Publications
2024
2023
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://www.biorxiv.org/content/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://www.biorxiv.org/content/10.1101/2023.12.22.573133v1
Jah, 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://www.biorxiv.org/content/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 Jun;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 Aug 8;9(5):e200090 (PMID 37560121)
2022
Dubocanin, D., Sedeno Cortes, AE., Ranchalis, J., Real, T., Mallory, B., Stergachis, AB., (2022) Single-molecule architecture and heterogeneity of human telomeric DNA and chromatin. bioRxiv https://biorxiv.org/cgi/content/short/2022.05.09.491186v1
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 https://www.biorxiv.org/content/10.1101/2022.09.25.509398v1 (in press)
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 https://www.medrxiv.org/content/10.1101/2022.09.09.22279746v1 (in press)
2021
*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
2020
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
2019
*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
2018
*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
2017
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
2016
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, in press
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
2015
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
2014
*Stergachis, AB., *Neph, S., Sandstrom, R., Haugen, E., Reynolds, A.P., Zhang, M., Byron, R., Canfield, T., Stelhing-Sun, S., Lee, K., Thurman, R.E., Vong, S., Bates, D., Neri, F., Diegel, M., Giste, E., Dunn, D., Vierstra, J., Hansen, R.S., Johnson, A.K., Sabo, P.J., Wilken, M.S., Reh, T.A., Treuting, P.M., Kaul, R., Groudine, M., Bender, M. A., Borenstein, E. and 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 Research 13, 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 Reports 8, 1–16
2013
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. Science 342, 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. Cell 154, 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 Genetics 45, 852-9
2012
*Neph, S., *Stergachis, AB., Reynolds, A., Sandstrom, R., Borenstein, E., and Stamatoyannopoulos, J. A. (2012). Circuitry and Dynamics of Human Transcription Factor Regulatory Networks. Cell 150, 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. Nature 489, 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 Research 22, 1689–1697.
ENCODE Project Consortium, [522 Authors], Stergachis, AB., [79 Authors] (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489, 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. Nature 489, 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.
2011
Stergachis, AB., MacLean, B., Lee, K., Stamatoyannopoulos, J. A., and MacCoss, M. J. (2011). Rapid empirical discovery of optimal peptides for targeted proteomics. Nature Methods 8, 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 Signaling 4, ra83–ra83.