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Publications

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Read about work that Cofactor has contributed to.

  1. HAND1 loss-of-function within the embryonic myocardium reveals survivable congenital cardiac defects and adult heart failure. Firulli BA, et al. Cardiovascular Research, 09 July 2019. https://doi.org/10.1093/cvr/cvz182
  2. Quantitative Genetic Mapping and Genome Assembly in the Lesser Wax Moth Achroia grisella. Koseva BS, et al. G3: GENES, GENOMES, GENETICS. 1 July 2019 vol. 9 no. 7 2349-2361; https://doi.org/10.1534/g3.119.400090
  3. Experimental Acute Exposure to Thirdhand Smoke and Changes in the Human Nasal Epithelial Transcriptome: A Randomized Clinical Trial. Pozuelos GL, Kagda MS, Schick S, Girke T, Volz DC, Talbot P. JAMA Netw Open. June 28, 20192(6):e196362. doi:10.1001/jamanetworkopen.2019.6362
  4. Comparative transcriptomic analysis of dermal wound healing reveals de novo skeletal muscle regeneration in Acomys cahirinus. Brant JO, Boatwright JL, Davenport R, Sandoval AGW, Maden M, Barbazuk WB. 29 May 2019. PLoS ONE 14(5): e0216228. https://doi.org/10.1371/journal.pone.0216228
  5. miR-301a promotes lung tumorigenesis by suppressing Runx3. Li et al. Molecular Cancer (2019) 18:99 23 May 2019. https://doi.org/10.1186/s12943-019-1024-0
  6. Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard. Migicovsky Z. et al. Horticulture Research volume 6, Article number: 64. 01 May 2019. https://doi.org/10.1038/s41438-019-0146-2
  7. Noninvasive Detection of High-risk Adenomas Using Stool-derived Eukaryotic RNA Sequences as Biomarkers. Barnell E, Kang Y, Wurtzler E, Griffith M, Chaudhuri AA, Griffith OL, Geneoscopy Scientists, Barnell A, Campbell K, Kruse KR, Gastroenterology (2019), doi: https:// doi.org/10.1053/j.gastro.2019.05.058
  8. Mce3R Stress-Resistance Pathway Is Vulnerable to Small-Molecule Targeting That Improves Tuberculosis Drug Activities. Yang X, et al. ACS Infect. Dis.2019571239-1251. 23 April 2019. https://doi.org/10.1021/acsinfecdis.9b00099
  9. RNA Sequencing Reveals Small and Variable Contributions of Infectious Agents to Transcriptomes of Postmortem Nervous Tissues From Amyotrophic Lateral Sclerosis, Alzheimer’s Disease and Parkinson’s Disease Subjects, and Increased Expression of Genes From DBennett JP, Kenney PM, Brohawn DG. Front. Neurosci., 28 March 2019 | https://doi.org/10.3389/fnins.2019.00235
  10. We have the tools to advance precision medicine, why are we using them? Messina DM. Clinical OMICS. Clinical OMICs. Mar 2019. Volume: 6 Issue 2: 27 March 2019. http://doi.org/10.1089/clinomi.06.02.19
  11. Alzheimer’s Disease Frontal Cortex Mitochondria Show a Loss of Individual Respiratory Proteins but Preservation of Respiratory Supercomplexes. Kenney PM, Bennett JP. International Journal of Alzheimer’s DiseaseVolume 2019, Article ID 4814783 https://doi.org/10.1155/2019/4814783
  12. Bacterial sepsis triggers an antiviral response that causes translation shutdown. Hato T, et al. J Clin Invest. 2 January 2019;129(1):296–309.https://doi.org/10.1172/JCI123284.
