Publications

Dubocanin D, Hartley GA, Sedeño Cortés AE, Mao Y, Hedouin S, Ranchalis J, Agarwal A, Logsdon GA, Munson KM, Real T, Mallory BJ, Eichler EE, Biggins S, O’Neill RJ, Stergachis AB. (2025). Conservation of dichromatin organization along regional centromeres. Cell Genomics. https://doi.org/10.1016/j.xgen.2025.100819

Dubocanin D, Kalygina A, Franklin JM, Chittenden C, Vollger MR, Neph S, Stergachis AB, Altemose N. (2025). Integrating single-molecule sequencing and deep learning to predict haplotype-specific 3D chromatin organization in a Mendelian condition. bioRxiv. https://doi.org/10.1101/2025.02.26.640261

Vollger MR, Korlach J, Eldred KC, Swanson E, Underwood JG, Bohaczuk SC, Mao Y, Cheng YH, Ranchalis J, Blue EE, Schwarze U, Munson KM, Saunders CT, Wenger AM, Allworth A, Chanprasert S, Duerden BL, Glass I, Horike-Pyne M, Kim M, Leppig KA, McLaughlin IJ, Ogawa J, Rosenthal EA, Sheppeard S, Sherman SM, Strohbehn S, Yuen AL, Stacey AW, University of Washington Center for Rare Disease Research, Undiagnosed Diseases Network, Reh TA, Byers PH, Bamshad MJ, Hisama FM, Jarvik GP, Sancak Y, Dipple KM, Stergachis AB. (2025). Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition. Nature Genetics, 57, 469–479.

Barrero DJ, Hedouin S, Mao Y, Asbury CL, Stergachis AB, O’Toole E, Biggins S. (2025). Centromeres in the thermotolerant yeast K. marxianus mediate attachment to a single microtubule. bioRxiv. https://doi.org/10.1101/2025.01.24.634737

Popchock AR, Hedouin S, Mao Y, Asbury CL, Stergachis AB, Biggins S. (2025). Stable centromere association of the yeast histone variant Cse4 requires its essential N-terminal domain. EMBO Journal, 44, 1488–1511.

Real TD, Hebbar P, Yoo D, Antonacci F, Pačar I, Diekhans M, Mikol GJ, Popoola OG, Mallory B, Vollger MR, Dishuck PC, Guitart X, Rozanski AN, Munson KM, Hoekzema K, Ranchalis JE, Neph SJ, Sedeño-Cortés AE, Paten B, Salama S, Stergachis AB, Eichler EE. (2025). Genetic diversity and regulatory features of human-specific NOTCH2NL duplications. bioRxiv. https://doi.org/10.1101/2025.03.14.643395

Folta A, Sedeño-Cortés A, McEwen A, Kao E, Gupta P, Stone J, Rubin A, Horike-Pyne M, Shirts B, Dubard-Gault M, Kumar R, Fowler D, Starita L, Hisama F, Stergachis AB. (2025). P215: Assessment of factors driving disparities in clinical uncertainty for patients seen in adult medical genetics clinics. Genetics in Medicine Open, 3(2), 102180.

Gupta P, McEwen A, Kao E, Sedeño Cortés A, Folta A, Horike-Pyne M, Shirts B, Kumar R, Hisama F, Fowler D, Starita L, Stergachis AB. (2025). P656: Using functional data for VUS reclassification in cancer predisposition genes. Genetics in Medicine Open, 3(2), 103025.

Park MS, Ovadiuc C, Folta A, McEwen A, Shirts B, Fowler D, Stergachis AB, Starita L, Kumar R. (2025). P713: Survey results reveal barriers and solutions to the use of functional data in variant interpretation. Genetics in Medicine Open, 3(2), 103082.

Park MS, Kumar RD, Ovadiuc C, Folta A, McEwen AE, Snyder A, Fowler DM, Rubin AF, Shirts BH, Starita LM, Stergachis AB. (2025). Insights on improving accessibility and usability of functional data to unlock its potential for variant interpretation. medRxiv. https://doi.org/10.1101/2025.01.25.25321117

Peter CJ, Agarwal A, Watanabe R, Kassim BS, Wang X, Lambert TY, Javidfar B, Evans V, Dawson T, Fridrikh M, Girdhar K, Roussos P, Nageshwaran SK, Tsankova NM, Sebra RP, Vollger MR, Stergachis AB, Hasson D, Akbarian S. (2024). Single chromatin fiber profiling and nucleosome position mapping in the human brain. Cell Reports Methods, 4(12), 100911.

