZN, Scharfe C, Yu T, Koeberl DD. Genet Med. 2023 Jun; 2023 Apr 9. PMID: 37031408.
Validation of a targeted metabolomics panel for improved second-tier newborn screening.Mak J, Peng G, Le A, Gandotra N, Enns GM, Scharfe C, Cowan TM. J Inherit Metab Dis. 2023 Mar; 2023 Feb 2. PMID: 36680545.
Nucleic Acid Quantification by Multi-Frequency Impedance Cytometry and Machine Learning.Kokabi M, Sui J, Gandotra N, Pournadali Khamseh A, Scharfe C, Javanmard M. Biosensors (Basel). 2023 Feb 24; 2023 Feb 24. PMID: 36979528.
A systems biology approach identifies the role of dysregulated PRDM6 in the development of hypertension.Gunawardhana KL, Hong L, Rugira T, Uebbing S, Kucharczak J, Mehta S, Karunamuni DR, Cabera-Mendoza B, Gandotra N, Scharfe C, Polimanti R, Noonan JP, Mani A. J Clin Invest. 2023 Feb 15; 2023 Feb 15. PMID: 36602864.

2022

Metabolic diversity in human populations and correlation with genetic and ancestral geographic distances.Peng G, Pakstis AJ, Gandotra N, Cowan TM, Zhao H, Kidd KK, Scharfe C. Mol Genet Metab. 2022 Nov; 2022 Oct 13. PMID: 36252453.
A multipurpose panel of microhaplotypes for use with STR markers in casework.Kidd KK, Pakstis AJ, Gandotra N, Scharfe C, Podini D. Forensic Sci Int Genet. 2022 Sep; 2022 Jun 3. PMID: 35696960.
dbRUSP: An Interactive Database to Investigate Inborn Metabolic Differences for Improved Genetic Disease Screening.Peng G, Zhang Y, Zhao H, Scharfe C. Int J Neonatal Screen. 2022 Aug 29; 2022 Aug 29. PMID: 36135348.
Population-Based Screening of Newborns: Findings From the NBS Expansion Study (Part One).Brower A, Chan K, Williams M, Berry S, Currier R, Rinaldo P, Caggana M, Gaviglio A, Wilcox W, Steiner R, Holm IA, Taylor J, Orsini JJ, Brunelli L, Adelberg J, Bodamer O, Viall S, Scharfe C, Wasserstein M, Chen JY, Escolar M, Goldenberg A, Swoboda K, Ficicioglu C, Matern D, Lee R, Watson M. Front Genet. 2022; 2022 Jul 22. PMID: 35938011.

2021

The population genetics characteristics of a 90 locus panel of microhaplotypes.Pakstis AJ, Gandotra N, Speed WC, Murtha M, Scharfe C, Kidd KK. Hum Genet. 2021 Dec; 2021 Oct 13. PMID: 34643790.
Multi-frequency impedance sensing for detection and sizing of DNA fragments.Sui J, Gandotra N, Xie P, Lin Z, Scharfe C, Javanmard M. Sci Rep. 2021 Mar 22; 2021 Mar 22. PMID: 33753781.
Massively parallel discovery of human-specific substitutions that alter enhancer activity.Uebbing S, Gockley J, Reilly SK, Kocher AA, Geller E, Gandotra N, Scharfe C, Cotney J, Noonan JP. Proc Natl Acad Sci U S A. 2021 Jan 12. PMID: 33372131.

2020

Timing of Newborn Blood Collection Alters Metabolic Disease Screening Performance.Peng G, Tang Y, Cowan TM, Zhao H, Scharfe C. Front Pediatr. 2020; 2021 Jan 20. PMID: 33553077.
Ethnic variability in newborn metabolic screening markers associated with false-positive outcomes.Peng G, Tang Y, Gandotra N, Enns GM, Cowan TM, Zhao H, Scharfe C. J Inherit Metab Dis. 2020 Sep; 2020 Apr 17. PMID: 32216101.
Validation of novel forensic DNA markers using multiplex microhaplotype sequencing.Gandotra N, Speed WC, Qin W, Tang Y, Pakstis AJ, Kidd KK, Scharfe C. Forensic Sci Int Genet. 2020 Jul; 2020 Mar 18. PMID: 32305739.
Reducing False-Positive Results in Newborn Screening Using Machine Learning.Peng G, Tang Y, Cowan TM, Enns GM, Zhao H, Scharfe C. Int J Neonatal Screen. 2020 Mar; 2020 Mar 3. PMID: 32190768.