  13. Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model. Wang H, et al. Molecular Neurodegeneration. volume 13, Article number: 65. 17 December 2018. https://doi.org/10.1186/s13024-018-0296-y
  14. RNA-Seq Analyses of the Role of miR-21 in Acute Pancreatitis. Li X, et al. Cell Physiol Biochem 2018;51:2198-2211. 7 December 2018. https://doi.org/10.1159/000495866
  15. Precision Biomarkers and Medicines Go Global. Patricia Fitzpatrick Dimond. Genetic Engineering & Biotechnology News (GEN). Nov 2018. http://doi.org/10.1089/gen.38.19.02
  16. Genomic characterization reveals significant divergence within Chlorella sorokiniana(Chlorellales, Trebouxiophyceae). Hovde BT, et al. Algal Research Volume 35, November 2018, Pages 449-461 https://doi.org/10.1016/j.algal.2018.09.012
  17. Thyroid hormone influences brain gene expression programs and behaviors in later generations by altering germ line epigenetic information. Martinez ME, Duarte CW, Stohn JP, Karaczyn A, Wu Z, DeMambro VE, Hernandez A. Molecular Psychiatry24 October 2018. https://doi.org/10.1038/s41380-018-0281-4
  18. The apolipoprotein N-acyl transferase Lnt is dispensable for growth in Acinetobacter Gwin CM, Prakash N, Belisario JC, Haider L, Rosen ML, Martinez LR, Rigel NW. Microbiology. 11 October 2018, Microbiology 164: 1547-1556, doi: 10.1099/mic.0.000726
  19. Exposure to maternal obesity alters gene expression in the preimplantation ovine conceptus. McCoski SR, et al. BMC Genomics volume 19, Article number: 737. 11 October 2018. https://doi.org/10.1186/s12864-018-5120-0
  20. Determination of quantitative trait nucleotides by concordance analysis between quantitative trait loci and marker genotypes of US Holsteins. Weller JI, et al. Journal of Dairy Science Volume 101, Issue 10, October 2018, Pages 9089-9107. https://doi.org/10.3168/jds.2018-14816
  21. Rapid Divergence of Genome Architectures Following the Origin of an Ectomycorrhizal Symbiosis in the Genus Amanita. Hess J, et al. Molecular Biology and Evolution, Volume 35, Issue 11, 18 September 2018, Pages 2786–2804, https://doi.org/10.1093/molbev/msy179
  22. Phylogenomics of montane frogs of the Brazilian Atlantic Forest is consistent with isolation in sky islands followed by climatic stability.Pie MR, et al. Biological Journal of the Linnean Society, Volume 125, Issue 1, September 2018, Pages 72–82, https://doi.org/10.1093/biolinnean/bly093
  23. Next generation sequencing analysis of soy glyceollins and 17-β estradiol: Effects on transcript abundance in the female mouse brain. Bamji SF, Rouchka E, Zhang Y, Li X, Kalbfleisch T, Corbitt C. Molecular and Cellular Endocrinology. Volume 471, 15 August 2018, Pages 15-21. https://doi.org/10.1016/j.mce.2017.05.007
  24. Chemistry in a Multidisciplinary, Interdisciplinary World. Ober C, Garelick H. Chemistry International, Volume 40, Issue 3, Pages 7–10, 06 August 2018. DOI: https://doi.org/10.1515/ci-2018-0304.
  25. RNA-Sequencing Reveals Similarities and Differences in Gene Expression in Vulnerable Brain Tissues of Alzheimer’s and Parkinson’s Diseases. Bennett JP, Keeney PM.  Journal of Alzheimer’s Disease Reports, vol. 2, no. 1, pp. 129-137, 21 July 2018. DOI: 10.3233/ADR-180072
  26. Integrative Conjugative Element ICEHs1 Encodes for Antimicrobial Resistance and Metal Tolerance in Histophilus somni. Bhatt K, Timsit E, Rawlyk N, Potter A, Liljebjelk K. Front Vet Sci. 2018; 5: 153. 10 Jul 2018. doi: 10.3389/fvets.2018.00153
  27. Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus. Barreto FS, et al. Nature Ecology & Evolution volume 2,pages1250–1257. 09 July 2018. https://doi.org/10.1038/s41559-018-0588-1
  28. Wheat differential gene expression induced by different races of Puccinia triticina. Neugebauer KA, Bruce M, Todd T, Trick HN, Fellers JP (2018) PLoS ONE 13(6): e0198350. https://doi. org/10.1371/journal.pone.0198350
  29. Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells. Tunstall T, et al. Genome Res. 2018 Jun;28(6):780-788. doi: 10.1101/gr.227603.117. Epub 2018 May 24. DOI: 10.1101/gr.227603.117
  30. Global Transcriptome Analysis of Brown Adipose Tissue of Diet-Induced Obese Mice. Cao J, et al. J. Mol. Sci.6 April 2018, 19(4), 1095; https://doi.org/10.3390/ijms19041095
  31. Noninvasive neuromodulation in essential tremor demonstrates relief in a sham-controlled pilot trial.Lin PT, Ross EK, Chidester P, Rosenbluth KH, Hamner SR, Wong SH, Sanger TD, Hallett M, Delp SL. Mov Disord. 2018 Jul;33(7):1182-1183. doi: 10.1002/mds.27350. Epub 2018 Apr 17. PubMed PMID: 29663525; PubMed Central PMCID: PMC6174932.