Bohaczuk SC, Amador ZJ, Li C, Mallory BJ, Swanson EG, Ranchalis J, Vollger MR, Munson KM, Walsh T, Hamm MO, Mao Y, Lieber A, Stergachis AB. (2024). Resolving the chromatin impact of mosaic variants with targeted Fiber-seq. Genome Research, 34(12), 2269–2278.

McEwen A, Gupta P, Conner E, Jose M, Starita L, Stergachis A, Shirts B. (2024). Functional data drive reclassification of variants of uncertain significance in cancer predisposition genes identified in adult genetics clinic patients. Journal of Molecular Diagnostics, 26(11), S18.

Jha A, Bohaczuk SC, Mao Y, Ranchalis J, Mallory BJ, Min AT, Hamm MO, Swanson E, Dubocanin D, Finkbeiner C, Li T, Whittington D, Noble WS, Stergachis AB, Vollger MR. (2024). DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools. Genome Research, 34(11), 1976–1986.

Tullius TW, Isaac RS, Dubocanin D, Ranchalis J, Churchman LS, Stergachis AB. (2024). RNA polymerases reshape chromatin architecture and couple transcription on individual fibers. Molecular Cell, 84(17), 3209–3222.e5.

Isaac RS, Tullius TW, Hansen KG, Dubocanin D, Couvillion M, Stergachis AB, Churchman LS. (2024). Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA. Nature Structural & Molecular Biology, 31(3), 568–577.

Hartley GA, Okhovat M, Hoyt SJ, Fuller E, Pauloski N, Alexandre N, Alexandrov I, Drennan R, Dubocanin D, Gilbert DM, Mao Y, McCann C, Neph S, Ryabov F, Sasaki T, Storer JM, Svendsen D, Troy W, Wells J, Core L, Stergachis A, Carbone L, O’Neill RJ. (2024). Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon. bioRxiv. https://doi.org/10.1101/2024.XX.XX.xxxxxx

Pak CM, Gilmore MJ, Bulkley JE, Chakraborty P, Dagan-Rosenfeld O, Foreman AKM, Gollob MH, Jenkins CL, Katz AE, Lee K, Meeks N, O’Daniel JM, Posey JE, Rego SM, Shah N, Steiner RD, Stergachis AB, Subramanian SL, Trotter T, Wallace K, Williams MS, Goddard KAB, Buchanan AH, Manickam K, Powell B, Hunter JE, ClinGen Resource. (2024). Implementing evidence-based assertions of clinical actionability in the context of secondary findings: Updates from the ClinGen Actionability Working Group. Genetics in Medicine, 26(8), 101164.

Bubb KL, Hamm MO, Min JK, Ramirez-Corona B, Mueth NA, Ranchalis J, Vollger MR, Trapnell C, Cuperus JT, Queitsch C, Stergachis AB. (2024). The regulatory potential of transposable elements in maize. bioRxiv. https://doi.org/10.1101/2024.XX.XX.xxxxxx

Vollger MR, Swanson EG, Neph SJ, Ranchalis J, Munson KM, Ho CH, Sedeno-Cortes AE, Fondrie WE, Bohaczuk SC, Mao Y, Parmalee NL, Mallory BJ, Harvey WT, Kwon Y, Garcia GH, Hoekzema K, Meyer JG, Cicek M, Eichler EE, Noble WS, Witten DM, Bennett JT, Ray JP, Stergachis AB. (2024). A haplotype-resolved view of human gene regulation. bioRxiv. https://doi.org/10.1101/2024.06.14.599122

Cheng YH, Bohaczuk SC, Stergachis AB. (2024). Functional categorization of gene regulatory variants that cause Mendelian conditions. Human Genetics, 143(4), 559–605.

