Publications

2023

• Arora U, Sullivan BA, Dumont BL (2023) Variation in the CENP-A sequence association landscape across diverse inbred mouse strains. Cell Rep, DOI: https://doi.10.1016/j..celrep.2023.113178.

2022

• Alkan C, Carbone L, Dennis M, Ernst J, Evrony G, Girirajan S, Leung DCY, Cheng CCY, MacAlpine D, Ting N, Ramsay M, Rowe H, Gould P, Enriquez-Gasca R, Sullivan B  (2022) Perspective: Implications of the first complete human genome assembly. Genome Res, 32: 595-598, doi:10.1101/gr.276723.122. 
• Altemose N, Logsdon GA, Bzikadze AV, Sidhwani S, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks, S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gertson JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O’Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH (2022) Complete genomic and epigenetic maps of human centromeres. Science, 376(6588):eabl4178, doi: 10.1126/science.abl4178.
• Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Cheng H, Chin C-S, Chose W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sovic I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti V, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O’Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM (2022) The complete sequence of a human genome. Science, 376(6588): 44-53.

2021

• DeBose-Scarlett E, Sullivan BA (2021) Genomic and epigenetic foundations of neocentromere formation. Annu Rev Genet 55:331-348; doi: 10.1146/annurev-genet-071719-020924.
• Miga KH, Sullivan BA (2021) Expanding studies of chromosome structure and function in the era of T2T genomics. Hum Mol Genet 30(R2):R198-R205; doi: 10.1093/hmg/ddab214.
• Sullivan BA (2021) The new year for chromosome research: a change of guard amidst a shifting scientific landscape and global pandemic. Chromosome Res 29, pages 127–130, doi: 10.1007/s10577-021-09647-4.

2020

• Hoffmann S, Izquierdo HM, Gamba R, Chardon F, Dumont M, Keizer V, Herve S, McNulty SM, Sullivan BA, Manel N, Fachinetti D (2020) A genetic memory initiates the epigenetic loop necessary to preserve centromere position. EMBO J, e105505, doi: 10.15252/embj.2020105505, PMCID: PMC7560200.
• Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Frederickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Thibaud-Nissen F, Schmitt AD, Belton J-M, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, ana Risque R, Graves Lindsay TA, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM (2020) Telomere-to-telomere assembly of a complete human X chromosome. Nature 585(7823):79-84, doi: 10.1038/s41586-020-2547-7, PMCID: PMC7484160.
• Sullivan BA (2020) De novo centromere formation: one’s company, two’s a crowd. Dev Cell, 52(3):257-258, doi.org/10.1016/j.devcel/2020.01.021.
• Sullivan LL, Sullivan BA (2020) Genomic and functional variation of human centromeres. Exp Cell Res, 389(2): 11896, doi: 10.1016/j.yexcr.2020.111896, PMCID: PMC7140587.
• Sullivan BA (2020) A sampling of methods to study chromosome and genome structure and function. Chromosome Res, 28(1):1-5, doi.org/10.1007/s10577-020-09629-y.

2019

• McNulty SM, Sullivan BA (2019) Going the distance: Neocentromeres make long-range contacts with heterochromatin. J Cell Biol, 218(1):5-7, doi: 10.1083/jcb.201811172, PMCID: PMC6363448.

2018

• McNulty SM, Sullivan BA (2018) Alpha satellite DNA biology: finding function in the recesses of the genome. Chromosome Res, 26(3):115-138, doi: 10.1007/s10577-018-9582-3, PMCID: PMC6121732.

2017

• Larsen PA*, Harris RA*, Liu Y, Murali SC, Campbell CR, Brown AD, Sullivan BA, Shelton J, Brown SJ, Raveendran M, Dudchencko O, Machol I, Lieberman E, Muzny DM, Gibbs RA, Yoder AD, Rogers J, Worley KC (2017) Hybrid de novo assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). BMC Biology, 15:110, doi: 10.1186/s12915-017-0439-6, PMCID: PMC5689209. (*joint first authors)
• McNulty SM, Sullivan BA (2017) Centromere Silencing Mechanisms. Prog Mol Subcell Biol 56:233-255, doi: 10.1007/978-3-319-58592-5_10.
• Iwata-Otsubo A, Dawicki-McKenna JM, Akera T, Falk SJ, Chmatal L, Yang K, Sullivan BA, Schultz RM, Lampson MA, Black BE (2017) Expanded satellite repeats amplify a discrete CENP-A nucleosome assembly site on chromosomes that drive in female meiosis. Curr Biol, 27:2365-2373, doi: 10.1016/j.cub.2017.06.069, PMCID: PMC5567862.
• McNulty SM, Sullivan LL, Sullivan BA (2017) Human centromeres produce chromosome-specific and array-specific alpha satellite transcripts that are complexed with CENP-A and CENP-C. Dev Cell, 42:226-240, doi: 10.1016/j.devcel/2017.07.001, PMCID: PMC5568664. [Read the preview by Mike Blower’s lab]
• Johnson WL*, Yewdell WT*, Bell JC, McNulty SM, Duda Z, O’Neill RJ, Sullivan BA, Straight AF (2017) RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin. eLife, 6:e25299, doi: 10.7554/eLife.25299, PMCID: PMC5538822. (*joint first authors)
• Sullivan LL, Chew K, Sullivan BA (2017) Alpha satellite DNA variation and function of the human centromere. Nucleus, 8(4):331-339, doi: 10.1080/19491034.2017.1308989, PMCID: PMC5597293.

