PUBLICATIONS

IMG_0950.jpg

  • Justin Wagner, Nathan D Olson, Lindsay Harris, Jennifer McDaniel, Haoyu Cheng, Arkarachai Fungtammasan, Yih-Chii Hwang, Richa Gupta, Aaron M Wenger, William J Rowell, Ziad M Khan, Jesse Farek, Yiming Zhu, Aishwarya Pisupati, Medhat Mahmoud, Chunlin Xiao, Byunggil Yoo, Sayed Mohammad Ebrahim Sahraeian, Danny E Miller, David Jaspez, Jose M Lorenzo-Salazar, Adrian Munoz-Barrera, Luis A Rubio-Rodriguez, Carlos Flores, Giuseppe Narzisi, Uday Shanker Evani, Wayne E Clarke, Joyce Lee, Christopher E Mason, Stephen E Lincoln, Karen H. Miga, Mark TW Ebbert, Alaina Shumate, Heng Li, Chen-Shan Chin, Justin M Zook, Fritz J Sedlazeck“Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes.” bioRxiv (2021). doi: https://doi.org/10.1101/2021.06.07.444885

  • Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J. Hoyt, Mark Diekhans, Glennis A. Logsdon, Michael Alonge, Stylianos E. Antonarakis, Matthew Borchers, Gerard G. Bouffard, Shelise Y. Brooks, Gina V. Caldas, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G. de Lima, Philip C. Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T. Fiddes, Giulio Formenti, Robert S. Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G.S. Grady, Tina A. Graves-Lindsay, Ira M. Hall, Nancy F. Hansen, Gabrielle A. Hartley, Marina Haukness, Kerstin Howe, Michael W. Hunkapiller, Chirag Jain, Miten Jain, Erich D. Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V. Maduro, Tobias Marschall, Ann M. McCartney, Jennifer McDaniel, Danny E. Miller, James C. Mullikin, Eugene W. Myers, Nathan D. Olson, Benedict Paten, Paul Peluso, Pavel A. Pevzner, David Porubsky, Tamara Potapova, Evgeny I. Rogaev, Jeffrey A. Rosenfeld, Steven L. Salzberg, Valerie A. Schneider, Fritz J. Sedlazeck, Kishwar Shafin, Colin J. Shew, Alaina Shumate, Yumi Sims, Arian F. A. Smit, Daniela C. Soto, Ivan Sović, Jessica M. Storer, Aaron Streets, Beth A. Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P. Walenz, Aaron Wenger, Jonathan M. D. Wood, Chunlin Xiao, Stephanie M. Yan, Alice C. Young, Samantha Zarate, Urvashi Surti, Rajiv C. McCoy, Megan Y. Dennis, Ivan A. Alexandrov, Jennifer L. Gerton, Rachel J. O’Neill, Winston Timp, Justin M. Zook, Michael C. Schatz, Evan E. Eichler† , Karen H. Miga† , Adam M. Phillippy† "The complete sequence of a human genome." bioRxiv (2021). doi: https://doi.org/10.1101/2021.05.26.445798

    (* denotes equal contribution, † denotes corresponding authorship)

  • Mitchell R. Vollger, Xavi Guitart, Philip C. Dishuck, Ludovica Mercuri, William T. Harvey, Ariel Gershman, Mark Diekhans, Arvis Sulovari, Katherine M. Munson, Alexandra M. Lewis, Kendra Hoekzema, David Porubsky, Ruiyang Li, Sergey Nurk, Sergey Koren, Karen H. Miga, Adam M. Phillippy, Winston Timp, Mario Ventura, Evan E. Eichler"Segmental duplications and their variation in a complete human genome." bioRxiv (2021). doi: https://doi.org/10.1101/2021.05.26.445678

  • Ariel Gershman, Michael E.G. Sauria, Paul W. Hook, Savannah J. Hoyt, Roham Razaghi, Sergey Koren, Nicolas Altemose, Gina V. Caldas, Mitchell R. Vollger, Glennis A. Logsdon, Arang Rhie, Evan E. Eichler, Michael C. Schatz, Rachel J. O’Neill, Adam M. Phillippy, Karen H. Miga†, Winston Timp† "Epigenetic patterns in a complete human genome." bioRxiv (2021). doi:https://doi.org/10.1101/2021.05.26.443420

  • Kishwar Shafin, Trevor Pesout, Pi-Chuan Chang, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel, Gunjan Baid, Jordan M. Eizenga, Karen H. Miga, Paolo Carnevali, Miten Jain, Andrew Carroll, Benedict Paten. "Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks." bioRxiv (2021). doi: https://doi.org/10.1101/2021.03.04.433952

