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* denotes equal contribution.

  1. Genetic demultiplexing and transcript start site identification from nanopore sequencing of 10x Genomics multiome libraries.
    (2026). J Mears, P Orchard, A Varshney, M Bose, CC Robertson, M Piper, E Pashos, V Dolgachev, N Manickam, P Jean, DW Kitzman, EB Fauman, F Damilano, RJ Roth Flach, B Nicklas, SCJ Parker
    bioRxiv. [bioRxiv DOI]
  2. Donor-matched iPSC model reveals context-dependent T2D genetic signals in fibro-adipogenic progenitors.
    (2026). C Ventresca, A Varshney, P Orchard, HTH Vu, Y Tsan, A Monteiro da Rocha, MR Erdos, L Kinnunen, TA Lakka, J Saramies, M Laakso, J Tuomilehto, K Mohlke, M Boehnke, LJ Scott, HA Koistinen, FS Collins, T Herron, S Bielas, SCJ Parker
    bioRxiv. [bioRxiv DOI]
  3. Genome writing and targeted delivery of the NKX6-3/ANK1 gene cluster and its type 2 diabetes GWAS variants to human iPSCs.
    (2026). N Chalhoub, A Varshney, W Zhang, S Uhl, JM Laurent, C McLoughlin, H Ashe, N Dale, X Mou, K Ramnarine, J Goldberg, D Paull, MT Maurano, R Brosh, D Fenyö, F Cipriani, SCJ Parker, JD Boeke
    bioRxiv. [bioRxiv DOI]
  4. RFX6 expression is central to the development and function of the neuroendocrine compartments of the pancreas and intestine and strongly affects diabetes risk.
    (2026). TSR Bate, Y Huang, X Luo, DC Saunders, JT Walker, V Rai, SCJ Parker, J Liu, M Brissova
    Diabetology International. [DOI]
  5. Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context-specific genetic regulation.
    (2026). A Varshney, N Manickam, P Orchard, A Tovar, Z Zhang, F Feng, MR Erdos, N Narisu, C Ventresca, K Nishino, V Rai, HM Stringham, AU Jackson, T Tamsen, C Gao, M Yang, OI Koues, JD Welch, CF Burant, LK Williams, C Jenkinson, RA DeFronzo, L Norton, J Saramies, TA Lakka, M Laakso, J Tuomilehto, KL Mohlke, JO Kitzman, HA Koistinen, J Liu, M Boehnke, FS Collins, LJ Scott, SCJ Parker
    Nature Genetics (accepted, in press). [bioRxiv DOI]
  6. Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions.
    (2026). A Tovar, Y Kyono, K Nishino, M Bose, A Varshney, SCJ Parker*, JO Kitzman*
    HGG Advances. [PubMed]
  7. Combining functional annotation and multi-trait fine-mapping methods improves fine-mapping resolution at glycaemic trait loci.
    (2026). J Soenksen, J Chen, A Varshney, S Martin, MAGIC Consortium, SCJ Parker, AP Morris, JL Asimit, I Barroso
    Human Molecular Genetics. [PubMed]
  8. Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed.
    (2025). P Orchard, TW Blackwell, L Kachuri, PJ Castaldi, MH Cho, SA Christenson, P Durda, S Gabriel, CP Hersh, S Huntsman, S Hwang, R Joehanes, M Johnson, X Li, H Lin, CT Liu, Y Liu, ACY Mak, AW Manichaikul, D Paik, A Saferali, JD Smith, KD Taylor, RP Tracy, J Wang, M Wang, JS Weinstock, J Weiss, HE Wheeler, Y Zhou, S Zoellner, JC Wu, L Mestroni, S Graw, MRG Taylor, VE Ortega, CW Johnson, W Gan, G Abecasis, DA Nickerson, N Gupta, K Ardlie, PG Woodruff, Y Zheng, RP Bowler, DA Meyers, A Reiner, C Kooperberg, E Ziv, VS Ramachandran, MG Larson, LA Cupples, EG Burchard, EK Silverman, SS Rich, N Heard-Costa, H Tang, JI Rotter, AV Smith, D Levy, NHLBI TOPMed Consortium Multi-Omics Working Group, NHLBI TOPMed Consortium, F Aguet*, L Scott*, LM Raffield*, SCJ Parker*
    medRxiv (accepted at Science). [medRxiv DOI]
  9. Opposite directions of association of higher physical activity and higher insulin resistance with human skeletal muscle cell type abundance and fiber-type-level gene expression.
