Publications
‡ Indicates co-first authorship
Annotations are in the spirit of the San Francisco Declaration On Research Assessment (SF DORA)
See also: Google Scholar Profile
SELECTED PEER-REVIEWED PUBLICATIONS, ANNOTATED
Altemose N (2022). [Review]
A classical revival: Human satellite DNAs enter the genomics era. Seminars in Cell and Developmental Biology, 128, 2-14. https://doi.org/10.1016/j.semcdb.2022.04.012 [open-access preprint available]
- Many open questions remain about the epigenetics and regulation of the newly assembled repetitive heterochromatic regions of the human genome. However, existing methods for mapping protein-DNA interactions utilize short DNA sequencing reads that cannot be reliably mapped to repetitive regions. To address this, we developed a sequencing method for mapping protein-DNA interactions on long, single, native molecules of DNA that retain endogenous CpG methylation information. Then, we applied this method to produce the first high-resolution maps of histone variants and centromere proteins across human centromeres. We joined forces with Aaron Straight’s group at Stanford, who are experts in centromere biology and who were working on a similar method.- This work was described in a news & views article in the same issue: Ahmad, K. Mapping beads on strings. Nat Methods (2022). https://rdcu.be/cOftR
Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, 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, Lucas JK, Aganezov S, Olson D, Gomes de Lima L, 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 A, F, Sullivan BA, Straight AF, Wheeler TJ, Gerton 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 (2021).
Complete genomic and epigenetic maps of human centromeres. Science, 375, eabl4178. https://doi.org/10.1126/science.abl4178 [free to read]
Altemose N, Maslan A, Rios-Martinez C, Lai A, White JA, Streets A (2020).
μDamID: a microfluidic approach for joint imaging and sequencing of protein-DNA interactions in single cells. Cell Systems, 11, 1-13. https://doi.org/10.1016/j.cels.2020.08.015 [open access, transparent review]
Li R‡, Bitoun E‡, Altemose N‡, Davies RW, Davies B, Myers SR (2019).
A high-resolution map of non-crossover events reveals impacts of genetic diversity on mammalian meiotic recombination. Nature Communications, 10(3900), 1-15. https://doi.org/10.1038/s41467-019-11675-y [open access, transparent review]
Altemose N, Noor N, Bitoun E, Tumian A, Imbeault M, Chapman R, Aricescu AR, Myers SR (2017).
A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis. eLife, 6, e28383. https://doi.org/10.7554/eLife.28383 [open access, transparent review]
Davies B‡, Hatton E‡, Altemose N, Hussin JG, Pratto F, Zhang G, Hinch AG, Moralli D, Biggs D, Diaz R, Preece C, Li R, Brick K, Green CM, Camerini-Otero RD, Myers SR, and Donnelly P (2016).
Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice. Nature, 530(7589), 171–176. https://doi.org/10.1038/nature16931 [free to read on PubMed Central]
- This study proposes the first molecular mechanism of speciation in any mammal, resulting from a collaboration between four research groups (Ben Davies, R. Dan Camerini-Otero, Simon Myers, Peter Donnelly). Using maps of PRDM9 binding and double-strand break formation, we discovered that PRDM9-related hybrid infertility can be explained by PRDM9 binding unequally to each homologous chromosome at each binding site. My contribution stems from an entire chapter of my thesis work. I helped design all experiments, led the breeding of hybrid mice, performed and analyzed the PRDM9 binding experiments, and generated the fourth and final main text figure. My data and analyses proved essential for illuminating the proposed mechanism and reaching the main conclusion of the paper. Our results have inspired further investigations into this speciation mechanism by others. A news and views summary of the article is available at: https://www.nature.com/articles/nature16870Altemose N, Hayden KE, Maggioni M, Willard HF (2014).
