School of Biomedical Sciences

R&D Lab Publications from 2009 – Present

 

 

22 A Panda And A Pirate Vol2

 


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Book and Book Chapters

Budowle, B., Schutzer, S.E., Breeze, R., Keim, P.S., and Morse, S.A. (eds.): Microbial Forensics, Second Edition, Academic Press, Amsterdam, 2011.

Budowle, B. and Williamson, P.C.: Microbial forensics – a scientific discipline for response to bioterrorism and biocrime. Jamieson A. and Moenssens A., eds., Wiley Encyclopedia of Forensic Science, John Wiley & Sons, Ltd., Chichester, UK, 2011, DOI: 10.1002/9780470061589.fsa1031.

Jianye Ge, DNA based kinship analysis and missing person identification, Forensic Science, Nova Publishers, 2011

B. Budowle, J. D. Churchill, J. L. King. The Next State-of-the-Art Forensic Genetics Technology: Massively Parallel Sequencing. Handbook of Forensic Genetics: Biodiversity and Heredity in Civil and Criminal Investigation: World Scientific; 2017. p. 249-91.

Mandape, S. Emerging Trends in Bioinformatics for Breast Cancer Molecular Research. ” Breast Cancer: Current Trends in Molecular Research “, Bentham Science Publishers (2012).


Select Publications

 


2022

M. Huang, M. Liu, H. Li, J. King, A. Smuts, B. Budowle, J. Ge, A machine learning approach for missing persons cases with high genotyping errors, Frontiers in Genetics. (2022).

B. Crysup, A.E. Woerner, A genotype likelihood function for DNA mixtures, Forensic Science International: Genetics. (2022).

S.D. Turner, V. Nagraj, M. Scholz, S. Jessa, C. Acevedo, J. Ge, A.E. Woerner, B. Budowle, Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples, Front Genet 13 (2022).

M.E. Bermejo Valladolid, J. Ge, B. Budowle, C. Infante Valdez, C.D. Neyra-Rivera, Genetic study with 21 autosomal STRs in five Peruvian macro regions for human identification purposes, Legal Medicine 57 (2022) 102073.

B.A. Cornejo-Moreno, M.A. Henríquez-García, S.L. Ramos-Aleman, X.P. Romero, E. Lazo-Mena, M. de Pleitez, C.M. Vullo, J. Ge, B. Budowle, Population data for 21 STRs for the Salvadoran population using GlobalFiler Express and GlobalFiler STR Amplification Kits, International Journal of Legal Medicine 136(2) (2022) 565-567.

J. Alfieri, M.D. Coble, C. Conroy, A. Dahl, D.R. Hares, B.S. Weir, C. Wolock, E. Zhao, H. Kingston, T.W. Zolandz, A new implementation of a semi-continuous method for DNA mixture interpretation, Forensic Science International: Reports 6 (2022) 100281.

E. Cropper, M. D. Coble, M. F. Kavlick, Assessment of human nuclear and mitochondrial DNA qPCR assays for quantification accuracy utilizing NIST SRM 2372a, Forensic Science International: Genetics. 59 (2022) 102711.

A. E. Woerner, B. Crysup, F. C. Hewitt, M. W. Gardner, M. A. Freitas, B. Budowle, Techniques for estimating genetically variable peptides and semi-continuous likelihoods from massively parallel sequencing data, Forensic Science International: Genetics.

H. Kelly, M. Coble, M. Kruijver, R. Wivell, J.-A. Bright, Exploring likelihood ratios assigned for siblings of the true mixture contributor as an alternate contributor, Journal of Forensic Sciences. 67 (2022) 1167-75.

A. J. Sherier, A. E. Woerner, B. Budowle, Determining Informative Microbial Single Nucleotide Polymorphisms for Human Identification, Applied and Environmental Microbiology. (2022) e00052-22.

L. Ceresa, J. Chavez, M. M. Bus, B. Budowle, E. Kitchner, J. Kimball, et al., Förster Resonance Energy Transfer-Enhanced Detection of Minute Amounts of DNA, Analytical Chemistry. 94 (2022) 5062-8.

B. Budowle, M. M Bus, L. Dungan, A. v. Daal, The forensic genomics toolbox is expanding, BioTechniques. 72 (2022) 5-7.

Turner SD, Nagraj VP, Scholz M et al. skater: an R package for SNP-based kinship analysis, testing, and evaluation [version 1; peer review: 1 approved, 1 approved with reservations]. F1000Research 2022, 11:18 (https://doi.org/10.12688/f1000research.76004.1)

B. Crysup, B. Budowle, A.E. Woerner, ProSynAR: a reference aware read merger, Bioinformatics (2022).

B. Budowle, M. M Bus, L. Dungan, A. v. Daal, The forensic genomics toolbox is expanding, BioTechniques (2022).

 


2021

B. Song, A.E. Woerner, J. Planz, mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes, BMC Bioinformatics 22(1) (2021) 12.

M. Baniasad, A. J. Reed, S. M. Lai, L. Zhang, K. Q. Schulte, A. R. Smith, et al., Optimization of proteomics sample preparation for forensic analysis of skin samples, Journal of Proteomics. 249 (2021) 104360.

A. J. Sherier, A. E. Woerner, B. Budowle, Population Informative Markers Selected Using Wright’s Fixation Index and Machine Learning Improves Human Identification Using the Skin Microbiome, Appl Environ Microbiol. 87 (2021) e0120821.

J. Ge, J.L. King, A. Smuts, B. Budowle, Precision DNA Mixture Interpretation with Single-Cell Profiling, Genes-Basel 12(11) (2021) 1649.

J.C. Cihlar, K.B. Kapema, B. Budowle, Validation of the Applied Biosystems RapidHIT ID instrument and ACE GlobalFiler Express sample cartridge, International Journal of Legal Medicine (2021).

Ceresa, L., Kitchner, E., Seung, M., Bus, M.M., Budowle, B., Chavez, J., Gryczynski, I., Gryczynski, Z., 2021. A novel approach to imaging and visualization of minute amounts of DNA in small volume samples. The Analyst. doi:10.1039/d1an01391b (2021).

J. Ge, J. King, S. Mandape, B. Budowle, Enhanced mixture interpretation with macrohaplotypes based on long-read DNA sequencing, International Journal of Legal Medicine (2021).

S.N. Mandape, U. Smart, J.L. King, M. Muenzler, K.B. Kapema, B. Budowle, A.E. Woerner, MMDIT: A tool for the deconvolution and interpretation of mitochondrial DNA mixtures, Forensic Science International: Genetics (2021).

M.M. Bus, E.A.d. Jong, J.L. King, W.v.d. Vliet, J. Theelen, B. Budowle, Reverse complement-PCR, an innovative and effective method for multiplexing forensically relevant single nucleotide polymorphism marker systems, BioTechniques (2021).

Kitchner E, Chavez J, Ceresa L, Bus MM, Budowle B, Gryczynski Z. A novel approach for visualization and localization of small amounts of DNA on swabs to improve DNA collection and recovery process. Analyst, 146(4), 1198-1206 (2021).

U. Smart, J. C. Cihlar, B. Budowle, International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions, Forensic Science International: Genetics. 54 (2021) 102551.

R. Li, B. Budowle, H. Sun, J. Ge, Linkage and linkage disequilibrium among the markers in the forensic MPS panels, Journal of Forensic Sciences. n/a (2021).

R. Moura-Neto, J. L. King, I. C. Mello, V. H. G. Dias, B. Crysup, A. Woerner, et al., Evaluation of Promega PowerSeq™ Auto/Y systems prototype on an admixed sample of Rio de Janeiro, Brazil: Population data, sensitivity, stutter and mixture studies, Forensic Sci Int Genet. 53 (2021).