2019

Assessment of network module identification across complex diseases.Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R, Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D. Nat Methods. 2019 Sep; 2019 Aug 30. PMID: 31471613.
Combining newborn metabolic and DNA analysis for second-tier testing of methylmalonic acidemia.Peng G, Shen P, Gandotra N, Le A, Fung E, Jelliffe-Pawlowski L, Davis RW, Enns GM, Zhao H, Cowan TM, Scharfe C. Genet Med. 2019 Apr; 2018 Sep 13. PMID: 30209273.
Elevated methylmalonic acidemia (MMA) screening markers in Hispanic and preterm newborns.Peng G, de Fontnouvelle CA, Enns GM, Cowan TM, Zhao H, Scharfe C. Mol Genet Metab. 2019 Jan; 2018 Nov 10. PMID: 30448007.

2018

Transplant Virus Detection Using Multiplex Targeted Sequencing.Tan SK, Shen P, Lefterova MI, Sahoo MK, Fung E, Odegaard JI, Davis RW, Pinsky BA, Scharfe C. J Appl Lab Med. 2018 Mar. PMID: 31245786.

2017

Common data elements for clinical research in mitochondrial disease: a National Institute for Neurological Disorders and Stroke project.Karaa A, Rahman S, Lombès A, Yu-Wai-Man P, Sheikh MK, Alai-Hansen S, Cohen BH, Dimmock D, Emrick L, Falk MJ, McCormack S, Mirsky D, Moore T, Parikh S, Shoffner J, Taivassalo T, Tarnopolsky M, Tein I, Odenkirchen JC, Goldstein A. J Inherit Metab Dis. 2017 May; 2017 Mar 16. PMID: 28303425.
Acylcarnitine Profiles Reflect Metabolic Vulnerability for Necrotizing Enterocolitis in Newborns Born Premature.Sylvester KG, Kastenberg ZJ, Moss RL, Enns GM, Cowan TM, Shaw GM, Stevenson DK, Sinclair TJ, Scharfe C, Ryckman KK, Jelliffe-Pawlowski LL. J Pediatr. 2017 Feb; 2016 Nov 8. PMID: 27836286.

2016

Next-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis.Lefterova MI, Shen P, Odegaard JI, Fung E, Chiang T, Peng G, Davis RW, Wang W, Kharrazi M, Schrijver I, Scharfe C. J Mol Diagn. 2016 Mar; 2016 Feb 1. PMID: 26847993.

2015

A Rapid, High-Quality, Cost-Effective, Comprehensive and Expandable Targeted Next-Generation Sequencing Assay for Inherited Heart Diseases.Wilson KD, Shen P, Fung E, Karakikes I, Zhang A, InanlooRahatloo K, Odegaard J, Sallam K, Davis RW, Lui GK, Ashley EA, Scharfe C, Wu JC. Circ Res. 2015 Sep 11; 2015 Aug 11. PMID: 26265630.
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, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, Terry SF, Zhang Z, Copeland WC, van Oven M, Prokisch H, Wallace DC, Attimonelli M, Krotoski D, Zuchner S, Gai X. Mol Genet Metab. 2015 Mar; 2014 Dec 4. PMID: 25542617.

2014

A functional screen for copper homeostasis genes identifies a pharmacologically tractable cellular system.Schlecht U, Suresh S, Xu W, Aparicio AM, Chu A, Proctor MJ, Davis RW, Scharfe C, St Onge RP. BMC Genomics. 2014 Apr 5; 2014 Apr 5. PMID: 24708151.

