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Items: 1 to 50 of 195

1.

CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases.

Singh DD, Hawkins RD, Lahesmaa R, Tripathi SK.

Semin Cell Dev Biol. 2019 Jun 19. pii: S1084-9521(18)30111-3. doi: 10.1016/j.semcdb.2019.05.007. [Epub ahead of print] Review.

PMID:
31112800
2.

Animal-assisted therapy for schizophrenia and related disorders: A systematic review.

Hawkins EL, Hawkins RD, Dennis M, Williams JM, Lawrie SM.

J Psychiatr Res. 2019 Aug;115:51-60. doi: 10.1016/j.jpsychires.2019.05.013. Epub 2019 May 16.

PMID:
31108372
3.

Superovulation alters global DNA methylation in early mouse embryo development.

Yu B, Smith TH, Battle SL, Ferrell S, Hawkins RD.

Epigenetics. 2019 Aug;14(8):780-790. doi: 10.1080/15592294.2019.1615353. Epub 2019 May 13.

PMID:
31060426
4.

Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States.

Battle SL, Doni Jayavelu N, Azad RN, Hesson J, Ahmed FN, Overbey EG, Zoller JA, Mathieu J, Ruohola-Baker H, Ware CB, Hawkins RD.

Stem Cell Reports. 2019 May 14;12(5):1129-1144. doi: 10.1016/j.stemcr.2019.04.004. Epub 2019 May 2.

5.

The Development and Evaluation of 'Farm Animal Welfare': An Educational Computer Game for Children.

Hawkins RD, Ferreira GARM, Williams JM.

Animals (Basel). 2019 Mar 13;9(3). pii: E91. doi: 10.3390/ani9030091.

6.

Folliculin regulates mTORC1/2 and WNT pathways in early human pluripotency.

Mathieu J, Detraux D, Kuppers D, Wang Y, Cavanaugh C, Sidhu S, Levy S, Robitaille AM, Ferreccio A, Bottorff T, McAlister A, Somasundaram L, Artoni F, Battle S, Hawkins RD, Moon RT, Ware CB, Paddison PJ, Ruohola-Baker H.

Nat Commun. 2019 Feb 7;10(1):632. doi: 10.1038/s41467-018-08020-0.

7.

Corrigendum: Intermediate-term memory in Aplysia involves neurotrophin signaling, transcription, and DNA methylation.

Yang Q, Antonov I, Castillejos D, Nagaraj A, Bostwick C, Kohn A, Moroz LL, Hawkins RD.

Learn Mem. 2019 Jan 16;26(2):60. doi: 10.1101/lm.049189.118. Print 2019 Feb. No abstract available.

8.

DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory sensory epithelium.

Yizhar-Barnea O, Valensisi C, Jayavelu ND, Kishore K, Andrus C, Koffler-Brill T, Ushakov K, Perl K, Noy Y, Bhonker Y, Pelizzola M, Hawkins RD, Avraham KB.

Sci Rep. 2018 Nov 26;8(1):17348. doi: 10.1038/s41598-018-35587-x.

9.

Intermediate-term memory in Aplysia involves neurotrophin signaling, transcription, and DNA methylation.

Yang Q, Antonov I, Castillejos D, Nagaraj A, Bostwick C, Kohn A, Moroz LL, Hawkins RD.

Learn Mem. 2018 Nov 15;25(12):620-628. doi: 10.1101/lm.047977.118. Print 2018 Dec. Erratum in: Learn Mem. 2019 Jan 16;26(2):60.

PMID:
30442770
10.

Autocrine signaling by an Aplysia neurotrophin forms a presynaptic positive feedback loop.

Jin I, Udo H, Nicholls R, Zhu H, Kandel ER, Hawkins RD.

Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):E11168-E11177. doi: 10.1073/pnas.1810649115. Epub 2018 Nov 5.

11.

Anterograde and retrograde signaling by an Aplysia neurotrophin forms a transsynaptic functional unit.

Jin I, Udo H, Kassabov S, Kosmidis S, Zhu H, Kandel ER, Hawkins RD.

Proc Natl Acad Sci U S A. 2018 Nov 13;115(46):E10951-E10960. doi: 10.1073/pnas.1810650115. Epub 2018 Oct 30.

12.

Reactivation of γ-globin in adult β-YAC mice after ex vivo and in vivo hematopoietic stem cell genome editing.

