Publications

Baldan J, Camacho-Roda J, Ballester M, Høj K, Kurilla A, Maurer C, Arcila-Barrera S, Lin X, Pan Z, Castro J, Mayorca-Guiliani  A, Rift C, Hasselby J, Bouwens L, Lefebvre V, David C, Parnas O, DelGiorno K, Erler J, Rooman I, Arnes L (2024) Resolution of Acinar Dedifferentiation Regulates Tissue Remodeling in Pancreatic Injury and Cancer Initiation. Gastroenterology 167(4):718-732.e18.

Hendriksen J, Locallo A, Maarup S, Debnath O, Ishaque N, Hasselbach B, Skjøth-Rasmussen B, Yde C, Poulsen H, Lassen U, Weischenfeldt J (2024) Immunotherapy drives mesenchymal tumor cell state shift and TME immune response in glioblastoma patients. Neuro Oncol, 26(8):1453-1466.

Sørensen F, Petanjek TL, Scheper M, Rydbirk R, Korshunova I, Anink J, Mühlebner A, Mills J, Petanjek Z, Aronica E, Khodosevich K (2024) Single-cell profiling of cortical tubers in tuberous sclerosis complex shows molecular structure preservation and massive reorganization of metabolism. bioRxiv, 2024.10.31.621014.

Khodosevich K^#, Dragicevic K, Howes O^# (2024) Drug targeting in psychiatric disorders – how to overcome the loss in translation? Nat Rev Drug Discov, 23(3):218-231.

Schmidt S, Hansen K, Krautz R, Rago D, Havelund J, Stigliani A, Faergeman NJ, Prézelin A, Rivière J, Couturier-Tarrade A, Akimov V, Blagoev B, Elfving B, Neess D, Vogel U, Khodosevich K, Hougaard KS, Sandelin A (2024). Pulmonary maternal immune activation does not cross the placenta but leads to fetal metabolic adaptation. Nat Commun 15(1):4711.

Scheper M, Sørensen F, Ruffolo G, Gaeta A, Lissner LJ, Anink JJ, Korshunova I, Jansen FE, Riney K, van Hecke W, Mühlebner A, Khodosevich K, Schubert D, Palma E, Mills JD, Aronica E (2024). Impaired GABAergic regulation and developmental immaturity in interneurons derived from the medial ganglionic eminence in the tuberous sclerosis complex. Acta Neuropathol 147(1):80.

Maciag G, Hansen S, Krizic K, Kellermann L, Inventor Zøylner M, Ulyanchenko S, Maimets M, Baattrup A, Riis L, Khodosevich K, Sato T, Bressan R, Nielsen O, Jensen K (2024). JAK/STAT signaling promotes the emergence of unique cell states in ulcerative colitis. Stem Cell Reports 19(8):1172-1188.

Szabó D, Franke V, Bianco S, Batiuk MY, Paul EJ, Kukalev A, Pfisterer UG, Irastorza-Azcarate I, Chiariello AM, Demharter S, Zea-Redondo L, Lopez-Atalaya JP, Nicodemi M, Akalin A, Khodosevich K, Ungless MA, Winick-Ng W, Pombo A (2024). A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons. bioRxiv, 2024.05.10.593308.

Khodosevich K^#, Sellgren CM^# (2023) Neurodevelopmental disorders—high-resolution rethinking of disease modeling. Mol Psychiatry 28(1):34-43.

Luinenburg M, Scheper M, Sorensen F, Anink J, Van Hecke W, Korshunova I, Jansen F, Riney K, van Eijsden P, Gosselaar P, Mills J, Kalf R, Zimmer T, Broekaart D, Khodosevich K, Aronica E, Muhlebner A (2023). Loss of maturity and homeostatic functions in Tuberous Sclerosis Complex-derived astrocytes. Front Cell Neurosci 17:1284394.

Kick F, Holze H, Rydbirk R, Khodosevich K (2023) CRMetrics - an R package for Cell Ranger Filtering and Metrics Visualisation. Research Square doi.org/10.21203/rs.3.rs-2853524/v1.