    (2025). DL Ciotlos, SC Hanks, A Varshney, MR Erdos, N Manickam, HM Stringham, P Orchard, EM Hill-Burns, N Narisu, LL Bonnycastle, MD Sweeney, J Saramies, M Laakso, J Tuomilehto, TA Lakka, KL Mohlke, M Boehnke, FS Collins, HA Koistinen, SCJ Parker, LJ Scott
    bioRxiv. [bioRxiv DOI]
  10. Massively parallel reporter assay reveals promoter-, position-, and strand-specific effects in transcription start sites.
    (2025). M Bose*, A Tovar*, Y Kyono, A Varshney, JO Kitzman*, SCJ Parker*
    bioRxiv. [bioRxiv DOI]
  11. Integrative multi-omics uncovers skeletal muscle enhancer programming of cardiorespiratory fitness.
    (2025). AM Weitzel, P Orchard, CR Evans, N Manickam, MK Treutelaar, SL Britton, LG Koch, JZ Li, SCJ Parker*, CF Burant*
    bioRxiv. [bioRxiv DOI]
  12. Genetic integration with cell-specific nucleosome positioning resolves causal relationships underlying chromatin accessibility profiles.
    (2025). X Wang, CC Robertson, A Varshney, N Manickam, P Orchard, M Laakso, J Tuomilehto, TA Lakka, KL Mohlke, M Boehnke, LJ Scott, HA Koistinen, FS Collins, SCJ Parker
    bioRxiv. [bioRxiv DOI]
  13. Skeletal muscle eQTL meta-analysis implicates genes in the genetic architecture of muscular and cardiometabolic traits.
    (2025). EP Wilson, KA Broadaway, VA Parsons, S Vadlamudi, N Narisu, SM Brotman, KW Currin, HM Stringham, MR Erdos, R Welch, JK Holtzman, TA Lakka, M Laakso, J Tuomilehto, M Boehnke, HA Koistinen, FS Collins, SCJ Parker, LJ Scott, KL Mohlke
    American Journal of Human Genetics. [PubMed]
  14. Extensive differential gene expression and regulation by sex in human skeletal muscle.
    (2025). SC Hanks, AS Mauger, A Varshney, DL Ciotlos, N Manickam, N Narisu, AJ Shumway, P Orchard, MR Erdos, M Sweeney, J Okamoto, AU Jackson, HM Stringham, LL Bonnycastle, X Zhou, TA Lakka, KL Mohlke, J Tuomilehto, M Laakso, M Boehnke, P Sethupathy, FS Collins, HA Koistinen, SCJ Parker, LJ Scott
    Cell Genomics. [PubMed]
  15. Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits.
    (2025). KW Currin, HJ Perrin, GK Pandey, AA Alkhawaja, S Vadlamudi, AE Musser, AS Etheridge, KA Broadaway, JD Rosen, A Varshney, AS Chaudhry, PJ Gallins, FA Wright, YH Zhou, SCJ Parker, LM Raffield, EG Schuetz, F Innocenti, KL Mohlke
    Genome Research. [PubMed]
  16. Accelerating Medicines Partnership in type 2 diabetes and common metabolic diseases: collaborating to maximize the value of genetic and genomic data.
    (2025). MC Costanzo, B Akolkar, M Claussnitzer, JC Florez, AL Gloyn, SFA Grant, KH Kaestner, AK Manning, KL Mohlke, SCJ Parker, PM Titchenell, MS Udler, MA Jones, TN Kamphaus, RA Fischer, MI McCarthy, MR Miller, M Boehnke, AMP T2D Consortium, AMP CMD Consortium, J Flannick, NP Burtt
    Diabetes. [PubMed]
  17. Genomic and phenotypic correlates of mosaic loss of chromosome Y in blood.
    (2025). YA Jakubek, X Ma, AM Stilp, F Yu, J Bacon, JW Wong, F Aguet, K Ardlie, DK Arnett, KC Barnes, JC Bis, TW Blackwell, LC Becker, E Boerwinkle, RP Bowler, MJ Budoff, AP Carson, J Chen, MH Cho, J Coresh, N Cox, PS de Vries, DL DeMeo, DW Fardo, M Fornage, X Guo, ME Hall, N Heard-Costa, B Hidalgo, MR Irvin, AD Johnson, E Jorgenson, EE Kenny, MD Kessler, D Levy, Y Li, JAC Lima, Y Liu, AE Locke, RJF Loos, MJ Machiela, RA Mathias, BD Mitchell, J Murabito, JC Mychaleckyj, K North, P Orchard, SCJ Parker, Y Pershad, PA Peyser, KA Pratte, BM Psaty, LM Raffield, S Redline, SS Rich, JI Rotter, SJ Shah, JA Smith, AP Smith, A Smith, M Taub, HK Tiwari, R Tracy, B Tuftin, AG Bick, VG Sankaran, AP Reiner, P Scheet, PL Auer
    American Journal of Human Genetics. [PubMed]
