Searching journal content for Alexander J. Hartemink in author.

Displaying results 1-10 of 14
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  1. Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
    • Kevin Moyung,
    • Yulong Li,
    • Heather K. MacAlpine,
    • Alexander J. Hartemink,
    • and David M. MacAlpine
    Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
  2. Research: Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase
    • Boning Chen,
    • Heather K. MacAlpine,
    • Alexander J. Hartemink,
    • and David M. MacAlpine
    Genome Res. December 2023 33: 2108-2118; Published in Advance December 11, 2023, doi:10.1101/gr.278273.123
  3. Method: Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
    • Kaixuan Luo,
    • Jianling Zhong,
    • Alexias Safi,
    • Linda K. Hong,
    • Alok K. Tewari,
    • Lingyun Song,
    • Timothy E. Reddy,
    • Li Ma,
    • Gregory E. Crawford,
    • and Alexander J. Hartemink
    Genome Res. June 2022 32: 1183-1198; Published in Advance May 24, 2022, doi:10.1101/gr.272203.120
  4. Research: Linking the dynamics of chromatin occupancy and transcription with predictive models
    • Trung Q. Tran,
    • Heather K. MacAlpine,
    • Vinay Tripuraneni,
    • Sneha Mitra,
    • David M. MacAlpine,
    • and Alexander J. Hartemink
    Genome Res. June 2021 31: 1035-1046; Published in Advance April 23, 2021, doi:10.1101/gr.267237.120
  5. Research: Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication
    • Vinay Tripuraneni,
    • Gonen Memisoglu,
    • Heather K. MacAlpine,
    • Trung Q. Tran,
    • Wei Zhu,
    • Alexander J. Hartemink,
    • James E. Haber,
    • and David M. MacAlpine
    Genome Res. May 2021 31: 775-788; Published in Advance April 2, 2021, doi:10.1101/gr.271155.120
  6. Research: Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding
    • Ian C. McDowell,
    • Alejandro Barrera,
    • Anthony M. D'Ippolito,
    • Christopher M. Vockley,
    • Linda K. Hong,
    • Sarah M. Leichter,
    • Luke C. Bartelt,
    • William H. Majoros,
    • Lingyun Song,
    • Alexias Safi,
    • D. Dewran Koçak,
    • Charles A. Gersbach,
    • Alexander J. Hartemink,
    • Gregory E. Crawford,
    • Barbara E. Engelhardt,
    • and Timothy E. Reddy
    Genome Res. September 2018 28: 1272-1284; Published in Advance August 10, 2018, doi:10.1101/gr.233346.117
    OPEN ACCESS ARTICLE
  7. Method: Mapping nucleosome positions using DNase-seq
    • Jianling Zhong,
    • Kaixuan Luo,
    • Peter S. Winter,
    • Gregory E. Crawford,
    • Edwin S. Iversen,
    • and Alexander J. Hartemink
    Genome Res. March 2016 26: 351-364; Published in Advance January 15, 2016, doi:10.1101/gr.195602.115
  8. Resource: Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach
    • Pablo Meyer,
    • Geoffrey Siwo,
    • Danny Zeevi,
    • Eilon Sharon,
    • Raquel Norel,
    • DREAM6 Promoter Prediction Consortium,
    • Eran Segal,
    • and Gustavo Stolovitzky
    Genome Res. November 2013 23: 1928-1937; Published in Advance August 15, 2013, doi:10.1101/gr.157420.113
  9. Resource: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    • Stephen G. Landt,
    • Georgi K. Marinov,
    • Anshul Kundaje,
    • Pouya Kheradpour,
    • Florencia Pauli,
    • Serafim Batzoglou,
    • Bradley E. Bernstein,
    • Peter Bickel,
    • James B. Brown,
    • Philip Cayting,
    • Yiwen Chen,
    • Gilberto DeSalvo,
    • Charles Epstein,
    • Katherine I. Fisher-Aylor,
    • Ghia Euskirchen,
    • Mark Gerstein,
    • Jason Gertz,
    • Alexander J. Hartemink,
    • Michael M. Hoffman,
    • Vishwanath R. Iyer,
    • Youngsook L. Jung,
    • Subhradip Karmakar,
    • Manolis Kellis,
    • Peter V. Kharchenko,
    • Qunhua Li,
    • Tao Liu,
    • X. Shirley Liu,
    • Lijia Ma,
    • Aleksandar Milosavljevic,
    • Richard M. Myers,
    • Peter J. Park,
    • Michael J. Pazin,
    • Marc D. Perry,
    • Debasish Raha,
    • Timothy E. Reddy,
    • Joel Rozowsky,
    • Noam Shoresh,
    • Arend Sidow,
    • Matthew Slattery,
    • John A. Stamatoyannopoulos,
    • Michael Y. Tolstorukov,
    • Kevin P. White,
    • Simon Xi,
    • Peggy J. Farnham,
    • Jason D. Lieb,
    • Barbara J. Wold,
    • and Michael Snyder
    Genome Res. September 2012 22: 1813-1831; doi:10.1101/gr.136184.111
    OPEN ACCESS ARTICLE
  10. Letter: Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading
    • Heather K. MacAlpine,
    • Raluca Gordân,
    • Sara K. Powell,
    • Alexander J. Hartemink,
    • and David M. MacAlpine
    Genome Res. February 2010 20: 201-211; Published in Advance December 7, 2009, doi:10.1101/gr.097873.109
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