Publications

    • Gibson SB, Damaraju N, Gustafson JG, Balton EV, Chanprasert S, Glass IA, Horike-Pyne M, Kumar RD, Leppig KA, Lundberg C, Ranchalis J, Rosenthal EA, Solomon AK, Stergachis AB, Wener M, UDN, Jarvik GP, Blue EE, Dipple KM, Dashnow H, Starita LM, Miller DE. (2026). Genome-wide detection and clinical prioritization of tandem repeat outliers using long-read sequencing. medRxiv. https://doi.org/10.64898/2026.04.30.26352103

    • Devaney JM, Chong JX, Lopes PC, Noya J, Berlyoung AS, Yusuff S, Lynch S, Brandon R, Hruska KS, Lochovsky L, Spangler J, McWalter K, Nykamp K, Poll SR, Stergachis AB, Greally J, Kruszka P, Dolzhenko E, Chen X, Robertson AV, Rowell WJ, Lake JA, Carroll A, Kueffner R, Eberle MA, Facio FM, Bamshad MJ, Johnson B. (2026). Sensitivity of HiFi long-read genome sequencing for difficult-to-detect pathogenic variants when applied to real-world clinical laboratory samples. Am J Hum Genet. https://doi.org/10.1016/j.ajhg.2026.04.001

    • Zakarian C, Smith JD, Wong CH, Frazar CD, Ryke E, McGee SR, Richardson M, Weiss JM, Munson KM, Hoekzema K, Mack T, Kwon Y, Ou J, Neph SJ, Sohn M-H, Minkina A, Bennett JT, Stergachis AB, Eichler EE, Wei C-L. (2026). Long-read MitoScope reveals tissue-resolved somatic mitochondrial variation and landscape of nuclear-embedded mitochondrial sequences. bioRxiv. https://doi.org/10.64898/2026.04.13.718259

    • Real TD, Hebbar P, Yoo D, Antonacci F, Pačar I, Dubocanin D, 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. (2026). Genetic diversity and regulatory features of human-specific NOTCH2NL duplications. Cell Genomics. https://doi.org/10.1016/j.xgen.2026.101194

    • Resnick R, Kao EY, Maynard C, Tabaghi S, Stergachis AB, Nazer B, Yang KD. (2026). Validation of the Madrid Genotype Score to Predict Pathogenic Variants in U.S. Dilated Cardiomyopathy Patients. JACC Advances. https://doi.org/10.1016/j.jacadv.2026.102648

    • Mack T, Lin J, Ren L, Sohn MH, Minkina A, Kwon Y, Yoo D, Sui Y, Munson KM, Hoekzema K, Mastrorosa FK, Sorensen M, Ayllon M, Sun KA, Koundiya N, Ou J, Noyes MD, Sedeño-Cortés A, Leonardson A, Jacques CN, Oliviera C, Frazar CD, Zakarian C, Jensen DM, Swanson EG, Ryke E, Kolar JT, Ranchalis J, Sutherlin L, Vollger MR, Loy K, Pham MM, Huang MF, Au NY, Nielsen PM, McGee SR, Neph S, Bohaczuk S, Shaffer T, Freeman V, Mao Y, Stillman BC, Richardson M, Smith JD, Weiss JM, Parmalee NL, Wei CL, Bennett JT, Stergachis AB, Eichler EE. (2026). Donor-specific assemblies enhance somatic structural variant detection in complex genomic regions. bioRxiv. https://doi.org/10.64898/2026.02.20.707061

    • Tejura M, Chen Y, McEwen AE, Stewart R, Sverchkov Y, Laval F, Woo I, Zeiberg D, Shen R, Fayer S, Stone J, Smith N, Casadei S, Wang ZR, Snyder M, Capodanno BJ, Gupta P, Benazouz M, Jain S, Heidl S, Muffley L, Dong S, Lin K, Hitz BC, Gabdank I, Da EY, Best S, Grindstaff S, Reinhart D, Rodriguez-Salas L, Seid O, Vandi AJ, Wenman C, Wheelock MK, Pendyala S, Holmes D, Xu A, Hosokai A, Tixhon M, Reno C, Ewald JD, Spirohn-Fitzgerald K, Teelucksingh T, Hao T, Chen ZS, Haghighi M, Hamid AK, Miglietta EA, Weisbart E, Coppin G, Lambourne L, Gebbia M, Atina AG, van Loggerenberg W, Fawcett KM, Steiner RD, Johnsen J, Stergachis AB, Iakoucheva LM, Singh S, Cimini BA, Roth FP, James RG, Vidal M, Taipale M, Carpenter AE, Calderwood MA, Craven M, Pejaver V, Rubin AF, Radivojac P, Fowler DM, Starita LM. (2026). A scalable approach to resolving variants of uncertain significance. bioRxiv. https://doi.org/10.64898/2026.02.14.705848

    • Jiang M, Hu C, Hedouin S, Andrade Latino A, Arimura Y, Stergachis AB, Biggins S. (2026). Native yeast kinetochore structures identify an essential inner kinetochore interaction. bioRxiv. https://doi.org/10.64898/2026.01.30.702844

    • Gupta P, Knerr S, Fowler D, Starita L, Stergachis AB. (2026). P506: Patient perspectives on communication and care after genetic variant reclassification. Genetics in Medicine Open, 4.