Li C, Psatha N, Sova P, Gil S, Wang H, Kim J, Kulkarni C, Valensisi C, Hawkins RD, Stamatoyannopoulos G, Lieber A.

Blood. 2018 Jun 28;131(26):2915-2928. doi: 10.1182/blood-2018-03-838540. Epub 2018 May 22.

13.

Three-dimensional genome architecture and emerging technologies: looping in disease.

Mishra A, Hawkins RD.

Genome Med. 2017 Sep 30;9(1):87. doi: 10.1186/s13073-017-0477-2. Review.

14.

First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor.

Moody JD, Levy S, Mathieu J, Xing Y, Kim W, Dong C, Tempel W, Robitaille AM, Dang LT, Ferreccio A, Detraux D, Sidhu S, Zhu L, Carter L, Xu C, Valensisi C, Wang Y, Hawkins RD, Min J, Moon RT, Orkin SH, Baker D, Ruohola-Baker H.

Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10125-10130. doi: 10.1073/pnas.1706907114. Epub 2017 Sep 1.

15.

Methylome Analysis of Human Bone Marrow MSCs Reveals Extensive Age- and Culture-Induced Changes at Distal Regulatory Elements.

Pasumarthy KK, Doni Jayavelu N, Kilpinen L, Andrus C, Battle SL, Korhonen M, Lehenkari P, Lund R, Laitinen S, Hawkins RD.

Stem Cell Reports. 2017 Sep 12;9(3):999-1015. doi: 10.1016/j.stemcr.2017.07.018. Epub 2017 Aug 24.

16.

Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases.

Valensisi C, Andrus C, Buckberry S, Doni Jayavelu N, Lund RJ, Lister R, Hawkins RD.

Cell Rep. 2017 Aug 8;20(6):1448-1462. doi: 10.1016/j.celrep.2017.07.036.

17.

Genome-wide, Single-Cell DNA Methylomics Reveals Increased Non-CpG Methylation during Human Oocyte Maturation.

Yu B, Dong X, Gravina S, Kartal Ö, Schimmel T, Cohen J, Tortoriello D, Zody R, Hawkins RD, Vijg J.

Stem Cell Reports. 2017 Jul 11;9(1):397-407. doi: 10.1016/j.stemcr.2017.05.026. Epub 2017 Jun 22.

18.

Corrigendum: Muscle-specific CRISPR/Cas9 dystrophin gene editing ameliorates pathophysiology in a mouse model for Duchenne muscular dystrophy.

Bengtsson NE, Hall JK, Odom GL, Phelps MP, Andrus CR, Hawkins RD, Hauschka SD, Chamberlain JR, Chamberlain JS.

Nat Commun. 2017 Jun 23;8:16007. doi: 10.1038/ncomms16007.

19.

Childhood Attachment to Pets: Associations between Pet Attachment, Attitudes to Animals, Compassion, and Humane Behaviour.

Hawkins RD, Williams JM, Scottish Society For The Prevention Of Cruelty To Animals Scottish Spca.

Int J Environ Res Public Health. 2017 May 6;14(5). pii: E490. doi: 10.3390/ijerph14050490.

20.

An Activating STAT3 Mutation Causes Neonatal Diabetes through Premature Induction of Pancreatic Differentiation.

Saarimäki-Vire J, Balboa D, Russell MA, Saarikettu J, Kinnunen M, Keskitalo S, Malhi A, Valensisi C, Andrus C, Eurola S, Grym H, Ustinov J, Wartiovaara K, Hawkins RD, Silvennoinen O, Varjosalo M, Morgan NG, Otonkoski T.

Cell Rep. 2017 Apr 11;19(2):281-294. doi: 10.1016/j.celrep.2017.03.055.

21.

Assessing Effectiveness of a Nonhuman Animal Welfare Education Program for Primary School Children.

Hawkins RD, Williams JM; Scottish Society for the Prevention of Cruelty to Animals.

J Appl Anim Welf Sci. 2017 Jul-Sep;20(3):240-256. doi: 10.1080/10888705.2017.1305272. Epub 2017 Apr 3.

PMID:
28368662
22.

Muscle-specific CRISPR/Cas9 dystrophin gene editing ameliorates pathophysiology in a mouse model for Duchenne muscular dystrophy.

Bengtsson NE, Hall JK, Odom GL, Phelps MP, Andrus CR, Hawkins RD, Hauschka SD, Chamberlain JR, Chamberlain JS.

