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Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation.

Bartman CR, Hamagami N, Keller CA, Giardine B, Hardison RC, Blobel GA, Raj A.

Mol Cell. 2019 Feb 7;73(3):519-532.e4. doi: 10.1016/j.molcel.2018.11.004. Epub 2018 Dec 13.


Erratum for Hardison et al., "Transient Nutrient Deprivation Promotes Macropinocytosis-Dependent Intracellular Bacterial Community Development".

Hardison RL, Heimlich DR, Harrison A, Beatty WL, Rains S, Moseley MA, Thompson JW, Justice SS, Mason KM.

mSphere. 2018 Oct 31;3(5). pii: e00562-18. doi: 10.1128/mSphere.00562-18. No abstract available.


Microevolution in response to transient heme-iron restriction enhances intracellular bacterial community development and persistence.

Hardison RL, Harrison A, Wallace RM, Heimlich DR, O'Bryan ME, Sebra RP, Pinkett HW, Justice SS, Mason KM.

PLoS Pathog. 2018 Oct 17;14(10):e1007355. doi: 10.1371/journal.ppat.1007355. eCollection 2018 Oct.


The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions.

Wang Y, Song F, Zhang B, Zhang L, Xu J, Kuang D, Li D, Choudhary MNK, Li Y, Hu M, Hardison R, Wang T, Yue F.

Genome Biol. 2018 Oct 4;19(1):151. doi: 10.1186/s13059-018-1519-9.


Transient Nutrient Deprivation Promotes Macropinocytosis-Dependent Intracellular Bacterial Community Development.

Hardison RL, Heimlich DR, Harrison A, Beatty WL, Rains S, Moseley MA, Thompson JW, Justice SS, Mason KM.

mSphere. 2018 Sep 12;3(5). pii: e00286-18. doi: 10.1128/mSphere.00286-18. Erratum in: mSphere. 2018 Oct 31;3(5):.


Integrative detection and analysis of structural variation in cancer genomes.

Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F.

Nat Genet. 2018 Oct;50(10):1388-1398. doi: 10.1038/s41588-018-0195-8. Epub 2018 Sep 10.


Liver Transplant Listing in Pediatric Acute Liver Failure: Practices and Participant Characteristics.

Squires JE, Rudnick DA, Hardison RM, Horslen S, Ng VL, Alonso EM, Belle SH, Squires RH.

Hepatology. 2018 Dec;68(6):2338-2347. doi: 10.1002/hep.30116. Epub 2018 Nov 1.


Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells.

Grevet JD, Lan X, Hamagami N, Edwards CR, Sankaranarayanan L, Ji X, Bhardwaj SK, Face CJ, Posocco DF, Abdulmalik O, Keller CA, Giardine B, Sidoli S, Garcia BA, Chou ST, Liebhaber SA, Hardison RC, Shi J, Blobel GA.

Science. 2018 Jul 20;361(6399):285-290. doi: 10.1126/science.aao0932.


Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points.

Heuston EF, Keller CA, Lichtenberg J, Giardine B, Anderson SM; NIH Intramural Sequencing Center, Hardison RC, Bodine DM.

Epigenetics Chromatin. 2018 May 28;11(1):22. doi: 10.1186/s13072-018-0195-z.


A Learning Collaborative Approach Increases Specificity of Diagnosis of Acute Liver Failure in Pediatric Patients.

Narkewicz MR, Horslen S, Hardison RM, Shneider BL, Rodriguez-Baez N, Alonso EM, Ng VL, Leonis MA, Loomes KM, Rudnick DA, Rosenthal P, Romero R, Subbarao GC, Li R, Belle SH, Squires RH; Pediatric Acute Liver Failure Study Group.

Clin Gastroenterol Hepatol. 2018 Nov;16(11):1801-1810.e3. doi: 10.1016/j.cgh.2018.04.050. Epub 2018 Apr 30.


Selenoproteins regulate stress erythroid progenitors and spleen microenvironment during stress erythropoiesis.

Liao C, Hardison RC, Kennett MJ, Carlson BA, Paulson RF, Prabhu KS.

Blood. 2018 Jun 7;131(23):2568-2580. doi: 10.1182/blood-2017-08-800607. Epub 2018 Apr 3.