J. Ge, B. Budowle, Forensic investigation approaches of searching relatives in DNA databases, Journal of Forensic Sciences. (2021).

E.K. Guevara, J.U. Palo, J.L. King, M.M. Buś, S. Guillén, B. Budowle, A. Sajantila, Autosomal STR and SNP characterization of populations from the Northeastern Peruvian Andes with the ForenSeqTM DNA Signature Prep Kit, Forensic Science International: Genetics 52 (2021).

B. Crysup, A. E. Woerner, J. L. King, B. Budowle, Graph Algorithms for Mixture Interpretation, Genes. 12 (2021) 185.

B. Crysup, B. Budowle, A.E. Woerner, ProDerAl: reference position dependent alignment, Bioinformatics (2021).

U. Smart, J.C. Cihlar, S.N. Mandape, M. Muenzler, J.L. King, B. Budowle, A.E. Woerner, A Continuous Statistical Phasing Framework for the Analysis of Forensic Mitochondrial DNA Mixtures, Genes-Basel 12(2) (2021) 128.

J.L. King, A.E. Woerner, S.N. Mandape, K.B. Kapema, R.S. Moura-Neto, R. Silva, B. Budowle, STRait Razor Online: An enhanced user interface to facilitate interpretation of MPS data, Forensic Science International: Genetics (2021).

A.E. Woerner, S. Mandape, J.L. King, M. Muenzler, B. Crysup, B. Budowle, Reducing noise and stutter in short tandem repeat loci with unique molecular identifiers, Forensic Science International: Genetics (2021).

K.Q. Schulte, F.C. Hewitt, T.E. Manley, A.J. Reed, M. Baniasad, N.C. Albright, M.E. Powals, D.S. LeSassier, A.R. Smith, L. Zhang, L.W. Allen, B.C. Ludolph, K.L. Weber, A.E. Woerner, M.A. Freitas, M.W. Gardner, Fractionation of DNA and protein from individual latent fingerprints for forensic analysis, Forensic Science International: Genetics 50 (2021) 102405.


2020

E.K. Guevara, J.U. Palo, S. Översti, J.L. King, M. Seidel, M. Stoljarova, F.R. Wendt, M.M. Bus, A. Guengerich, W.B. Church, S. Guillén, L. Roewer, B. Budowle, A. Sajantila, Genetic assessment reveals no population substructure and divergent regional and sex-specific histories in the Chachapoyas from northeast Peru, PLoS One 15(12) (2020) e0244497.

J.C. Cihlar, C. Amory, R. Lagacé, C. Roth, W. Parson, B. Budowle, Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel, Genes-Basel 11(11) (2020) 1345.

P.A. Barrio, P. Martín, A. Alonso, P. Müller, M. Bodner, B. Berger, W. Parson, B. Budowle, Massively parallel sequence data of 31 autosomal STR loci from 496 Spanish individuals revealed concordance with CE-STR technology and enhanced discrimination power, Forensic Science International: Genetics 42 (2019) 49-55.

J. Ge, B. Budowle, Forensic investigation approaches of searching relatives in DNA databases, Journal of Forensic Sciences.

J. Churchill Cihlar, C. Strobl, R. Lagace, M. Muenzler, W. Parson, B. Budowle, Distinguishing Mitochondrial DNA and NUMT Sequences Amplified with the Precision ID mtDNA Whole Genome Panel, Mitochondrion (2020).

J. Ge, B. Budowle, How many familial relationship testing results could be wrong?, PLOS Genetics 16(8) (2020) e1008929.

B. Budowle, M.M. Bus, M.A. Josserand, D.L. Peters, A standalone humanitarian DNA identification database system to increase identification of human remains of foreign nationals, International Journal of Legal Medicine (2020).

A.E. Woerner, J.C. Cihlar, U. Smart, B. Budowle, Numt identification and removal with RtN!, Bioinformatics (2020).

A.E. Woerner, F.C. Hewitt, M.W. Gardner, M.A. Freitas, K.Q. Schulte, D.S. LeSassier, M. Baniasad, A.J. Reed, M.E. Powals, A.R. Smith, N.C. Albright, B.C. Ludolph, L. Zhang, L.W. Allen, K. Weber, B. Budowle, An algorithm for random match probability calculation from peptide sequences, Forensic Science International: Genetics 47 (2020).

J.C. Cihlar, D. Peters, C. Strobl, W. Parson, B. Budowle, The lot-to-lot variability in the mitochondrial genome of controls, Forensic Science International: Genetics (2020).

 


2019

A. Ambers, M. M. Bus, J. L. King, B. Jones, J. Durst, J. E. Bruseth, et al., Forensic genetic investigation of human skeletal remains recovered from the La Belle shipwreck, Forensic Science International. (2019) 110050.

R. E. Kieser, M. M. Buś, J. L. King, W. van der Vliet, J. Theelen, B. Budowle, Reverse Complement PCR: A Novel One-Step PCR System for Typing Highly Degraded DNA for Human Identification, Forensic Science International: Genetics.

D. S. LeSassier, K. Q. Schulte, T. E. Manley, A. R. Smith, M. L. Powals, N. C. Albright, et al., Artificial fingerprints for cross-comparison of forensic DNA and protein recovery methods, PLOS ONE. 14 (2019) e0223170.

K. Butler Gettings, D. Ballard, M. Bodner, L. A. Borsuk, J. King, W. Parson, et al., Report from the STRAND Working Group on the 2019 STR Sequence Nomenclature Meeting, Forensic Science International: Genetics.

F. R. Wendt, B. Budowle, Pharmacogenetics and the postmortem molecular autopsy, Wiley Interdisciplinary Reviews: Forensic Science. 0 e1361.

R. E. Kieser, B. Budowle, Rolling circle amplification: A (random) primer on the enrichment of an infinite linear DNA template, Wiley Interdisciplinary Reviews: Forensic Science. 0 e1359.

K. Elwick, M. M. Bus, J. L. King, J. Chang, S. Hughes-Stamm, B. Budowle, Utility of the Ion S5™ and MiSeq FGx™ sequencing platforms to characterize challenging human remains, Legal Medicine. (2019).

U. Smart, B. Budowle, A. Ambers, R. Soares Moura-Neto, R. Silva, A. E. Woerner, A novel phylogenetic approach for de novo discovery of putative nuclear mitochondrial (pNumt) haplotypes, Forensic Science International: Genetics. (2019).

C. Strobl, J. Churchill Cihlar, R. Lagacé, S. Wootton, C. Roth, N. Huber, et al., Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel, Forensic Science International: Genetics. 42 (2019) 244-51.

A. J. Sherier, R. E. Kieser, N. M. M. Novroski, F. R. Wendt, J. L. King, A. E. Woerner, et al., Copan microFLOQ® Direct Swab collection of bloodstains, saliva, and semen on cotton cloth, International Journal of Legal Medicine. (2019).

F. R. Wendt, A.-L. Rahikainen, J. L. King, A. Sajantila, B. Budowle, A genome-wide association study of tramadol metabolism from post-mortem samples, The Pharmacogenomics Journal. (2019).

A. E. Woerner, J. L. King, B. Budowle, Compound stutter in D2S1338 and D12S391, Forensic Science International: Genetics. (2019).

F. R. Wendt, N. M. Novroski, A.-L. Rahikainen, A. Sajantila, B. Budowle, A pathway-driven predictive model of tramadol pharmacogenetics, European Journal of Human Genetics. (2019) 1.