  32. Bronchoalveolar lavage (BAL) cells in idiopathic pulmonary fibrosis express a complex pro-inflammatory, pro-repair, angiogenic activation pattern, likely associated with macrophage iron accumulation. Lee J, Arisi I, Puxeddu E, Mramba LK, Amicosante M, Swaisgood CM, Pallante M, Brantly ML, Skold M, Saltini C. PLoS One. 13(4): e0194803. 12 April 2018. https://doi.org/10.1371/journal.pone.0194803
  33. Influence of Intestinal Microbiota Transplantation and NleH Expression on Citrobacter rodentiumColonization of Mice. Wang G, Feuerbacher LA, Hardwidge PR. Pathogens. 2018 Mar 30;7(2). pii: E35. doi: 10.3390/pathogens7020035.
  34. Offspring sex impacts DNA methylation and gene expression in placentae from women with diabetes during pregnancy. Alexander J, Teague AM, Chen J, Aston CE, Leung Y-K, Chernausek S, et al. PLoS ONE 13(2): 22 February 2018. e0190698. https://doi.org/10.1371/journal.pone.0190698
  35. Genomic heterogeneity of ALKfusion breakpoints in non-small-cell lung cancer. Rosenbaum JN, et al. Modern Pathologyvolume31, pages 791–808. 12 January 2018.  https://doi.org/10.1038/modpathol.2017.181
  36. Micro RNA’s (miRNA’s) may help explain expression of multiple genes in Alzheimer’s Frontal Cortex. Bennett JP, Keeney PM. J Syst Integr Neurosci, 2017 Volume 3(5): 9-9 doi: 10.15761/JSIN.1000178
  37. The molecular basis for an ancient colour mutant in sweet pea (Lathyrus odoratus). Cronk QCB. Canadian Journal of Plant Science, 26 October 2017, 98(3): 591-600, https://doi.org/10.1139/cjps-2017-0238
  38. Divergence of the Venom Exogene Repertoire in Two Sister Species of Turriconus. Li Q, et al. Genome Biology and Evolution, Volume 9, Issue 9, September 2017, Pages 2211–2225, https://doi.org/10.1093/gbe/evx157
  39. MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts. Abernathy DG, et al. Cell Stem Cell Volume 21, Issue 3, 7 September 2017, Pages 332-348.e9. https://doi.org/10.1016/j.stem.2017.08.002
  40. Genome sequencing and comparative genomics reveal a repertoire of putative pathogenicity genes in chilli anthracnose fungus Colletotrichum truncatum. Rao S, Nandineni MR. PLoS One 12(8): e0183567. 28 August 2017. https://doi.org/10.1371/journal.pone.0183567
  41. A new strategy for aromatic ring alkylation in cylindrocyclophane biosynthesis. Nakamura H, Schultz EE, Balskus EP. Nature Chemical Biologyvol 13, pages916–921. 26 June 2017. https://doi.org/10.1038/nchembio.2421
  42. Tissue organization alters gene expression in equine induced trophectoderm cells. Reinholt BM, et al. General and Comparative Endocrinology. Volume 247, 1 June 2017, Pages 174-182. https://doi.org/10.1016/j.ygcen.2017.01.030
  43. β-Lactone formation during product release from a nonribosomal peptide synthetase. Schaffer JE, Reck MR, Prasad NK, Wencevicz TA. Nature Chemical Biologyvolume 13, pages 737–744. 15 May 2017. https://doi.org/10.1038/nchembio.2374
