Publications
From the Lab
Li C, Georgakopoulou A, Mishra A, Gil S, Hawkins RD, Yannaki E, Lieber A. (2021) In vivo HSPC gene therapy with base editors allows for efficient reactivation of fetal γ-globin in β-YAC mice. Blood Adv 5(4):1122-1135.
Yu B#,*, Doni Jayavelu N#, Battle SL#, Mar JC, Zimmerman SE, Schimmel T, Cohen J, Hawkins, RD*. (2020) Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation. PLoS One 15(11):e241698 #Co-first author. *Co-Corresponding Author.
Battle SL & Hawkins RD. “Epigenome dynamics in in vitro and in vivo mammalian embryonic stem cell systems”. The Epigenetics of Pluripotent Stem Cells. Eds. Eran Meshorer & Guiseppe Testa. Elsevier. 2020. (book chapter)
Doni Jayavelu N, Jajodia A, Mishra A, Hawkins RD. (2020) Candidate silencer elements for the human and mouse genomes. Nature Commun. 11(1):1061
Li C, Mishra AS, Gil S, Wang M, Georgakopoulou A, Papayannopoulou T, Hawkins RD, Lieber A. (2019) Targeted Integration and High-Level Transgene Expression in AAVS1 Transgenic Mice after In Vivo HSC Transduction with HDAd5/35++ Vectors. Mol Ther. 27(12):2195-221..
Singh DD, Hawkins RD, Lahesmaa R, Tripathi SK. (2019) CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases. Semin Cell Dev Biol. 96:32-43.
Yu B*, Smith TH, Battle SL, Ferrell S, Hawkins RD*. (2019) Superovulation alters global DNA methylation in early mouse embryo development. Epigenetics. 14(8):780-790. *Co-Corresponding Author.
Battle SL, Doni Jayavelu N, Azad RN, Hesson J, Ahmed FN, Overbey EG, Zoller JA, Mathieu J, Ruohola-Baker H, Ware CB, Hawkins RD. (2019) Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States. Stem Cell Reports. 12(5):1129-1144.
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. (2019) Folliculin regulates mTORC1/2 and WNT pathways in early human pluripotency. Nat Commun. 10(1):632.
Yizhar-Barnea O*, Valensisi C*, Doni Jayavelu N, Kishore J, Andrus C, Koffler-Brill T, Ushakov K, Perl K, Noy Y, Bhonker Y, Pelizzola M, Hawkins RD**, Avraham KB**. (2018) DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory sensory epithelium. Sci Reports. 8:17348. *co-first author. **Co-Corresponding Author.
Li C, Psatha N, Sova P, Gil S, Wang H, Kim J, Kulkarni C, Valensisi C, Hawkins RD, Stamatoyannopoulos G, Lieber A. (2018) Reactivation of γ-globin in adult β-YAC mice after ex vivo and in vivo hematopoietic stem cell genome editing. Blood. 131(26):2915-2928.
Mishra A, and Hawkins RD. (2017) Three-dimensional genome architecture and emerging technologies: looping in disease. Genome Medicine. 9:87.
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. (2017) First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor. PNAS. 114(38):10125-10130.
Pasumarthy KK*, Doni Jayavelu N*, Kilpinen L, Andrus C, Battle SL, Korhonen M, Lehenkari P, Lund R, Laitinen S, Hawkins RD. (2017) Methylome analysis in human bone marrow MSCs reveals extensive age- and culture-induced changes at distal regulatory elements. Stem Cell Reports. 9: 1-17. *co-first author.
Valensisi C, Andrus C, Buckberry S, Doni Jayavelu N, Lund RJ, Lister R, Hawkins RD. (2017) Epigenomic landscapes of hESC-derived neural rosettes: modeling neural tube formation and diseases. Cell Reports. 20(6):1448-1462.
Yu B, Dong X, Gravina S, Kartal Ö, Schimmel T, Cohen J, Tortoriello D, Zody R, Hawkins RD, Vijg J. (2017) Genome-wide, Single-Cell DNA Methylomics Reveals Increased Non-CpG Methylation during Human Oocyte Maturation. Stem Cell Reports. 9(1):397-407.