F. R. Wendt, N. M. Novroski, A.-L. Rahikainen, A. Sajantila, B. Budowle, Supervised Classification of CYP2D6 Genotype and Metabolizer Phenotype With Postmortem Tramadol-Exposed Finns, The American journal of forensic medicine and pathology. 40 (2019) 8-18.

J.-A. Bright, K. Cheng, Z. Kerr, C. McGovern, H. Kelly, T. R. Moretti, et al., STRmix™ collaborative exercise on DNA mixture interpretation, Forensic Science International: Genetics. (2019).

A. E. Woerner, N. M. Novroski, F. R. Wendt, A. Ambers, R. Wiley, S. E. Schmedes, et al., Forensic human identification with targeted microbiome markers using nearest neighbor classification, Forensic Science International: Genetics. 38 (2019) 130-9.


2018

N. M. M. Novroski, F. R. Wendt, A. E. Woerner, M. M. Bus, M. Coble, B. Budowle, Expanding beyond the current core STR loci: An exploration of 73 STR markers with increased diversity for enhanced DNA mixture deconvolution, Forensic Science International: Genetics.

X. Zeng, K. Elwick, C. Mayes, M. Takahashi, J. L. King, D. Gangitano, et al., Assessment of impact of DNA extraction methods on analysis of human remain samples on massively parallel sequencing success, International Journal of Legal Medicine. (2018).

R. Houston, C. Mayes, J. L. King, S. Hughes-Stamm, D. Gangitano, Massively parallel sequencing of 12 autosomal STRs in Cannabis sativa, ELECTROPHORESIS. (2018).

J. S. Buckleton, J.-A. Bright, K. Cheng, B. Budowle, M. D. Coble, NIST Interlaboratory Studies Involving DNA Mixtures (MIX13): A modern analysis, Forensic Science International: Genetics.

I. S. Junttila, A. Vuorio, B. Budowle, T. Laukkala, A. Sajantila, Challenges in investigation of diabetes-related aviation fatalities—an analysis of 1491 subsequent aviation fatalities in USA during 2011–2016, International Journal of Legal Medicine. 132 (2018) 1713-8.

A. Alonso, P. A. Barrio, P. Müller, S. Köcher, B. Berger, P. Martin, et al., Current state-of-art of STR sequencing in forensic genetics, Electrophoresis. 39 (2018) 2655-68.

R. Silva, D. M. De Almeida, B. C. A. Cabral, V. H. G. Dias, I. C. De Toledo E Mello, T. Péterürményi, et al., Microbial enrichment and gene functional categories revealed on the walls of a spent fuel pool of a nuclear power plant, PLoS ONE. 13 (2018).

N. M. M. Novroski, A. E. Woerner, B. Budowle, Potential highly polymorphic short tandem repeat markers for enhanced forensic identity testing, Forensic Science International: Genetics. (2018).

J. S. Buckleton, J. A. Bright, S. Gittelson, T. R. Moretti, A. J. Onorato, F. R. Bieber, et al., The Probabilistic Genotyping Software STRmix: Utility and Evidence for its Validity, J Forensic Sci. (2018).

A.E. Woerner, A. Ambers, F.R. Wendt, J.L. King, R.S. Moura-Neto, R. Silva, B. Budowle, Evaluation of the Precision ID mtDNA Whole Genome Panel on two massively parallel sequencing systems, Forensic Science International: Genetics  (2018).

J. L. King, J. D. Churchill, N. M. M. Novroski, X. Zeng, D. Warshauer, L. H. Seah, et al., Increasing the discrimination power of ancestry- and identity-informative SNP loci within the ForenSeq™ DNA Signature Prep Kit, Forensic Science International: Genetics. (2018).

E. M. Greytak, D. H. Kaye, B. Budowle, C. Moore, S. L. Armentrout, Privacy and genetic genealogy data, Science. 361 (2018) 857.

N. M. M. Novroski, A. E. Woerner, B. Budowle, Insertion within the flanking region of the D10S1237 locus, Forensic Science International: Genetics. 35 (2018) e4-e6.

J. D. Churchill, M. Stoljarova, J. L. King, B. Budowle, Massively parallel sequencing-enabled mixture analysis of mitochondrial DNA samples, International Journal of Legal Medicine. (2018) 1-10.

F. R. Wendt, A. Sajantila, R. S. Moura-Neto, A. E. Woerner, B. Budowle, Full-gene haplotypes refine CYP2D6 metabolizer phenotype inferences, International Journal of Legal Medicine. 132 (2018) 1007-24.

A. Vuorio, B. Budowle, A. Sajantila, T. Laukkala, I. Junttila, S. E. Kravik, et al., Duty of notification and aviation safety—A study of fatal aviation accidents in the United States in 2015, International Journal of Environmental Research and Public Health. 15 (2018).

F. R. Wendt, A. E. Woerner, A. Sajantila, R. S. Moura-Neto, B. Budowle, Exploring the 1000 Genomes Project haplotype reporting for the CYP2D6 pharmacogene, International Journal of Legal Medicine. (2018) 1-4.

B. Martínez-Jarreta, C. Sosa, C. Laliena, B. Budowle, R. E. M. Hedges, Stable Isotope and Radiocarbon Dating of the Remains of the Medieval Royal House of Aragon (Spain) Shed Light on Their Diets, Life Histories and Identities, Archaeometry. 60 (2018) 366-82.

B. C. A. Cabral, L. Hoffmann, B. Budowle, T. P. Ürményi, R. S. Moura-Neto, S. M. F. O. Azevedo, et al., Planktonic microbial profiling in water samples from a Brazilian Amazonian reservoir, MicrobiologyOpen. 7 (2018).

T. Laukkala, A. Vuorio, R. Bor, B. Budowle, P. Navathe, E. Pukkala, et al., Copycats in pilot aircraft-assisted suicides after the germanwings incident, International Journal of Environmental Research and Public Health. 15 (2018).

C. Phillips, K. B. Gettings, J. L. King, D. Ballard, M. Bodner, L. Borsuk, et al., “The devil’s in the detail”: Release of an expanded, enhanced and dynamically revised forensic STR Sequence Guide, Forensic Science International: Genetics. (2018).

F. R. Wendt, A. Sajantila, B. Budowle, Predicted activity of UGT2B7, ABCB1, OPRM1, and COMT using full-gene haplotypes and their association with the CYP2D6-inferred metabolizer phenotype, Forensic Science International: Genetics. 33 (2018) 48-58.

Ambers A, Vanek D, Votrubova J, Sajantila A, Budowle B. Improved Y-STR typing for disaster victim identification, missing persons investigations, and historical human skeletal remains. International Journal of Legal Medicine 2018 https://doi.org/10.1007/s00414-018-1794-8

Ambers A, Wiley R, Novroski N, Budowle B. Direct PCR amplification of DNA from human bloodstains, saliva, and touch samples collected with microFLOQ® swabs. Forensic Science International: Genetics 32 (2018) 80-87.


2017

A. Woerner, J. King, B. Budowle, Flanking Variation Influences Rates of Stutter in Simple Repeats, Genes. 8 (2017) 329.

S. E. Schmedes, A. E. Woerner, N. M. M. Novroski, F. R. Wendt, J. L. King, K. M. Stephens, et al., Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification, Forensic Science International: Genetics.

K. Elwick, X. Zeng, J. King, B. Budowle, S. Hughes-Stamm, Comparative tolerance of two massively parallel sequencing systems to common PCR inhibitors, International Journal of Legal Medicine. (2017).

K.B. Gettings, L.A. Borsuk, D. Ballard, M. Bodner, B. Budowle, L. Devesse, J. King, W. Parson, C. Phillips, P.M. Vallone, STRSeq: A catalog of sequence diversity at human identification Short Tandem Repeat loci, Forensic Science International: Genetics.