  • Glennis A. Logsdon, Mitchell R. Vollger, PingHsun Hsieh, Yafei Mao, Mikhail A. Liskovykh, Sergey Koren, Sergey Nurk, Ludovica Mercuri, Philip C. Dishuck, Arang Rhie, Leonardo G. de Lima, David Porubsky, Andrey V. Bzikadze, Milinn Kremitzki, Tina A. Graves-Lindsay, Chirag Jain, Kendra Hoekzema, Shwetha C. Murali, Katherine M. Munson, Carl Baker, Melanie Sorensen, Alexandra M. Lewis, Urvashi Surti, Jennifer L. Gerton, Vladimir Larionov, Mario Ventura, Karen H. Miga, Adam M. Phillippy, Evan E. Eichler.. "The structure, function and evolution of a complete human chromosome 8." Nature 593.7857 (2021): 101-107

  • Leah Bury, Brittania Moodie, Jimmy Ly, Liliana S McKay, Karen H. Miga, Iain M Cheeseman. “Alpha-satellite RNA transcripts are repressed by centromere-nucleolus associations.” eLife 2020;9:e59770 DOI: 10.7554/eLife.59770

  • Sergey Nurk, Brian P. Walenz, Arang Rhie, Mitchell R. Vollger, Glennis A. Logsdon, Robert Grothe, Karen H. Miga, Evan E. Eichler, Adam M. Phillippy, and Sergey Koren. "HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads." Genome Res. (2020)doi:10.1101/gr.263566.120

  • Mikheenko, Alla, Andrey V. Bzikadze, Alexey Gurevich, Karen H. Miga, and Pavel A. Pevzner. TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats." Bioinformatics 36, no. Supplement_1 (2020): i75-i83.

  • Karen H. Miga*†, Sergey Koren*, Arang Rhie, Mitchell R. Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A. Logsdon, Valerie A. Schneider, Tamara Potapova, Jonathan Wood, William Chow, Joel Armstrong, Jeanne Fredrickson, Evgenia Pak, Kristof Tigyi, Milinn Kremitzki, Christopher Markovic, Valerie Maduro, Amalia Dutra, Gerard G. Bouffard, Alexander Chang, Nancy F. Hansen, Françoise Thibaud-Nissen, Anthony D. Schmitt, Jon-Matthew Belton, Siddarth Selvaraj, Megan Y. Dennis, Daniela C. Soto, Ruta Sahasrabudhe, Gulhan Kaya, Josh Quick, Nicholas J. Loman, Nadine Holmes, Matthew Loose, Urvashi Surti, Rosa ana Risques, Tina A. Graves Lindsay, Robert Fulton, Ira Hall, Benedict Paten, Kerstin Howe, Winston Timp, Alice Young, James C. Mullikin, Pavel A. Pevzner, Jennifer L. Gerton, Beth A. Sullivan, Evan E. Eichler, Adam M. Phillippy†. "Telomere-to-telomere assembly of a complete human X chromosome." bioRxiv (2019): 735928. 

  • Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E. Olsen, Colleen Bosworth, Joel Armstrong, Kristof Tigyi, Nicholas Maurer, Sergey Koren, Fritz J. Sedlazeck, Tobias Marschall, SimonMayes, Vania Costa, Justin M. Zook, Kelvin J. Liu, Duncan Kilburn, Melanie Sorensen, Katy M. Munson, Mitchell R. Vollger, Evan E. Eichler, Sofie Salama, David Haussler, Richard E. Green, Mark Akeson, Adam Phillippy, Karen H. Miga, Paolo Carnevali, Miten Jain, Benedict Paten. “Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit.” bioRxiv 715722; doi:  . 

  • Yael Nechemia-Arbely*, Karen H. Miga*, Ofer Shoshani, Aaron Aslanian, Moira A. McMahon, Ah Young Lee, Daniele Fachinetti, John R. Yates III, Bing Ren, Don Cleveland. DNA replication-mediated error correction of ectopic CENP-A deposition maintains centromere identity. Nature cell biology 21.6 (2019): 743.