    • McEwen A, Gupta P, Folta A, Kao E, Sedeno-Cortes A, Horike-Pyne M, ... Stergachis AB. (2026). P646: Integrating functional data in variant classification: Navigating conflict, calibration, and low-penetrance. Genetics in Medicine Open, 4.

    • 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.

    • 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

    • Swanson EG, Mao Y, Mallory BJ, Vollger MR, Bohaczuk SC, Oliveira CB, Lyon DB, Ranchalis J, Parmalee NL, Cohen BA, Bennett JT, Stergachis AB. (2025). Mapping single-cell diploid chromatin fiber architectures using DAF-seq. Nature Biotechnology. https://doi.org/10.1038/s41587-025-02914-3

    • Inan RA, DiStefano MT, Amr SS, Beißbarth T, Starita LM, Stergachis AB, Abou Tayoun A, Hufnagel RB, Vona B. (2025). A Comparative Survey of Functional Evidence Use in Hearing and Vision Loss Genetics. medRxiv. https://doi.org/10.1101/2025.11.25.25339647

    • McEwen AE, Stone J, Tejura M, Gupta P, Capodanno BJ, Da EY, Grindstaff SB, Moore N, Reinhart D, Snyder AE, Stergachis AB, Starita LM, Fowler DM, Rubin AF. (2025). MaveMD: A functional data resource for genomic medicine. medRxiv. https://doi.org/10.1101/2025.11.15.25336228

    • Fayer S, Garge RK, Hopkins M, Friedman CE, McGee AV, Rico J, Powell RL, McDermot E, Smith NT, Pendyala S, Richardson ME, Smith E, Bowen BM, Resnick R, Gupta P, Stergachis AB, Gifford C, Pinglay S, Yang KC, Fowler DM, Starita LM. (2025). Editing stem cell genomes at scale to measure variant effects in diverse cell and genetic contexts. medRxiv. https://doi.org/10.1101/2025.11.12.25340127

    • Cheng YHH, Sedeño-Cortés AE, Ranchalis JE, Munson KM, Vollger MR, ... Stergachis AB, ... (2025). Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditions. medRxiv. https://doi.org/10.1101/2025.11.07.25339764

    • iguera Altolaguirre C, Stergachis AB, Sweetser DA, Gold NB. (2025). Late-onset multiple acyl-CoA dehydrogenase deficiency presenting as hyperammonemia and encephalopathy: case series. The Neurohospitalist, 15(4), 372–376.

    • Folta A, Sedeño Cortés AE, Gupta P, McEwen AE, Kao EY, Horike-Pyne M, Stone J, Shirts BH, Dubard-Gault ME, Fowler DM, Starita LM, Hisama FM, Stergachis AB. (2025). Imprecision medicine: Systematic gaps in reporting variants of uncertain significance (VUS) and their reclassifications. Genetics in Medicine, 27(9), 101501. https://doi.org/10.1016/j.gim.2025.101501

    • Kondamudi N, Stein EJ, Bevan GH, Stergachis AB, Hisama F, Nazer B, Chatterjee NA. (2025). Association of Left Ventricular Summit Arrhythmias With Pathogenic Genetic Variants. JACC: Clinical Electrophysiology, 11(4), 830–832. https://doi.org/10.1016/j.jacep.2024.12.008

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

    • 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.

    • 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.

    • 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

    • Kondamudi N, Bevan G, Nazer B, Stergachis AB, Hisama F, Chatterjee N. (2024). Association of left ventricular summit arrhythmias with pathogenic gene variants. Circulation, 150(Suppl_1), A4143995–A4143995.

    • McEwen A, Gupta P, Conner E, Jose M, Starita L, Stergachis AB, 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–S18.

    • Stergachis AB, Folta A, Sedeno-Cortes A, Jose M, Horike-Pyne M, ... (2024). P390: Assessing and addressing the burden of VUSs within adult medical genetics practices. Genetics in Medicine Open, 2.

    • Lenahan A, Glass I, Stergachis AB, Paschal C, Blue E, Allworth A, Cristian I, ... (2024). P364: Mosaic copy gain of 16p with supernumerary chromosome formation: An emerging phenotype. Genetics in Medicine Open, 2.

    • 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

    • 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.