  18. Adipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits.
    (2025). SM Brotman, JS El-Sayed Moustafa, L Guan, KA Broadaway, D Wang, AU Jackson, R Welch, KW Currin, M Tomlinson, S Vadlamudi, HM Stringham, AL Roberts, TA Lakka, A Oravilahti, L Fernandes Silva, N Narisu, MR Erdos, T Yan, LL Bonnycastle, CK Raulerson, Y Raza, X Yan, SCJ Parker, J Kuusisto, P Pajukanta, J Tuomilehto, FS Collins, M Boehnke, MI Love, HA Koistinen, M Laakso, KL Mohlke*, KS Small*, LJ Scott*
    Nature Genetics. [PubMed]
  19. CelLink: integrating single-cell multi-omics data with weak feature linkage and imbalanced cell populations.
    (2025). X Luo, Y Huang, H Zeng, Y Tao, X Bao, F Feng, AL Hopkirk, T Pham, TSR Bate, DC Saunders, P Orchard, C Robertson, S Shrestha, JM Spraggins, JP Cartailler, SCJ Parker, M Brissova, J Liu
    Nucleic Acids Research. [PubMed]
  20. Molecular responses in abdominal subcutaneous adipose tissue after a session of endurance exercise: effects of exercise intensity.
    (2025). C Ahn, T Zhang, T Rode, G Yang, OK Chugh, S Ellis, S Ghayur, S Mehta, R Salzman, H Jiang, SCJ Parker, CF Burant, JF Horowitz
    Journal of Physiology. [PubMed]
  21. Efferocytosis-induced metabolic shift in bone macrophages drives lactate production and modulates inflammation and osteoclastogenesis.
    (2025). R Kannan, NJ Carruthers, AJ Koh, GG Kleer, K Nakamura, SCJ Parker, LK McCauley, H Roca
    Frontiers in Immunology. [PubMed]
  22. Functional dissection of metabolic trait-associated gene regulation in steady state and stimulated human skeletal muscle cells.
    (2024). K Nishino, JO Kitzman, SCJ Parker, A Tovar
    bioRxiv. [bioRxiv DOI]
  23. Building a literature knowledge base towards transparent biomedical AI.
    (2024). Y Huang, Z Han, X Luo, X Luo, Y Gao, M Zhao, F Tang, Y Wang, J Chen, C Li, X Lu, T Jiao, J Qiu, F Deng, L Guan, H Shang, F Feng, THH Vu, T Bate, D Xue, JP Cartailler, M Stitzel, S Chen, M Brissova, SCJ Parker, J Liu
    bioRxiv. [bioRxiv DOI]
  24. Untangling the genetics of beta cell dysfunction and death in type 1 diabetes.
    (2024). CC Robertson*, RM Elgamal*, BA Henry-Kanarek*, P Arvan, S Chen, S Dhawan, DL Eizirik, JS Kaddis, G Vahedi, SCJ Parker*, KJ Gaulton*, SA Soleimanpour*
    Molecular Metabolism. [DOI]
  25. The methodological and ethical concerns of genetic studies of same-sex sexual behavior.
    (2024). C Ventresca, DO Martschenko, R Wedow, M Civelek, J Tabery, J Carlson, SCJ Parker, PS Ramos
    American Journal of Human Genetics. [DOI]
  26. Human vascularized macrophage-islet organoids to model immune-mediated pancreatic β cell pyroptosis upon viral infection.
    (2024). L Yang, Y Han, T Zhang, X Dong, J Ge, A Roy, J Zhu, T Lu, JJ Vandana, N de Silva, CC Robertson, JZ Xiang, C Pan, Y Sun, J Que, T Evans, C Liu, W Wang, A Naji, SCJ Parker, RE Schwartz, S Chen
    Cell Stem Cell. [DOI]
  27. Cntools: A computational toolbox for cellular neighborhood analysis from multiplexed images.
    (2024). Y Tao, F Feng, X Luo, CV Reihsmann, AL Hopkirk, JP Cartailler, M Brissova, SCJ Parker, DC Saunders, J Liu
    PLoS Computational Biology. [PubMed]
  28. Integrative single-cell multi-omics profiling of human pancreatic islets identifies T1D-associated genes and regulatory signals.
