The Parker Lab
Research
News
People
Tools
Jobs
Contact

Read our papers at Google Scholar or PubMed.

  1. Single-cell gene expression and chromatin accessibility profiling of human pancreatic islets at basal and stimulatory conditions nominates mechanisms of type 1 diabetes genetic risk. (2023). R D’Oliveira Albanus, X Tang, HJ Taylor, N Manickam, M Erdos, N Narisu, Y Han, P Orchard, A Varshney, C Liu, A Naji, HPAP Consortium, FS Collins, S Chen, SCJ Parker; bioRxiv. [DOI]
  2. Retrograde mitochondrial signaling governs the identity and maturity of metabolic tissues. (2023). GL Pearson*, EM Walker*, N Lawlor, 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; bioRxiv. [DOI]
  3. Non-coding variants altering a conserved cis-regulatory element cause dominant hereditary congenital facial palsy. (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, SCJ Parker, TA Hadlock, EW Jabs, FS Collins, BD Webb, LA Pennacchio, I Manoli, EC Engle; (in review).
  4. Fixing reference errors efficiently improves sequencing results. (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 (accepted). [bioRxiv DOI]
  5. 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, SC Parker, M Boehnke, C Langenberg, E Wheeler, KL Mohlke; The American Journal of Human Genetics. [DOI]
  6. 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]
  7. 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]
  8. RFX6-mediated dysregulation defines human β cell dysfunction in early type 2 diabetes. (2021). JT Walker*, DC Saunders*, V Rai*, C Dai, P Orchard, AL Hopkirk, CV Reihsmann, Y Tao, S Fan, S Shrestha, A Varshney, JJ Wright, YD Pettway, C Ventresca, S Agarwala, R Aramandla, G Poffenberger, R Jenkins, NJ Hart, DL Greiner, LD Shultz, R Bottino, Human Pancreas Analysis Program, J Liu, SCJ Parker*, AC Powers*, M Brissova*; bioRxiv. [DOI]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. 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, S 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]
  17. 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]
  18. 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. Bottinger, Thomas A Buchanan, Mickaël Canouil, Mark J Caulfield, John C. Chambers, Daniel I. Chasman, Yii-Der Ida Chen, Ching-Yu Cheng, Francis S. Collins, Adolfo Correa, Francesco Cucca, H. Janaka de Silva, George Dedoussis, Sölve Elmståhl, Michele K. Evans, Ele Ferranni, Luigi Ferruci, Jose C Florez, Paul Franks, Timothy M Frayling, Philippe Froguel, Bruna Gigante, Mark O. Goodarzi, Penny Gordon-Larsen, Harald Grallert, Niels Grarup, Sameline Grimsgaard, Leif Groop, Vilmundur Gudnason, Xiuqing Guo, Anders Hamsten, Torben Hansen, Caroline Hayward, Susan R. Heckbert, Bernardo L Horta, Wei Huang, Erik Ingelsson, Pankow S James, Jost B Jonas, J. Wouter Jukema, Pontiano Kaleebu, Robert Kaplan, Sharon L.R. Kardia, Norihiro Kato, Sirkka M. Keinanen-Kiukaanniemi, Bong-Jo Kim, Mika Kivimaki, Heikki A. Koistinen, Jaspal S. Kooner, Antje Körner, Peter Kovacs, Diana Kuh, Meena Kumari, Zoltan Kutalik, Markku Laakso, Timo A. Lakka, Lenore J Launer, Karin Leander, Huaixing Li, Xu Lin, Lars Lind, Cecilia Lindgren, Simin Liu, Ruth J.F. Loos, Patrik Magnusson, Anubha Mahajan, Andres Metspalu, Dennis O Mook-Kanamori, Trevor A Mori, Patricia B Munroe, Inger Njølstad, Jeffrey R O’Connell, Albertine J Oldehinkel, Ken K Ong, Sandosh Padmanabhan, Colin N.A. Palmer, Nicholette D Palmer, Oluf Pedersen, Craig E Pennell, David J Porteous, Peter P. Pramstaller, Michael A. Province, Bruce M. Psaty, Lu Qi, Leslie J. Raffel, Rainer Rauramaa, Susan Redline, Paul M Ridker, Frits R. Rosendaal, Timo E. Saaristo, Manjinder Sandhu, Jouko Saramies, Neil Schneiderman, Peter Schwarz, Laura J. Scott, Elizabeth Selvin, Peter Sever, Xiao-ou Shu, P Eline Slagboom, Kerrin S Small, Blair H Smith, Harold Snieder, Tamar Sofer, Thorkild I.A. Sørensen, Tim D Spector, Alice Stanton, Claire J Steves, Michael Stumvoll, Liang Sun, Yasuharu Tabara, E Shyong Tai, Nicholas J Timpson, Anke Tönjes, Jaakko Tuomilehto, Teresa Tusie, Matti Uusitupa, Pim van der Harst, Cornelia van Duijn, Veronique Vitart, Peter Vollenweider, Tanja GM Vrijkotte, Lynne E Wagenknecht, Mark Walker, Ya X Wang, Nick J Wareham, Richard M Watanabe, Hugh Watkins, Wen B Wei, Ananda R Wickremasinghe, Gonneke Willemsen, James F Wilson, Tien-Yin Wong, Jer-Yuarn Wu, Anny H Xiang, Lisa R Yanek, Loïc Yengo, Mitsuhiro Yokota, Eleftheria Zeggini, Wei Zheng, Alan B Zonderman, Jerome I Rotter, Anna L Gloyn, Mark I. McCarthy, Josée Dupuis, James B Meigs, Robert Scott, Inga Prokopenko, Aaron Leong, Ching-Ti Liu, Stephen CJ Parker*, Karen L. Mohlke*, Claudia Langenberg*, Eleanor Wheeler*, Andrew P. Morris*, Inês Barroso*, & The Meta-Analysis of Glucose and Insulin-related Traits Consortium (MAGIC); Nature Genetics. [DOI]
  19. BAF60a deficiency uncouples chromatin accessibility and cold sensitivity from white fat browning. (2020). T. Liu, L. Mi, J. Xiong, P. Orchard, Q. Yu, L. Yu, X. Zhao, Z. Meng, S.C.J. Parker, J.D. Lin, S. Li; Nature Communications. [DOI]