Nat Commun. 2017 Feb 14;8:14454. doi: 10.1038/ncomms14454. Erratum in: Nat Commun. 2017 Jun 23;8:16007.

23.

Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer.

Celik S, Logsdon BA, Battle S, Drescher CW, Rendi M, Hawkins RD, Lee SI.

Genome Med. 2016 Jun 10;8(1):66. doi: 10.1186/s13073-016-0319-7.

24.

Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells.

Konki M, Pasumarthy K, Malonzo M, Sainio A, Valensisi C, Söderström M, Emani MR, Stubb A, Närvä E, Ghimire B, Laiho A, Järveläinen H, Lahesmaa R, Lähdesmäki H, Hawkins RD, Lund RJ.

Sci Rep. 2016 Feb 25;6:22190. doi: 10.1038/srep22190.

25.

Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC Differentiation Potential.

Kyttälä A, Moraghebi R, Valensisi C, Kettunen J, Andrus C, Pasumarthy KK, Nakanishi M, Nishimura K, Ohtaka M, Weltner J, Van Handel B, Parkkonen O, Sinisalo J, Jalanko A, Hawkins RD, Woods NB, Otonkoski T, Trokovic R.

Stem Cell Reports. 2016 Feb 9;6(2):200-12. doi: 10.1016/j.stemcr.2015.12.009. Epub 2016 Jan 14.

26.

cChIP-seq: a robust small-scale method for investigation of histone modifications.

Valensisi C, Liao JL, Andrus C, Battle SL, Hawkins RD.

BMC Genomics. 2015 Dec 21;16:1083. doi: 10.1186/s12864-015-2285-7.

27.

Hyperpolarization-activated, cyclic nucleotide-gated cation channels in Aplysia: Contribution to classical conditioning.

Yang Q, Kuzyk P, Antonov I, Bostwick CJ, Kohn AB, Moroz LL, Hawkins RD.

Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):16030-5. doi: 10.1073/pnas.1501731113. Epub 2015 Dec 14.

28.

Identification of global regulators of T-helper cell lineage specification.

Kanduri K, Tripathi S, Larjo A, Mannerström H, Ullah U, Lund R, Hawkins RD, Ren B, Lähdesmäki H, Lahesmaa R.

Genome Med. 2015 Nov 20;7:122. doi: 10.1186/s13073-015-0237-0.

29.

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition.

Sperber H, Mathieu J, Wang Y, Ferreccio A, Hesson J, Xu Z, Fischer KA, Devi A, Detraux D, Gu H, Battle SL, Showalter M, Valensisi C, Bielas JH, Ericson NG, Margaretha L, Robitaille AM, Margineantu D, Fiehn O, Hockenbery D, Blau CA, Raftery D, Margolin AA, Hawkins RD, Moon RT, Ware CB, Ruohola-Baker H.

Nat Cell Biol. 2015 Dec;17(12):1523-35. doi: 10.1038/ncb3264. Epub 2015 Nov 16.

30.

Comprehensive identification and analysis of human accelerated regulatory DNA.

Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins RD, Akey JM.

Genome Res. 2015 Sep;25(9):1245-55. doi: 10.1101/gr.192591.115. Epub 2015 Jun 23.

31.

Associative learning in invertebrates.

Hawkins RD, Byrne JH.

Cold Spring Harb Perspect Biol. 2015 Apr 15;7(5). pii: a021709. doi: 10.1101/cshperspect.a021709. Review.

32.

Functional analysis of a chromosomal deletion associated with myelodysplastic syndromes using isogenic human induced pluripotent stem cells.

Kotini AG, Chang CJ, Boussaad I, Delrow JJ, Dolezal EK, Nagulapally AB, Perna F, Fishbein GA, Klimek VM, Hawkins RD, Huangfu D, Murry CE, Graubert T, Nimer SD, Papapetrou EP.

Nat Biotechnol. 2015 Jun;33(6):646-55. doi: 10.1038/nbt.3178. Epub 2015 Mar 23.

33.

Epigenomics of autoimmune diseases.

Gupta B, Hawkins RD.

Immunol Cell Biol. 2015 Mar;93(3):271-6. doi: 10.1038/icb.2015.18. Review.

PMID:
25776989
34.

Nonassociative learning in invertebrates.

Byrne JH, Hawkins RD.