    (2025). R D’Oliveira Albanus, X Zhang, Z Zhao, HJ Taylor, X Tang, Y Han, P Orchard, A Varshney, T Zhang, N Manickam, MR Erdos, N Narisu, L Taylor, X Saavedra, X Liu, A Zhong, B Li, T Zhou, A Naji, C Liu, FS Collins, SCJ Parker*, S Chen*
    Cell Reports. [PubMed]
  29. Retrograde mitochondrial signaling governs the identity and maturity of metabolic tissues.
    (2025). EM Walker*, GL Pearson*, N Lawlor, AM Stendahl, A Lietzke, V Sidarala, J Zhu, T Stromer, EC Reck, J Li, A Renberg, K Mohamed, VS Parekh, IX Zhang, B Thompson, D Zhang, SA Duplaga, L Haataja, SCJ Parker, P Arvan, L Yin, BA Kaufman, LS Satin, L Sussel, ML Stitzel, SA Soleimanpour
    Science. [PubMed]
  30. Non-coding variants alter Gata2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis.
    (2023). AP Tenney, SJ Garnai, M Kosicki, CD Robson, BJ Barry, Z Zhang, WM Chan, TE Collins, A Gelber, BM Pratt, A Varshney, M Lek, C Van Ryzin, FM Facio, TJ Lehky, C Zalewski, KA King, CC Brewer, A Thurm, J Snow, N Narisu, LL Bonnycastle, A Swift, PS Chines, JL Bell, S Mohan, MC Whitman, SE Staffieri, JE Elder, JL Demer, A Torres, E Rachid, C Al-Haddad, RM Boustany, DA Mackey, SH Orkin, SCJ Parker, TA Hadlock, EW Jabs, FS Collins, BD Webb, LA Pennacchio, I Manoli, EC Engle
    Nature Genetics. [DOI]
  31. FixItFelix: improving genomic analysis by fixing reference errors.
    (2023). S Behera, J LeFaive, P Orchard, M Mahmoud, LF Paulin, J Farek, DC Soto, SCJ Parker, AV Smith, MY Dennis, JM Zook, FJ Sedlazeck
    Genome Biology. [DOI]
  32. Loci for insulin processing and secretion provide insight into type 2 diabetes risk.
    (2023). KA Broadaway, X Yin, A Williamson, VA Parsons, EP Wilson, AH Moxley, S Vadlamudi, A Varshney, AU Jackson, V Ahuja, SR Bornstein, LJ Corbin, GE Delgado, OP Dwivedi, LF Silva, TM Frayling, H Grallert, S Gustafsson, L Hakaste, U Hammar, C Herder, S Herrmann, K Højlund, DA Hughes, ME Kleber, CM Lindgren, C-T Liu, J Luan, A Malmberg, AP Moissl, AP Morris, N Perakakis, A Peters, JR Petrie, M Roden, PEH Schwarz, S Sharma, A Silveira, RJ Strawbridge, T Tuomi, AR Wood, P Wu, B Zethelius, D Baldassarre, JG Eriksson, T Fall, JC Florez, A Fritsche, B Gigante, A Hamsten, E Kajantie, M Laakso, J Lahti, DA Lawlor, L Lind, W März, JB Meigs, J Sundström, NJ Timpson, R Wagner, M Walker, NJ Wareham, H Watkins, I Barroso, S O’Rahilly, N Grarup, SCJ Parker, M Boehnke, C Langenberg, E Wheeler*, KL Mohlke*
    The American Journal of Human Genetics. [DOI]
  33. Three-dimensional chromatin re-organization during muscle stem cell aging.
    (2023). BA Yang, JA Larouche, KM Sabin, PM Fraczek, SCJ Parker, CA Aguilar
    Aging Cell. [DOI]
  34. Whole genome sequence association analysis of fasting glucose and fasting insulin levels in diverse cohorts from the NHLBI TOPMed program.
    (2022). D DiCorpo, SM Gaynor, EM Russell, KE Westerman, LM Raffield, TD Majarian, P Wu, C Sarnowski, HM Highland, A Jackson, NR Hasbani, PS de Vries, JA Brody, B Hidalgo, X Guo, JA Perry, JR O’Connell, S Lent, ME Montasser, BE Cade, D Jain, H Wang, R D’Oliveira Albanus, A Varshney, LR Yanek, L Lange, ND Palmer, M Almeida, JM Peralta, S Aslibekyan, AS Baldridge, AG Bertoni, LF Bielak, C-S Chen, Y-DI Chen, WJ Choi, MO Goodarzi, JS Floyd, MR Irvin, RR Kalyani, T. N Kelly, S Lee, C-T Liu, D Loesch, JE Manson, RL Minster, T Naseri, JS Pankow, LJ Rasmussen-Torvik, AP Reiner, MS Reupena, E Selvin, JA Smith, DE Weeks, H Xu, J Yao, W Zhao, SCJ Parker, A Alonso, DK Arnett, J Blangero, E Boerwinkle, A Correa, LA Cupples, JE Curran, R Duggirala, J He, SR Heckbert, SLR Kardia, RW Kim, C Kooperberg, S Liu, RA Mathias, ST McGarvey, BD Mitchell, AC Morrison, PA Peyser, BM Psaty, S Redline, AR Shuldiner, KD Taylor, RS Vasan, KA Viaud-Martinez, JC Florez, JG Wilson, R Sladek, SS Rich, JI Rotter, X Lin, J Dupuis, JB Meigs, J Wessel, AK Manning
    Communications Biology. [DOI]