Health Related Quality of Life and Neurocognitive Outcomes in the First Year after Pediatric Acute Liver Failure.

Sorensen LG, Neighbors K, Hardison RM, Loomes KM, Varni JW, Ng VL, Squires RH, Alonso EM; Pediatric Acute Liver Failure Study Group.

J Pediatr. 2018 May;196:129-138.e3. doi: 10.1016/j.jpeds.2018.01.030. Epub 2018 Mar 16.


Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility.

Behera V, Evans P, Face CJ, Hamagami N, Sankaranarayanan L, Keller CA, Giardine B, Tan K, Hardison RC, Shi J, Blobel GA.

Nat Commun. 2018 Feb 22;9(1):782. doi: 10.1038/s41467-018-03082-6.


Between form and function: the complexity of genome folding.

Oudelaar AM, Hanssen LLP, Hardison RC, Kassouf MT, Hughes JR, Higgs DR.

Hum Mol Genet. 2017 Oct 1;26(R2):R208-R215. doi: 10.1093/hmg/ddx306. Review.


Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation.

Zhang Y, Hardison RC.

Nucleic Acids Res. 2017 Sep 29;45(17):9823-9836. doi: 10.1093/nar/gkx659.


Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element.

Huang P, Keller CA, Giardine B, Grevet JD, Davies JOJ, Hughes JR, Kurita R, Nakamura Y, Hardison RC, Blobel GA.

Genes Dev. 2017 Aug 15;31(16):1704-1713. doi: 10.1101/gad.303461.117. Epub 2017 Sep 15.


HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.

Yang T, Zhang F, Yardımcı GG, Song F, Hardison RC, Noble WS, Yue F, Li Q.

Genome Res. 2017 Nov;27(11):1939-1949. doi: 10.1101/gr.220640.117. Epub 2017 Aug 30.


Evolution of hemoglobin loci and their regulatory elements.

Philipsen S, Hardison RC.

Blood Cells Mol Dis. 2018 May;70:2-12. doi: 10.1016/j.bcmd.2017.08.001. Epub 2017 Aug 9. Review.


Cognitive decline and brain amyloid-β accumulation across 3 years in adults with Down syndrome.

Hartley SL, Handen BL, Devenny D, Mihaila I, Hardison R, Lao PJ, Klunk WE, Bulova P, Johnson SC, Christian BT.

Neurobiol Aging. 2017 Oct;58:68-76. doi: 10.1016/j.neurobiolaging.2017.05.019. Epub 2017 Jun 2.


An Aggregate Biomarker Risk Score Predicts High Risk of Near-Term Myocardial Infarction and Death: Findings From BARI 2D (Bypass Angioplasty Revascularization Investigation 2 Diabetes).

Ghasemzadeh N, Brooks MM, Vlachos H, Hardison R, Sikora S, Sperling L, Quyyumi AA, Epstein SE.

J Am Heart Assoc. 2017 Jul 3;6(7). pii: e003587. doi: 10.1161/JAHA.116.003587.


The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries.

Hsu SC, Gilgenast TG, Bartman CR, Edwards CR, Stonestrom AJ, Huang P, Emerson DJ, Evans P, Werner MT, Keller CA, Giardine B, Hardison RC, Raj A, Phillips-Cremins JE, Blobel GA.

Mol Cell. 2017 Apr 6;66(1):102-116.e7. doi: 10.1016/j.molcel.2017.02.027.


Lactate and Lactate: Pyruvate Ratio in the Diagnosis and Outcomes of Pediatric Acute Liver Failure.

Feldman AG, Sokol RJ, Hardison RM, Alonso EM, Squires RH, Narkewicz MR; Pediatric Acute Liver Failure Study Group.

J Pediatr. 2017 Mar;182:217-222.e3. doi: 10.1016/j.jpeds.2016.12.031. Epub 2017 Jan 12.


A genome-editing strategy to treat β-hemoglobinopathies that recapitulates a mutation associated with a benign genetic condition.

Traxler EA, Yao Y, Wang YD, Woodard KJ, Kurita R, Nakamura Y, Hughes JR, Hardison RC, Blobel GA, Li C, Weiss MJ.

Nat Med. 2016 Sep;22(9):987-90. doi: 10.1038/nm.4170. Epub 2016 Aug 15.