  • Yannick Delpu, Thomas McNamara, Patrick Griffin, Suhail Kaleem, Shubhada Narayan, Carl Schildkraut, 

    Karen H. Miga, Mamta Tahiliani. Chromosomal rearrangements at hypomethylated Satellite 2 sequences are associated with impaired replication efficiency and increased fork stalling. bioRxiv doi: 

  • Sasha A. Langley, Karen H. Miga, Gary H. Karpen, Charles H. Langley. Diverse haplotypes span human centromeres and include archaic lineages within and out of Africa. eLife 8 (2019): e42989

  • Glennis A. Logsdon, Craig W. Gambogi, Mikhail A. Liskovykh, Evelyne J. Barrey, Vladimir Larionov, Karen H. Miga, Patrick Heun, and Ben E. Black. Human Artificial Chromosomes that Bypass Centromeric DNA. Cell 178.3 (2019): 624-639.

  • ​Quan Zhu, Nien Hoong, Aaron Aslanian, Toshiro Hara, Christopher Benner, Sven Heinz, Karen H. Miga, Eugene Ke, Sachin Verma, Jan Soroczynski, John R. Yates III, Tony Hunter, Inder M. Verma. "Heterochromatin-Encoded Satellite RNAs Induce Breast Cancer." Molecular cell (2018). Jun 7;70(5):842-853.e7. doi: 10.1016/j.molcel.2018.04.023​

  • Miten Jain*, Hugh Olsen*, Dan Turner, David Stoddart, Benedict Paten, David Haussler, Huntington F. Willard, Mark Akeson, and Karen H. Miga†. Linear assembly of a human Y chromosome centromere. Nature Biotechnology (2018) doi:10.1038/nbt.4109

  • Miten Jain*, Sergey Koren*, Karen H Miga*, Josh Quick*, Arthur C Rand*, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes, Sunir Malla, Hannah Marriott, Tom Nieto, Justin O'Grady, Hugh E Olsen, Brent S Pedersen, Arang Rhie, Hollian Richardson, Aaron Quinlan, Terrance P Snutch, Louise Tee, Benedict Paten, Adam M. Phillippy, Jared T Simpson, Nicholas James Loman, Matthew Loose. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology (2018) doi:10.1038/nbt.4060 

  • Yael Nechemia-Arbely, Daniele Fachinetti, Karen H. Miga, Nikolina Sekulic, Gautam Soni, Adeline Karwei Wong, Ah Young Lee, Kristen Nguyen, Cees Dekker, Bing Ren, Ben E. Black, and Don W. Cleveland.  Human centromeric CENP-A-containing chromatin is a homotypic, octameric nucleosome with loosely held DNA termini at all cell cycle points. The Journal of Cell Biology (2017): 216(3):607-621.

  • Karen H. Miga†. Chromosome-specific centromere sequences provide an estimate of ancestral chromosome 2 fusion event in hominin genomes. J Heredity (2016): esw039 

  • Adam M Novak, Glenn Hickey, Erik Garrison, Sean Blum, Abram Connelly, Alexander Dilthey, Jordan Eizenga, M. A. Saleh Elmohamed, Sally Guthrie, André Kahles, Stephen Keenan, Jerome Kelleher, Deniz Kural, Heng Li, Michael F Lin, Karen H. Miga, Nancy Ouyang, Goran Rakocevic, Maciek Smuga-Otto, Alexander Wait Zaranek, Richard Durbin, Gil McVean, David Haussler, Benedict Paten. Community Genome Graphs. bioRxiv doi: 

  • Volkan Sevim, Ali Bashir, Chen-Shan Chin, and Karen H. Miga. Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing. Bioinformatics (2016): btw101.

  • Karen H. Miga†, Christopher Eisenhart and W. James Kent. Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments. Nucleic acids research (2015): gkv671

  • Miten Jain, Ian T. Fiddes, Karen H. Miga, Hugh E. Olsen, Benedict Paten, and Mark Akeson. Improved data analysis for the MinION nanopore sequencer. Nature methods (2015); 12(4):351-6.

  • Kate R. Rosenbloom, Joel Armstrong, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadoo, Maximilian Haeussler, Rachel A. Harte, Steve Heitner, Glenn Hickey, Angie S. Hinrichs, Robert Hubley, Donna Karolchik, Katrina Learned, Brian T. Lee, Chin H. Li, Karen H. Miga, Ngan Nguyen, Benedict Paten, Brian J. Raney, Arian F. A. Smit, Matthew L. Speir, Ann S. Zweig, David Haussler, Robert M. Kuhn and W. James Kent. The UCSC Genome Browser database: 2015 update. Nucleic acids research 43.D1 (2015): D670-D681

  • Indri Erliandri, Haiqing Fu, Megumi Nakano, Jung-Hyun Kim, Karen H. Miga, Mikhail Liskovykh, William C. Earnshaw, Hiroshi Masumoto, Natalay Kouprina, Mirit I. Aladjem, and Vladimir Larionov. Replication of alpha-satellite DNA arrays in endogenous human centromeric regions and in human artificial chromosome. Nucleic acids research 42, no. 18 (2014): 11502-11516. 