2016

• Sullivan LL, Maloney KA, Towers AJ, Gregory SG, Sullivan BA (2016) Human centromere repositioning within euchromatin after partial chromosome deletion. Chromosome Res 24(4):451-466, doi: 10.1007/s10577-016-9536-6, PMCID: PMC5366066.
• Aldrup-MacDonald ME*, Kuo ME*, Sullivan LL*, Chew K, Sullivan BA (2016) Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles. Genome Res 26:1301-1311, doi: 10.1101/gr.206706.116, PMCID: PMC5052062 (*joint first authors)  [press releases: https://www.eurekalert.org/pub_releases/2016-08/du-vi083016.php; http://www.wfdd.org/story/predictive-power-junk-your-genome-0].
• Ross JE, Woodlief KS, Sullivan BA (2016) Inheritance of the CENP-A chromatin domain is spatially and temporally constrained at human centromeres. Epigenetics Chromatin 9:20, doi: 10.1186/s13072-016-0071-7, PMCID: PMC4888493.

2015

• Ross JE*, McNulty SM*, Sullivan BA (2015) The epigenetics of centromere function. in “Epigenetics: Current Research and Emerging Trends” (BP Chadwick, editor), pp. 133-166, Caister Academic Press. (*joint first authors)

2014

• Stimpson KM, Sullivan LL, Kuo ME, Sullivan BA (2014) Nucleolar organization, ribosomal DNA array stability, and acrocentric chromosome integrity are linked to telomere function. PLoS ONE 9(3): e92432. doi: 10.1371/journal.pone.0092432, PMCID: PMC3963894.
• Scott KC and Sullivan BA (2014) Neocentromeres: A place for everything and everything in its place. Trends Genet 30:66-74, PMCID: PMC3913482.
• Aldrup-MacDonald ME and Sullivan BA (2014) The past, present, and future of human centromere genomics. Genes 5:33-50, doi: 10.3390/genes5010033, PMCID: PMC3966626.

2013

• Earnshaw WC, Allshire RC, Black BE, Bloom K, Brinkley BR, Brown W, Cheeseman IM, Choo KHA, Copenhaver GP, DeLuca JG, Desai A, Diekmann S, Erhardt S, Fitzgerald-Hayes M, Foltz, D, Fukagawa T, Gassmann R, Gerlich DW, Glover DM, Gorbsky GJ, Harrison SC, Heun P, Hirota T, Jansen LET, Karpen G, Kops GJPL, Lampson MA, Lens SM, Losada A, Luger K, Maiato H, Maddox PS, Margolis RL, Masumoto H, McAinsh AD, Mellone BG, Meraldi P, Musacchio A, Oegema K, O’Neill RJ, Salmon ED, Scott KC, Straight AF, Stukenberg PT, Sullivan BA, Sullivan KF, Sunkel CE, Swedlow JR, Walczak CE, Warburton PE, Westermann S, Willard HF, Wordem L, Yanagida M, Yen TJ, Yoda K, Cleveland DW (2013) Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant. Chromosome Res 21:101–106, doi: 10.1007/s10577-013-9347-y, PMCID: PMC3627038.

2012

• Maloney KA, Sullivan LL, Matheny JE, Strome ED, Merrett SL, Ferris A, Sullivan BA (2012) Functional epialleles at an endogenous human centromere. Proc Natl Acad Sci USA 109(34):13704-13709, PMCID: PMC3427087.
• Stimpson KM, Matheny JE, Sullivan BA. (2012) Dicentric chromosomes: unique models to study centromere function and inactivation.  Chromosome Res doi: 10.1007/s10577-012-9302-3, PMCID: PMC3557915. pdf
• Stimpson KM, Sullivan BA. (2012) Centromeres poised en pointe: CDKs put a hold on CENP-A assembly.  Dev Cell 22(1):1-2.

