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Kastriti, ME., Maksimov, D., Krupinova, J (...) Kharchenko, PV., Adameyko, I. (2026). Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover. Nat Genet. 58(9):2270-2283

Gonzalez Lopez, M., Katsura, KA., Neves, VCM (...) Adameyko, I., Krivanek, J. (2026). Embryonic and postnatal macrophages are necessary for proper tooth development and homeostasis. Nat Commun. 17(1)

Schwarz, LA., Dotter, CP., Isaev, S (...) Bock, C., Novarino, G. (2026). Cortical development dynamics across autism spectrum disorder mouse models. Nature. 656(8126):159-172

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Poverennaya, I., Murtazina, A., Li, L (...) Chagin, AS., Adameyko, I. (2026). Ribosomal modifications are associated with mesenchymal fate selection in the neural crest lineage. Nat Commun. 17(1)

Palmer, CR., Song, J., Yang, B (...) Ren, B., Zhang, K. (2026). Single-cell multiomic human brain atlas reveals regulatory drivers of cortical regionality. Nat Commun. 17(1)

Mitchel, J., Gordon, MG., Perez, RK (...) Ye, CJ., Kharchenko, PV. (2025). Coordinated, multicellular patterns of transcriptional variation that stratify patient cohorts are revealed by tensor decomposition. Nat Biotechnol. 43(7):1192-1201

Gustafsson, K., Isaev, S., Mirsanaye, K (...) Kharchenko, PV., Scadden, DT. (2025). Mesenchymal thymic niche cells enable regeneration of the adult thymus and T cell immunity. Nat Biotechnol.

Embaie, BT., Sarkar, H., Alchahin, AM (...) Kharchenko, PV., Baryawno, N. (2025). Comparative Single-Cell Transcriptomics of Human Neuroblastoma and Preclinical Models Reveals Conservation of an Adrenergic Cell State. Cancer Res. 85(6):1015-1034

Toghani, D., Gupte, S., Zeng, S (...) Spencer, JA., Silberstein, L. (2025). Niche-derived Semaphorin 4A safeguards functional identity of myeloid-biased hematopoietic stem cells. Nat Aging. 5(4):558-575

Keller, MS., Gold, I., McCallum, C (...) Kharchenko, PV., Gehlenborg, N. (2025). Vitessce: integrative visualization of multimodal and spatially resolved single-cell data. Nat Methods. 22(1):63-67

Olsen, TK., Otte, J., Mei, S (...) Kharchenko, PV., Baryawno, N. (2024). Joint single-cell genetic and transcriptomic analysis reveal pre-malignant SCP-like subclones in human neuroblastoma. Mol Cancer. 23(1):180

Kalhor, K., Chen, CJ., Lee, HS (...) Fan, JB., Zhang, K. (2024). Mapping human tissues with highly multiplexed RNA in situ hybridization. Nat Commun. 15(1):2511

Mei, S., Alchahin, AM., Embaie, BT (...) Kogner, P., Baryawno, N. (2024). Single-cell analyses of metastatic bone marrow in human neuroblastoma reveals microenvironmental remodeling and metastatic signature. JCI Insight. 9(6)

Zhang, Y., Petukhov, V., Biederstedt, E (...) Zhang, K., Kharchenko, PV. (2024). Gene panel selection for targeted spatial transcriptomics. Genome Biol. 25(1):35

Mei, S., Alchahin, AM., Tsea, I (...) Sykes, DB., Baryawno, N. (2024). Single-cell analysis of immune and stroma cell remodeling in clear cell renal cell carcinoma primary tumors and bone metastatic lesions. Genome Med. 16(1):1

Gao, T., Soldatov, R., Sarkar, H (...) Loh, PR., Kharchenko, PV. (2023). Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes. Nat Biotechnol. 41(3):417-426

Parry, EM., Lemvigh, CK., Deng, S (...) Jain, N., Wu, CJ. (2023). ZNF683 marks a CD8⁺ T cell population associated with anti-tumor immunity following anti-PD-1 therapy for Richter syndrome. Cancer Cell. 41(10):1803-1816.e8

Gao, T., Kastriti, ME., Ljungström, V (...) Park, PJ., Kharchenko, PV. (2023). A pan-tissue survey of mosaic chromosomal alterations in 948 individuals. Nat Genet. 55(11):1901-1911

Jain, S., Pei, L., Spraggins, JM (...) Börner, K., Snyder, MP. (2023). Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol. 25(8):1089-1100