  35. Genetic risk converges on regulatory networks mediating early type 2 diabetes.
    (2023). JT Walker*, DC Saunders*, V Rai*, H Chen, P Orchard, C Dai, YD Pettway, AL Hopkirk, CV Reihsmann, Y Tao, S Fan, S Shrestha, A Varshney, LE Petty, JJ Wright, C Ventresca, S Agarwala, R Aramandla, G Poffenberger, R Jenkins, S Mei, NJ Hart, S Phillipe, H Kang, DL Greiner, LD Shultz, R Bottino, Human Pancreas Analysis Program, J Liu, JE Below, SCJ Parker*, AC Powers*, M Brissova*
    Nature. [DOI]
  36. Rare Non-coding Variation Identified by Large Scale Whole Genome Sequencing Reveals Unexplained Heritability of Type 2 Diabetes.
    (2020).J Wessel, TD Majarian, HM Highland, S Raghavan, MD Szeto, NR Hasbani, PS de Vries, JA Brody, C Sarnowski, D DiCorpo, X Yin, B Hidalgo, X Guo, J Perry, JR O’Connell, S Lent, ME Montasser, BE Cade, D Jain, H Wang, P Wu, S Bonàs-Guarch, RD Albanus, A Leong, I Miguel-Escalada, A Varshney, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Anthropometry, DIAMANTE, GL Kinney, LR Yanek, L Lange, M Almeida, JM Peralta, S Aslibekyan, AS Baldridge, AG Bertoni, LF Bielak, DW Bowden, CS Chen, YDI Chen, SH Choi, WJ Choi, D Darbar, JS Floyd, BI Freedman, MO Goodarzi, R Irvin, RR Kalyani, T Kelly, S Lee, CT Liu, D Loesch, JE Manson, R Nassir, ND Palmer, JS Pankow, LJ Rasmussen-Torvik, AP Reiner, E Selvin, AH Shadyab, JA Smith, DE Weeks, LC Weng, H Xu, J Yao, Z Yoneda, W Zhao, J Ferrer, A Mahajan, MI McCarthy, SCJ Parker, A Alonso, DK Arnett, J Blangero, E Boerwinkle, MH Cho, A Correa, LA Cupples, JE Curran, R Duggirala, PT Ellinor, J He, SR Heckbert, SLR Kardia, RW Kim, C Kooperberg, S Liu, SA Lubitz, RA Mathias, S McGarvey, BD Mitchell, AC Morrison, PA Peyser, BM Psaty, S Redline, D Roden, MB Shoemaker, NL Smith, KD Taylor, RS Vasan, KA Viaud-Martinez, JC Florez, JG Wilson, R Sladek, J Dupuis, SS Rich, JI Rotter, JB Meigs, AK Manning
    medRxiv. [DOI]
  37. Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits.
    (2021). P. Orchard*, N. Manickam*, A. Varshney, V. Rai, J. Kaplan, C. Lalancette, K. Gallagher, C.F. Burant, S.C.J. Parker
    Genome Research. [DOI]
  38. Combinatorial transcription factor profiles predict mature and functional human islet α and β cells.
    (2021). S Shrestha, DC Saunders, JT Walker, J Camunas-Soler, X-Q Dai, R Haliyur, R Aramandla, G Poffenberger, N Prasad, R Bottino, R Stein, J-P Cartailler, SCJ Parker, PE MacDonald, SE Levy, AC Powers, M Brissova
    JCI Insight. [DOI]
  39. Chromatin information content landscapes inform transcription factor and DNA interactions.
    (2021). R D'Oliveira Albanus, Y Kyono, J Hensley, A Varshney, P Orchard, JO Kitzman, SCJ Parker
    Nature Communications. [DOI]
