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  1. Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle. (accepted). DL Taylor*, LJ Scott*, AU Jackson, N Narisu, G Hemani, MR Erdos, PS Chines, A Swift, J Idol, JP Didion, RP Welch, L Kinnunen, J Saramies, TA Lakka, M Laakso, J Tuomilehto, SCJ Parker, HA Koistinen, GD Smith, M Boehnke, E Birney*, FS Collins*; PNAS
  2. Genomic annotation of disease-associated variants reveals shared functional contexts. (2019). Y Kyono, JO Kitzman*, SCJ Parker*; Diabetologia [DOI]
  3. Multiomic profiling identifies cis-regulatory networks underlying human pancreatic β cell identity and function. (2019). N Lawlor, EJ Márquez, P Orchard, N Narisu, MS Shamim, A Thibodeau, A Varshney, R Kursawe, MR Erdos, M Kanke, H Gu, E Pak, A Dutra, S Russell, X Li, E Piecuch, O Luo, PS Chines, C Fuchbserger, NIH Intramural Sequencing Center, P Sethupathy, AP Aiden, Y Ruan, EL Aiden, FS Collins, D Ucar, SCJ Parker*, and ML Stitzel*; Cell Reports [DOI]
  4. Cell specificity of human regulatory annotations and their genetic effects on gene expression. (2019). A Varshney, H VanRenterghem, P Orchard, AP Boyle*, ML Stitzel*, D Ucar*, SCJ Parker; Genetics [DOI]
  5. Genome-wide chromatin accessibility and transcriptome profiling show minimal epigenome changes and coordinated transcriptional dysregulation of hedgehog signaling in Danforth’s short tail mice. (2018). P Orchard*, JS White*, PE Thomas*, A Mychalowych, A Kiseleva, J Hensley, B Allen, SCJ Parker*, CE Keegan*; Human Molecular Genetics [DOI]
  6. BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues. (2018). LS Zou, MR Erdos, DL Taylor, PS Chines, A Varshney, et al; BMC Genomics [DOI]
  7. YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU. (2018). D Quang, Y Guan, and SCJ Parker Bioinformatics [DOI]
  8. Global dynamics of stage-specific transcription factor binding during thymocyte development. (2018). T Hosoya*, R D’Oliveira Albanus*, J Hensley, G Myers, Y Kyono, J Kitzman, SCJ Parker, and JD Engel Scientific Reports [DOI]
  9. Interactions between genetic variation and cellular environment in skeletal muscle gene expression. (2018). DL Taylor, DA Knowles, LJ Scott, AH Ramirez, F Paolo Casale, BN Wolford, et al PLoS ONE [DOI]
  10. A Common Type 2 Diabetes Risk Variant Potentiates Activity of an Evolutionarily Conserved Islet Stretch Enhancer and Increases C2CD4A and C2CD4B Expression. (2018). I Kycia, BN Wolford, JR Huyghe, C Fuchsberger, S Vadlamudi, R Kursawe, et al American Journal of Human Genetics [DOI]
  11. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls. (2017). J Flannick, C Fuchsberger, A Mahajan, TM Teslovich, V Agarwala, KJ Gaulton, et al Scientific Data [DOI]
  12. A type 2 diabetes-associated functional regulatory variant in a pancreatic islet enhancer at the ADCY5 locus. (2017). TS Roman, ME Cannon, S Vadlamudi, ML Buchkovich, BN Wolford, RP Welch, et al Diabetes [DOI]
  13. Large meta-analysis of genome wide association studies identifies five loci for lean body mass. (2017). MC Zillikens, S Demissie, YH Hsu, LM Yerges-Armstrong, WC Chou, L Stolk, et al Nature Communications 8(1), 80 [DOI]
  14. Genetic regulatory signatures underlying islet gene expression and type 2 diabetes. (2017). A Varshney, LJ Scott, RP Welch, MR Erdos, PS Chines, N Narisu, et al Proceedings of the National Academy of Sciences [DOI]
  15. The genetic architecture of type 2 diabetes. (2016). C Fuchsberger, J Flannick, TM Teslovich, A Mahajan, V Agarwala, KJ Gaulton, et al Nature [DOI]
  16. The genetic regulatory signature of type 2 diabetes in human skeletal muscle. (2016). LJ Scott, MR Erdos, JR Huyghe, RP Welch, AT Beck, BN Wolford, et al Nature Communications 7, 11764 [DOI]
  17. Super Enhancers in Cancers, Complex Disease, and Developmental Disorders. (2015). AR Niederriter, A Varshney, SCJ Parker, DM Martin Genes 6 (4), 1183-1200 [DOI]
  18. Motif signatures in stretch enhancers are enriched for disease-associated genetic variants. (2015). DX Quang, MR Erdos, SCJ Parker, FS Collins Epigenetics & chromatin 8 (1), 1-14 [DOI]
  19. Super-enhancers delineate disease-associated regulatory nodes in T cells. (2015). G Vahedi, Y Kanno, Y Furumoto, K Jiang, SCJ Parker, MR Erdos, et al Nature 2015 [DOI]