Hirz, T., Mei, S., Sarkar, H (...) Kharchenko, PV., Sykes, DB. (2023). Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses. Nat Commun. 14(1):663

Huebner, AJ., Gorelov, RA., Deviatiiarov, R (...) Kharchenko, PV., Hochedlinger, K. (2023). Dissection of gastric homeostasis in vivo facilitates permanent capture of isthmus-like stem cells in vitro. Nat Cell Biol. 25(3):390-403

Faure, L., Soldatov, R., Kharchenko, PV., Adameyko, I. (2023). scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data. Bioinformatics. 39(1)

Purroy, N., Tong, YE., Lemvigh, CK (...) Gohil, SH., Wu, CJ. (2022). Single-cell analysis reveals immune dysfunction from the earliest stages of CLL that can be reversed by ibrutinib. Blood. 139(14):2252-2256

Petukhov, V., Xu, RJ., Soldatov, RA (...) Moffitt, JR., Kharchenko, PV. (2022). Cell segmentation in imaging-based spatial transcriptomics. Nat Biotechnol. 40(3):345-354

Haase, C., Gustafsson, K., Mei, S (...) Scadden, DT., Lin, CP. (2022). Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging. Nat Methods. 19(12):1622-1633

Batiuk, MY., Tyler, T., Dragicevic, K (...) Kharchenko, PV., Khodosevich, K. (2022). Upper cortical layer-driven network impairment in schizophrenia. Sci Adv. 8(41):eabn8367

Alchahin, AM., Mei, S., Tsea, I (...) Kharchenko, PV., Baryawno, N. (2022). A transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma. Nat Commun. 13(1):5747

Verhoeven, BM., Mei, S., Olsen, TK (...) Johnsen, JI., Baryawno, N. (2022). The immune cell atlas of human neuroblastoma. Cell Rep Med. 3(6):100657

Buonomo, EL., Mei, S., Guinn, SR (...) Kharchenko, PV., Sharpe, AH. (2022). Liver stromal cells restrict macrophage maturation and stromal IL-6 limits the differentiation of cirrhosis-linked macrophages. J Hepatol. 76(5):1127-1137

Osumi-Sutherland, D., Xu, C., Keays, M (...) Lein, E., Teichmann, SA. (2021). Cell type ontologies of the Human Cell Atlas. Nat Cell Biol. 23(11):1129-1135

Bergen, V., Soldatov, RA., Kharchenko, PV., Theis, FJ. (2021). RNA velocity-current challenges and future perspectives. Mol Syst Biol. 17(8):e10282

Kameneva, P., V Artemov, A., Kastriti, ME (...) Kharchenko, PV., Adameyko, I. (2021). Evolutionary switch in expression of key markers between mouse and human leads to mis-assignment of cell types in developing adrenal medulla. Cancer Cell. 39(5):590-591

Kfoury, Y., Baryawno, N., Severe, N (...) Sykes, DB., Kharchenko, PV. (2021). Human prostate cancer bone metastases have an actionable immunosuppressive microenvironment. Cancer Cell. 39(11):1464-1478.e8

(2021). A multimodal cell census and atlas of the mammalian primary motor cortex. Nature. 598(7879):86-102

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Bedoya-Reina, OC., Li, W., Arceo, M (...) Kogner, P., Schlisio, S. (2021). Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors. Nat Commun. 12(1):5309

Girskis, KM., Stergachis, AB., DeGennaro, EM (...) Greenberg, ME., Walsh, CA. (2021). Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions. Neuron. 109(20):3239-3251.e7

Tasdemir-Yilmaz, OE., Druckenbrod, NR., Olukoya, OO (...) Goodrich, LV., Segal, RA. (2021). Diversity of developing peripheral glia revealed by single-cell RNA sequencing. Dev Cell. 56(17):2516-2535.e8

Seplyarskiy, VB., Soldatov, RA., Koch, E (...) Kharchenko, PV., Sunyaev, S. (2021). Population sequencing data reveal a compendium of mutational processes in the human germ line. Science. 373(6558):1030-1035

Kharchenko, PV. (2021). The triumphs and limitations of computational methods for scRNA-seq. Nat Methods. 18(7):723-732

Kameneva, P., Artemov, AV., Kastriti, ME (...) Kharchenko, PV., Adameyko, I. (2021). Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin. Nat Genet. 53(5):694-706

Kupari, J., Usoskin, D., Parisien, M (...) Diatchenko, L., Ernfors, P. (2021). Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain. Nat Commun. 12(1):1510