  44. DNA methylation assessment from human slow- and fast-twitch skeletal muscle fibers. Begue G, Raue U, Jemiolo B, Trappe S. Journal of Applied Physiology. Volume 122 Issue 4. 11 April 2017. Pages 952-967. https://doi.org/10.1152/japplphysiol.00867.2016
  45. Hormone-like peptides in the venoms of marine cone snails. Robinson SD, et al. General and Comparative Endocrinology Volume 244, 1 April 2017, Pages 11-18. https://doi.org/10.1016/j.ygcen.2015.07.012
  46. Microanalyte MDx Goes Mainstream. Philippe Desjardins. Genetic Engineering & Biotechnology News (GEN). Mar 2017. Volume: 37 Issue 6: March 15, 2017. http://doi.org/10.1089/gen.37.06.13
  47. The Larson Blue coat color phenotype in Holsteins: Characteristics and effects on body temperature regulation and production in lactating cows in a hot climate. Dikmen S, Dahl GE, Cole JB, Null DJ, Hansen PJ. Journal of Animal Science, Volume 95, Issue 3, March 2017, Pages 1164–1169,https://doi.org/10.2527/jas.2016.1148
  48. Stress-responsive pathways and small RNA changes distinguish variable developmental phenotypes caused by MSH1 loss. Shao MR, et al. BMC Plant Biology volume 17, Article number: 47. 20 February 2017.  https://doi.org/10.1186/s12870-017-0996-4
  49. Collagen synthesis disruption and downregulation of core elements of TGF-β, Hippo, and Wnt pathways in keratoconus corneas. Kabza M, et al. European Journal of Human Genetics 1 February 2017. 25, 582–590; doi:10.1038/ejhg.2017.4
  50. Identification of microsporidia host-exposed proteins reveals a repertoire of rapidly evolving proteins. Reinke AW, Balla KM, Bennett EJ, Troemel ER. Nature Communicationsvolume 8, Article number: 14023. 09 January 2017. https://doi.org/10.1038/ncomms14023
  51. Discovery of short linear motif‐mediated interactions through phage display of intrinsically disordered regions of the human proteome. Davey NE, et al. The FEBS Journal Volume 284, Issue 3. 21 December 2016. https://doi.org/10.1111/febs.13995
  52. Transcriptome discovery in non-model wild fish species for the development of quantitative transcript abundance assays. Hahn CM, et al. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics Volume 20, December 2016, Pages 27-40. https://doi.org/10.1016/j.cbd.2016.07.001
  53. The ubiquitin ligase CRL2ZYG11targets cyclin B1 for degradation in a conserved pathway that facilitates mitotic slippage. Balachandran RS, et al. The Journal of Cell Biology Oct 2016, 215 (2) 151-166; DOI: 10.1083/jcb.201601083
  54. Pharmacological properties of microneurotrophin drugs developed for treatment of amyotrophic lateral sclerosis. Bennett JP, O’Brien LC, Brohawn DG. Biochemical Pharmacology. Volume 117, 1 October 2016, Pages 68-77 https://doi.org/10.1016/j.bcp.2016.08.001
  55. DNMT3A-Dependent DNA Methylation May Act As a Tumor Suppressor-Not a Tumor Promoter-during AML Progression. Spencer D, Russler-Germain D, Helton NM, Lamprecht TL, Shinawi, M, Westervelt P, Payton JE, Fulton RS, Wilson RK, Walter MJ, Link DC, DiPersio JF, & Ley TJ. (2016).  Blood,128(22), 1050.