  20. GBshape: a genome browser database for DNA shape annotations. (2015). TP Chiu, L Yang, T Zhou, BJ Main, SCJ Parker, SV Nuzhdin, TD Tullius, et al Nucleic acids research 43 (D1), D103-D109 [DOI] 6x
  21. Comparative analysis of metazoan chromatin organization.. Nature (2014), 449-452 [DOI] 33x
  22. Somatic mutations in MAP3K5 attenuate its proapoptotic function in melanoma through increased binding to thioredoxin. (2014). TD Prickett, B Zerlanko, JJ Gartner, SCJ Parker, K Dutton-Regester, et al Journal of Investigative Dermatology 134 (2), 452-460 [DOI]
  23. Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. (2013). SCJ Parker, ML Stitzel, DL Taylor, JM Orozco, MR Erdos, JA Akiyama, et al Proceedings of the National Academy of Sciences 110 (44), 17921-17926 [DOI] 59x
  24. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. (2013). JJ Gartner, SCJ Parker, TD Prickett, K Dutton-Regester, ML Stitzel, JC Lin, et al Proceedings of the National Academy of Sciences 110 (33), 13481-13486 [DOI] 34x
  25. Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes.. PLoS Genet 8 (8), e1002871 [DOI] 8x
  26. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.. PLoS Genet 8 (6), e1002789-e1002789 [DOI] 38x
  27. Somatic mutations in Pyk2 in melanoma alter protein activity, interactions and localization. (2012). MD Willard, IH Wulur, Y Samuels, TD Barber, J Gartner, SCJ Parker Cancer Research 72 (8 Supplement), 100-100 [DOI]
  28. An integrated encyclopedia of DNA elements in the human genome.. Nature 2012 2917x
  29. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. (2011). EP Bishop, R Rohs, SCJ Parker, SM West, P Liu, RS Mann, B Honig, et al ACS chemical biology 6 (12), 1314-1320 [DOI] 40x
  30. Accurate and comprehensive sequencing of personal genomes. (2011). SS Ajay, SCJ Parker, HO Abaan, KVF Fajardo, EH Margulies Genome research 21 (9), 1498-1505 [DOI] 92x
  31. A bioinformatics approach for determining sample identity from different lanes of high-throughput sequencing data. (2011). RL Goldfeder, SCJ Parker, SS Ajay, H Ozel Abaan, EH Margulies PloS one 6 (8) [DOI]
  32. DNA shape, genetic codes, and evolution. (2011). SCJ Parker, TD Tullius Current opinion in structural biology 21 (3), 342-347 [DOI] 22x
  33. A user's guide to the encyclopedia of DNA elements (ENCODE).. PLoS Biology 9 (4), e1001046 656x
  34. A Computational Method to Search for DNA Structural Motifs in Functional Genomic Elements. (2011). SCJ Parker, A Harlap, TD Tullius Yeast Systems Biology 367-379 [DOI]
  35. Evolutionary Constraint on DNA Shape in the Human Genome. (2011). TD Tullius, SCJ Parker, EH Margulies Evolutionary Biology–Concepts Biodiversity, Macroevolution and Genome ... [DOI]
  36. Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.. Cell metabolism 12 (5), 443-455 94x
  37. Human NPY promoter variation rs16147: T> C as a moderator of prefrontal NPY gene expression and negative affect. (2010). WH Sommer, J Lidström, H Sun, D Passer, R Eskay, SCJ Parker, SH Witt, et al Human mutation 31 (8), E1594-E1608 [DOI] 47x
  38. Family-based analysis of candidate genes for polycystic ovary syndrome.. The Journal of Clinical Endocrinology & Metabolism 95 (5), 2306-2315 75x
  39. Local DNA topography correlates with functional noncoding regions of the human genome. (2009). SCJ Parker, L Hansen, HO Abaan, TD Tullius, EH Margulies Science 324 (5925), 389-392 [DOI] 148x
  40. The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome. (2008). SCJ Parker, EH Margulies, TD Tullius Genome Informatics 20, 199-211 [DOI]
  41. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.. Nature 447 (7146), 799-816 [DOI] 3370x
  42. Detection of DNA structural motifs in functional genomic elements. (2007). JA Greenbaum, SCJ Parker, TD Tullius Genome research 17 (6), 940-946 [DOI] 29x
  43. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. (2006). AM Gustafson, ES Snitkin, SCJ Parker, C DeLisi, S Kasif Bmc Genomics 7 (1), 265 89x
  44. DNA sequence and analysis of human chromosome 8.. Nature 439, 331-335 [DOI] 79x
  45. Finishing the euchromatic sequence of the human genome.. Nature 431 (7011), 931-945 2707x
  46. Computational method for identification of functionally significant non-coding sequences: studies of Hox cluster organization. (2000). SCJ Parker, J daSilva, EJ Stellwag AMERICAN ZOOLOGIST 40 (6), 1164-1165
  47. HOX gene evolution among telosts.. AMERICAN ZOOLOGIST 39 (5), 14A-14A