R. S. Moura-Neto, I. C. T. Mello, R. Silva, A. P. C. Maette, C. G. Bottino, A. Woerner, et al., Evaluation of InnoTyper® 21 in a sample of Rio de Janeiro population as an alternative forensic panel, International Journal of Legal Medicine. (2017).

J. D. Churchill, N. M. M. Novroski, J. L. King, L. H. Seah, B. Budowle, Population and performance analyses of four major populations with Illumina’s FGx Forensic Genomics System, Forensic Science International: Genetics. 30 (2017) 81-92.

X. Zeng, J. L. King, B. Budowle, Investigation of the STR loci noise distributions of PowerSeq™ Auto System, Croatian medical journal. 58 (2017) 214.

A. Heraclides, E. Bashiardes, E. Fernández-Domínguez, S. Bertoncini, M. Chimonas, V. Christofi, et al., Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots, PLOS ONE. 12 (2017) e0179474.

A. E. Woerner, J. L. King, B. Budowle, Fast STR allele identification with STRait Razor 3.0, Forensic Science International: Genetics. 30 (2017) 18-23.

B. Young, J. L. King, B. Budowle, L. Armogida, A technique for setting analytical thresholds in massively parallel sequencing-based forensic DNA analysis, PLOS ONE. 12 (2017) e0178005.

J. L. King, F. R. Wendt, J. Sun, B. Budowle, STRait Razor v2s: Advancing sequence-based STR allele reporting and beyond to other marker systems, Forensic Science International: Genetics. (2017).

H. Brown, R. Thompson, G. Murphy, D. Peters, B. La Rue, J. King, et al., Development and Validation of a Novel Multiplexed DNA Analysis System, InnoTyper ® 21, Forensic Science International: Genetics. (2017).

F. R. Wendt, J. L. King, N. M. M. Novroski, J. D. Churchill, J. Ng, R. F. Oldt, et al., Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans, Forensic Science International: Genetics. 28 (2017) 146-54.

S. Gittelson, T. R. Moretti, A. J. Onorato, B. Budowle, B. S. Weir, J. Buckleton, The factor of 10 in forensic DNA match probabilities, Forensic Science International: Genetics. 28 (2017) 178-87.

R. Wiley, K. Sage, B. Larue, B. Budowle, Internal Validation of the RapidHIT ® ID System, Forensic Science International: Genetics. (2017).

S. E. Schmedes, A. E. Woerner, B. Budowle, Forensic human identification using skin microbiomes, Appl Environ Microbiol. (2017).

A. J. Pakstis, L. Kang, L. Liu, Z. Zhang, T. Jin, E. L. Grigorenko, et al., Increasing the reference populations for the 55 AISNP panel: the need and benefits, International Journal of Legal Medicine. (2017) 1-5.

B. Budowle, C. Capt, R. Chakraborty, J. Ge, Paternity calculations in a di-spermy case, International Journal of Legal Medicine. 131 (2017) 339-43.

F. R. Wendt, A. Sajantila, R. S. Moura-Neto, A. E. Woerner, B. Budowle, Full-gene haplotypes refine CYP2D6 metabolizer phenotype inferences, International Journal of Legal Medicine. (2017) 1-18.

F. R. Wendt, A. Sajantila, B. Budowle, Predicted activity of UGT2B7, ABCB1, OPRM1, and COMT using full-gene haplotypes and their association with the CYP2D6-inferred metabolizer phenotype, Forensic Science International: Genetics. 33 (2018) 48-58.

Votrubova J, Ambers A, Budowle B, Vanek D. Comparison of standard capillary electrophoresis based genotyping method and ForenSeq™ DNA Signature Prep kit (Illumina) on a set of challenging samples, Forensic Science International: Genetics Supplement Series (2017) http://dx.doi.org/10.1016/j.fsigss.2017.09.027

Vanek D, Budowle B, Dubska-Votrubova J, Ambers A, et al. Results of a collaborative study on DNA identification of aged bone samples, Croatian Medical Journal 58 (2017) 229-239.

B. Budowle, S. E. Schmedes, F. R. Wendt, Increasing the reach of forensic genetics with massively parallel sequencing, Forensic Science, Medicine and Pathology. 13 (2017) 342-9.

A. Vuorio, T. Laukkala, P. Navathe, B. Budowle, R. Bor, A. Sajantila, Bipolar disorder in aviation medicine, Aerospace medicine and human performance. 88 (2017) 42-7.

A. Vuorio, S. Asmayawati, B. Budowle, R. Griffiths, T. Strandberg, J. Kuoppala, et al., General aviation pilots over 70 years old, Aerospace medicine and human performance. 88 (2017) 142-5.


2016

A. D. Ambers, J. D. Churchill, J. L. King, M. Stoljarova, H. Gill-King, M. Assidi, et al., More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing, BMC Genomics. 17 (2016) 750.

N. M. M. Novroski, J. L. King, J. D. Churchill, L. H. Seah, B. Budowle, Characterization of genetic sequence variation of 58 STR loci in four major population groups, Forensic Science International: Genetics. 25 (2016) 214-26.

F. R. Wendt, D. H. Warshauer, X. Zeng, J. D. Churchill, N. M. M. Novroski, B. Song, et al., Massively parallel sequencing of 68 insertion/deletion markers identifies novel microhaplotypes for utility in human identity testing, Forensic Science International: Genetics. 25 (2016) 198-209.

F. R. Wendt, J. D. Churchill, N. M. Novroski, J. L. King, J. Ng, R. F. Oldt, et al., Genetic analysis of the Yavapai Native Americans from West-Central Arizona using the Illumina MiSeq FGx™ Forensic Genomics System, Forensic Science International: Genetics. (2016).

J. D. Churchill, J. L. King, R. Chakraborty, B. Budowle, Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality, International journal of legal medicine. (2016) 1-12.

C. Phillips, W. Parson, J. Amigo, J. L. King, M. D. Coble, C. R. Steffen, et al., D5S2500 is an ambiguously characterized STR: Identification and description of forensic microsatellites in the genomics age, Forensic Science International: Genetics. (2016)

X. Zeng, D. H. Warshauer, J. L. King, J. D. Churchill, R. Chakraborty, B. Budowle, Empirical testing of a 23-AIMs panel of SNPs for ancestry evaluations in four major US populations, International journal of legal medicine. (2016) 1-6.

F. Wendt, X. Zeng, J. Churchill, J. L. King, B. Budowle., Analysis of short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci from single source samples using a custom HaloPlex Target Enrichment System panel. American Journal of Forensic Medicine and Pathology. (2016)

W. Parson, D. Ballard, B. Budowle, J. M. Butler, K. B. Gettings, P. Gill, et al., Massively Parallel Sequencing of forensic STRs: Considerations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements, Forensic Science International: Genetics. (2016)

A.-L. Rahikainen, J. U. Palo, W. de Leeuw, B. Budowle, A. Sajantila, DNA quality and quantity from up to 16 years old post-mortem blood stored on FTA cards, Forensic science international. 261 (2016) 148-53.

K. L. McCulloh, J. Ng, R. F. Oldt, J. A. Weise, J. Viray, B. Budowle, et al., The genetic structure of native Americans in North America based on the Globalfiler® STRs, Legal Medicine. 23 (2016) 49-54.

F. R. Bieber, J. S. Buckleton, B. Budowle, J. M. Butler, M. D. Coble, Evaluation of forensic DNA mixture evidence: protocol for evaluation, interpretation, and statistical calculations using the combined probability of inclusion, BMC genetics. 17 (2016) 125.