Specht, H., Emmott, E., Petelski, AA (...) Koller, A., Slavov, N. (2021). Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. Genome Biol. 22(1):50

Kagan, J., Moritz, RL., Mazurchuk, R (...) Smith, RD., Srivastava, S. (2020). National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions. J Proteome Res. 19(5):1900-1912

Pfisterer, U., Petukhov, V., Demharter, S (...) Kharchenko, PV., Khodosevich, K. (2020). Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis. Nat Commun. 11(1):5038

Krivanek, J., Soldatov, RA., Kastriti, ME (...) Kharchenko, PV., Adameyko, I. (2020). Dental cell type atlas reveals stem and differentiated cell types in mouse and human teeth. Nat Commun. 11(1):4816

Bachireddy, P., Ennis, C., Nguyen, VN (...) Kharchenko, PV., Wu, CJ. (2020). Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect. Sci Transl Med. 12(561)

(2019). The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature. 574(7777):187-192

Barkas, N., Petukhov, V., Nikolaeva, D (...) Khodosevich, K., Kharchenko, PV. (2019). Joint analysis of heterogeneous single-cell RNA-seq dataset collections. Nat Methods. 16(8):695-698

Soldatov, R., Kaucka, M., Kastriti, ME (...) Kharchenko, PV., Adameyko, I. (2019). Spatiotemporal structure of cell fate decisions in murine neural crest. Science. 364(6444)

La Manno, G., Soldatov, R., Zeisel, A (...) Linnarsson, S., Kharchenko, PV. (2018). RNA velocity of single cells. Nature. 560(7719):494-498

Petukhov, V., Guo, J., Baryawno, N (...) Samsonova, MG., Kharchenko, PV. (2018). dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments. Genome Biol. 19(1):78

Fan, J., Lee, HO., Lee, S (...) Park, WY., Kharchenko, PV. (2018). Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data. Genome Res. 28(8):1217-1227

Lake, BB., Chen, S., Sos, BC (...) Kharchenko, PV., Zhang, K. (2018). Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. Nat Biotechnol. 36(1):70-80

Hoggatt, J., Singh, P., Tate, TA (...) Scadden, DT., Pelus, LM. (2018). Rapid Mobilization Reveals a Highly Engraftable Hematopoietic Stem Cell. Cell. 172(1-2):191-204.e10

Lake, BB., Codeluppi, S., Yung, YC (...) Linnarsson, S., Zhang, K. (2017). A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. Sci Rep. 7(1):6031

Furlan, A., Dyachuk, V., Kastriti, ME (...) Ernfors, P., Adameyko, I. (2017). Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla. Science. 357(6346)

Wang, L., Fan, J., Francis, JM (...) Livak, KJ., Wu, CJ. (2017). Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Res. 27(8):1300-1311

Alekseyenko, AA., Walsh, EM., Zee, BM (...) Kuroda, MI., French, CA. (2017). Ectopic protein interactions within BRD4-chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma. Proc Natl Acad Sci U S A. 114(21):E4184-E4192

Yuan, GC., Cai, L., Elowitz, M (...) Shivdasani, R., Tirosh, I. (2017). Challenges and emerging directions in single-cell analysis. Genome Biol. 18(1):84

Akle, V., Stankiewicz, AJ., Kharchenko, V (...) Kharchenko, PV., Zhdanova, IV. (2017). Circadian Kinetics of Cell Cycle Progression in Adult Neurogenic Niches of a Diurnal Vertebrate. J Neurosci. 37(7):1900-1909

Fan, J., Salathia, N., Liu, R (...) Chun, J., Kharchenko, PV. (2016). Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nat Methods. 13(3):241-4

Yu, VWC., Yusuf, RZ., Oki, T (...) Kharchenko, PV., Scadden, DT. (2016). Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells. Cell. 167(5):1310-1322.e17

Wang, L., Brooks, AN., Fan, J (...) Kharchenko, PV., Wu, CJ. (2016). Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. Cancer Cell. 30(5):750-763

Zhang, X., Chen, MH., Wu, X (...) Sharp, PA., Walsh, CA. (2016). Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex. Cell. 166(5):1147-1162.e15

Silberstein, L., Goncalves, KA., Kharchenko, PV (...) Hu, GF., Scadden, DT. (2016). Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators. Cell Stem Cell. 19(4):530-543

Burger, JA., Landau, DA., Taylor-Weiner, A (...) Getz, G., Wu, CJ. (2016). Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition. Nat Commun. 7:11589