Khodosevich K, Dragicevic K, Howes O (2023) Drug targeting in psychiatric disorders – how to overcome the loss in translation? Nat Rev Drug Discovery, s41573-023-00847-7 

Lemcke R, Egebjerg C, Berendtsen NT, Egerod KL, Thomsen AR, Pers TH, Christensen JP, Kornum BR (2023) Molecular consequences of peripheral Influenza A infection on cell populations in the murine hypothalamus. Elife, 12:RP87515

Palani NP, Horvath C, Timshel PN, Folkertsma P, Grønning AGB, Henriksen TI, Peijs L, Jensen VH, Sun W, Jespersen NZ, Wolfrum C, Pers TH, Nielsen S, Scheele C (2023) Adipogenic and SWAT cells separate from a common progenitor in human brown and white adipose depots. Nat Metab, 5(6):996-1013.

Lee J, Møller AF, Chae S, Bussek A, Park TJ, Kim Y, Lee HS, Pers TH, Kwon T, Sedzinski J, Natarajan KN (2023) A single-cell, time-resolved profiling of Xenopus mucociliary epithelium reveals nonhierarchical model of development. Sci Adv, 9(14):eadd5745.

O'Rourke C, Salati M, Rae C, Carpino G, Leslie H, Pea A, Prete M, Bonetti L, Amato F, Montal R, Upstill-Goddard R, Nixon C, Sanchon-Sanchez P, Kunderfranco P, Sia D, Gaudio E, Overi D, Cascinu S, Hogdall D, Pugh S, Domingo E, Primrose J, Bridgewater J, Spallanzani A, Gelsomino F, Llovet J, Calvisi D, Boulter L, Caputo F, Lleo A, Jamieson N, Luppi G, Dominici M, Andersen J, Braconi C (2023) Molecular portraits of patients with intrahepatic cholangiocarcinoma who diverge as rapid progressors or long survivors on chemotherapy. Gut, doi: 10.1136/gutjnl-2023-330748

Ford S, Buus T, Nastasi C, Geisler C, Bonefeld C, Ødum  N, Woetmann A (2023) In vitro differentiated human CD4+ T cells produce hepatocyte growth factor. Front Immunol, 14:1210836

Karin F, Ferretti E (2023) Derivation of Human Extraembryonic Mesoderm-like Cells from Primitive Endoderm. Int J Mol Sci, 24(14):11366

Schmøkel S, Nordentoft  I, Lindskrog S, Lamy P, Knudsen M, Jensen J, Dyrskjøt L (2023) Improved protocol for single-nucleus RNA-sequencing of frozen human bladder tumor biopsies. Nucleus, 14(1):2186686

Pærregaard S, Wulff L, Schussek S, Niss K, Mörbe U, Jendholm J, Wendland K, Andrusaite A, Brulois K, Nibbs R, Sitnik K, Mowat A, Butcher E, Brunak S, Agace W (2023) The small and large intestine contain related mesenchymal subsets that derive from embryonic Gli1+ precursors. Nat Commun, 14(1):2307

Peiffer L, Gambichler T, Buus T, Horny K, Gravemeyer J, Furtmann F, Spassova I, Kubat L, Susok L, Stranzenbach R, Srinivas N, Ødum N, Becker J (2023) Phenotypic plasticity of malignant T cells in blood and skin of a Sézary syndrome patient revealed by single cell transcriptomics. Front Oncol, 13:1090592

Gluud M, Pallesen E, Buus T, Gjerdrum L, Lindahl L, Kamstrup M, Bzorek M, Danielsen R, Bech R, Monteiro E, Blümel E, Willerslev-Olsen A, Lykkebo-Valløe A, Vadivel C, Krejsgaard T, Bonefeld C, Geisler C, Becker J, Koralov S, Iversen L, Litman T, Woetmann A, Ødum N (2023) Malignant T cells induce skin barrier defects through cytokine-mediated JAK/STAT signaling in cutaneous T-cell lymphoma. Blood, 141 (2): 180–193.