  • Nicolas Altemose, Karen H. Miga†, Mauro Maggioni, and Huntington F. Willard. Genomic   Characterization of Large Heterochromatic Gaps in the Human Genome Assembly. PLOS Comput Biol. 2014 May 15;10(5):e1003628.

  • Karen H. Miga, Yulia Newton, Miten Jain, Nicolas F. Altemose, Huntington F. Willard and W. James Kent.  Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res. 2014 Apr;24(4):697-707.

(Karen E. Hayden is my maiden name)

  • Karen E. Hayden*, Erin D. Strome*, Stephanie E. Merrett, Hye-Ran Lee, and Huntington F. Willard.  Defining Centromere Competent Sequence Features in the Human Genome. Mol Cell Biol. 2013 Feb;33(4):763-7.

  • Karen E. Hayden† and Huntington F Willard.  Composition and organization of active centromere sequences in complex genomes.  BMC Genomics. 2012 Jul 20;13(1):324

  • Hye-Ran Lee, Karen E. Hayden, and Huntington F. Willard.   Organization and molecular evolution of CENP-A-associated satellite DNA families in a basal primate genome. Genome Biol Evol. 2011 Aug 9       

  • Kaitlin M. Stimpson, Ihn Young Song, Anna Jauch, Heidi Holtgreve-Grez, Karen E. Hayden, Joanna M. Bridger, and Beth A. Sullivan. Telomere Disruption Results in Non-random Formation of De Novo Dicentric Human Chromosomes That Are Stabilized by Partial Centromeric Deletion. PLOS Genet. 2010 Aug 12;6(8) 

  • Tera L. Newman, Eray Tuzun, V. Anne Morrison, Karen E. Hayden, Mario Ventura, Sean D. McGrath, Mariano Rocchi, and Evan E. Eichler. A genome-wide survey of structural variation between human and chimpanzee. Genome Res. 2005 Oct;15(10):1344-56.

  • Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome.  (…,Karen E. Hayden [authorship order 26 out of 67], …) Nature. 2005 Sep 1;437(7055):69-87.

  • Chris T. Yohn, Zhaoshi Jiang, Sean D. McGrath, Karen E. Hayden, Philipp Khaitovich, Matthew E. Johnson, Marla Y. Eichler, John D McPherson, Shaying Zhao, Savante Pääbo, and Evan E. Eichler. Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans.  PLOS Biol. 2005 Apr;3(4):e110.

  • Massimo Pigliucci and Karen Hayden. "Phenotypic plasticity is the major determinant of changes in phenotypic integration in Arabidopsis." New Phytologist 152.3 (2001): 419-430.

  • Guy D. Griffin, Waleed Khalaf, Karen E. Hayden, Estelle J. Miller, Vinay R. Dowray, Amy L. Creekmore, Carl W. Carruthers, M. Wendy Williams, and Paul C. Gailey. Power frequency magnetic field exposure and gap junctional communication in Clone 9 cells. Bioelectrochemistry 51, no. 2 (2000): 117-123.

Invited book chapters and reviews

  • Karen H. Miga† and Ivan Alexandrov. "Variation and Evolution of Human Centromeres: A Field Guide and Perspective." Annual Review of Genetics (2021) (in press)

  • Karen H. Miga†. "Breaking through the unknowns of the human reference genome." Nature (2021): 217-218

  • Karen H. Miga and Ting Wang. "The Need for a Human Pangenome Reference Sequence." Annual Review of Genomics and Human Genetics 22 (2021).

  • Karen H. Miga†."Centromere studies in the era of ‘telomere-to-telomere’genomics." Experimental cell research (2020): 112127.

  • Karen H. Miga†. Centromeric Satellite DNAs: Hidden Sequence Variation in the Human Population. Genes 10, no. 5 (2019): 352.

  • Karen H. Miga†. (2017) The promises and challenges of genomic studies of human centromeres. Ben E. Black (Ed.), Centromeres and Kinetochores, Progress in Molecular and Subcellular Biology, © Springer-Verlag Berlin Heidelbarg

  • Karen H. Miga†. Completing the human genome: progress and challenges of a satellite DNA assembly. Chromosome Research 23.3 (2015): 421-426.

  •  Karen E. Hayden†.  Human Centromere Genomics:  This Time it’s Personal.  Chromosome Res. 2012 Jul;20(5):621-33.