  20. Quantification, dynamic visualization, and validation of bias in ATAC-seq data with ataqv. (2020). P Orchard, Y Kyono, J Hensley, JO Kitzman, SCJ Parker; Cell Systems. [DOI]
  21. Influence of genetic variants on gene expression in human pancreatic islets – implications for type 2 diabetes. (2020). A Viñuela*, A Varshney*, M van de Bunt*, RB Prasad*, O Asplund, A Bennett, M Boehnke, A Brown, MR Erdos, J Fadista, O Hansson, G Hatem, C Howald, AK Iyengar, P Johnson, U Krus, PE MacDonald, A Mahajan, JE Manning Fox, N Narisu, V Nylander, P Orchard, N Oskolkov, NI Panousis, A Payne, ML Stitzel, S Vadlamudi, R Welch, FS Collins, KL Mohlke, AL Gloyn, LJ Scott, ET Dermitzakis, L Groop, SCJ Parker, MI McCarthy; Nature Communications. [DOI]
  22. Single cell ATAC-seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures. (2019). V Rai*, DX Quang*, MR Erdos, DA Cusanovich, RM Daza, N Narisu, LS Zou, JP Didion, Y Guan, J Shendure*, SCJ Parker*, FS Collins*; Molecular Metabolism. [DOI]
  23. Machine learning to predict anti-TNF drug responses of rheumatoid arthritis patients by integrating clinical and genetic markers. (2019). Y Guan, H Zhang, D Quang, Z Wang, SCJ Parker, DA Pappas, JM Kremer, F Zhu; Arthritis Rheumatol. [DOI]
  24. Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle. (2019). 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 [DOI]
  25. Genomic annotation of disease-associated variants reveals shared functional contexts. (2019). Y Kyono, JO Kitzman*, SCJ Parker*; Diabetologia [DOI]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU. (2018). D Quang, Y Guan, and SCJ Parker Bioinformatics [DOI]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. 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]
  36. 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]
  37. 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]
  38. The genetic architecture of type 2 diabetes. (2016). C Fuchsberger, J Flannick, TM Teslovich, A Mahajan, V Agarwala, KJ Gaulton, et al Nature [DOI]
  39. 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]
  40. Super Enhancers in Cancers, Complex Disease, and Developmental Disorders. (2015). AR Niederriter, A Varshney, SCJ Parker, DM Martin Genes 6 (4), 1183-1200 [DOI]
  41. 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]
  42. 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]
  43. 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
  44. Comparative analysis of metazoan chromatin organization.. Nature (2014), 449-452 [DOI] 33x
  45. 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]
  46. 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
  47. 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
  48. Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes.. PLoS Genet 8 (8), e1002871 [DOI] 8x
  49. 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
  50. 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]
  51. An integrated encyclopedia of DNA elements in the human genome.. Nature 2012 2917x
  52. 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
  53. 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
  54. 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]
  55. DNA shape, genetic codes, and evolution. (2011). SCJ Parker, TD Tullius Current opinion in structural biology 21 (3), 342-347 [DOI] 22x
  56. A user's guide to the encyclopedia of DNA elements (ENCODE).. PLoS Biology 9 (4), e1001046 656x
  57. 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]
  58. Evolutionary Constraint on DNA Shape in the Human Genome. (2011). TD Tullius, SCJ Parker, EH Margulies Evolutionary Biology–Concepts Biodiversity, Macroevolution and Genome ... [DOI]
  59. Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.. Cell metabolism 12 (5), 443-455 94x
  60. 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
  61. Family-based analysis of candidate genes for polycystic ovary syndrome.. The Journal of Clinical Endocrinology & Metabolism 95 (5), 2306-2315 75x
  62. 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
  63. 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]
  64. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.. Nature 447 (7146), 799-816 [DOI] 3370x
  65. Detection of DNA structural motifs in functional genomic elements. (2007). JA Greenbaum, SCJ Parker, TD Tullius Genome research 17 (6), 940-946 [DOI] 29x
  66. 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
  67. DNA sequence and analysis of human chromosome 8.. Nature 439, 331-335 [DOI] 79x
  68. Finishing the euchromatic sequence of the human genome.. Nature 431 (7011), 931-945 2707x
  69. 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
  70. HOX gene evolution among telosts.. AMERICAN ZOOLOGIST 39 (5), 14A-14A

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