  40. A transcription start site map in human pancreatic islets reveals functional regulatory signatures.
    (2021). A Varshney, Y Kyono, VR Elangovan, C Wang, MR Erdos, N Narisu, R D'Oliveira Albanus, P Orchard, ML Stitzel, FS Collins, JO Kitzman, SCJ Parker
    Diabetes. [DOI]
  41. Genetic effects on liver chromatin accessibility identify disease regulatory variants.
    (2021). KW Currin, MR Erdos, N Narisu, V Rai, S Vadlamudi, HJ Perrin, JR Idol, T Yan, RD Albanus, KA Broadaway, AmyS Etheridge, LL Bonnycastle, P Orchard, JP Didion, AS Chaudhry, NIH Intramural Sequencing Core, F Innocenti, EG Schuetz, LJ Scott, SCJ Parker, FS Collins*, KL Mohlke*
    American Journal of Human Genetics. [DOI]
  42. CHD7 promotes neural progenitor differentiation in embryonic stem cells via altered chromatin accessibility and nascent gene expression.
    (2020). H Yao, DF Hannum, Y Zhai, SF Hill, RD Albanus, W Lou, JM Skidmore, G Sanchez, A Saiakhova, S Bielas, P Scacheri, M Ljungman, SCJ Parker, DM Martin
    Scientific Reports. [DOI]
  43. ACE2 expression in adipose tissue is associated with COVID-19 cardio-metabolic risk factors and cell type composition.
    (2020). JS El-Sayed Moustafa*, AU Jackson*, SM Brotman*, L Guan*, S Villicaňa, AL Roberts, A Zito, L Bonnycastle, MR Erdos, N Narisu, HM Stringham, R Welch, T Yan, T Lakka, SCJ Parker, J Tuomilehto, FS Collins, P Pajukanta, M Boehnke, HA Koistinen, M Laakso, M Falchi, JT Bell, LJ Scott**, KL Mohlke**, KS Small**
    International Journal of Obesity. [DOI]
  44. Multi-omic profiling of pituitary thyrotropic cells and progenitors.
    (2021). AZ Daly, LA Dudley, MT Peel, SA Liebhaber, SCJ Parker, SA Camper
    BMC Biology. [DOI]
  45. The trans-ancestral genomic architecture of glycaemic traits.
    (2021). Ji Chen*, Cassandra N. Spracklen*, Gaëlle Marenne*, Arushi Varshney*, Laura J Corbin*, Jian’an Luan, Sara Willems, Ying Wu, Xiaoshuai Zhang, Momoko Horikoshi, Thibaud S Boutin, Reedik Mägi, Johannes Waage, Achilleas Pitsilides, Ruifang Li-Gao, Kei Hang, Jie Yao, Mila D Anasanti, Audrey Y Chu, Annique Claringbould, Jani Heikkinen, Jaeyoung Hong, Jouke-Jan Hottenga, Shaofeng Huo, Marika A. Kaakinen, Tin Louie, Winfried März, Hortensia Moreno-Macias, Anne Ndungu, Sarah C. Nelson, Ilja M. Nolte, Kari North, Chelsea K. Raulerson, Debashree Ray, Rebecca Rohde, Denis Rybin, Claudia Schurmann, Xueling Sim, Loz Southam, Isobel Stewart, Carol A. Wang, Yujie Wang, Peitao Wu, Weihua Zhang, Tarunveer S. Ahluwalia, Emil VR Appel, Lawrence F. Bielak, Jennifer A. Brody, Noel P Burtt, Claudia P Cabrera, Brian E Cade, Jin Fang Chai, Xiaoran Chai, Li-Ching Chang, Chien-Hsiun Chen, Brian H Chen, Kumaraswamy N Chitrala, Yen-Feng Chiu, Hugoline G. de Haan, Graciela E Delgado, Ayse Demirkan, Qing Duan, Jorgen Engmann, Segun A Fatumo, Javier Gayán, Franco Giulianini, Jung Ho Gong, Stefan Gustafsson, Yang Hai, Fernando P Hartwig, Jing He, Yoriko Heianza, Tao Huang, Alicia Huerta-Chagoya, Mi Yeong Hwang, Richard A. Jensen, Takahisa Kawaguchi, Katherine A Kentistou, Young Jin Kim, Marcus E Kleber, Ishminder K Kooner, Shuiqing Lai, Leslie A Lange, Carl D Langefeld, Marie Lauzon, Man Li, Symen Ligthart, Jun Liu, Marie Loh, Jirong Long, Valeriya Lyssenko, Massimo Mangino, Carola Marzi, May E Montasser, Abhishek Nag, Masahiro Nakatochi, Damia Noce, Raymond Noordam, Giorgio