Saarimaki-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. (2017) An activating STAT3 mutation causes neonatal diabetes through premature induction of pancreatic differentiation. Cell Reports. 19(2):281-294.
Bengtsson NE, Hall JK, Odom GL, Phelps MP, Andrus CR, Hawkins RD, Hauschka SD, Chamberlain JR, Chamberlain JS. (2017) Muscle-specific CRISPR/Cas9 dystrophin gene editing ameliorates pathophysiology in a mouse model for Duchenne muscular dystrophy. Nat Commun. 8:14454.
Celik S, Logsdon BA, Battle S, Drescher CW, Rendi M, Hawkins RD, Lee SI. (2016) Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer. Genome Med. 8(1):66.
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. (2016) Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells. Sci Rep. 6:22190. *co-first author.
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. (2016) Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC Differentiation Potential. Stem Cell Reports. 6(2):200-12.
Valensisi C, Liao JL, Andrus C, Battle SL, Hawkins RD. (2015) cChIP-seq: a robust small-scale method for investigation of histone modifications. BMC Genomics. 16(1):1083.
Kanduri K, Tripathi S, Larjo A, Mannerström H, Ullah U, Lund R, Hawkins RD, Ren B, Lähdesmäki H, Lahesmaa R. (2015) Identification of global regulators of T-helper cell lineage specification. Genome Med. 7(1):122.
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. (2015) The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition. Nat Cell Biol. 17(12):1523-35.
Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins RD, Akey JM. (2015) Comprehensive identification and analysis of human regulatory DNA. Genome Research. 25(9):1245-1255.
Kotini AG, Chang C, 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. (2015) Functional dissection of hemizygous chromosomal deletions with human induced pluripotent stem cell models of myelodysplastic syndromes. Nat Biotechnology. 33(6):646-655.
Gupta B, and Hawkins RD. (2015) Epigenomics of Autoimmune Diseases. Immunology and Cell Biology. 93:271-276.
Ware CB, Nelson AM, Mecham B, Hesson J, Zhou W, Jonlin E, Jimenez-Caliani AJ, Deng X, Cavanaugh C, Cook S, Tesar PJ, Okada J, Margaretha L, Sperber H, Choi M, Blau CA, Treuting P, Hawkins RD, Cirulli V, Ruohola-Baker H. (2014) Derivation of Naïve Human Embryonic Stem Cells. PNAS. 111(12):4484-4489.
Hawkins RD*, Larjo A, Tripathi SK, Wagner U, Luu Y, Lonneberg T, Raghav S, Lee LK, Lund R, Ren, B, Lähdesmäki H*, Lahesmaa R*. (2013). Global Chromatin State Analysis Reveals Lineage-Specific Enhancers During the Initiation of Human T helper 1 and T helper 2 Polarization. Immunity. 38(6):1271-1284. *Co-Corresponding Author.
Hawkins RD, & Ren B. “Epigenetics of Pluripotency”. Environmental Epigenetics. Eds. Randy Jirtle & Frederick L. Tyson. Springer. 2013. (book chapter)
Sajan SA, and Hawkins RD. (2012) Methods for Identification of Higher-Order Chromatin Structure. Annu Rev Genomics Hum Genet. 13:59-82.
Elo LL, Kallio A, Laajala TD, Hawkins RD, Korpelainen E, Aittokallio T. (2012) Optimized detection of transcription factor binding sites in ChIP-seq experiments. Nucleic Acid Research 40(1):e1.
Yu B#,*, Doni Jayavelu N#, Battle SL#, Mar JC, Zimmerman SE, Schimmel T, Cohen J, Hawkins, RD*. (2020) Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation. PLoS One 15(11):e241698 #Co-first author. *Co-Corresponding Author.
Battle SL & Hawkins RD. “Epigenome dynamics in in vitro and in vivo mammalian embryonic stem cell systems”. The Epigenetics of Pluripotent Stem Cells. Eds. Eran Meshorer & Guiseppe Testa. Elsevier. 2020. (book chapter)
Doni Jayavelu N, Jajodia A, Mishra A, Hawkins RD. (2020) Candidate silencer elements for the human and mouse genomes. Nature Commun. 11(1):1061
Li C, Mishra AS, Gil S, Wang M, Georgakopoulou A, Papayannopoulou T, Hawkins RD, Lieber A. (2019) Targeted Integration and High-Level Transgene Expression in AAVS1 Transgenic Mice after In Vivo HSC Transduction with HDAd5/35++ Vectors. Mol Ther. 27(12):2195-221..