M. R. Lindberg, S. E. Schmedes, F. C. Hewitt, J. L. Haas, K. L. Ternus, D. R. Kadavy, et al., A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes, PLOS ONE. 11 (2016) e0167600.


2015

X. Zeng, R. Chakraborty, J. King, B. LaRue, R. Moura-Neto, B. Budowle, Selection of highly informative SNP markers for population affiliation of major US populations, International Journal of Legal Medicine. (2015) 1-12.

A. Ambers, M. Turnbough, R. Benjamin, H. Gill-King, J. L. King, A. Sajantila, B. Budowle, Modified DOP-PCR for Improved STR Typing of Degraded DNA from Human Skeletal Remains and Bloodstains. Legal Medicine. (2015)

D. H. Warshauer, J. D. Churchill, N. M. M. Novroski, J. L. King, B. Budowle, Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing. Genomics, Proteomics & Bioinformatics. (2015)

J. D. Churchill, S. E. Schmedes, J. L. King, B. Budowle, Evaluation of the Illumina® Beta Version ForenSeq™ DNA Signature Prep Kit for Use in Genetic Profiling, Forensic Science International: Genetics. (2015)

S. Schmedes, J. King, B. Budowle, Correcting inconsistencies and errors in bacterial genome metadata using an automated curation tool in Excel (AutoCurE), Frontiers in Bioengineering and Biotechnology. (2015)

M. Stoljarova, J. King, M. Takahashi, A. Aaspõllu, B. Budowle, Whole mitochondrial genome genetic diversity in an Estonian population sample, International Journal of Legal Medicine. (2015) 1-5.

X. Zeng, J. King, S. Hermanson, J. Patel, D. R. Storts, B. Budowle, An Evaluation of the PowerSeq™ Auto system: A Multiplex Short Tandem Repeat Marker Kit Compatible with Massively Parallel Sequencing, Forensic Science International: Genetics. (2015)
J. D. Churchill, J. Chang, J. Ge, N. Rajagopalan, S. C. Wootton, C. W. Chang, R. Lagace, W. Liao, J. L. King, B. Budowle. Blind study evaluation illustrates utility of the Ion PGM system for use in human identity DNA typing, Croatian Medical Journal. (2015)

S. B. Seo, X. Zeng, J. King, B. LaRue, M. Assidi, M Al-Qahtani, A. Sajantila, B. Budowle, Underlying Data for Sequencing the Mitochondrial Genome with the Massively Parallel Sequencing Platform Ion Torrent™ PGM™, BMC Genomics. (2015)

Zeng, J. L. King, M. Stoljarova, D. H. Warshauer, B. L. LaRue, A. Sajantila,et al.,High Sensitivity Multiplex Short Tandem Repeat Loci Analyses with Massively Parallel Sequencing, Forensic Science International:Genetics.(2015)


2014

 

R. S. Moura-Neto, R. Silva, I. C. Mello, T. Nogueira, A. A. Al-Deib, B. LaRue, et al., Evaluation of a 49 InDel Marker HID panel in two specific populations of South America and one population of Northern Africa, International Journal of Legal Medicine. (2014) 1-5.

D. Warshauer, C. Davis, C. Holt, Y. Han, P. Walichiewicz, T. Richardson, et al., Massively parallel sequencing of forensically relevant single nucleotide polymorphisms using TruSeq™ forensic amplicon, International Journal of Legal Medicine. (2014) 1-6

C. Davis, D. Peters, D. Warshauer, J. King, B. Budowle, Sequencing the hypervariable regions of human mitochondrial DNA using massively parallel sequencing: Enhanced data acquisition for DNA samples encountered in forensic testing, Legal Medicine. (2014)

D. H. Warshauer, J. L. King, B. Budowle, STRait Razor v2. 0: The Improved STR Allele Identification Tool–Razor, Forensic Science International: Genetics. (2014)

S. Flores, J. Sun, J. King, A. Eisenberg, B. Budowle, Allele frequencies for 15 autosomal STR loci and haplotype data for 17 Y-STR loci in a population from Belize, International Journal of Legal Medicine. (2014) 1-2

B. L. LaRue, A. Moore, J. L. King, P. L. Marshall, B. Budowle, An evaluation of the RapidHIT® system for reliably genotyping reference samples, Forensic Science International: Genetics.

J. L. King, A. Sajantila, B. Budowle, mitoSAVE: Mitochondrial sequence analysis of variants in Excel, Forensic Science International: Genetics. 12 (2014) 122-5.

J. L. King, B. L. LaRue, N. M. Novroski, M. Stoljarova, S. B. Seo, X. Zeng, et al., High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq, Forensic Science International: Genetics. 12 (2014) 128-35.

A. Ambers, M. Turnbough, R. Benjamin, J. King, B. Budowle, Assessment of the role of DNA repair in damaged forensic samples, International Journal of Legal Medicine. (2014) 1-9.

Ambers, Angie, Harrell Gill-King, Dennis Dirkmaat, Robert Benjamin, Jonathan King, and Bruce Budowle. “Autosomal and Y-STR analysis of degraded DNA from the 120-year-old skeletal remains of Ezekiel Harper.”Forensic Science International: Genetics 9 (2014): 33-41.

P. L. Marshall, M. Stoljarova, S. E. Schmedes, J. L. King, B. Budowle, A high volume extraction and purification method for recovering DNA from human bone, Forensic Science International: Genetics. (2014).

P. L. Marshall, M. Stoljarova, B. L. Larue, J. L. King, B. Budowle, Evaluation of a Novel Material, Diomics X-Swab™, for Collection of DNA, Forensic Science International: Genetics. (2014).

P. L. Marshall, J. L. King, B. Budowle, Utility of amplification enhancers in low copy number DNA analysis, International Journal of Legal Medicine. (2014) 1-10.

Seo, Seung Bum, et al. “Reduction of stutter ratios in short tandem repeat loci typing of low copy number DNA samples.” Forensic Science International: Genetics 8.1 (2014): 213-218.

Ge, J. and Budowle, B.: Modeling one complete versus triplicate analyses in Low Template DNA typing. Int. J. Leg. Med. (in press).

Flores, S.K., Sun, J., King, J., and Budowle, B.: Validation of the GlobalFiler™ Express PCR Amplification Kit for the direct amplification of single-source DNA samples on a high-throughput automated workflow. Forens. Sci. Int. Genet. (in press).


2013

Budowle, B., Schmedes, S., and Murch, R.S. (2013) The microbial forensics pathway for use of massively parallel sequencing technologies. The science and applications of microbial genomics. Institute of Medicine, Washington, DC, The National Academies Press. Seo, Seung Bum, et al. “Single nucleotide polymorphism typing with massively parallel sequencing for human identification.” International journal of legal medicine (2013): 1-8.

Jin, Hong Xuan, Seung Bum Seo, Hye Young Lee, Sohee Cho, Jianye Ge, Jonathan King, Bruce Budowle, and Soong Deok Lee. “Differences of PCR efficiency between two-step PCR and standard three-step PCR protocols in short tandem repeat amplification.” Australian Journal of Forensic Sciencesahead-of-print (2013): 1-11.

Budowle, B., D. H. Warshauer, S. B. Seo, J. L. King, C. Davis, and B. LaRue. “Deep Sequencing Provides Comprehensive Multiplex Capabilities.” Forensic Science International: Genetics Supplement Series4, no. 1 (2013): e334-e335.