Pistis, Michael Preuss, Laura Raffield, Laura J. Rasmussen-Torvik, Stephen S Rich, Neil R Robertson, Rico Rueedi, Kathleen Ryan, Serena Sanna, Richa Saxena, Katharina E Schraut, Bengt Sennblad, Kazuya Setoh, Albert V Smith, Lorraine Southam, Thomas Sparsø, Rona J Strawbridge, Fumihiko Takeuchi, Jingyi Tan, Stella Trompet, Erik van den Akker, Peter J Van der Most, Niek Verweij, Mandy Vogel, Heming Wang, Chaolong Wang, Nan Wang, Helen R Warren, Wanqing Wen, Tom Wilsgaard, Andrew Wong, Andrew R Wood, Tian Xie, Mohammad Hadi Zafarmand, Jing-Hua Zhao, Wei Zhao, Najaf Amin, Zorayr Arzumanyan, Arne Astrup, Stephan JL Bakker, Damiano Baldassarre, Marian Beekman, Richard N Bergman, Alain Bertoni, Matthias Blüher, Lori L. Bonnycastle, Stefan R Bornstein, Donald W Bowden, Qiuyin Cai, Archie Campbell, Harry Campbell, Yi Cheng Chang, Eco J.C. de Geus, Abbas Dehghan, Shufa Du, Gudny Eiriksdottir, Aliki Eleni Farmaki, Mattias Frånberg, Christian Fuchsberger, Yutang Gao, Anette P Gjesing, Anuj Goel, Sohee Han, Catharina A Hartman, Christian Herder, Andrew A. Hicks, Chang-Hsun Hsieh, Willa A. Hsueh, Sahoko Ichihara, Michiya Igase, M. Arfan Ikram, W. Craig Johnson, Marit E Jørgensen, Peter K Joshi, Rita R Kalyani, Fouad R. Kandeel, Tomohiro Katsuya, Chiea Chuen Khor, Wieland Kiess, Ivana Kolcic, Teemu Kuulasmaa, Johanna Kuusisto, Kristi Läll, Kelvin Lam, Deborah A Lawlor, Nanette R. Lee, Rozenn N. Lemaitre, Honglan Li, Lifelines Cohort Study, Shih-Yi Lin, Jaana Lindström, Allan Linneberg, Jianjun Liu, Carlos Lorenzo, Tatsuaki Matsubara, Fumihiko Matsuda, Geltrude Mingrone, Simon Mooijaart, Sanghoon Moon, Toru Nabika, Girish N. Nadkarni, Jerry L. Nadler, Mari Nelis, Matthew J Neville, Jill M Norris, Yasumasa Ohyagi, Annette Peters, Patricia A. Peyser, Ozren Polasek, Qibin Qi, Dennis Raven, Dermot F Reilly, Alex Reiner, Fernando Rivideneira, Kathryn Roll, Igor Rudan, Charumathi Sabanayagam, Kevin Sandow, Naveed Sattar, Annette Schürmann, Jinxiu Shi, Heather M Stringham, Kent D. Taylor, Tanya M. Teslovich, Betina Thuesen, Paul RHJ Timmers, Elena Tremoli, Michael Y Tsai, Andre Uitterlinden, Rob M van Dam, Diana van Heemst, Astrid van Hylckama Vlieg, Jana V Van Vliet-Ostaptchouk, Jagadish Vangipurapu, Henrik Vestergaard, Tao Wang, Ko Willems van Dijk, Yongbing Xiang, Tatijana Zemunik, Goncalo R Abecasis, Linda S. Adair, Carlos Alberto Aguilar-Salinas, Marta E Alarcón-Riquelme, Ping An, Larissa Aviles-Santa, Diane M Becker, Lawrence J Beilin, Sven Bergmann, Hans Bisgaard, Corri Black, Michael Boehnke, Eric Boerwinkle, Bernhard O Böhm, Klaus Bønnelykke, D I. Boomsma, Erwin P. 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  73. 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, KL van Bueren, PS Chines, N Narisu, BL Black, A Visel, LA Pennacchio, FS Collins
    Proceedings of the National Academy of Sciences 110 (44), 17921-17926 [DOI]
  74. 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, S Davis, VL Simhadri, S Jha, N Katagiri, V Gotea, JK Teer, X Wei, MA Morken, UK Bhanot, G Chen, LL Elnitski, MA Davies, JE Gershenwald, H Carter, R Karchin, W Robinson, S Robinson, SA Rosenberg, FS Collins, G Parmigiani, AA Komar, C Kimchi-Sarfaty, NK Hayward, EH Margulies, Y Samuels
    Proceedings of the National Academy of Sciences 110 (33), 13481-13486 [DOI]
  75. Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes.