Cold Spring Harb Perspect Biol. 2015 Feb 26;7(5). pii: a021675. doi: 10.1101/cshperspect.a021675. Review.

35.

Integrative analysis of 111 reference human epigenomes.

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.

Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248.

36.

Factors influencing perception of effort (session rating of perceived exertion) during elite soccer training.

Gaudino P, Iaia FM, Strudwick AJ, Hawkins RD, Alberti G, Atkinson G, Gregson W.

Int J Sports Physiol Perform. 2015 Oct;10(7):860-4. doi: 10.1123/ijspp.2014-0518. Epub 2015 Feb 11.

PMID:
25671338
37.

Derivation of naive human embryonic stem cells.

Ware CB, Nelson AM, Mecham B, Hesson J, Zhou W, Jonlin EC, Jimenez-Caliani AJ, Deng X, Cavanaugh C, Cook S, Tesar PJ, Okada J, Margaretha L, Sperber H, Choi M, Blau CA, Treuting PM, Hawkins RD, Cirulli V, Ruohola-Baker H.

Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4484-9. doi: 10.1073/pnas.1319738111. Epub 2014 Mar 12.

38.

Systematic bias between running speed and metabolic power data in elite soccer players: influence of drill type.

Gaudino P, Iaia FM, Alberti G, Hawkins RD, Strudwick AJ, Gregson W.

Int J Sports Med. 2014 Jun;35(6):489-93. doi: 10.1055/s-0033-1355418. Epub 2013 Oct 28.

PMID:
24165959
39.
40.

Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization.

Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R.

Immunity. 2013 Jun 27;38(6):1271-84. doi: 10.1016/j.immuni.2013.05.011. Epub 2013 Jun 20.

41.

Epigenomic analysis of multilineage differentiation of human embryonic stem cells.

Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B.

Cell. 2013 May 23;153(5):1134-48. doi: 10.1016/j.cell.2013.04.022. Epub 2013 May 9.

42.

A field-test battery for elite, young soccer players.

Hulse MA, Morris JG, Hawkins RD, Hodson A, Nevill AM, Nevill ME.

Int J Sports Med. 2013 Apr;34(4):302-11. doi: 10.1055/s-0032-1312603. Epub 2012 Nov 9.

PMID:
23143702
43.

Methods for identifying higher-order chromatin structure.

Sajan SA, Hawkins RD.

Annu Rev Genomics Hum Genet. 2012;13:59-82. doi: 10.1146/annurev-genom-090711-163818. Epub 2012 Jun 6. Review.

PMID:
22703176
44.

Spontaneous transmitter release recruits postsynaptic mechanisms of long-term and intermediate-term facilitation in Aplysia.

Jin I, Udo H, Rayman JB, Puthanveettil S, Kandel ER, Hawkins RD.

Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):9137-42. doi: 10.1073/pnas.1206846109. Epub 2012 May 22.

45.

Spontaneous transmitter release is critical for the induction of long-term and intermediate-term facilitation in Aplysia.

Jin I, Puthanveettil S, Udo H, Karl K, Kandel ER, Hawkins RD.

Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):9131-6. doi: 10.1073/pnas.1206914109. Epub 2012 May 22.

46.

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.

Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B.

Genome Res. 2012 Feb;22(2):246-58. doi: 10.1101/gr.125872.111. Epub 2011 Dec 7.

47.

Nonlinear temporal integration of brain stimulation reward.

Hawkins RD.

Behav Neurosci. 2011 Dec;125(6):892-9. doi: 10.1037/a0026180.

PMID:
22122150
48.

Optimized detection of transcription factor-binding sites in ChIP-seq experiments.

Elo LL, Kallio A, Laajala TD, Hawkins RD, Korpelainen E, Aittokallio T.

Nucleic Acids Res. 2012 Jan;40(1):e1. doi: 10.1093/nar/gkr839. Epub 2011 Oct 18.

49.

Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency.

Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z, Kuan S, Yu P, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Ren B.

Cell Res. 2011 Oct;21(10):1393-409. doi: 10.1038/cr.2011.146. Epub 2011 Aug 30.

50.

Rapid increase in clusters of synaptophysin at onset of homosynaptic potentiation in Aplysia.

Jin I, Udo H, Hawkins RD.

Proc Natl Acad Sci U S A. 2011 Jul 12;108(28):11656-61. doi: 10.1073/pnas.1102695108. Epub 2011 Jun 27.

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