Publications

Featured publications

The following is a list of short news items that describe the five most recent publications which featured the work of Bioinformatics Core members: Find out more about how we can lend our bioinformatics and statistical expertise to help you with your research.

• Finding variations in canine tumors may provide insight into common pathways for human cancer
• New paper involving assembly of PacBio reads from a tricky part of the dog genome, published in Immunogenetics
• New RNA-Seq paper published in Parasites & Vectors journal
• New PLOS Genetics paper identifies first genetic variant associated with a hoof wall specific phenotype
• The Bioinformatics Core helps understand the effects of ibuprofen contamination on the transcriptome of an inland fish

Full Publication List

This list includes all publications that feature Bioinformatics Core members as co-authors, and most of the papers where we are acknowledged for providing assistance and/or software that was developed in the Core.

2017

• [Acknowledged, Software] — Milk Bioactive Peptide Database: A comprehensive database of milk protein-derived bioactive peptides and novel visualization. Søren D Nielsen, Robert L Beverly, Yunyao Qu, Davis C Dallas. Food Chemistry. In revision.

2016

• [Co-authors] — Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus. Madison-Villar, M. J., Cheng Sun, Nelson C. Lau, Matthew L. Settles, and Rachel Lockridge Mueller. Journal of molecular evolution 83, no. 3-4 (2016): 126-136.
• [Acknowledged] — Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation. Shore, Sabrina, et al. PloS one 11.11 (2016): e0167009.
• [Acknowledged] — A resistance to thyroid hormone syndrome mutant operates through the target gene repertoire of the wild-type thyroid hormone receptor. Jimenez, Robyn, and Martin L. Privalsky. Molecular and Cellular Endocrinology (2017).
• [Co-authors] — Refinement of the canine CD1 locus topology and investigation of antibody binding to recombinant canine CD1 isoforms. Schjaerff, Mette, Stefan M. Keller, Joseph Fass, Lutz Froenicke, Robert A. Grahn, Leslie Lyons, Verena K. Affolter, Annemarie T. Kristensen, and Peter F. Moore. Immunogenetics 68, no. 3 (2016): 191-204.
• [Acknowledged] — Finished genome sequences of Xanthomonas fragariae, the cause of bacterial angular leaf spot of strawberry. Henry, Peter M., and Johan HJ Leveau. Genome announcements 4.6 (2016): e01271-16.
• [Acknowledged] — The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa. Gouran H, Gillespie H, Nascimento R, Chakraborty S, Zaini PA, Jacobson A, Phinney BS, Dolan D, Durbin-Johnson BP, Antonova ES, Lindow SE. Scientific Reports. 2016 Aug 5;6:31098.
• [Co-authors] — Effects of high temperatures on threatened estuarine fishes during periods of extreme drought. Ken M. Jeffries, Richard E. Connon, Brittany E. Davis, Lisa M. Komoroske, Monica T. Britton, Ted Sommer, Anne E. Todgham, Nann A. Fangue. Journal of Experimental Biology 2016 219: 1705-1716; doi: 10.1242/jeb.134528
• [Co-authors] — Chromosomal Aberrations in Canine Gliomas Define Candidate Genes and Common Pathways in Dogs and Humans. Peter J. Dickinson, BVSc, PhD, Dan York, BA, PhD, Robert J. Higgins, BVSc, PhD, Richard A. LeCouteur, BVSc, PhD, Nikhil Joshi, MS, and Danika Bannasch, DVM, PhD. 2016 May 31. Journal of Neuropathology and Experimental Neurology. Vol. 0, No. 0, 2016, pp. 1–11.
• [Software] — Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Schirmer, Melanie, et al. Nucleic acids research (2015): gku1341.