Seo, Seung Bum, Hong Xuan Jin, Hye Young Lee, Jianye Ge, Jonathan L. King, Sung Hee Lyoo, Dong Hoon Shin, and Soong Deok Lee. “Improvement of short tandem repeat analysis of samples highly contaminated by humic acid.” Journal of forensic and legal medicine 20, no. 7 (2013): 922-928.

Budowle, B.: Editors’ Pick: ENCODE and its first impractical application. BMC Investigative Genetics 4(4), 2013.

Alenizi, M., Ge, J., Ismael, S., Alenezi, H., AlAwadhi, A., AlDuaij, W., AlSaleh, B., Ghulloom, Z., and Budowle, B.: Population genetic analyses of the 15 STR loci of seven forensically-relevant populations residing in
Kuwait. Forens. Sci. Int. Genet. 7(4):e106-107, 2013.

Warshauer, D.H.; Lin, D., Hari, K., Jain, R., Davis, C., LaRue, B., King, J., and Budowle, B.: STRait Razor: A length-based forensic STR allele-calling tool for use with second generation sequencing data. Forens.
Sci. Int. Genet. 7:409–417, 2013.

Budowle, B., Warshauer, D.H., Seo, S.B., King, J.L., Davis, C., and LaRue, B.: Massively parallel sequencing provides comprehensive multiplex capabilities. Forensic Sci. Int.: Genetics Supplement Series 4:e334–e335, 2013.

LaRue, B.L., Lagacé, R., Chang, C., Holt, A., Hennessy, L., Ge, J., King, J.L., Chakraborty, R., and Budowle, B.: Characterization of 114 insertion/deletion (INDEL) polymorphisms, and selection of a global INDEL panel
for human identification. Leg. Med. 16(1):26-32, 2014.

Budowle, B.: Editors’ pick: re-‘colon’-ization of healthy microbiota after recurrent C. difficile infection. Invest. Genet. 4(1):28, 2013.

Kayser, M., Sajantila, A., and Budowle, B.: A tribute to DNA fingerprinting. 4(1):19, 2013.


2012

LaRue, B.L., King, J.L., and Budowle, B.: A validation Study of the Nucleix DSI-Semen Kit – a Methylation-Based Assay for Semen Identification. Int. J. Leg. Med. 127(2):299-308, 2013.

Keating, B., Bansal, A.T., Walsh, S., Millman, J., Newman, J., Kidd, K., Budowle, B., Eisenberg, A., Donfack, J., Gasparini, P., Budimlija, Z., Henders, A.K., Chandrupatla, H., Duffy, D.L., Gordon, S.D., Hysi, P., Liu,
F., Medland, S.E., Rubin, L., Martin, N.G., Spector, T.D., and Kayser M.: First all-in-one inference tool for DNA forensics: parallel genome-wide inference of bio-geographic ancestry, appearance, relatedness and gender with Identitas forensic chip. Int. J. Leg. Med. 127(3):559-572, 2013.

Marshall, P. L., King, J. L., Lawrence, N. P., Lazarev, A., Gross, V. S., & Budowle, B. (2012). Pressure cycling technology (PCT) reduces effects of inhibitors of the PCR.International journal of legal medicine, 1-13.

Schmedes, S., Marshall, P., King, J.L., and Budowle, B. (2012) Effective removal of co-purified inhibitors from extracted DNA samples using synchronous coefficient of drag alteration (SCODA) technology. Int J Legal Med 127:749-755.

Budowle B, Ge J, Chakraborty R, Gill-King H. Response to: Use of prior odds for missing persons identifications – authors’ reply. Investig Genet. 2012 Feb 1;3(1):3.

Ge J, Eisenberg A, Budowle B. Developing criteria and data to determine best options for expanding the core CODIS loci. Investig Genet. 2012 Jan 6;3:1.

Lee SB, Clabaugh KC, Silva B, Odigie KO, Coble MD, Loreille O, Scheible M, Fourney RM, Stevens J, Carmody GR, Parsons TJ, Pozder A, Eisenberg AJ, Budowle B, Ahmad T, Miller RW, Crouse CA. Assessing a
novel room temperature DNA storage medium for forensic biological samples. Forensic Sci Int Genet. 2012 Jan;6(1):31-40. Epub 2011 Feb 15.

Davis CP, King JL, Budowle B, Eisenberg AJ, Turnbough MA. Extraction platform evaluations: a comparison of AutoMate Express?, EZ1? Advanced XL, and Maxwell? 16 Bench-top DNA extraction systems.
Leg Med (Tokyo). 2012 Jan;14(1):36-9. Epub 2011 Dec 17.

Alvarez-Cubero MJ, Saiz M, Martinez-Gonzalez LJ, Alvarez JC, Eisenberg AJ, Budowle B, Lorente JA. Genetic identification of missing persons: DNA analysis of human remains and compromised samples. Pathobiology. 2012;79(5):228-38. Epub 2012 Jun 21.

Ge J, Budowle B. Kinship index variations among populations and thresholds for familial searching. PLoS One. 2012;7(5):e37474. Epub 2012 May 16.

Myers BA, King JL, Budowle B. Evaluation and comparative analysis of direct amplification of STRs using PowerPlex 18D and Identifier Direct systems. Forensic Sci Int Genet. 2012 Sep;6(5):640-5. Epub
2012 Mar 8.

Planz JV, Sannes-Lowery KA, Duncan DD, Manalili S, Budowle B, Chakraborty R, Hofstadler SA, Hall TA. Automated analysis of sequence polymorphism in STR alleles by PCR and direct electrospray ionization
mass spectrometry. Forensic Sci Int Genet. 2012 Sep;6(5):594-606. Epub 2012 Mar 8.

Li B, Ge J, Wu F, Ye L, Budowle B, Chen Y. Population genetic analyses of the STR loci of the AmpFlSTR NGM SElect kit for Han population in Fujian Province, China. Int J Legal Med. 2012 Jul 22. [Epub
ahead of print]

Warshauer DH, King J, Eisenberg AJ, Budowle B. Validation of the PLEX-ID(TM) mass spectrometry mitochondrial DNA assay. Int J Legal Med. 2012 Jul 21. [Epub ahead of print]

Warshauer DH, Marshall P, Kelley S, King J, Budowle B. An evaluation of the transfer of saliva-derived DNA. Int J Legal Med. 2012 Jul 15. [Epub ahead of print]

Davis C, Ge J, King J, Malik N, Weirich V, Eisenberg AJ, Budowle B. Variants observed for STR locus SE33: a concordance study. Forensic Sci Int Genet. 2012 Jul;6(4):494-7. Epub 2011 Dec 30.

Li L, Ge J, Zhang S, Guo J, Zhao S, Li C, Tang H, Davis C, Budowle B, Hou Y, Liu Y. Maternity exclusion with a very high autosomal STRs kinship index. Int J Legal Med. 2012 Jul;126(4):645-8. Epub 2012
Mar 27.

Larue BL, Ge J, King JL, Budowle B. A validation study of the Qiagen Investigator DIPplex? kit; an INDEL-based assay for human identification. Int J Legal Med. 2012 Jul;126(4):533-40. Epub 2012 Jan 15.

Davis C, Ge J, Sprecher C, Chidambaram A, Thompson J, Ewing M, Fulmer P, Rabbach D, Storts D, Budowle B. Prototype PowerPlex(?) Y23 System: A concordance study. Forensic Sci Int Genet. 2012 Jun
29.

Davis C, Illescas M, Tirado C, Lopez R, Budowle B, Cruz TD. A Case of Amelogenin Y-null: A simple primer binding site mutation or unusual genetic anomaly? Leg Med (Tokyo). 2012 Jun 19.

Budowle B. Editors’ Pick: Normal aging versus Alzheimer’s disease – expression patterns may discern the differences. Investig Genet. 2012 May 18;3(1):11.