Singh DD, Hawkins RD, Lahesmaa R, Tripathi SK. (2019) CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases. Semin Cell Dev Biol. 96:32-43.
Yu B*, Smith TH, Battle SL, Ferrell S, Hawkins RD*. (2019) Superovulation alters global DNA methylation in early mouse embryo development. Epigenetics. 14(8):780-790. *Co-Corresponding Author.
Battle SL, Doni Jayavelu N, Azad RN, Hesson J, Ahmed FN, Overbey EG, Zoller JA, Mathieu J, Ruohola-Baker H, Ware CB, Hawkins RD. (2019) Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States. Stem Cell Reports. 12(5):1129-1144.
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. (2019) Folliculin regulates mTORC1/2 and WNT pathways in early human pluripotency. Nat Commun. 10(1):632.
Yizhar-Barnea O*, Valensisi C*, Doni Jayavelu N, Kishore J, Andrus C, Koffler-Brill T, Ushakov K, Perl K, Noy Y, Bhonker Y, Pelizzola M, Hawkins RD**, Avraham KB**. (2018) DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory sensory epithelium. Sci Reports. 8:17348. *co-first author. **Co-Corresponding Author.
Li C, Psatha N, Sova P, Gil S, Wang H, Kim J, Kulkarni C, Valensisi C, Hawkins RD, Stamatoyannopoulos G, Lieber A. (2018) Reactivation of γ-globin in adult β-YAC mice after ex vivo and in vivo hematopoietic stem cell genome editing. Blood. 131(26):2915-2928.
Mishra A, and Hawkins RD. (2017) Three-dimensional genome architecture and emerging technologies: looping in disease. Genome Medicine. 9:87.
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. (2017) First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor. PNAS. 114(38):10125-10130.
Pasumarthy KK*, Doni Jayavelu N*, Kilpinen L, Andrus C, Battle SL, Korhonen M, Lehenkari P, Lund R, Laitinen S, Hawkins RD. (2017) Methylome analysis in human bone marrow MSCs reveals extensive age- and culture-induced changes at distal regulatory elements. Stem Cell Reports. 9: 1-17. *co-first author.
Valensisi C, Andrus C, Buckberry S, Doni Jayavelu N, Lund RJ, Lister R, Hawkins RD. (2017) Epigenomic landscapes of hESC-derived neural rosettes: modeling neural tube formation and diseases. Cell Reports. 20(6):1448-1462.
Yu B, Dong X, Gravina S, Kartal Ö, Schimmel T, Cohen J, Tortoriello D, Zody R, Hawkins RD, Vijg J. (2017) Genome-wide, Single-Cell DNA Methylomics Reveals Increased Non-CpG Methylation during Human Oocyte Maturation. Stem Cell Reports. 9(1):397-407.
Saarimaki-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. (2017) An activating STAT3 mutation causes neonatal diabetes through premature induction of pancreatic differentiation. Cell Reports. 19(2):281-294.
Bengtsson NE, Hall JK, Odom GL, Phelps MP, Andrus CR, Hawkins RD, Hauschka SD, Chamberlain JR, Chamberlain JS. (2017) Muscle-specific CRISPR/Cas9 dystrophin gene editing ameliorates pathophysiology in a mouse model for Duchenne muscular dystrophy. Nat Commun. 8:14454.
Celik S, Logsdon BA, Battle S, Drescher CW, Rendi M, Hawkins RD, Lee SI. (2016) Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer. Genome Med. 8(1):66.
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. (2016) Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells. Sci Rep. 6:22190. *co-first author.
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. (2016) Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC Differentiation Potential. Stem Cell Reports. 6(2):200-12.
Valensisi C, Liao JL, Andrus C, Battle SL, Hawkins RD. (2015) cChIP-seq: a robust small-scale method for investigation of histone modifications. BMC Genomics. 16(1):1083.