2011

• Sullivan LL, Boivin CD, Mravinac B, Song IY, Sullivan BA. (2011) Genomic size of CENP-A domain is proportional to total alpha satellite array size at human centromeres and expands in cancer cells. Chromosome Res (19)4:457-470, PMCID: PMC3565466.

2010

• Stimpson KM, Sullivan BA. (2011) Histone H3K4 methylation keeps centromeres open for business. EMBO J 30(2):233-234, PMCID: PMC3025472.
• Sullivan BA. (2010) Optical mapping of protein-DNA complexes on chromatin fibers. Methods Mol Biol 659:99-115.
• Stimpson KM, Song IY, Jauch A, Holtgreve-Grez H, Hayden KE, Bridger JM, Sullivan BA. (2010) Telomere disruption results in non-random formation of de novo dicentric chromosomes involving acrocentric human chromosomes. PLOS Genet 6(8):e1001061, PMCID: PMC2920838.
• Stimpson KM, Sullivan BA. (2010) Epigenomics of centromere assembly and function. Curr Opin Cell Biol 22:772-80.

2009

• Balakumaran BS, Porrello A, Hsu DS, Glover W, Foye A, Leung JY, Sullivan BA, Hahn WC, Loda M, Febbo PG. (2009) MYC Activity Mitigates Response to Rapamycin in Prostate Cancer through Eukaryotic Initiation Factor 4E-Binding Protein 1-Mediated Inhibition of Autophagy. Cancer Res 69(19):7803-10.
• Mravinac B, Sullivan LL, Reeves JW, Yan CM, Kopf KS, Farr CJ, Schueler MG, Sullivan BA. (2009) Histone modifications within the human X centromere region. PLoS ONE 4(8):e6602, PMCID: PMC2719913.
• Gopalakrishnan S, Sullivan BA, Trazzi S, Della Valle G, Robertson KD. (2009) DNMT3B interacts with constitutive centromere protein CENP-C to modulate DNA methylation and the histone code at centromeric regions. Human Mol Genet 18:3178–3193, PMCID: PMC2722982.
• Kim JH, Ebersole T, Kouprina N, Noskov VN, Ohzeki J, Masumoto H, Mravinac B, Sullivan BA, Pavlicek A, Dovat S, Pack SD, Kwon YW, Flanagan PT, Loukinov D, Lobanenkov V, Larionov V. (2009) Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing. Genome Res 19(4):533-44, PMCID: PMC2665773.
• Gao F, Ponte JF, Levy M, Papageorgis P, Cook NM, Ozturk S, Lambert AW, Thiagalingam A, Abdolmaleky HM, Sullivan BA, Thiagalingam S. (2009) hBub1 negatively regulates p53 mediated early cell death upon mitotic checkpoint activation. Cancer Biol Ther 8(7):55-63.

2006

• Dai J, Sullivan BA, and Higgins JM. (2006) Regulation of mitotic chromosome cohesion by haspin and aurora B. Dev Cell 11:741-750 (BAS-cover illustration).
• Schueler MG, Sullivan BA. (2006) Structural and functional dynamics of human centromeric chromatin. Annu Rev Genomics Hum Genet 7:301-13.
• Lam AL, Boivin CD, Bonney CF, Rudd MK, Sullivan BA. (2006) Human centromeric chromatin is a dynamic chromosomal domain that can spread over non-centromeric DNA. Proc Natl Acad Sci USA 103:4186-4191, PMCID: PMC1449668.

2005

• Scott KC, Sullivan BA. (2005) Epigenetic Inheritance and RNAi at the centromere and heterochromatin. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, (Section editor: R. Nicholls), Edited by Lynn Jorde (John Wiley & Sons), doi: 10.1002/04701153X.g103322.
• Wilson KC, Cattel DJ, Wan Z, Rahangdale S, Ren F, Kornfeld H, Sullivan BA, Cruikshank WW, Center DM. (2005) Regulation of prointerleukin-16 and p27Kip1 in primary human T lymphocytes, Cell Immunol 237:17-27.
• Lam AL, Pazin DE, Sullivan BA. (2005) Control of gene expression and assembly of chromosomal subdomains by chromatin regulators with antagonistic functions. Chromosoma 114:242-51.

2004

• Sullivan, BA. (2004) Centromeres. In Encyclopedia of Biological Chemistry. (W.J. Lennarz and M.D. Lane eds), Elsevier, Oxford, Vol.1, pp. 367-371.
• Sullivan BA, Karpen GH. (2004) Centromeric chromatin displays a histone modification pattern that is distinct from both euchromatin and heterochromatin. Nat Struc Mol Biol 11:1076-1083 (+ cover illustration), PMCID: PMC1283111.