2015

• [Acknowledged] — De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes. Ashrafi et al. BMC Genomics. 2012, 13, October 30
• [Acknowledged] — Enhanced biological processes associated with alopecia in polar bears (Ursus maritimus). Bowen et al. Science of The Total Environment. 2015, 5(29), October 1
• [Software]  — Genome sequence of Anoxybacillus ayderensis AB04T isolated from the Ayder hot spring in Turkey. Bleed et al. Standards in Genomic Science. 2015, 10&(70), September 26
• [Co-authors] — RNA-seq analyses of changes in the Anopheles gambiae transcriptome associated with resistance to pyrethroids in Kenya: identification of candidate-resistance genes and candidate-resistance SNPs. Mariangela Bonizzoni, Eric Ochomo, William Dunn et al. Parasites & Vectors. 2015, 8(474), September 17
• [Co-authors] — Identifying rhesus macaque gene orthologs using heterospecific human CNV probes. Jillian Ng, Joseph N. Fass, Blythe Durbin-Johnson, David Glenn Smith,, Sree Kanthaswamy. Genomics Data. 2015, 6, September 16
• [Software] — Self-renewing diploid Axin2+ cells fuel homeostatic renewal of the liver. Wang et al. Nature. 2015, 524(7564), August 5
• [Co-authors] — YeATS – a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut. Sandeep Chakraborty, Monica Britton, Jill Wegrzyn et al. F1000 Research. 2015, 4(155), June 17
• [Software] — Genome Sequence of Anoxybacillus thermarum AF/04T, Isolated from the Euganean Hot Springs in Abano Terme, Italy. Genome Announcement. 2015, 3 (3), May 21
• [Co-authors] — Complete genome sequence of canine papillomavirus type 16.  Jennifer Luff, Michelle Mader, Monica Britton, Joseph Fass et al. Genome Announcements. 2015, 3 (3), May 7
• [Software] — A cysteine-clamp gene drives embryo polarity in the midge Chironomus. Klomp et al. Science. 2015, 348(6238), May 7
• [Co-authors] — SERPINB11 Frameshift Variant Associated with Novel Hoof Specific Phenotype in Connemara Ponies. Carrie J. Finno, Carlynn Stevens, Amy Young, Verena Affolter, Nikhil A. Joshi et al. PLOS Genetics. 2015, 11 (4), April 13
• [Software] — Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.). Keller at al. Theoretical and Applied Genetics. 2015, 128 (5), Mar 5
• [Co-authors] — Chronic exposures to low and high concentrations of ibuprofen elicit different gene response patterns in a euryhaline fish. Jeffries KM, Brander SM, Britton MT, Fangue NA, Connon RE. Environmental Science and Pollution Resesarch. 2015, March 4
• [Acknowledged], [Software] — RNA-Seq Analysis of Spatiotemporal Gene Expression Patterns During Fruit Development Revealed Reference Genes for Transcript Normalization in Plums. Kim et al. Plant Molecular Biology Reporter. 2015, February 28
• [Acknowledged] — Mitochondrial complex I deficiency leads to inflammation and retinal ganglion cell death in the Ndufs4 mouse. Yu et al. Human Molecular Genetics. 2015, 24 (10), February 4
• [Acknowledged] — Next-generation sequencing workflow for assembly of nonmodel mitogenomes exemplified with North Pacific albatrosses (Phoebastria spp.). Lounsberry et al. Molecular Ecology. 2015, 15 (4), January 13
• [Software] — The Ordospora colligata Genome: Evolution of Extreme Reduction in Microsporidia and Host-To-Parasite Horizontal Gene Transfer. Pombert et al. Mbio. 2015, 6(1), January 13
• [Acknowledged], [Software] — Quantitative Proteomics Reveals Dynamic Changes in the Plasma Membrane During Arabidopsis Immune Signaling. Elmore  et al. Molecular and Cellular Proteomics. 2012, 11(4), January 3

2014

• [Software]  — Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes. Davis-Richardson et al. Frontiers in Microbiology. 2014, 5, December 10
• [Software] —  Biofilm formation by virulent and non-virulent strains of Haemophilus parasuis. Bello-Ortí et al. Veterinary Research. 2014, 45(104), November 27
• [Software]  — Genome-wide transcriptional profiling of Botrytis cinerea genes targeting plant cell walls during infections of different hosts. Blanco-Ulate et al. Frontiers in Plant Science. 2014, 5, September 3
• [Software] — A Lack of Parasitic Reduction in the Obligate Parasitic Green Alga Helicosporidium. Pombert et al. PLOS Genetics. 2014, 10(5), May 8
• [Acknowledged] — Analysis of the Salivary Gland Transcriptome of Frankliniella occidentalis. Stafford-Banks et al. PLOS ONE. 2014, April 15
• [Software]  — Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing. Henry  et al. Plant Cell. 2014, 26(4), April 11
• [Software] — On Optimal Read Trimming in NGS and Its Complexity. Hedkte et al. Chapter in Algorithms for Computational Biology. 