2013

Multiplex target capture with double-stranded DNA probes.Shen P, Wang W, Chi AK, Fan Y, Davis RW, Scharfe C. Genome Med. 2013; 2013 May 29. PMID: 23718862.
Rare variant detection using family-based sequencing analysis.Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi AK, Davis RW, Huff V, Scharfe C, Wang W. Proc Natl Acad Sci U S A. 2013 Mar 5; 2013 Feb 20. PMID: 23426633.

2012

Forward chemical genetics in yeast for discovery of chemical probes targeting metabolism.St Onge R, Schlecht U, Scharfe C, Evangelista M. Molecules. 2012 Nov 5; 2012 Nov 5. PMID: 23128089.
SRMA: an R package for resequencing array data analysis.Zhang N, Xu Y, O'Hely M, Speed TP, Scharfe C, Wang W. Bioinformatics. 2012 Jul 15; 2012 May 10. PMID: 22581181.

2011

High-quality DNA sequence capture of 524 disease candidate genes.Shen P, Wang W, Krishnakumar S, Palm C, Chi AK, Enns GM, Davis RW, Speed TP, Mindrinos MN, Scharfe C. Proc Natl Acad Sci U S A. 2011 Apr 19; 2011 Apr 5. PMID: 21467225.
Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing.Wang W, Shen P, Thiyagarajan S, Lin S, Palm C, Horvath R, Klopstock T, Cutler D, Pique L, Schrijver I, Davis RW, Mindrinos M, Speed TP, Scharfe C. Nucleic Acids Res. 2011 Jan; 2010 Sep 15. PMID: 20843780.

2010

Semi-automated library preparation for high-throughput DNA sequencing platforms.Farias-Hesson E, Erikson J, Atkins A, Shen P, Davis RW, Scharfe C, Pourmand N. J Biomed Biotechnol. 2010; 2010 Jun 8. PMID: 20625503.

2009

Mapping gene associations in human mitochondria using clinical disease phenotypes.Scharfe C, Lu HH, Neuenburg JK, Allen EA, Li GC, Klopstock T, Cowan TM, Enns GM, Davis RW. PLoS Comput Biol. 2009 Apr; 2009 Apr 24. PMID: 19390613.
Mitochondrial DNA analysis by multiplex denaturing high-performance liquid chromatography and selective sequencing in pediatric patients with cardiomyopathy.Schrijver I, Pique LM, Traynis I, Scharfe C, Sehnert AJ. Genet Med. 2009 Feb. PMID: 19265752.

2006

MitoP2: the mitochondrial proteome database--now including mouse data.Prokisch H, Andreoli C, Ahting U, Heiss K, Ruepp A, Scharfe C, Meitinger T. Nucleic Acids Res. 2006 Jan 1. PMID: 16381964.
Proteome analysis of mitochondrial outer membrane from Neurospora crassa.Schmitt S, Prokisch H, Schlunck T, Camp DG 2nd, Ahting U, Waizenegger T, Scharfe C, Meitinger T, Imhof A, Neupert W, Oefner PJ, Rapaport D. Proteomics. 2006 Jan. PMID: 16294304.
The role of selection in the evolution of human mitochondrial genomes.Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K, Passarino G, Underhill PA, Scharfe C, Torroni A, Scozzari R, Modiano D, Coppa A, de Knijff P, Feldman M, Cavalli-Sforza LL, Oefner PJ. Genetics. 2006 Jan; 2005 Sep 19. PMID: 16172508.

2005

Identifying new candidate genes for hereditary facial paresis on chromosome 3q21-q22 by RNA in situ hybridization in mouse.van der Zwaag B, Burbach JP, Scharfe C, Oefner PJ, Brunner HG, Padberg GW, van Bokhoven H. Genomics. 2005 Jul; 2005 Apr 20. PMID: 15953540.

2004

Integrative analysis of the mitochondrial proteome in yeast.Prokisch H, Scharfe C, Camp DG 2nd, Xiao W, David L, Andreoli C, Monroe ME, Moore RJ, Gritsenko MA, Kozany C, Hixson KK, Mottaz HM, Zischka H, Ueffing M, Herman ZS, Davis RW, Meitinger T, Oefner PJ, Smith RD, Steinmetz LM. PLoS Biol. 2004 Jun; 2004 Jun 15. PMID: 15208715.
MitoP2, an integrated database on mitochondrial proteins in yeast and man.Andreoli C, Prokisch H, Hörtnagel K, Mueller JC, Münsterkötter M, Scharfe C, Meitinger T. Nucleic Acids Res. 2004 Jan 1. PMID: 14681457.