Yuan L, Ge J, Lu D, Yang X. Population data of 21 non-CODIS STR loci in Han population of northern China. Int J Legal Med. 2012 Jul;126(4):659-64. Epub 2012 Jan 13.

Oh CS, Lee SJ, Park JB, Lee SD, Seo SB, Kim HY, Kim J, Kim YS, Shin DH. Autosomal Short Tandem Repeat Analysis of Ancient DNA by Coupled Use of Mini- and Conventional STR Kits. J Forensic Sci. 2012
May;57(3):820-5.

Zhang AH, Lee HY, Seo SB, Lee HJ, Jin HX, Cho SH, Lyoo SH, Kim KH, Lee JW, Lee SD. Y Haplogroup Distribution in Korean and Other Populations. Kor J Legal Med. 2012 May;36(1):34-44.


2011

Ge, J., Yan, J., Budowle, B., Chakraborty, R.,and Eisenberg, A.: Issues on China forensic DNA database. Chinese Journal of Forensic Medicine, 2011, 26(3): 252-255.

Tate CM, Nu?ez AN, Goldstein CA, Gomes I, Robertson JM, Kavlick MF, Budowle B. Evaluation of circular DNA substrates for whole genome amplification prior to forensic analysis. Forensic Sci Int Genet. 2012 Mar;6(2):185-90. Epub 2011 May 12.

Frumkin D, Wasserstrom A, Budowle B, Davidson A. DNA methylation-based forensic tissue identification. Forensic Sci Int Genet. 2011 Nov;5(5):517-24. Epub 2010 Dec 31.

Kavlick MF, Lawrence HS, Merritt RT, Fisher C, Isenberg A, Robertson JM, Budowle B. Quantification of human mitochondrial DNA using synthesized DNA standards. J Forensic Sci. 2011 Nov;56(6):1457-63. doi:
10.1111/j.1556-4029.2011.01871.x. Epub 2011 Sep 2.

Ge J, Chakraborty R, Eisenberg A, Budowle B. Comparisons of familial DNA database searching strategies. J Forensic Sci. 2011 Nov;56(6):1448-56. doi: 10.1111/j.1556-4029.2011.01867.x. Epub 2011 Aug 9.

Davis C, Ge J, Chidambaram A, King J, Turnbough M, Collins M, Dym O, Chakraborty R, Eisenberg AJ, Budowle B. Y-STR loci diversity in native Alaskan populations. Int J Legal Med. 2011 Jul;125(4):559-63. Epub 2011 Mar 30.

Ge J, Eisenberg A, Yan J, Chakraborty R, Budowle B. Pedigree likelihood ratio for lineage markers. Int J Legal Med. 2011 Jul;125(4):519-25. Epub 2010 Sep 21.

Budowle B, Ge J, Chakraborty R, Gill-King H. Use of prior odds for missing persons identifications. Investig Genet. 2011 Jun 27;2(1):15.

Núnéz C, Sosa C, Baeta M, Geppert M, Turnbough M, Phillips N, Casalod Y, Bolea M, Roby R, Budowle B, Martínez-Jarreta B. Genetic analysis of 7 medieval skeletons from the Aragonese Pyrenees. Croat Med J. 2011 Jun;52(3):336-43.

Chakraborty R, Ge J, Budowle B. Response to: DNA identification by pedigree likelihood ratio accommodating population substructure and mutations- authors’ reply. Investig Genet. 2011 Mar 25;2(1):8. Budowle B, Kayser M, Sajantila A. The demise of the United Kingdom’s forensic science service (FSS): loss of world-leading engine of innovation and development in the forensic sciences. Investig Genet. 2011 Feb 1;2(1):4.

Budowle B, van Daal A. Comment on “A universal strategy to interpret DNA profiles that does not require a definition of low copy number” by Peter Gill and John Buckleton, 2010, Forensic Sci. Int. Genetics 4, 221-227. Forensic Sci Int Genet. 2011 Jan;5(1):15. Epub 2010 Jun 8.

Budowle B, Ge J, Chakraborty R, Eisenberg AJ, Green R, Mulero J, Lagace R, Hennessy L. Population genetic analyses of the NGM STR loci. Int J Legal Med. 2011 Jan;125(1):101-9. Epub 2010 Sep 29.

Ge J, Budowle B, Chakraborty R. Choosing relatives for DNA identification of missing persons. J Forensic Sci. 2011 Jan;56 Suppl 1:S23-8. doi: 10.1111/j.1556-4029.2010.01631.x. Epub 2010 Dec 13. Ge J, Budowle B, Chakraborty R. Comments on “Interpreting Y chromosome STR haplotype mixture”. Leg Med (Tokyo). 2011 Jan;13(1):52; author reply 52-3. Epub 2010 Oct 16.

Budowle, B. and van Daal, A.: Reply to Comments by Buckleton and Gill on “Low copy number typing has yet to achieve ‘general acceptance'” by Budowle, B., et al, 2009. Forensic Sci. Int. Genetics: Supplement Series 2, 551-552. Forens. Sci. Int. Genetics 5(1):12-14, 2011.

Bos KI, Schuenemann VJ, Golding GB, Burbano HA, Waglechner N, Coombes BK, McPhee JB, DeWitte SN, Meyer M, Schmedes S, Wood J, Earn DJ, Herring DA, Bauer P, Poinar HN, Krause J. A draft genome of Yersinia pestis from victims of the Black Death. Nature. 2011 Oct 12;478(7370):506-10.

Schuenemann VJ, Bos K, DeWitte S, Schmedes S, Jamieson J, Mittnik A, Forrest S, Coombes BK, Wood JW, Earn DJ, White W, Krause J, Poinar HN. Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death. Proc Natl Acad Sci USA. 2011 Sep 20;108(38):E746-52. Epub 2011 Aug 29.

Davis CP, Chelland LA, Pavlova VR, Illescas MJ, Brown KL, Dawson Cruz T. “Traditional Multiplex STR Amplification of Low Template DNA Samples with the Addition of Proofreading Enzymes.” Journal of Forensic Sciences. (2011) 56(3):726-32 DOI: 10.1111/j.1556-4029.2011.01727.x


2010

Sajantila A, Palo JU, Ojanper I, Davis C, Budowle B. Pharmacogenetics in medico-legal context. Forensic Sci Int. 2010 Dec 15;203(1-3):44-52.

Nu?ez C, Baeta M, Sosa C, Casalod Y, Ge J, Budowle B, Martínez-Jarreta B. Reconstructing the population history of Nicaragua by means of mtDNA, Y-chromosome STRs, and autosomal STR markers. Am J
Phys Anthropol. 2010 Dec;143(4):591-600. doi: 10.1002/ajpa.21355. Epub 2010 Aug 18.

Ge J, Budowle B, Planz JV, Eisenberg AJ, Ballantyne J, Chakraborty R. US forensic Y-chromosome short tandem repeats database. Leg Med (Tokyo). 2010 Nov;12(6):289-95.

Balamurugan K, Kanthimathi S, Vijaya M, Suhasini G, Duncan G, Tracey M, Budowle B. Genetic variation of 15 autosomal microsatellite loci in a Tamil population from Tamil Nadu, Southern India. Leg Med (Tokyo). 2010 Nov;12(6):320-3. Epub 2010 Sep 1.

Ge J, Budowle B, Chakraborty R. DNA identification by pedigree likelihood ratio accommodating population substructure and mutations. Investig Genet. 2010 Oct 4;1(1):8.