Batiuk M, Tyler T, Dragicevic K, Mei S, Rydbirk R, Petukhov V, Deviatiiarov R, Sedmak D, Frank E, Feher V, Habek N, Hu Q, Igolkina A, Roszik L, Pfisterer U, Garcia-Gonzalez D, Petanjek Z, Adorjan I, Kharchenko P, Khodosevich K (2022) Upper cortical layer–driven network impairment in schizophrenia. Sci Adv 8, doi:10.1126/SCIADV.ABN8367

Petukhov V, Igolkina A, Rydbirk R, Mei S, Christoffersen L, Khodosevich K, Kharchenko P (2022). Case-control analysis of single-cell RNA-seq studies. bioRxiv 2022.03.15.484475.

Kim D, Kim J, Yu Y, Kim Y, Baek S, Won KJ (2022) Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition. Nucl Acid Res, 13:7298–7309

Malwade S, Gasthaus J, Bellardita C, Andelic M, Moric B, Korshunova I, Kiehn O, Vasistha NA, Khodosevich K (2022) Identification of vulnerable interneuron subtypes in 15q13.3 microdeletion syndrome using single-cell transcriptomics. Biol Psychiatry, 91(8): 727-739

Pedersen  C,  Dam  S, Barnkob M, Leipold  M,  Purroy N, Rassenti L, Kipps  T, Nguyen J, Lederer  J, Gohil  S, Wu C, Olsen L (2022) cyCombine allows for robust integration of single-cell cytometry datasets within and across technologies. Nat Commun, 13(1):1698

Bergmann T, Liu Y, Skov J, Mogus L, Lee J, Pfisterer U, Hand L, Asenjo-Martinez A, Vargas I, Seemann S, Tsz J, Lee H, Patikas N, Kornum B, Denham M, Hyttel P, Witter M, Gorodkin J, Pers T, Hemberg M, Khodosevich K, Hall V (2022) Production of human entorhinal stellate cell-like cells by forward programming shows an important role of Foxp1 in reprogramming. Front Cell Dev Biol, 10: 1–23

Kohler K, Goldhammer N, Demharter S, Pfisterer U, Khodosevich K, Rønnov-Jessen L, Petersen O, Villadsen R, Kim J (2022) Ductal keratin 15+ luminal progenitors in normal breast exhibit a basal-like breast cancer transcriptomic signature. npj Breast Cancer, 8: 1–12

Pazarlar B, Aripaka S, Petukhov V, Pinborg L, Khodosevich K, Mikkelsen J (2022) Expression profile of synaptic vesicle glycoprotein 2A, B, and C paralogues in temporal neocortex tissue from patients with temporal lobe epilepsy (TLE). Mol Brain, 15: 45

• Herrera A,  Cheng A, Mimitou E, Seffens A, George D, Bar-Natan M, Heguy A, Ruggles K, Scher J, Hymes K, Latkowski J, Ødum N, Kadin M, Ouyang Z, Geskin L, Smibert P, Buus T, Koralov S (2021) Multimodal single-cell analysis of cutaneous T-cell lymphoma reveals distinct subclonal tissue-dependent signatures. Blood, 138 (16): 1456–1464

• Ivanova E, Devlin J, Buus T, Koide A, Shwetar J, Cornelius A, Samanovic M, Herrera A, Mimitou E, Zhang C, Desvignes L, Odum N, Smibert P, Ulrich R, Mulligan M, Koide S, Ruggles K, Herati R, Koralov S (2021) SARS-CoV-2 mRNA vaccine elicits a potent adaptive immune response in the absence of IFN-mediated inflammation observed in COVID-19. medRxiv, 2021.04.20.21255677

• Buus T, Herrera A, Ivanova E, Mimitou E, Cheng A, Herati R, Papagiannakopoulos T, Smibert P, Odum N, Koralov S (2021) Improving oligo-conjugated antibody signal in multimodal single-cell analysis. eLife, doi.org/10.7554/eLife.61973