Kanduri K, Tripathi S, Larjo A, Mannerström H, Ullah U, Lund R, Hawkins RD, Ren B, Lähdesmäki H, Lahesmaa R. (2015) Identification of global regulators of T-helper cell lineage specification. Genome Med. 7(1):122.
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. (2015) The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition. Nat Cell Biol. 17(12):1523-35.
Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins RD, Akey JM. (2015) Comprehensive identification and analysis of human regulatory DNA. Genome Research. 25(9):1245-1255.
Kotini AG, Chang C, 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. (2015) Functional dissection of hemizygous chromosomal deletions with human induced pluripotent stem cell models of myelodysplastic syndromes. Nat Biotechnology. 33(6):646-655.
Gupta B, and Hawkins RD. (2015) Epigenomics of Autoimmune Diseases. Immunology and Cell Biology. 93:271-276.
Ware CB, Nelson AM, Mecham B, Hesson J, Zhou W, Jonlin E, Jimenez-Caliani AJ, Deng X, Cavanaugh C, Cook S, Tesar PJ, Okada J, Margaretha L, Sperber H, Choi M, Blau CA, Treuting P, Hawkins RD, Cirulli V, Ruohola-Baker H. (2014) Derivation of Naïve Human Embryonic Stem Cells. PNAS. 111(12):4484-4489.
Hawkins RD*, Larjo A, Tripathi SK, Wagner U, Luu Y, Lonneberg T, Raghav S, Lee LK, Lund R, Ren, B, Lähdesmäki H*, Lahesmaa R*. (2013). Global Chromatin State Analysis Reveals Lineage-Specific Enhancers During the Initiation of Human T helper 1 and T helper 2 Polarization. Immunity. 38(6):1271-1284. *Co-Corresponding Author.
Hawkins RD, & Ren B. “Epigenetics of Pluripotency”. Environmental Epigenetics. Eds. Randy Jirtle & Frederick L. Tyson. Springer. 2013. (book chapter)
Sajan SA, and Hawkins RD. (2012) Methods for Identification of Higher-Order Chromatin Structure. Annu Rev Genomics Hum Genet. 13:59-82.
Elo LL, Kallio A, Laajala TD, Hawkins RD, Korpelainen E, Aittokallio T. (2012) Optimized detection of transcription factor binding sites in ChIP-seq experiments. Nucleic Acid Research 40(1):e1.
Previous work
Epigenomic Roadmap Consortium, et al. (2015) Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-330.
Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, et al. (2013). Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells. Cell. 153(5):1134-1148.
Hon G, 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. (2012) Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Research 22(2):246-58.
Hawkins RD†, Hon GC†, Yang C, Antosiewicz JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Kuan S, Yu P, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Ren B. (2011) Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Research. 21: 1393-1409. †Equal contribution of work.
Alvarado DM, Hawkins RD, Bashiardes S, Veile RA, Powder KE, Speck J, Warchol ME, Lovett M. (2011) An RNAi-Based Screen of Transcription Factor Gene Pathways During Sensory Regeneration in the Avian Inner Ear. J Neurosci. 31: 4535-4543.
Lister R†, Pelizzola M†, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O’Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomas JA, Evans RM, Ecker JR. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 471: 68-73. †Equal contribution of work.
Egelhofer TA†, Minoda A†, KlugmanS†, Kolasinska-Zwierz P, Alekseyenko AA, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Rechtsteiner A, Riddle NC, Schwartz YB, Vielle A, Elgin SCR, Kuroda MI, Park PJ, Pirrotta V, Ren B, Ahringer J, Strome S, Karpen G^, Hawkins RD^, and Lieb JD^ (2010) Assessment of histone-modification antibody quality. Nature Structural & Molecular Biology. 18:91-94. †Equal contribution of work; ^Co-corresponding Authors.
Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28(10): 1097-1105.