Swanson EG, Mao Y, Mallory BJ, Vollger MR, Ranchalis J, Bohaczuk SC, Parmalee NL, Bennett JT, Stergachis AB. (2024). Deaminase-assisted single-molecule and single-cell chromatin fiber sequencing. bioRxiv. https://doi.org/10.1101/2024.11.06.622310

Vollger MR, Korlach J, Eldred KC, Swanson E, Underwood JG, Cheng Y-HH, Ranchalis J, Mao Y, Blue EE, Schwarze U, Munson KM, Saunders CT, Wenger AM, Allworth A, Chanprasert S, Duerden BL, Glass I, Horike-Pyne M, Kim M, Leppig KA, McLaughlin IJ, Ogawa J, Rosenthal EA, Sheppeard S, Sherman SM, Strohbehn S, Yuen AL, University of Washington Center for Mendelian Genomics (UW-CMG), Undiagnosed Diseases Network (UDN), Reh TA, Byers PH, Bamshad MJ, Hisama FM, Jarvik GP, Sancak Y, Dipple KM, Stergachis AB. (2023). Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition. bioRxiv. https://doi.org/10.1101/2023.09.26.559521v1

Tullius TW, Isaac RS, Ranchalis R, Dubocanin D, Churchman LS, Stergachis AB. (2023). RNA polymerases reshape chromatin and coordinate transcription on individual fibers. bioRxiv. https://doi.org/10.1101/2023.12.22.573133v1

Jha A, Bohaczuk SC, Mao Y, Ranchalis J, Mallory BJ, Min A, Hamm MP, Swanson E, Finkbeiner C, Li T, Whittington D, Noble WS, Stergachis AB, Vollger MR. (2023). DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools. bioRxiv. https://doi.org/10.1101/2023.04.20.537673v3

Debo BM, Mallory B, Stergachis AB. (2023). Evaluation of N6-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes. Genome Research, 33, 427–434.

Pujol-Giménez J, Mirzaa G, Blue E, Albano G, Allworth A, Bennett J, Byers P, Chanprasert S, Chen J, Doherty D, Folta A, Gillentine M, Glass I, Hing A, Horike-Pyne M, Leppig K, Miller D, Parhin A, Ranchalis J, Raskind W, Rosenthal E, Schwarze U, Sheppeard S, Strohbehn S, Sybert V, Timms A, Wener M, Bamshad MJ, Dipple K, Hisama F, Jarvik G, Hediger M, Stergachis AB. (2023). Dominant-negative variant in SLC1A4 causes an autosomal dominant epilepsy syndrome. Annals of Clinical and Translational Neurology, 10(6), 1046–1053. PMID: 37194416

Stergachis AB, Blue EE, Gillentine MA, Wang L, Schwarze U, Sedeño Cortés A, Ranchalis J, Allworth A, Bland AE, Chanprasert S, Chen J, Doherty D, Folta AB, Glass I, Horike-Pyne M, Huang AY, Khan AT, Leppig KA, Miller DE, Mirzaa M, Parhin A, Raskind W, Rosenthal EA, Sheppeard S, Strohbehn S, Sybert VP, Tran TT, Wener M, UW-CMG, UDN, Byers PH, Nelson SF, Bamshad MJ, Dipple KM, Jarvik GP, Hoppins S, Hisama FM. (2023). Full-length isoform sequencing for resolving the molecular basis of Charcot-Marie-Tooth 2A. Neurology Genetics, 9(5), e200090. PMID: 37560121

Debo BM, Mallory B, Stergachis AB. (2022). Evaluation of N6-adenine DNA-immunoprecipitation-based genomic profiling in eukaryotes. bioRxiv. https://doi.org/10.1101/2022.03.02.482749

Dubocanin D, Sedeño Cortés AE, Ranchalis J, Real T, Mallory B, Stergachis AB. (2022). Single-molecule architecture and heterogeneity of human telomeric DNA and chromatin. bioRxiv. https://doi.org/10.1101/2022.05.09.491186

Isaac RS, Tullius TW, Hansen KG, Dubocanin D, Couvillion M, Stergachis AB, Churchman LS. (2022). Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA. bioRxiv (in press). https://doi.org/10.1101/2022.09.25.509398

Galey M, Reed P, Wenger T, Beckman E, Chang IJ, Paschal CR, Buchan JG, Lockwood CM, Puia-Dumitrescu M, Garalde DR, Guillory J, Markham AJ, Stergachis AB, Bamshad MJ, Eichler EE, Miller DE. (2022). 3-hour genome sequencing and targeted analysis to rapidly assess genetic risk. medRxiv (in press). https://doi.org/10.1101/2022.09.09.22279746