• Petukhov V, Xu R, Soldatov RA, Cadinu P, Khodosevich K, Moffitt J, Kharchenko P. (2021) Cell segmentation in imaging-based spatial transcriptomics. Nat Biotech, 10.1038/s41587-021-01044-w

• Kim J, T Jakobsen S, Natarajan KN, Won KJ. (2021) TENET: gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data. Nucleic Acids Res, 49(1):e1
  
  
• Batiuk MY, Tyler T, Mei S, Rydbirk R, Petukhov V, Sedmak D, Erzsebet F, Feher V, Habek N, Qiwen H, Igolkina A, Roszik L, Pfisterer U, Petanjek Z, Adorjan I, Kharchenko P, Khodosevich K. (2021) Selective vulnerability of supragranular layer neurons in schizophrenia. bioRxiv, 2020.11.17.386458.
  
  
• Susmita Malwade, Janina Gasthaus, Carmelo Bellardita, Matej Andelic, Barna Morie, Irina Korshunova, Ole Kiehn, Navneet A. Vasistha, Konstantin Khodosevich (2021) Identification of vulnerable interneuron subtypes in 15q13.3 microdeletion syndrome using single-cell transcriptomics. Biological Psychiatry, 2021, doi: 10.1016/j.biopsych.2021.09.012 

• Mariani L, Guo X, Menezes N, Drozd AM, Cakal SD, Wang Q, Ferretti E (2021) A TALE/HOX code unlocks WNT signalling response towards paraxial mesoderm. Nat Commun 12, 5136
  

• Guangzheng Weng, Junil Kim, Kyoung Jae Won. (2021) VeTra: a tool for trajectory inference based on RNA velocity. Bioinformatics, btab364

• Møller AF, Natarajan KN (2020) Predicting gene regulatory networks from cell atlases. Life Sci Alliance, 3(11):e202000658
  
  
• Petukhov V, Soldatov RA, Khodosevich K, Kharchenko P. (2020) Bayesian segmentation of spatially resolved transcriptomics data. bioRxiv, 2020.10.05.326777.
  
  
• Pfisterer, Demharter S., Petukhov V., Meichsner J., Thompson J., Batiuk M., Asenjo Martinez A., Vasistha N., Thakur A., Mikkelsen J., Adorjan I., Pinborg L., Pers T., von Engelhardt J., Kharchenko P., Khodosevich K. (2020) Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis. Nat Commun, 11(1):1-19
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• Sanz Morello B., Pfisterer U., Hansen N., Demharter S., Thakur A., Fujii K., Levitskiy S., Montalant A., Korshunova I., Mammen P., Kamenski P., Noguchi S., Aldana Garcia B., Hougaard K., Perrier J., Khodosevich K. (2020) Unique isoform in oxidative phosphorylation machinery supports the function of fast-spiking neurons. EMBO J, 39:e105759
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• Terkelsen MK, Bendixen SM, Hansen D, Scott EAH, Moeller AF, Nielsen R, Mandrup S, Schlosser A, Andersen TL, Sorensen GL, Krag A, Natarajan KN, Detlefsen S, Dimke H, Ravnskjaer K. (2020) Transcriptional Dynamics of Hepatic Sinusoid-Associated Cells After Liver Injury. Hepatology, 72(6):2119-2133
  