  56. Cattle Immunized with a Recombinant Subunit Vaccine Formulation Exhibits a Trend towards Protection against Histophilus somniBacterial Challenge. Madampage CA, Wilson D, Townsend H, Crockford G, Rawlyk N, Dent D, et al. 8 August 2016. PLoS ONE 11(8): e0159070. https://doi.org/10.1371/journal.pone.0159070
  57. RNAseq Analyses Identify Tumor Necrosis Factor-Mediated Inflammation as a Major Abnormality in ALS Spinal Cord. Brohawn DG, O’Brien LC, Bennett JP Jr (2016) PLoS ONE 11(8): e0160520. https://doi.org/10.1371/journal.pone.0160520
  58. Transcriptome Discovery in Non-Model Wild Fish Species for the Development of Quantitative Transcript Abundance Assays. Hahn CM, Lwanowicz LR, Comman RS, Mazik PM, Blazer VS. Comp Biochem and Phys Part D: Genomics and Proteomics. ePub 12 July 2016. doi:10.1016/j.cbd.2016.07.001
  59. Transcriptome differences in the rumen of beef steers with variation in feed intake and gain. Kern RJ, et al. Gene. Volume 586, Issue 1, 15 July 2016, Pages 12-26. https://doi.org/10.1016/j.gene.2016.03.034
  60. Identification of microsporidia host-exposed proteins reveals a repertoire of large paralogous gene families and rapidly evolving proteins. Reinke AW, Balla KM, Bennett EJ, Troemel ER. bioRxiv 3 June 2016. doi: http://dx.doi.org/10.1101/056788
  61. D27 MACROPHAGES: RESOLVERS, RESPONDERS OR BOTH?: Alveolar Macrophage Activation Pattern In Idiopathic Pulmonary Fibrosis (ipf): Bronchoalveolar Lavage (bal) Transcriptome Analysis. Swaisgood, C M; Arisi, I; Mariani, F; Puxeddu, E; Amicosante, M; et al. American Journal of Respiratory and Critical Care Medicine; New York 193, (2016): 1.
  62. Comparative and Transcriptome Analyses Uncover Key Aspects of Coding- and Long Noncoding RNAs in Flatworm Mitochondrial Genomes. Ross E, Blair DGuerrero-Hernández CSánchez Alvarado A. G3 (Bethesda).2016 May 3;6(5):1191-200. doi: 10.1534/g3.116.028175.
  63. The complete mitochondrial genome of black-footed ferret, Mustela nigripes (Mustela, Mustelinae). Zhao RB, Zhou CY, Lu ZX, Hu P, Liu, JQ, Tan WW, Yang Mitochondrial DNA A DNA MappSeq Anal.2016 May;27(3):1595-6. doi: 10.3109/19401736.2014.958685
  64. Transcriptome-wide patterns of divergence during allopatric evolution. Pereira RJBarreto FSPierce NTCarneiro MBurton RS. Mol Ecol.2016 Apr;25(7):1478-93. doi: 10.1111/mec.13579. Epub 2016 Mar 15.
  65. Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies(Diopsidae). Baker RHNarechania ADeSalle RJohns PMReinhardt JAWilkinson GS. Genome Biol Evol.2016 Mar 26;8(3):896-914. doi: 10.1093/gbe/evw043.
  66. Systemic Reprogramming of Translation Efficiencies on Oxygen Stimulus. Ho JJ, Wang M, Audas TE, Kwon D, Carlsson SK, Timpano S, Evagelou SL, Brothers S, Gonzalgo ML, Krieger JR, Chen S, Uniacke J, Lee S. Cell Rep. 2016 Feb 16;14(6):1293-300. doi: 10.1016/j.celrep.2016.01.036.
  67. A large microRNA cluster on chromosome 19 is a transcriptional hallmark of WHO type A and AB thymomas. Radovich M, Solzak JP, Hancock BA, Conces ML, Atale R, Porter RF, Zhu J, Glasscock J, Kesler KA, Badve SS, Schneider BP, Loehrer PJ. British Journal of Cancer. 2016 Feb 16;114(4):477-84. doi: 10.1038/bjc.2015.425
  68. Comparative Genomic Analysis of Mannheimia haemolyticafrom Bovine Sources. Klima CLCook SRZaheer RLaing CGannon VPXu YRasmussen JPotter AHendrick SAlexander TWMcAllister TA. PLoS One.2016 Feb 29;11(2):e0149520. doi: 10.1371/journal.pone.0149520
  69. A novel gastrointestinal microbiome modulator from soy pods reduces absorption of dietary fat in mice. Boue S, Fortgang I, Levy RJ Jr, Bhatnager D, Burow M, Fahey G, Heiman ML. Obesity (Silver Spring). 2016 Jan;24(1):87-95. doi: 10.1002/oby.21197
  70. Using RNA Sequencing and In Silico Subtraction to Identify Resistance Gene Analog Markers for Lr16 in Wheat. Harrison NR, Fritz AK, Glasscock JI, Ahmed S, Messina DN, St. Amand P, Fellers JP. 2015 Plant Genome 8. doi:10.3835/plantgenome2014.08.0040
  71. Reverse vaccinology as an approach for developing Histophilus somni vaccine candidates. Madampage CA, Rawlyk N, Crockford G, Wang Y, White AP, Brownlie R, Van Donkersgoed J, Dorin C, Potter A. 2015 Nov;43(6):444-51. doi: 10.1016/j.biologicals.2015.09.001.