Masuda, T., Wang, X., Maeda, M (...) Kharchenko, PV., Maeda, T. (2016). Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin. Science. 351(6270):285-9

Bersani, F., Lee, E., Kharchenko, PV (...) Ting, DT., Haber, DA. (2015). Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer. Proc Natl Acad Sci U S A. 112(49):15148-53

Alekseyenko, AA., Walsh, EM., Wang, X (...) Kuroda, MI., French, CA. (2015). The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains. Genes Dev. 29(14):1507-23

Welling, M., Chen, HH., Muñoz, J (...) Heck, AJ., Geijsen, N. (2015). DAZL regulates Tet1 translation in murine embryonic stem cells. EMBO Rep. 16(7):791-802

Zhou, H., Schmidt, SC., Jiang, S (...) Kieff, E., Zhao, B. (2015). Epstein-Barr virus oncoprotein super-enhancers control B cell growth. Cell Host Microbe. 17(2):205-16

Alekseyenko, AA., McElroy, KA., Kang, H (...) Kharchenko, PV., Kuroda, MI. (2015). BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes. Curr Protoc Mol Biol. 109:21.30.1-21.30.32

Schmidt, SC., Jiang, S., Zhou, H (...) Kieff, E., Zhao, B. (2015). Epstein-Barr virus nuclear antigen 3A partially coincides with EBNA3C genome-wide and is tethered to DNA through BATF complexes. Proc Natl Acad Sci U S A. 112(2):554-9

Usoskin, D., Furlan, A., Islam, S (...) Linnarsson, S., Ernfors, P. (2015). Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. Nat Neurosci. 18(1):145-53

Kharchenko, PV., Silberstein, L., Scadden, DT. (2014). Bayesian approach to single-cell differential expression analysis. Nat Methods. 11(7):740-2

Landau, DA., Clement, K., Ziller, MJ (...) Meissner, A., Wu, CJ. (2014). Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell. 26(6):813-825

Ho, JW., Jung, YL., Liu, T (...) Karpen, GH., Park, PJ. (2014). Comparative analysis of metazoan chromatin organization. Nature. 512(7515):449-52

Alekseyenko, AA., Gorchakov, AA., Zee, BM (...) Kharchenko, PV., Kuroda, MI. (2014). Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs. Genes Dev. 28(13):1445-60

Alekseyenko, AA., Gorchakov, AA., Kharchenko, PV., Kuroda, MI. (2014). Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification. Proc Natl Acad Sci U S A. 111(7):2488-93

Jiang, S., Willox, B., Zhou, H (...) Kieff, E., Zhao, B. (2014). Epstein-Barr virus nuclear antigen 3C binds to BATF/IRF4 or SPI1/IRF4 composite sites and recruits Sin3A to repress CDKN2A. Proc Natl Acad Sci U S A. 111(1):421-6

Ferrari, F., Jung, YL., Kharchenko, PV (...) Kuroda, MI., Park, PJ. (2013). Comment on "Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters". Science. 340(6130):273

Ferrari, F., Plachetka, A., Alekseyenko, AA (...) Park, PJ., Kuroda, MI. (2013). "Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts. Cell Rep. 5(3):629-36

Portal, D., Zhou, H., Zhao, B (...) Lu, Y., Kieff, E. (2013). Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2. Proc Natl Acad Sci U S A. 110(46):18537-42

Woo, CJ., Kharchenko, PV., Daheron, L., Park, PJ., Kingston, RE. (2013). Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters. Mol Cell Biol. 33(16):3274-85

Apostolou, E., Ferrari, F., Walsh, RM (...) Park, PJ., Hochedlinger, K. (2013). Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell. 12(6):699-712

Wang, CI., Alekseyenko, AA., LeRoy, G (...) Garcia, BA., Kuroda, MI. (2013). Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol. 20(2):202-9

(2012). An integrated encyclopedia of DNA elements in the human genome. Nature. 489(7414):57-74

Riddle, NC., Jung, YL., Gu, T (...) Park, PJ., Elgin, SC. (2012). Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genet. 8(9):e1002954

Landt, SG., Marinov, GK., Kundaje, A (...) Wold, BJ., Snyder, M. (2012). ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22(9):1813-31

Schwartz, YB., Linder-Basso, D., Kharchenko, PV (...) Karpen, GH., Pirrotta, V. (2012). Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res. 22(11):2188-98

Lee, E., Iskow, R., Yang, L (...) Kharchenko, PV., Park, PJ. (2012). Landscape of somatic retrotransposition in human cancers. Science. 337(6097):967-71