    (2012). SCJ Parker, Gartner J, Cardenas-Navia I, Wei X, Ozel Abaan H, Ajay SS, Hansen NF, Song L, Bhanot UK, Killian JK, Gindin Y, Walker RL, Meltzer PS, Mullikin JC, Furey TS, Crawford GE, Rosenberg SA, Samuels Y, Margulies EH
    PLoS Genet 8 (8), e1002871 [DOI]
  76. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.
    (2012). Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, SCJ Parker, Margulies EH, Wray GA, Furey TS, Crawford GE
    PLoS Genet 8 (6), e1002789 [DOI]
  77. 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]
  78. An integrated encyclopedia of DNA elements in the human genome.
    (2012). The ENCODE Project Consortium
    Nature 489 (7414), 57-74 [DOI]
  79. 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, TD Tullius
    ACS Chemical Biology 6 (12), 1314-1320 [DOI]
  80. 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]
  81. 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]
  82. DNA shape, genetic codes, and evolution.
    (2011). SCJ Parker, TD Tullius
    Current Opinion in Structural Biology 21 (3), 342-347 [DOI]
  83. A user's guide to the encyclopedia of DNA elements (ENCODE).
    (2011). The ENCODE Project Consortium
    PLoS Biology 9 (4), e1001046 [DOI]
  84. 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]
  85. Evolutionary Constraint on DNA Shape in the Human Genome.
    (2011). TD Tullius, SCJ Parker, EH Margulies
    Evolutionary Biology–Concepts Biodiversity, Macroevolution and Genome ... [DOI]
  86. Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.
    (2010). Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, SCJ Parker, Boyle AP, Scott LJ, , Margulies EH, Boehnke M, Furey TS, Crawford GE, Collins FS
    Cell Metabolism 12 (5), 443-455 [DOI]
  87. 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, US Zimmermann, V Nieratschker, M Rietschel, EH Margulies, M Palkovits, M Laucht, M Heilig
    Human Mutation 31 (8), E1594-E1608 [DOI]
  88. Family-based analysis of candidate genes for polycystic ovary syndrome.
    (2010). Ewens KG, Stewart DR, Ankener W, Urbanek M, McAllister JM, Chen C, Baig KM, SCJ Parker, Margulies EH, Legro RS, Dunaif A, Strauss 3rd JF, Spielman RS
    The Journal of Clinical Endocrinology & Metabolism 95 (5), 2306-2315 [DOI]
  89. 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]
  90. 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]
  91. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
    (2007). ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Demirtas’s ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, SCJ Parker, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children’s Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CWH, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JNS, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PIW, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VVB, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ
    Nature 447 (7146), 799-816 [DOI]
  92. Detection of DNA structural motifs in functional genomic elements.
    (2007). JA Greenbaum, SCJ Parker, TD Tullius
    Genome Research 17 (6), 940-946 [DOI]
  93. 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 [DOI]
  94. DNA sequence and analysis of human chromosome 8.
    (2006). Nusbaum C, Mikkelsen TS, Zody MC, Asakawa S, Taudien S, Garber M, Kodira CD, Schueler MG, Shimizu A, Whittaker CA, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Yang X, Allen NR, Anderson S, Asakawa T, Blechschmidt K, Bloom T, Borowsky ML, Butler J, Cook A, Corum B, DeArellano K, DeCaprio D, Dooley KT, Dorris L, Engels R, Glöckner G, Hafez N, Hagopian DS, Hall JL, Ishikawa SK, Jaffe DB, Kamat A, Kudoh J, Lehmann R, Lokitsang T, Macdonald P, Major JE, Matthews CD, Mauceli E, Menzel U, Mihalev AH, Minoshima S, Murayama Y, Naylor JW, Nicol R, Nguyen C, O’Leary SB, O’Neill K, SCJ Parker, Polley A, Raymond CK, Reichwald K, Rodriguez J, Sasaki T, Schilhabel M, Siddiqui R, Smith CL, Sneddon TP, Talamas JA, Tenzin P, Topham K, Venkataraman V, Wen G, Yamazaki S, Young SK, Zeng Q, Zimmer AR, Rosenthal A, Birren BW, Platzer M, Shimizu N, Lander ES
    Nature 439 (7074), 331-335 [DOI]
  95. Finishing the euchromatic sequence of the human genome.
    (2004). International Human Genome Sequencing Consortium
    Nature 431 (7011), 931-945 [DOI]
  96. 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
  97. HOX gene evolution among teleosts.
    (1999). EJ Stellwag, JL Scemama, YA Mohamud, SCJ Parker
    American Zoologist 39 (5), 14A

Stephen CJ Parker, Ph.D | scjp@umich.edu | Ann Arbor, MI