Hawkins RD†, Hon GC†, Ren B. (2010) Next-Generation Genomics: An Integrative Approach. Nature Reviews Genetics 11(7); 476-486. †Equal contribution of work
Elo LL†, Järvenpää H†, Tuomela S*, Raghav S*, Ahlfors H, Laurila K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Oresic, M, Lähdesmäki H, Rasool O, Rao KV, Aittokallio T, Lahesmaa R. (2010) Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity 32: 852-862. †Equal contribution of work
Hawkins RD †, Hon GC †, Lee LK, Ngo Q, Lister R, Pelizzola M, Kuan S, Edsall LE, Ye Z, Espinoza C, Antosiewicz-Bourget J, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B. (2010) Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6: 279-491. †Equal contribution of work
Lister R†, Pelizzola M†, Dowen RH, Hawkins RD, Hon GC, Tonti-Filippini J, Nery JR, Lee LK, Edsall LE, Antosiewicz-Bourget J, Ruotti V, Elwell A, Hernandez A, Stewart R, Millar AH, Thomson JA, Ren B, Ecker JR. (2009) Human DNA methylomes at single-base resolution reveal widespread cell-specific epigenetic signatures. Nature 462: 315-322. †Equal contribution of work
Hon GC, Hawkins RD, Ren, B. (2009) Predictive chromatin signatures in the mammalian genome. Hum Mol Genet. 18(R2): R195-201. (Review)
Heintzman ND†, Hon G†, Hawkins RD†, Kheradpour P, Ching KA, Stuart RK, Harp LF, Ching CW, Liu H, Zhang X, Green RD, Crawford GE, Kellis M, and Ren B. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112. †Equal contribution of work
Li Y, Reddy MA, Miao F, Shanmugam N, Yee JK, Hawkins D, Ren B, Natarajan R. (2008) Role of the histone H3 lysine 4 methyltransferase, SET7/9, in the regulation of NF-kappa B dependent inflammatory genes: Relevance to diabetes and inflammation. J Biol Chem. 283(39):26771-81.
Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacher PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu, XS. (2008). Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. Mar;18(3):393-403.
Heintzman, ND, Stuart RK, Hon G, Fu YW, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE and Ren B. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genetics, 39: 311-318.
Hawkins RD†, Bashiardes S†, Powder KE, Sajan SA, Bhonagiri V, Alvarado DM, Speck J, Warchol ME, and Lovett M. (2007). Large scale gene expression profiles of regenerating inner ear sensory epithelia. PLoS ONE 2(6): e525. †Equal contribution of work
Hawkins RD, and Ren B. (2006) Genome-wide Location Analysis: insights on transcriptional regulation. Hum Mol Genet. 15(1): R1-7. (Review)
Hawkins RD, Helms CA, Winston JB, Warchol ME, and Lovett M. (2006) Applying genomics to the avian inner ear: development of subtractive cDNA resources for exploring sensory function and hair cell regeneration. Genomics 87: 801-808.
Hawkins RD, and Lovett M. (2004) The developmental genetics of auditory hair cells. Hum Mol Genet. 13(2): R289-296. (Review)
Hawkins RD, Bashiardes S, Helms CA, Hu L, Saccone NL, Warchol ME, and Lovett M. (2003) Gene expression differences in quiescent versus regenerating hair cells of avian sensory epithelia: implications for human hearing and balance disorders. Hum Mol Genet. 12: 1261-1272.
Lai JY, Yu J, Hawkins RD, and Falck JR. (1995) Two-Carbon elongation/annulation of alcohols to nitriles. Tetrahedron Lett. 36: 5691-5694.
Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, et al. (2013). Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells. Cell. 153(5):1134-1148.
Hon G, 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. (2012) Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Research 22(2):246-58.
Hawkins RD†, Hon GC†, Yang C, Antosiewicz JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Kuan S, Yu P, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Ren B. (2011) Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Research. 21: 1393-1409. †Equal contribution of work.
Alvarado DM, Hawkins RD, Bashiardes S, Veile RA, Powder KE, Speck J, Warchol ME, Lovett M. (2011) An RNAi-Based Screen of Transcription Factor Gene Pathways During Sensory Regeneration in the Avian Inner Ear. J Neurosci. 31: 4535-4543.
Lister R†, Pelizzola M†, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O’Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomas JA, Evans RM, Ecker JR. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 471: 68-73. †Equal contribution of work.