2003

A tRNA(Ala) mutation causing mitochondrial myopathy clinically resembling myotonic dystrophy.Horváth R, Lochmüller H, Scharfe C, Do BH, Oefner PJ, Müller-Höcker J, Schoser BG, Pongratz D, Auer DP, Jaksch M. J Med Genet. 2003 Oct. PMID: 14569122.
Role of duplicate genes in genetic robustness against null mutations.Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, Li WH. Nature. 2003 Jan 2. PMID: 12511954.

2002

Childhood onset mitochondrial myopathy and lactic acidosis caused by a stop mutation in the mitochondrial cytochrome c oxidase III gene.Horváth R, Scharfe C, Hoeltzenbein M, Do BH, Schröder C, Warzok R, Vogelgesang S, Lochmüller H, Müller-Höcker J, Gerbitz KD, Oefner PJ, Jaksch M. J Med Genet. 2002 Nov. PMID: 12414820.
Systematic screen for human disease genes in yeast.Steinmetz LM, Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, Jones T, Chu AM, Giaever G, Prokisch H, Oefner PJ, Davis RW. Nat Genet. 2002 Aug; 2002 Jul 22. PMID: 12134146.
Evolutionary rate in the protein interaction network.Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. Science. 2002 Apr 26. PMID: 11976460.

2001

Frequency of mitochondrial transfer RNA mutations and deletions in 225 patients presenting with respiratory chain deficiencies.Jaksch M, Kleinle S, Scharfe C, Klopstock T, Pongratz D, Müller-Höcker J, Gerbitz KD, Liechti-Gallati S, Lochmuller H, Horvath R. J Med Genet. 2001 Oct. PMID: 11584044.

2000

The complete form of X-linked congenital stationary night blindness is caused by mutations in a gene encoding a leucine-rich repeat protein.Pusch CM, Zeitz C, Brandau O, Pesch K, Achatz H, Feil S, Scharfe C, Maurer J, Jacobi FK, Pinckers A, Andreasson S, Hardcastle A, Wissinger B, Berger W, Meindl A. Nat Genet. 2000 Nov. PMID: 11062472.
A novel mutation in the thiamine responsive megaloblastic anaemia gene SLC19A2 in a patient with deficiency of respiratory chain complex I.Scharfe C, Hauschild M, Klopstock T, Janssen AJ, Heidemann PH, Meitinger T, Jaksch M. J Med Genet. 2000 Sep. PMID: 10978358.
MITOP, the mitochondrial proteome database: 2000 update.Scharfe C, Zaccaria P, Hoertnagel K, Jaksch M, Klopstock T, Dembowski M, Lill R, Prokisch H, Gerbitz KD, Neupert W, Mewes HW, Meitinger T. Nucleic Acids Res. 2000 Jan 1. PMID: 10592209.

1999

MITOP: database for mitochondria-related proteins, genes and diseases.Scharfe C, Zaccaria P, Hoertnagel K, Jaksch M, Klopstock T, Lill R, Prokisch H, Gerbitz KD, Mewes HW, Meitinger T. Nucleic Acids Res. 1999 Jan 1. PMID: 9847163.

1998

Diabetes insipidus, diabetes mellitus, optic atrophy and deafness (DIDMOAD) caused by mutations in a novel gene (wolframin) coding for a predicted transmembrane protein.Strom TM, Hörtnagel K, Hofmann S, Gekeler F, Scharfe C, Rabl W, Gerbitz KD, Meitinger T. Hum Mol Genet. 1998 Dec. PMID: 9817917.

1997

Report of the second international workshop on human chromosome 10 mapping 1997.Meitinger T, Scharfe C, Call K, Moschonas N. Cytogenet Cell Genet. 1997. PMID: 9465886.