Alekseyenko, AA., Ho, JW., Peng, S (...) Kuroda, MI., Park, PJ. (2012). Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genet. 8(4):e1002646

Seplyarskiy, VB., Kharchenko, P., Kondrashov, AS., Bazykin, GA. (2012). Heterogeneity of the transition/transversion ratio in Drosophila and Hominidae genomes. Mol Biol Evol. 29(8):1943-55

Kharchenko, PV., Xi, R., Park, PJ. (2011). Evidence for dosage compensation between the X chromosome and autosomes in mammals. Nat Genet. 43(12):1167-9; author reply 1171-2

Egelhofer, TA., Minoda, A., Klugman, S (...) Hawkins, RD., Lieb, JD. (2011). An assessment of histone-modification antibody quality. Nat Struct Mol Biol. 18(1):91-3

Simon, MD., Wang, CI., Kharchenko, PV (...) Kuroda, MI., Kingston, RE. (2011). The genomic binding sites of a noncoding RNA. Proc Natl Acad Sci U S A. 108(51):20497-502

Kharchenko, PV., Alekseyenko, AA., Schwartz, YB (...) Karpen, GH., Park, PJ. (2011). Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 471(7339):480-5

Larschan, E., Bishop, EP., Kharchenko, PV (...) Park, PJ., Kuroda, MI. (2011). X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature. 471(7336):115-8

Ho, JW., Bishop, E., Karchenko, PV (...) White, KP., Park, PJ. (2011). ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics. 12:134

Eaton, ML., Prinz, JA., MacAlpine, HK (...) Kharchenko, PV., MacAlpine, DM. (2011). Chromatin signatures of the Drosophila replication program. Genome Res. 21(2):164-74

Riddle, NC., Minoda, A., Kharchenko, PV (...) Elgin, SC., Karpen, GH. (2011). Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res. 21(2):147-63

Day, DS., Luquette, LJ., Park, PJ., Kharchenko, PV. (2010). Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol. 11(6):R69

Tolstorukov, MY., Kharchenko, PV., Park, PJ. (2010). Analysis of primary structure of chromatin with next-generation sequencing. Epigenomics. 2(2):187-197

Roy, S., Ernst, J., Kharchenko, PV (...) White, KP., Kellis, M. (2010). Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 330(6012):1787-97

Woo, CJ., Kharchenko, PV., Daheron, L., Park, PJ., Kingston, RE. (2010). A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell. 140(1):99-110

Gorchakov, AA., Alekseyenko, AA., Kharchenko, P., Park, PJ., Kuroda, MI. (2009). Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X. Genes Dev. 23(19):2266-71

Tolstorukov, MY., Kharchenko, PV., Goldman, JA., Kingston, RE., Park, PJ. (2009). Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Res. 19(6):967-77

Kharchenko, PV., Tolstorukov, MY., Park, PJ. (2008). Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 26(12):1351-9

Alekseyenko, AA., Peng, S., Larschan, E (...) Park, PJ., Kuroda, MI. (2008). A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell. 134(4):599-609

Kharchenko, PV., Woo, CJ., Tolstorukov, MY., Kingston, RE., Park, PJ. (2008). Nucleosome positioning in human HOX gene clusters. Genome Res. 18(10):1554-61

Orford, K., Kharchenko, P., Lai, W (...) Park, PJ., Scadden, DT. (2008). Differential H3K4 methylation identifies developmentally poised hematopoietic genes. Dev Cell. 14(5):798-809

Wright, MA., Kharchenko, P., Church, GM., Segrè, D. (2007). Chromosomal periodicity of evolutionarily conserved gene pairs. Proc Natl Acad Sci U S A. 104(25):10559-64

Vitkup, D., Kharchenko, P., Wagner, A. (2006). Influence of metabolic network structure and function on enzyme evolution. Genome Biol. 7(5):R39

Kharchenko, P., Chen, L., Freund, Y., Vitkup, D., Church, GM. (2006). Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics. 7:177

Kharchenko, P., Church, GM., Vitkup, D. (2005). Expression dynamics of a cellular metabolic network. Mol Syst Biol. 1:2005.0016

Kharchenko, P., Vitkup, D., Church, GM. (2004). Filling gaps in a metabolic network using expression information. Bioinformatics. 20 Suppl 1:i178-85

Segrè, D., Zucker, J., Katz, J (...) Wright, MA., Church, GM. (2003). From annotated genomes to metabolic flux models and kinetic parameter fitting. OMICS. 7(3):301-16