Prevalence and Significance of Autoantibodies in Children With Acute Liver Failure.

Narkewicz MR, Horslen S, Belle SH, Rudnick DA, Ng VL, Rosenthal P, Romero R, Loomes KM, Zhang S, Hardison RM, Squires RH; Pediatric Acute Liver Failure Study Group.

J Pediatr Gastroenterol Nutr. 2017 Feb;64(2):210-217. doi: 10.1097/MPG.0000000000001363.


A guide to translation of research results from model organisms to human.

Hardison RC.

Genome Biol. 2016 Jul 26;17(1):161. doi: 10.1186/s13059-016-1026-9. Review.


A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition.

Hsiung CC, Bartman CR, Huang P, Ginart P, Stonestrom AJ, Keller CA, Face C, Jahn KS, Evans P, Sankaranarayanan L, Giardine B, Hardison RC, Raj A, Blobel GA.

Genes Dev. 2016 Jun 15;30(12):1423-39. doi: 10.1101/gad.280859.116.


Jointly characterizing epigenetic dynamics across multiple human cell types.

Zhang Y, An L, Yue F, Hardison RC.

Nucleic Acids Res. 2016 Aug 19;44(14):6721-31. doi: 10.1093/nar/gkw278. Epub 2016 Apr 19.


Unlinking an lncRNA from Its Associated cis Element.

Paralkar VR, Taborda CC, Huang P, Yao Y, Kossenkov AV, Prasad R, Luan J, Davies JO, Hughes JR, Hardison RC, Blobel GA, Weiss MJ.

Mol Cell. 2016 Apr 7;62(1):104-10. doi: 10.1016/j.molcel.2016.02.029. Epub 2016 Mar 31.


Finding partners to play the music of regulation.

Hardison RC.

Blood. 2016 Mar 31;127(13):1624-6. doi: 10.1182/blood-2016-02-697169.


Comprehensive Proteomic and Metabolomic Signatures of Nontypeable Haemophilus influenzae-Induced Acute Otitis Media Reveal Bacterial Aerobic Respiration in an Immunosuppressed Environment.

Harrison A, Dubois LG, St John-Williams L, Moseley MA, Hardison RL, Heimlich DR, Stoddard A, Kerschner JE, Justice SS, Thompson JW, Mason KM.

Mol Cell Proteomics. 2016 Mar;15(3):1117-38. doi: 10.1074/mcp.M115.052498. Epub 2015 Dec 28.


SBR-Blood: systems biology repository for hematopoietic cells.

Lichtenberg J, Heuston EF, Mishra T, Keller CA, Hardison RC, Bodine DM.

Nucleic Acids Res. 2016 Jan 4;44(D1):D925-31. doi: 10.1093/nar/gkv1263. Epub 2015 Nov 20.


Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution.

Han GC, Vinayachandran V, Bataille AR, Park B, Chan-Salis KY, Keller CA, Long M, Mahony S, Hardison RC, Pugh BF.

Mol Cell Biol. 2015 Oct 26;36(1):157-72. doi: 10.1128/MCB.00806-15. Print 2016 Jan 1.


The effects of normal aging on amyloid-β deposition in nondemented adults with Down syndrome as imaged by carbon 11-labeled Pittsburgh compound B.

Lao PJ, Betthauser TJ, Hillmer AT, Price JC, Klunk WE, Mihaila I, Higgins AT, Bulova PD, Hartley SL, Hardison R, Tumuluru RV, Murali D, Mathis CA, Cohen AD, Barnhart TE, Devenny DA, Mailick MR, Johnson SC, Handen BL, Christian BT.

Alzheimers Dement. 2016 Apr;12(4):380-90. doi: 10.1016/j.jalz.2015.05.013. Epub 2015 Jun 13.


Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility.

Dogan N, Wu W, Morrissey CS, Chen KB, Stonestrom A, Long M, Keller CA, Cheng Y, Jain D, Visel A, Pennacchio LA, Weiss MJ, Blobel GA, Hardison RC.

Epigenetics Chromatin. 2015 Apr 23;8:16. doi: 10.1186/s13072-015-0009-5. eCollection 2015.


Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution.