*Girskis, KM., *Stergachis, AB., *DeGennaro, EM., Doan, RN., Qian, X., Johnson, MB., Wang, PP., Sejourne, GM., Nagy, MA., Pollina, EA., Sousa, AMM., Shin, T., Kenny, CK., Scotellaro, JL., Debo, BM., Gonzalez, DM., Rento, LM., Yeh. RC., Song, JHT., Beaudin, M., Fan, J., Kharchenko, PV., Sestan, N., Greenberg, ME., Walsh, CA., (2021) Rewiring of human neurodevelopmental gene regulatory programs by Human Accelerated Regions (HARs). Neuron, 109, 1-13 (See press release here)

Stergachis, AB., Krier, JB., Merugumala, SK., Berry, GT., Lin, AP., (2021) Clinical utility of brain MRS imaging of patients with adult-onset non-cirrhotic hyperammonemia. Molecular Genetics and Metabolism Reports, 27, 100742

Stergachis, AB., Debo, BM., Haugen, E., Churchman, LS., Stamatoyannopoulos, JA., (2020) Single-molecule regulatory architectures captured by chromatin fiber sequencing, Science, 368, 1449-54 (pdf)

Stergachis, AB., Weiss, ST., Green, RC., (2020) Biobanks could identify medically actionable findings relevant for COVID-19 Clinical Care, Nature Medicine, 26, 991

Stergachis, AB., Mogensen, KM., Khoury, CC., Lin, AP., Peake, RWA., Baker, JJ., Barkoudah, E., Sahai, I., Sweetser, DA., Berry, GT., Krier, JB. (2020) A retrospective study of adult patients with non-cirrhotic hyperammonemia, Journal of Inherited Metabolic Disease, 43, 1165–1172

Federation, AJ., Nandakumar, V., Searle, BC., Stergachis, A., Wang, H., Pino. LK., Merrihew, G., Ting, YS., Howard, N., Kutyavin, T., MacCoss, MJ., Stamatoyannopoulos, JA., (2020) Highly Parallel Quantification and Compartment Localization of Transcription Factors and Nuclear Proteins Cell Reports, 30, 2463-2471

*Stergachis, AB., *Pujol-Giménez, J., Gyimesi, G., Fuster, D., Albano, G., Troxler, M., Picker, J., Rosenberg, PA., Bergin, A., Peters, J., El Achkar, CM., Harini, C., Manzi, S., Rotenberg, A., Hediger, MA., Rodan, LH. (2019) Recurrent SLC1A2 variants cause epilepsy via a dominant negative mechanism. Annals of Neurology, 85, 921-926

Li, GZ., Tio, MC., Pak, LM., Krier, J., Tullius, SG., Riella, LV., Malek, SK., Stergachis, AB., (2019) Non-Cirrhotic Hyperammonemia after Deceased Donor Kidney Transplantation: A Case Report. American Journal of Transplantation,19, 3197–3201

Eberly LA., [185 Authors], Stergachis A., [40 Authors] (2019) Identification of Racial Inequities in Access to Specialized Inpatient Heart Failure Care at an Academic Medical Center Circulation Heart Failure, 12, e006214

*Stouffs K, *Stergachis AB., Vanderhasselt T, Dica A, Janssens S, Vandervore L, Gheldof A, Bodamer O, Keymolen K, Seneca S, Liebaers I, Jayaraman D, Hill HE, Partlow JN, Walsh CA, Jansen AC. (2018) Expanding the clinical spectrum of biallelic ZNF335 variants. Clin Genet., 94, 246-251

Boueiz A, Pham B, Chase R, Lamb A, Lee S, Naing ZZC, Cho MH, Parker MM, Sakornsakolpat P, Hersh CP, Crapo JD, Stergachis AB., Tal-Singer R, DeMeo DL, Silverman EK, Zhou X, Castaldi PJ; COPDGene investigators. (2018) Integrative Genomics Analysis Identifies ACVR1B as a Candidate Causal Gene of Emphysema Distribution. Am J Respir Cell Mol Biol.Oct 18

Kenagy, RD., Kikuchi, S., Chen, L., Wijelath, ES., Stergachis, AB., Stamatoyannopoulos, J., Tang, GL., Clowes, AW., Sobel, M. (2017) A single nucleotide polymorphism of cyclin-dependent kinase inhibitor 1B (p27Kip1) associated with human vein graft failure affects growth of human venous adventitial cells but not smooth muscle cells. J Vasc Surg., 1, 309-317

Bollinger, JG., Stergachis, AB., Johnson, RS., Egertson, JD., MacCoss, MJ. (2016) Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards. Methods Mol Biol., 1410, 207-21