  
• Yuste, R., Hawrylycz, M., Aalling, N., Aguilar-Valles, A., Arendt, D., Arnedillo, R.A., Ascoli, G.A., Bielza, C., Bokharaie, V., Bergmann, T.B., Bystron, I., Capogna, M., Chang, Y., Clemens, A., de Kock, C.P.J., DeFelipe, J., Dos Santos, S.E., Dunville, K., Feldmeyer, D., Fiáth, R., Fishell, G.J., Foggetti, A., Gao, X., Ghaderi, P., Goriounova, N.A., Güntürkün, O., Hagihara, K., Hall, V.J., Helmstaedter, M., Herculano, S., Hilscher, M.M., Hirase, H., Hjerling-Leffler, J., Hodge, R., Huang, J., Huda, R., Khodosevich, K., Kiehn, O., Koch, H., Kuebler, E.S., Kühnemund, M., Larrañaga, P., Lelieveldt, B., Louth, E.L., Lui, J.H., Mansvelder, H.D., Marin, O., Martinez-Trujillo, J., Moradi Chameh, H., Nath, A., Nedergaard, M., Němec, P., Ofer, N., Pfisterer, U.G., Pontes, S., Redmond, W., Rossier, J., Sanes, J.R., Scheuermann, R., Serrano-Saiz, E., Steiger, J.F., Somogyi, P., Tamás, G., Tolias, A.S., Tosches, M.A., García, M.T., Vieira, H.M., Wozny, C., Wuttke, T. V., Yong, L., Yuan, J., Zeng, H., Lein, E. (2020) A community-based transcriptomics classification and nomenclature of neocortical cell types. Nat Neurosci, 23(12): 1456-1468
  
  
• Teves JM, Won KJ. (2020) Mapping Cellular Coordinates through Advances in Spatial Transcriptomics Technology. Mol Cells, 43(7):591-599
  
  
• Wan S, Kim J, Won KJ. (2020) SHARP: hyperfast and accurate processing of single-cell RNA-seq data via ensemble random projection. Genome Res, 30(2):205-213
  
  
• Genetic mapping of etiologic brain cell types for obesity. Timshel PN, Thompson JJ, Pers TH. Elife. 2020 Sep 21;9:e55851. doi: 10.7554/eLife.55851.
  
  
• Transcriptomic analysis links diverse hypothalamic cell types to fibroblast growth factor 1-induced sustained diabetes remission. Bentsen MA, Rausch DM, Mirzadeh Z, Muta K, Scarlett JM, Brown JM, Herranz-Pérez V, Baquero AF, Thompson J, Alonge KM, Faber CL, Kaiyala KJ, Bennett C, Pyke C, Ratner C, Egerod KL, Holst B, Meek TH, Kutlu B, Zhang Y, Sparso T, Grove KL, Morton GJ, Kornum BR, García-Verdugo JM, Secher A, Jorgensen R, Schwartz MW, Pers TH. Nat Commun. 2020 Sep 7;11(1):4458. doi: 10.1038/s41467-020-17720-5.
  
  
• Modeling neural tube development by differentiation of human embryonic stem cells in a microfluidic WNT gradient. Rifes P, Isaksson M, Rathore GS, Aldrin-Kirk P, Møller OK, Barzaghi G, Lee J, Egerod KL, Rausch DM, Parmar M, Pers TH, Laurell T, Kirkeby A. Nat Biotechnol. 2020 Nov;38(11):1265-1273. doi: 10.1038/s41587-020-0525-0. Epub 2020 May 25. PMID: 32451506

• Barkas N., Petukhov V., Nikolaeva D., Lozinsky Y., Demharter S., Khodosevich K., Kharchenko P. (2019) Joint analysis of heterogeneous single-cell RNA-seq dataset collections. Nat Methods, 16(8): 695-698
  
  
• Natarajan KN. (2019) Single-Cell Tagged Reverse Transcription (STRT-Seq). Methods Mol Biol. 1979:133-153.
  
  
• Guiu J., Hannezo E., Yui S., Demharter S., Ulyanchenko S., Maimets M., Jørgensen A., Perlman S., Lundvall L., Mamsen L., Larsen A., Olesen R., Andersen C., Langhoff Thuesen L., Juul Hare C., Pers T., Khodosevich K., Simons B., Jensen K. (2019) Tracing the origin of adult intestinal stem cells. Nature, 570(7759):107-111

Buus T, Willerslev-Olsen A, Fredholm S, Blümel E, Nastasi C, Gluud M, Hu T, Lindahl L, Iversen L, Fogh H, Gniadecki R, Litvinov I, Persson J, Bonefeld C, Geisler C, Christensen J, Krejsgaard T, Litman T, Woetmann A, Ødum N (2018) Single-cell heterogeneity in Sézary syndrome. Blood Adv, 2 (16): 2115–2126