Denas O, Sandstrom R, Cheng Y, Beal K, Herrero J, Hardison RC, Taylor J.

BMC Genomics. 2015 Feb 14;16:87. doi: 10.1186/s12864-015-1245-6.


The effects of chromatin organization on variation in mutation rates in the genome.

Makova KD, Hardison RC.

Nat Rev Genet. 2015 Apr;16(4):213-23. doi: 10.1038/nrg3890. Epub 2015 Mar 3. Review.


Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system.

Jain D, Mishra T, Giardine BM, Keller CA, Morrissey CS, Magargee S, Dorman CM, Long M, Weiss MJ, Hardison RC.

Genom Data. 2015 Jun 1;4:1-7.


Analysis of the bypass angioplasty revascularization investigation trial using a multistate model of clinical outcomes.

Zhang X, Li Q, Rogatko A, Tighiouart M, Hardison RM, Brooks MM, Kelsey SF, Kaul S, Bairey Merz CN.

Am J Cardiol. 2015 Apr 15;115(8):1073-9. doi: 10.1016/j.amjcard.2015.01.543. Epub 2015 Feb 2.


Functions of BET proteins in erythroid gene expression.

Stonestrom AJ, Hsu SC, Jahn KS, Huang P, Keller CA, Giardine BM, Kadauke S, Campbell AE, Evans P, Hardison RC, Blobel GA.

Blood. 2015 Apr 30;125(18):2825-34. doi: 10.1182/blood-2014-10-607309. Epub 2015 Feb 18.


Pluripotent stem cells reveal erythroid-specific activities of the GATA1 N-terminus.

Byrska-Bishop M, VanDorn D, Campbell AE, Betensky M, Arca PR, Yao Y, Gadue P, Costa FF, Nemiroff RL, Blobel GA, French DL, Hardison RC, Weiss MJ, Chou ST.

J Clin Invest. 2015 Mar 2;125(3):993-1005. doi: 10.1172/JCI75714. Epub 2015 Jan 26.


dCaP: detecting differential binding events in multiple conditions and proteins.

Chen KB, Hardison R, Zhang Y.

BMC Genomics. 2014;15 Suppl 9:S12. doi: 10.1186/1471-2164-15-S9-S12. Epub 2014 Dec 8.


Topologically associating domains are stable units of replication-timing regulation.

Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM.

Nature. 2014 Nov 20;515(7527):402-5. doi: 10.1038/nature13986.


Principles of regulatory information conservation between mouse and human.

Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP.

Nature. 2014 Nov 20;515(7527):371-375. doi: 10.1038/nature13985.


A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.


Genome accessibility is widely preserved and locally modulated during mitosis.

Hsiung CC, Morrissey CS, Udugama M, Frank CL, Keller CA, Baek S, Giardine B, Crawford GE, Sung MH, Hardison RC, Blobel GA.

Genome Res. 2015 Feb;25(2):213-25. doi: 10.1101/gr.180646.114. Epub 2014 Nov 4.


Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis.

Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ.

Genome Res. 2014 Dec;24(12):1932-44. doi: 10.1101/gr.164178.113. Epub 2014 Oct 15.


Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis.

Wu W, Morrissey CS, Keller CA, Mishra T, Pimkin M, Blobel GA, Weiss MJ, Hardison RC.

Genome Res. 2014 Dec;24(12):1945-62. doi: 10.1101/gr.164830.113. Epub 2014 Oct 15.


Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3366. No abstract available.


Extubating in the operating room after adult cardiac surgery safely improves outcomes and lowers costs.

Badhwar V, Esper S, Brooks M, Mulukutla S, Hardison R, Mallios D, Chu D, Wei L, Subramaniam K.

J Thorac Cardiovasc Surg. 2014 Dec;148(6):3101-9.e1. doi: 10.1016/j.jtcvs.2014.07.037. Epub 2014 Jul 31.


A comprehensive and high-resolution genome-wide response of p53 to stress.

Chang GS, Chen XA, Park B, Rhee HS, Li P, Han KH, Mishra T, Chan-Salis KY, Li Y, Hardison RC, Wang Y, Pugh BF.

Cell Rep. 2014 Jul 24;8(2):514-27. doi: 10.1016/j.celrep.2014.06.030. Epub 2014 Jul 17.

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