Searle, BC., Egertson, JD., Bollinger, JG., Stergachis, AB., MacCoss, MJ. (2015) Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments. Mol Cell Proteomics, 9, 2331-40

Stamatoyannopoulos, J. A. (2014) Conservation of trans-acting circuitry during mammalian regulatory evolution. Nature, 515, 365-70

Sharma, V., Eckels, J., Taylor, G. K., Shulman, N. J., Stergachis, AB., Joyner, S. A., Yan, P., Whiteaker, J. R., Halusa, G. N., Schilling, B., Gibson, B. W., Colangelo, C. M., Paulovich, A. G., Carr, S. A., Jaffe, J. D., MacCoss, M. J., MacLean, B. (2014) Panorama: A Targeted Proteomics Knowledge Base Journal of Proteome Research13, 4205-10

Sullivan, A. M., Arsovski, A. A., Lempe, J., Bubb, K. L., Weirauch, M. T., Sabo, P. J., Sandstrom, R., Thurman, R. E., Neph, S., Reynolds, A. P., Stergachis, AB., Vernot, B., Johnson, A. K., Haugen, E., Sullivan, S. T., Dargiel, A., Neri, J., Weaver, M., Diegel, M., Mnaimneh, S., Yang, A., Hughes, T. R., Nemhauser, J. L., Queitsch, C., Stamatoyannopoulos, J. A., (2014) Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. Cell Reports8, 1–16

Stergachis, AB., Haugen, E., Shafer, A., Fu, W., Vernot, B., Reynolds, A., Raubitschek, A., Ziegler, A., LeProust, E. M., Akey, J. M., Stamatoyannopoulos, J. A., (2013) Exonic transcription factor binding directs codon choice and affects protein evolution. Science342, 1367-1372

*Stergachis, AB., *Neph, S., Reynolds, A., Humbert, R., Vernot, B., Miller, B., Thurman, R.E., Sandstrom, R., Haugen, H., Akey, J.M., and Stamatoyannopoulos, J.A. (2013) Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell154, 888-903

Mercer, T.R., Edwards, S.L., Clark, M.B., Neph, S.J., Wang, H., Stergachis, AB., John S., Sandstrom, R., Li G., Sandhu, K.S., et. al. (2013). DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements. Nature Genetics45, 852-9

*Neph, S., *Stergachis, AB., Reynolds, A., Sandstrom, R., Borenstein, E., and Stamatoyannopoulos, J. A. (2012). Circuitry and Dynamics of Human Transcription Factor Regulatory Networks. Cell150, 1274–1286.

*Neph, S., *Vierstra, J., *Stergachis, AB., *Reynolds, A. P., Haugen, E., Vernot, B., Thurman, R. E., John, S., Sandstrom, R., Johnson, A. K., et al. (2012). An expansive human regulatory lexicon encoded in transcription factor footprints. Nature489, 83–90.

Vernot, B., Stergachis, AB., Maurano, M. T., Vierstra, J., Neph, S., Thurman, R. E., Stamatoyannopoulos, J. A., and Akey, J. M. (2012). Personal and population genomics of human regulatory variation. Genome Research22, 1689–1697.

ENCODE Project Consortium, [522 Authors], Stergachis, AB., [79 Authors] (2012). An integrated encyclopedia of DNA elements in the human genome. Nature489, 57–74.

Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, AB., Wang, H., Vernot, B., et al. (2012). The accessible chromatin landscape of the human genome. Nature489, 75–82.

Liu, B. A., Engelmann, B. W., Jablonowski, K., Higginbotham, K., Stergachis, AB., and Nash, P. D. (2012). SRC Homology 2 Domain Binding Sites in Insulin, IGF-1 and FGF receptor mediated signaling networks reveal an extensive potential interactome. Cell Communication and Signaling: CCS 10, 27.

Stergachis, AB., MacLean, B., Lee, K., Stamatoyannopoulos, J. A., and MacCoss, M. J. (2011). Rapid empirical discovery of optimal peptides for targeted proteomics. Nature Methods8, 1041–1043.

Liu, B. A., Shah, E., Jablonowski, K., Stergachis, A., Engelmann, B., and Nash, P. D. (2011). The SH2 Domain-Containing Proteins in 21 Species Establish the Provenance and Scope of Phosphotyrosine Signaling in Eukaryotes. Science Signaling4, ra83–ra83.