Egelhofer TA†, Minoda A†, KlugmanS†, Kolasinska-Zwierz P, Alekseyenko AA, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Rechtsteiner A, Riddle NC, Schwartz YB, Vielle A, Elgin SCR, Kuroda MI, Park PJ, Pirrotta V, Ren B, Ahringer J, Strome S, Karpen G^, Hawkins RD^, and Lieb JD^ (2010) Assessment of histone-modification antibody quality. Nature Structural & Molecular Biology. 18:91-94. †Equal contribution of work; ^Co-corresponding Authors.
Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28(10): 1097-1105.
Hawkins RD†, Hon GC†, Ren B. (2010) Next-Generation Genomics: An Integrative Approach. Nature Reviews Genetics 11(7); 476-486. †Equal contribution of work
Elo LL†, Järvenpää H†, Tuomela S*, Raghav S*, Ahlfors H, Laurila K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Oresic, M, Lähdesmäki H, Rasool O, Rao KV, Aittokallio T, Lahesmaa R. (2010) Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity 32: 852-862. †Equal contribution of work
Hawkins RD †, Hon GC †, Lee LK, Ngo Q, Lister R, Pelizzola M, Kuan S, Edsall LE, Ye Z, Espinoza C, Antosiewicz-Bourget J, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B. (2010) Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6: 279-491. †Equal contribution of work
Lister R†, Pelizzola M†, Dowen RH, Hawkins RD, Hon GC, Tonti-Filippini J, Nery JR, Lee LK, Edsall LE, Antosiewicz-Bourget J, Ruotti V, Elwell A, Hernandez A, Stewart R, Millar AH, Thomson JA, Ren B, Ecker JR. (2009) Human DNA methylomes at single-base resolution reveal widespread cell-specific epigenetic signatures. Nature 462: 315-322. †Equal contribution of work
Hon GC, Hawkins RD, Ren, B. (2009) Predictive chromatin signatures in the mammalian genome. Hum Mol Genet. 18(R2): R195-201. (Review)
Heintzman ND†, Hon G†, Hawkins RD†, Kheradpour P, Ching KA, Stuart RK, Harp LF, Ching CW, Liu H, Zhang X, Green RD, Crawford GE, Kellis M, and Ren B. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112. †Equal contribution of work
Li Y, Reddy MA, Miao F, Shanmugam N, Yee JK, Hawkins D, Ren B, Natarajan R. (2008) Role of the histone H3 lysine 4 methyltransferase, SET7/9, in the regulation of NF-kappa B dependent inflammatory genes: Relevance to diabetes and inflammation. J Biol Chem. 283(39):26771-81.
Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacher PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu, XS. (2008). Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. Mar;18(3):393-403.
Heintzman, ND, Stuart RK, Hon G, Fu YW, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE and Ren B. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genetics, 39: 311-318.
Hawkins RD†, Bashiardes S†, Powder KE, Sajan SA, Bhonagiri V, Alvarado DM, Speck J, Warchol ME, and Lovett M. (2007). Large scale gene expression profiles of regenerating inner ear sensory epithelia. PLoS ONE 2(6): e525. †Equal contribution of work
Hawkins RD, and Ren B. (2006) Genome-wide Location Analysis: insights on transcriptional regulation. Hum Mol Genet. 15(1): R1-7. (Review)
Hawkins RD, Helms CA, Winston JB, Warchol ME, and Lovett M. (2006) Applying genomics to the avian inner ear: development of subtractive cDNA resources for exploring sensory function and hair cell regeneration. Genomics 87: 801-808.
Hawkins RD, and Lovett M. (2004) The developmental genetics of auditory hair cells. Hum Mol Genet. 13(2): R289-296. (Review)
Hawkins RD, Bashiardes S, Helms CA, Hu L, Saccone NL, Warchol ME, and Lovett M. (2003) Gene expression differences in quiescent versus regenerating hair cells of avian sensory epithelia: implications for human hearing and balance disorders. Hum Mol Genet. 12: 1261-1272.
Lai JY, Yu J, Hawkins RD, and Falck JR. (1995) Two-Carbon elongation/annulation of alcohols to nitriles. Tetrahedron Lett. 36: 5691-5694.