  72. Fungal endophyte infection of ryegrass reprograms host metabolism and alters development. Dupont PYEaton CJWargent JJFechtner SSolomon PSchmid JDay RCScott BCox MP. New Phytol.2015 Dec;208(4):1227-40. doi: 10.1111/nph.13614.
  73. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Boothby TCTenlen JRSmith FWWang JRPatanella KANishimura EOTintori SCLi QJones CDYandell MMessina DNGlasscock J, Goldstein B. Proc Natl Acad Sci U S A.2015 Dec 29;112(52):15976-81. doi: 10.1073/pnas.1510461112.
  74. Hormone-like peptides in the venoms of marine cone snails. Robinson SD, Li Q, Bandyopadhyay PK, Gajewiak J, Yandell M, Papenfuss AT, Purcell AW, Norton RS, Safavi-Hemami H. Gen Comp Endocrinol. 2015 Aug 22. pii: S0016-6480(15)00214-2. doi: 10.1016/j.ygcen.2015.07.012.10.1016/j.ygcen.2015.07.012.
  75. Single nucleotide polymorphisms in the bovine Histophilus somni genome; a comparison of new and oldisolates. Madampage CA, Rawlyk N, Crockford G, Van Donkersgoed J, Dorin C, Potter A. Can J Vet Res. 2015 Jul;79(3):190-200.
  76. Characterization of the nocardiopsin biosynthetic gene cluster reveals similarities to and differences from therapamycin and FK-506 pathways. Bis DM, Ban YH, James ED, Alqahtani N, Viswanathan R, Lane AL. Chembiochem. 2015 Apr 13;16(6):990-7. doi: 10.1002/cbic.201500007.
  77. RNA-seq reveals regional differences in transcriptome response to heat stress in the marine snail Chlorostoma funebralis Gleason LU and Burton RS. 2015. Mol Ecol, 24: 610–627. doi:10.1111/mec.13047
  78. Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns. Esteban DJ, Hysa B, Bartow-McKenney C. PLoS One. 2015 Aug 6;10(8):e0134588. doi: 10.1371/journal.pone.0134588..
  79. A core gene set describes the molecular basis of mutualism and antagonism in Epichloe. Eaton CJ, et al. Mol Plant Microbe Interact. 2015 Mar;28(3):218-31. doi: 10.1094/MPMI-09-14-0293-FI.
  80. The Triboliumm castaneum cell line TcA: a new tool kit for cell biology. Silver K, et al. Sci Rep. 2014 Oct 30;4:6840. doi: 10.1038/srep06840.
  81. RNA-sequencing analysis of Trichophyton rubrum transcriptome in response to sublethal doses of acriflavine. Persinoti GF, et al. BMC Genomics 2014, 15(Suppl 7):S1  doi:10.1186/1471-2164-15-S7-S1
  82. Divergence with gene flow in a population of thermophilic bacteria: a potential role for spatially varying selection. Wall CA, Koniges GJ, Miller SR. Molecular Ecology, 23: 3371–3383. doi: 10.1111/mec.12812
  83. Discovery of the lomaiviticin biosynthetic gene cluster in Salinispora pacifica. Janso JE, et al. Tetrahedron Volume 70, Issues 27–28, 8 July 2014, Pages 4156–4164. doi:10.1016/j.tet.2014.03.009
  84. Meiotic Drive Impacts Expression and Evolution of X-Linked Genes in Stalk-Eyed Flies. Reinhardt, JA, et al. PLoS Genet. 2014 May 15;10(5):e1004362. doi: 10.1371/journal.pgen.1004362.