2013

• [Co-authors] — Probing functional polymorphisms in the dengue vector, Aedes aegypti. Mariangela Bonizzoni, Monica Britton, Osvaldo Marinotti, William Augustine Dunn, Joseph Fass and Anthony A James. BMC Genomics. 2013, 14(739), October 29
• [Acknowledged] — RNA-Seq Analysis Identifies a Novel Set of Editing Substrates for Human ADAR2 Present in Saccharomyces cerevisiae. Eifler et al. Biochemistry. 2013, 52(45), October 31
• [Acknowledged] — Gene Regulatory Networks Elucidating Huanglongbing Disease Mechanisms. Martinelli et al. PLOS ONE. 2013, 8(9), September 25
• [Co-authors] — Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes. Kanthaswamy S, Ng J, Ross CT, Trask JS, Smith DG, Buffalo VS, Fass JN, Lin D. Genomics. 2013 Jan;101(1):30-7. doi: 10.1016/j.ygeno.2012.09.001. Epub 2012 Sep 12. PMID:22982528 | PMCID:PMC3534948
• [Acknowledged] — The Influence of Gene Flow on Species Tree Estimation: A Simulation Study. Leaché et al. Systematic Biology. 2013, 63(1), August 13
• [Software] — Replication protein A subunit 3 and the iron efficiency response in soybean. Atwood et al. Plant, Cell, and Environment. 2013, 37(1), July 22
• [Software] — Gene Content and Diversity of the Loci Encoding Biosynthesis of Capsular Polysaccharides of the 15 Serovar Reference Strains of Haemophilus parasuis. Howell et al. Journal of Bacteriology. 2013, 195(18), July 19
• [Acknowledged] — Identification of SNPs in Closely Related Temperate Japonica Rice Cultivars Using Restriction Enzyme-Phased Sequencing. Kim and Tai. PLOS ONE. 2013, 8(3), March 26
• [Software] — High resolution genotyping by restriction enzyme-phased sequencing of advanced backcross lines of rice exhibiting differential cold stress recovery. Kim and Tai. Euphytica. 2013, 192(1), March 6
• [Co-authors] — Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Keith R. Bradnam, Joseph N. Fass, et al. Genome Research 2013, 21 (12) PMID:23870653 | PMCID:PMC3844414
• [Software] — Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi. Pombert et al. Eukaryotic Cell. 2015, 12(4), January 4

2012

• [Co-authors] — Differentiating Inbred Mouse Strains from Each Other and Those with Single Gene Mutations Using Hair Proteomics. Robert H. Rice , Katie M. Bradshaw, Blythe P. Durbin-Johnson, David M. Rocke, Richard A. Eigenheer, Brett S. Phinney, John P. Sundberg. PLOS ONE. 2012, December 14
• [Acknowledged]  — De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes. Ashrafi et al. BMC Genomics. 2012, 13, October 30
• [Acknowledged] — Induced Pluripotency and Oncogenic Transformation Are Related Processes. Riggs et al. Stem Cells and Development. 2012, 22(1), October 26
• [Co-authors] — Multiple clonal MLL fusions in a patient receiving CHOP-based chemotherapy. Shih SJ, Fass J, Buffalo V, Lin D, Singh SP, Diaz MO, Vaughan AT.  Br J Haematol. 2012 Oct;159(1):50-7. doi: 10.1111/j.1365-2141.2012.09248.x. Epub 2012 Jul 30.  PMID:22845170 | PMCID:PMC3444640
• [Co-authors] — Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms. You FM, Deal KR, Wang J, Britton MT, Fass JN, Lin D, Dandekar AM, Leslie CA, Aradhya M, Luo MC, Dvorak J. BMC Genomics. 2012 Jul 31;13:354. doi: 10.1186/1471-2164-13-354. PMID:22849334 | PMCID:PMC3527177
• [Co-authors] — High density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.). Pedro J. Martínez-García , Dan E. Parfitt, Ebenezer A. Ogundiwin, Joseph Fass, Helen M. Chan, Riaz Ahmad, Susan Lurie, Abhaya Dandekar, Thomas M. Gradziel, Carlos H. Crisosto. Tree Genetics & Genomes. 2012, 9(1), June 24
• [Co-authors] — Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing. Monson-Miller J, Sanchez-Mendez DC, Fass J, Henry IM, Tai TH, Comai L.  BMC Genomics. 2012 February 14;13:72. doi: 10.1186/1471-2164-13-72.  PMID:22333298 | PMCID:PMC3305632
• [Co-authors] — Transcriptome profiling of citrus fruit response to huanglongbing disease. Martinelli F, Uratsu SL, Albrecht U, Reagan RL, Phu ML, Britton M, Buffalo V, Fass J, Leicht E, Zhao W, Lin D, D’Souza R, Davis CE, Bowman KD, Dandekar AM.   PLoS One. 2012;7(5):e38039. doi: 10.1371/journal.pone.0038039. Epub 2012 May 31. PMID:22675433 | PMCID:PMC3364978
• [Acknowledged] — Case Study of Sequence Capture Enrichment Technology: Identification of Variation Underpinning Developmental Syndromes in an Amniote Model. Robb and Delaney. Genes. 2012, 3(2), March 26