Ge J, Budowle B, Planz JV, Chakraborty R. Haplotype block: a new type of forensic DNA markers. Int J Legal Med. 2010 Sep;124(5):353-61. Epub 2009 Dec 22.

Cummings CA, Bormann Chung CA, Fang R, Barker M, Brzoska P, Williamson PC, Beaudry J, Matthews M, Schupp J, Wagner DM, Birdsell D, Vogler AJ, Furtado MR, Keim P, Budowle B. Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing. Investig Genet. 2010 Sep 1;1(1):5.

Kayser M, Budowle B, Sajantila A. Welcome to investigative genetics. Investig Genet. 2010 Sep 1;1(1):1.

Polanskey D, Den Hartog BK, Elling JW, Fisher CL, Kepler RB, Budowle B. Comparison of mitotyper rules and phylogenetic-based mtDNA nomenclature systems. J Forensic Sci. 2010 Sep;55(5):1184-9. doi:
10.1111/j.1556-4029.2010.01477.x. Epub 2010 Jul 26.

Budowle B, Polanskey D, Fisher CL, Den Hartog BK, Kepler RB, Elling JW. Automated alignment and nomenclature for consistent treatment of polymorphisms in the human mitochondrial DNA control region. J
Forensic Sci. 2010 Sep;55(5):1190-5. doi: 10.1111/j.1556-4029.2010.01478.x. Epub 2010 Jul 26.

Tom BK, Koskinen MT, Dayton M, Mattila AM, Johnston E, Fantin D, Denise S, Spear T, Smith DG, Satkoski J, Budowle B, Kanthaswamy S. Development of a nomenclature system for a canine STR multiplex reagent kit. J Forensic Sci. 2010 May;55(3):597-604. Epub 2010 Mar 25.

Ge J, Budowle B, Chakraborty R. Interpreting Y chromosome STR haplotype mixture. Leg Med (Tokyo). 2010 May;12(3):137-43. Epub 2010 Mar 25.

Nilsson M, Possnert G, Edlund H, Budowle B, Kjellstr?m A, Allen M. Analysis of the putative remains of a European patron saint–St. Birgitta. PLoS One. 2010 Feb 16;5(2):e8986.

Budowle, B.: Low copy number typing still lacks robustness and reliability. Profiles in DNA 13(2), 2010; At: www.promega.com/profiles/1302/1302_02.html.

Budowle, B.: Familial searching: extending the investigative lead potential of DNA typing. Profiles in DNA 13(2), 2010, Available at: www.promega.com/profiles/1302/1302_07.html.

Ni W, Xu J, Huang Y, Liu T, and Ge J. Acronym Extraction using SVM with Uneven Margins. Proceedings of the 2nd IEEE Symposium on Web Society. Beijing, 2010.


2009

Maybruck JL, Hanson E, Ballantyne J, Budowle B, Fuerst PA. A comparative analysis of two different sets of Y-chromosome short tandem repeats (Y-STRs) on a common population panel. Forensic Sci Int Genet.
2009 Dec;4(1):11-20. Epub 2009 May 17.

Schutzer SE, Keim P, Czerwinski K, Budowle B. Use of forensic methods under exigent circumstances without full validation. Sci Transl Med. 2009 Nov 25;1(8):8cm7.

Hall TA, Sannes-Lowery KA, McCurdy LD, Fisher C, Anderson T, Henthorne A, Gioeni L, Budowle B, Hofstadler SA. Base composition profiling of human mitochondrial DNA using polymerase chain reaction and direct
automated electrospray ionization mass spectrometry. Anal Chem. 2009 Sep 15;81(18):7515-26.

Budowle B, Ge J, Aranda XG, Planz JV, Eisenberg AJ, Chakraborty R. Texas population substructure and its impact on estimating the rarity of Y STR haplotypes from DNA evidence*. J Forensic Sci. 2009
Sep;54(5):1016-21. Epub 2009 Jul 15.

Kanthaswamy S, Tom BK, Mattila AM, Johnston E, Dayton M, Kinaga J, Erickson BJ, Halverson J, Fantin D, DeNise S, Kou A, Malladi V, Satkoski J, Budowle B, Smith DG, Koskinen MT. Canine population data
generated from a multiplex STR kit for use in forensic casework. J Forensic Sci. 2009 Jul;54(4):829-40. Epub 2009 May 26.

Dayton M, Koskinen MT, Tom BK, Mattila AM, Johnston E, Halverson J, Fantin D, DeNise S, Budowle B, Smith DG, Kanthaswamy S. Developmental validation of short tandem repeat reagent kit for forensic DNA
profiling of canine biological material. Croat Med J. 2009 Jun;50(3):268-85.

Budowle B, Eisenberg AJ, van Daal A. Validity of low copy number typing and applications to forensic science. Croat Med J. 2009 Jun;50(3):207-17.

Ge J, Budowle B, Aranda XG, Planz JV, Eisenberg AJ, Chakraborty R. Mutation rates at Y chromosome short tandem repeats in Texas populations. Forensic Sci Int Genet. 2009 Jun;3(3):179-84. Epub 2009 Feb 14.

Budowle B, van Daal A. Extracting evidence from forensic DNA analyses: future molecular biology directions. Biotechniques. 2009 Apr;46(5):339-40, 342-50.

Budowle, B., Eisenberg, A.J., Gonzalez, S., Planz, J.V. Sannes-Lowery, K.A., Hall, T.A., Paulsen, J.E., and Hofstadler, S.A.: Validation of mass spectrometry analysis of mitochondrial DNA. Forens. Sci. Int. Gen. Suppl. Series 2:527-528, 2009.

Cummings, C.A., Bormann Chung, C.A., Fang, R., Barker, M., Brzoska, P.M., Williamson, P., Beaudry, J.A., Matthews, M., Schupp, J.M., Wagner, D.M., Furtado, M.R., Keim, P., and Budowle, B.: Whole-genome typing of Bacillus anthracis isolates by next-generation sequencing accurately and rapidly identifies strain-specific diagnostic polymorphisms. Forens. Sci. Int. Gen. Suppl. Series 2:300-301, 2009.

Budowle, B., Eisenberg, A.J., and van Daal, A.: Low copy number typing has yet to achieve “General Acceptance”. Forens. Sci. Int. Gen. Suppl. Series 2:551-552, 2009.

Planz, J.V., Budowle, B., Hall, T., Eisenberg, A.J., Sannes-Lowery, K., and Hofstadler, S.A.: Enhanced resolution and statistical power by using mass spectrometry for detection of SNPs within the short tandem repeats. Forens. Sci. Int. Gen. Suppl. Series 2:529-531, 2009.

Hofstadler, S.A., Hall, T.A., Sannes-Lowery, K.A., Manalili, S., Paulsen, J.E., McCurdy, L.D., Gioeni, L., Penella, T., Eisenberg, A.J., Planz, J.V., and Budowle, B.: Analysis of DNA forensic markers using high throughput mass spectrometry. Forens. Sci. Int. Gen. Suppl. Series 2:524-526, 2009.

Den Hartog, B.K., Elling, J.W., and Budowle, B.: The Impact of Jumping Alignments on mtDNA Population Analysis and Database Searching. Forens. Sci. Int. Gen. Suppl. Series 2:315-316, 2009.

Roby, R.K., Gonzalez, S.D., Phillips, N.R., Planz, J.V., Thomas, J.L., Pantoja Astudillo, J.A., Ge, J., Aguirre Morales, E., Eisenberg, A.J., Chakraborty, R., Bustos, P., and Budowle, B.: Autosomal STR allele frequencies and Y-STR and mtDNA haplotypes in Chilean sample populations Forens. Sci. Int. Gen. Suppl. Series 2:532-533, 2009.