Genomic characterization of large heterochromatic gaps in the human genome assembly. PLoS Computational Biology, 10(5), e1003628. https://doi.org/10.1371/journal.pcbi.1003628 [open access]
ADDITIONAL PEER-REVIEWED PUBLICATIONS
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, The Telomere-To-Telomere Consortium (74 authors), Surti U, 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, 375, eabj6987, https://doi.org/10.1126/science.abj6987 [free to read]
Gershman A, Sauria MEG, Guitart X, Vollger MR, Hook PW, Hoyt SJ, Jain M, Shumate A, Razaghi R, Koren S, Altemose N, Caldas GV, Logsdon GA, Rhie A, Eichler EE, Schatz MC, O’Neill RJ, Phillippy AM, Miga KH, Timp W (2022). Epigenetic patterns in a complete human genome. Science, 375, eabj5089, https://doi.org/10.1126/science.abj5089 [free to read]
Hoyt SJ, Storer JM, Hartley GA, Grady PGS, Gershman A, de Lima LG, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Rhie A, Core LJ, Gerton JL, Makalowski W, Olson D, Rosen J, Smit AFA, Straight AF, Vollger MR, Wheeler TJ, Schatz MC, Eichler EE, Phillippy AM, Timp W, Miga KH, O’Neill RJ (2022). From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science, 375, eabk3112, https://doi.org/10.1126/science.abk3112 [free to read]
Gupta A, Shamsi F, Altemose N, Dorlhiac GF, Cypess AM, White AP, Yosef N, Patti ME, Tseng Y-H, Streets A (2022). Characterization of transcript enrichment and detection bias in single-nuclei RNA-seq for mapping of distinct human adipocyte lineages. Genome Research, 32, 242-257, https://doi.org/10.1101/gr.275509.121 [open-access preprint available]
Grist S, Geldert A, Gopal A, Su A, Balch H, Herr A, Rampazzi S, Smullin S, Starr N, Rempel D, Agarwal P, Altemose N, Chen T, Hu G, Tung M, Pillarisetti A, Robinowitz D, Shless J (2021). Current understanding of ultraviolet-C decontamination of N95 filtering facepiece respirators. Applied Biosafety, eprint. https://doi.org/10.1089/apb.20.0051 [open access]
Nakatsuka N, Patterson N, Patsopoulos N, De Jager P, Altemose N, Tandon A, Beecham AH, McCauley JL, Isobel N, Hauser S, Hafler DA, Oksenberg JR, Reich D (2020). Two genetic variants explain the association of European ancestry with multiple sclerosis risk in African-Americans. Scientific Reports, 10, 16902. https://doi.org/10.1038/s41598-020-74035-7 [open access]
Lai A, Altemose N, White JA, Streets AM (2019). On-ratio PDMS bonding for multilayer microfluidic device fabrication. Journal of Micromechanics and Microengineering, 29(10), 107001. https://doi.org/10.1088/1361-6439/ab341e [open-access preprint available]
Williams AL, Genovese G, Dyer T, Altemose N, Truax K, Jun G, Patterson N, Myers SR, Curran JE, Duggirala R, Blangero J, Reich D, Przeworski M, on behalf of the T2D-GENES Consortium (2015). Non-crossover gene conversions show strong GC bias and unexpected clustering in humans. eLife 4. https://doi.org/10.7554/eLife.04637 [open access]
Hinch AG, Altemose N, Noor N, Donnelly P, Myers SR (2014). Recombination in the human pseudoautosomal region PAR1. PLoS Genetics 10(7), e1004503–e1004503. https://doi.org/10.1371/journal.pgen.1004503 [open access]
Miga KH, Newton Y, Jain M, Altemose N, Willard HF, Kent WJ (2014). Centromere reference models for human chromosomes X and Y satellite arrays. Genome Research 24(4), 697–707. https://doi.org/10.1101/gr.159624.113 [open access]
Genovese G, Handsaker R, Li H, Altemose N, Lindgren AM, Chambert K, Pasaniuc B, Price AL, Reich D, Morton CC, Pollak MR, Wilson JG, McCarroll SA (2013). Using population admixture to help complete maps of the human genome. Nature Genetics 45, 406-414. https://doi.org/10.1038/ng.2565 [free to read on PubMed Central]