2011

• [Co-authors] — Assemblathon 1: a competitive assessment of de novo short read assembly methods. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, et al.    Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16. PMID:21926179 | PMCID:PMC3227110
• [Co-authors] —Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection. Ahmad R, Parfitt DE, Fass J, Ogundiwin E, Dhingra A, Gradziel TM, Lin D, Joshi NA, Martinez-Garcia PJ, Crisosto CH.   BMC Genomics. 2011 Nov 22;12:569. doi: 10.1186/1471-2164-12-569. PMID:22108025 | PMCID:PMC3253712
• [Co-authors] — Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila. Fass JN, Joshi NA, Couvillion MT, Bowen J, Gorovsky MA, Hamilton EP, Orias E, Hong K, Coyne RS, Eisen JA, Chalker DL, Lin D, Collins K.  G3 (Bethesda). 2011 Nov;1(6):515-22. doi: 10.1534/g3.111.000927. Epub 2011 Nov 1. PMID:22384362 | PMCID:PMC3276166
• [Co-authors] — Exploring the Transcriptome Landscape of Pomegranate Fruit Peel for Natural Product Biosynthetic Gene and SSR Marker Discovery. Ono NN, Britton MT, Fass JN, Nicolet CM, Lin D, Tian L.   J Integr Plant Biol. 2011 Sep 12. doi: 10.1111/j.1744-7909.2011.01073.x. [Epub ahead of print]  PMID:21910825
• [Co-authors] — Discovery of rare mutations in populations: TILLING by sequencing. Tsai H, Howell T, Nitcher R, Missirian V, Watson B, Ngo KJ, Lieberman M, Fass J, Uauy C, Tran RK, Khan AA, Filkov V, Tai TH, Dubcovsky J, Comai L. Plant Physiol. 2011 Jul;156(3):1257-68. doi: 10.1104/pp.110.169748. Epub 2011 Apr 29. PMID:21531898 | PMCID:PMC3135940

2010

• [Co-authors] — A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development. Katz E, Fon M, Eigenheer RA, Phinney BS, Fass JN, Lin D, Sadka A, Blumwald E.   Proteome Sci. 2010 Dec 16;8:68. doi: 10.1186/1477-5956-8-68.  PMID:21162737 | PMCID:PMC3017515
• [Co-authors] — Mitochondrial DNA variant discovery and evaluation in human Cardiomyopathies through next-generation sequencing. Zaragoza MV, Fass J, Diegoli M, Lin D, Arbustini E.    PLoS One. 2010 Aug 20;5(8):e12295. doi: 10.1371/journal.pone.0012295.  PMID:20808834 | PMCID:PMC2924892
• [Co-authors] — Analysis of early host responses for asymptomatic disease detection and management of specialty crops. Dandekar AM, Martinelli F, Davis CE, Bhushan A, Zhao W, Fiehn O, Skogerson K, Wohlgemuth G, D’Souza R, Roy S, Reagan RL, Lin D, Cary R, Pardington P, Gupta G. Crit Rev Immunol. 2010;30(3):277-89. Review. PMID:20370635

2008

• [Co-authors] — Functional consequences of overexpressing the gap junction Cx43 in the cardiogenic potential of pluripotent human embryonic stem cells. Moore JC, Tsang SY, Rushing SN, Lin D, Tse HF, Chan CW, Li RA. Biochem Biophys Res Commun. 2008 Dec 5;377(1):46-51. doi: 10.1016/j.bbrc.2008.09.076. Epub 2008 Sep 25. PMID: 18823947