  85. Prophage Induction and Differential RecA and UmuDAb Transcriptome Regulation in the DNA Damage Responses of Acinetobacter baumannii and Acinetobacter baylyi. Hare JM. PLoS One. 2014 Apr 7;9(4):e93861. doi: 10.1371/journal.pone.0093861
  86. Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3. McClure M, et al. PLoS One. 2014 Mar 25;9(3):e92769. doi: 10.1371/journal.pone.0092769. eCollection 2014.
  87. Characterizing the heterogeneity of triple-negative breast cancers using microdissected normal ductal epithelium and RNA-sequencing. Radovich M, et al. Breast Cancer Research and Treatment. January 2014, Volume 143, Issue 1, pp 57-68. DOI: 10.1007/s10549-013-2780-y
  88. In vivo determination of direct targets of the nonsense-mediated decay pathway in Drosophila. Chapin A. et al. G3 (Bethesda). 2014 Mar 20;4(3):485-96. doi: 10.1534/g3.113.009357.
  89. Prokaryotes: Draft Genome Sequences of Two Alginate-Overproducing Variants of Pseudomonas aeruginosa, PAO1-VE2 and PAO1-VE13 Yeshi Yin, T. Ryan Withers, Richard M. Niles, Shannon L. Johnson, and Yu, HD. Genome Announc. November/December 2013 1:e01031-13; doi:10.1128/genomeA.01031-13
  90. Transposon fingerprinting using low coverage whole genome shotgun sequencing in Cacao (Theobroma cacao L.) and related species. Sveinsson S, Gill N, Kane NC, Cronk Q. BMC Genomics. 2013 Jul 24;14:502. doi: 10.1186/1471-2164-14-502
  91. Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem. Brown SP, Callaham MA, Oliver AK, Jumpponen A. FEMS Microbiol Ecol. 2013 Jul 19. doi: 10.1111/1574-6941.12181.
  92. Characterization of the Burkholderia thailandensis SOS response using whole transcriptome shotgun sequencing. Ulrich RL, Deshazer D, Kenny TA, Ulrich MP, Moravusova A, Opperman T, Bavari S, Bowlin TL, Moir DT, Panchal RG. Appl Environ Microbiol. 2013 Jul 19.
  93. Identification of purple sea urchin telomerase RNA using a next-generation sequencing based approach. Li Y, Podlevsky JD, Marz M, Qi X, Hoffmann S, Stadler PF, Chen JJ. 2013 Jun;19(6):852-60. doi: 10.1261/rna.039131.113.
  94. Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans. Tamayo JV, Gujar M, Macdonald SJ, Lundquist EA. BMC Genomics. 2013 May 4;14:304. doi: 10.1186/1471-2164-14-304.
  95. Draft Genome Sequence of a Mannheimia haemolytica Serotype 6 Isolate Collected from the Nasopharynx of a Beef Calf with Bovine Respiratory Disease. Klima CL, Cook SR, Hahn KR, Amoako KK, Alexander TW, Hendrick S, McAllister TA. Genome Announc. 2013 Apr 4;1(2):e0005113. doi: 10.1128/genomeA.00051-13.
  96. Alternative strategies for development of a reference transcriptome for quantification of allele specific expression in organisms having sparse genomic resources Shen Y, Garcia T, Pabuwal V, Boswell M, Pasquali A, Beldorth I, Warren W, Schartl M, Cresko WA, Walter RB. Comp Biochem Physiol Part D Genomics Proteomics. 2013 Mar;8(1):11-6. doi: 10.1016/j.cbd.2012.10.006.
  97. The common ancestral core of vertebrate and fungal telomerase RNAs. Qi X, Li Y, Honda S, Hoffmann S, Marz M, Mosig A, Podlevsky JD, Stadler PF, Selker EU, Chen JJ. Nucleic Acids Res. 2013 Jan 7;41(1):450-62. doi: 10.1093/nar/gks980.
  98. Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus. Ogura A, Yoshida MA, Moritaki T, Okuda Y, Sese J, Shimizu KK, Sousounis K, Tsonis PA. Sci Rep. 2013;3:1432. doi: 10.1038/srep01432.
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