2002

• Sullivan, BA. (2002) Centromere round-up at the heterochromatin corral. Trends Biotech 20:89-92.
• Blower MD*, Sullivan BA*, Karpen GH. (2002) Conserved organization of centromeric chromatin in flies and humans. Dev Cell 2:319-330 (*joint first authors; BAS-cover illustration), PMCID: PMC3192492.
• Hoskins RA, Smith CD, Carlson JW, Carvalho AB, Halpern A, Kaminker JS, Kennedy C, Mungall CJ, Sullivan BA, Sutton GG, Yasuhara JC, Wakimoto BT, Myers EW, Celniker SE, Rubin GM, Karpen GH. (2002) Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol 3:85.1-85.16, PMCID: PMC151187.

2001

• Sullivan BA, Blower MD, Karpen GH. (2001) Determining centromere identity: cyclical stories and forking paths. Nat Rev Genet 2:584-596.
• Sullivan B, Karpen G. (2001) Centromere identity in Drosophila is not determined in vivo by replication timing. J Cell Biol 154:683-690.
• Gong Y, RB Slee et al. (2001) LDL Receptor-Related Protein 5 (LRP5) affects bone accrual and eye development. Cell 107:513–523.

2000

• Sullivan BA, Bickmore WA. (2000) Unusual chromosome architecture and behaviour at an HSR. Chromosoma 109:173-180.

1999

• Sullivan BA & PE Warburton (1999) Studying the progression of vertebrate chromosomes through mitosis by immunofluorescence and FISH. In Chromosome Structural Analysis: A Practical Approach, p 81-101, Edited by Dr. Wendy Bickmore (IRL Press).

1998

• Sullivan BA & HF Willard (1998) Stable dicentric X chromosomes with two functional centromeres. Nat Genet 20:227-228.

1997

• Flejter, WL, B Issa, BA Sullivan, JC Carey, & AR Brothman (1997) Variegated aneuploidy in two siblings with microcephaly, growth deficiency, and minor somatic anomalies. Amer J Med Genet 75:45-51.
• Depinet TW, JL Zackowski, WC Earnshaw, S Kaffe, GS Sekhon, R Stallard, BA Sullivan, GH Vance, DL Van Dyke, HF Willard, AB Zinn, & S Schwartz (1997) Characterization of neo-centromeres in marker chromosomes lacking detectable alpha-satellite DNA. Hum Mol Genet 6:1195-1204.
• Warburton PE, CA Cooke, S Bourassa, O Vafa, BA Sullivan, G Stetten, G Gimelli, D Warburton, C Tyler-Smith, KF Sullivan, GG Poirier, & WC Earnshaw (1997) Immunolocalization of CENP-A, a kinetochore-specific histone H3 variant, suggests a distinct nucleosome structure at the inner kinetochore plate of active centromeres. Curr Biol 7:901-904.

1996

• Sullivan BA, S Schwartz, & HF Willard (1996) Centromeres of human chromosomes. Environ Mol Mutagenesis 28:182-191.
• Sullivan BA, LJ Jenkins, J Leana-Cox, E Karson, & S Schwartz (1996) Evidence for structural heterogeneity from molecular cytogenetic analysis of dicentric Robertsonian translocations. Amer J Hum Genet 59:167-175, PMCID: PMC1915107.

1995

• Sullivan BA, CA Schiffer, SR Patil, D Hulseberg, J Leana-Cox, & S Schwartz (1995) Application of FISH to rearrangements associated with chronic myelogenous leukemia. Cancer Genet Cytogenet 82:93-99.
• Sullivan BA & S Schwartz (1995) Identification of centromeric antigens in dicentric Robertsonian translocations: CENP-C and CENP-E are essential components of functional centromeres. Hum Mol Genet 4:2189-2198 (+ cover illustration).

1994

• Sullivan BA, DJ Wolff, and S Schwartz (1994) Analysis of centromeric activity in dicentric Robertsonian translocations: Implications for a functional acrocentric hierarchy. Chromosoma 103:459-467.

1993

• Leana-Cox J, S Levin, R Surana, E Wulfsberg, CL Keene, LJ Raffel, B Sullivan, and S Schwartz (1993) Characterization of de novo duplications in eight patients by using fluorescence in situ hybridization with chromosome-specific DNA libraries. Amer J Hum Genet 52:1067-1073.
• Sullivan BA, Leana-Cox J, and S Schwartz (1993) Clarification of subtle reciprocal rearrangements using fluorescence in situ hybridization. Amer J Med Genet 47:223-230.