Article

Coordinated IFN-γ/TNF axis drives selective loss of activated enteric glia in inflammatory bowel diseases.
Bubeck, Marvin, Penkert, Klara A. ORCID: https://orcid.org/0000-0002-9948-533X, Limberger, Heidi, González Acera, Miguel, Plattner, Christina, Ziegler, Svenja, Muppirala, Anoohya, Forster, Patrycja, Jakob, Manuel, Gamez-Belmonte, Reyes, Erkert, Lena, Kulkarni, Subhash, Günther, Claudia, Atreya, Raja, Kühl, Anja A., Hegazy, Ahmed N., Hildner, Kai, Trajanoski, Zlatko, Siegmund, Britta, Neurath, Markus F., Rao, Meenakshi, Progatzky, Fränze, Lie, Dieter Chichung, Becker, Christoph, Romagnani, Chiara, Ludwig, Leif S. ORCID: https://orcid.org/0000-0002-2916-2164, Klose, Christoph S.N. and Patankar, Jay V.
Cellular and Molecular Gastroenterology and Hepatology : 101827. 12 June 2026 (In Press)

IBDome: an integrated molecular, histopathological, and clinical atlas of inflammatory bowel diseases.
Plattner, Christina, Sturm, Gregor, Kühl, Anja A., Atreya, Raja, Carollo, Sandro, Rieder, Dietmar, Gronauer, Raphael, Günther, Michael, Ormanns, Steffen, Manzl, Claudia, Wirtz, Stefan, Meneghetti, Asier Rabasco, Hegazy, Ahmed N., Patankar, Jay V., Carrero, Zunamys I., Grabherr, Felix, Meyer, Moritz, Adolph, Timon E., Tilg, Herbert, Neurath, Markus F., Kather, Jakob Nikolas, Becker, Christoph, Siegmund, Britta and Trajanoski, Zlatko
Gastroenterology 10 June 2026 (In Press)

Transcriptomic profiling reveals substrate- and shear stress-dependent maturation of human small intestinal epithelial cells.
Alzain, Nadra, Almalla, Ahed, Sandu, Ketaki, Gerbeth, Lorenz, Ziegler, Jörn F., Gutwein, Catharina, Weidner, Patrick ORCID: https://orcid.org/0000-0003-2448-5981, Glauben, Rainer, Weinhart, Marie and Siegmund, Britta
Frontiers in Pharmacology 17 : 1706106. 1 May 2026

Single-cell template strand sequencing reveals culture-induced chromosomal instability in a gibbon cell line.
Daponte, Alessia, Chirico, Gerardina, Paparella, Annalisa, Montanari, Annalaura, Manzari, Caterina, Macino, Martina ORCID: https://orcid.org/0000-0002-8730-9005, Dionisi Dyck, Oliver ORCID: https://orcid.org/0000-0002-0410-1736, De Leonardis, Francesco, Maggiolini, Flavia Angela Maria, L'Abbate, Alberto, Montinaro, Francesco, Louzada, Sandra, Ventura, Mario, Sanders, Ashley D. ORCID: https://orcid.org/0000-0003-3945-0677, Antonacci, Francesca and Catacchio, Claudia Rita
Genome Research 36 (5): 938-948. May 2026

Early gut-vascular barrier breakdown precedes colitis onset in murine models.
Abdou, Mariam Mohamed, Kreiß, Lucas, Schmid, Benjamin, Thoma, Oana-Maria, Krüger, René, Bénard, Alan, Müller, Tanja M., Knauss, Annkathrin, Gabel, Michael, González-Acera, Miguel, Lyu, Yanmin, Petter, Katja, Lindemann, Aylin, Saad, Mina Saad Aziz, Eichhorn, Philip, Becker, Christoph, Naschberger, Elisabeth, Zundler, Sebastian, Weigmann, Benno, Rath, Timo, Atreya, Raja, Kühl, Anja A., Trajanoski, Zlatko, Friedrich, Oliver, Waldner, Maximilian J., Neurath, Markus F., Herrmann, Martin, Schürmann, Sebastian, Britzen-Laurent, Nathalie and Stürzl, Michael
Cellular and molecular gastroenterology and hepatology : 101795. 29 April 2026 (In Press)

Characterization of intestinal immune responses in generalized human and murine lipodystrophy.
Letizia, Marilena, Omar, Toka, Weidner, Patrick ORCID: https://orcid.org/0000-0003-2448-5981, Jakob, Manuel O., Freise, Inka, Krug, Susanne M., Löscher, Britt-Sabina, Rosati, Elisa, Obermayer, Benedikt, Gamez-Belmonte, Reyes, Hecker, Julia, Ziegler, Jörn-Felix, Weixler, Benjamin, Asbach, Patrick, Kunkel, Desiree, Stumvoll, Michael, Miehle, Konstanze, Becker, Christoph, Klose, Christoph S.N., Glauben, Rainer, Beule, Dieter, Kühl, Anja A, Conrad, Thomas, Tacke, Frank, Wirtz, Stefan, Franke, Andre, Sanders, Ashley D. ORCID: https://orcid.org/0000-0003-3945-0677, Siegmund, Britta and Weidinger, Carl
Journal of Clinical Investigation 136 (6): e192322. 16 March 2026

Fecal detection of calprotectin subunits links inflammatory bowel disease activity with chronicity of intestinal inflammation.
Jukic, Almina, Hilbe, Richard, Zundel, Luis, Willeit, Peter, Faserl, Klaus, Plattner, Christina, Zollner, Andreas, Meyer, Moritz, Siegmund, Kerstin, Klepsch, Victoria, Marteau, Valentin, Vich Vila, Arnau, Schwärzler, Julian, Vouk, Kathrin, Kozsar, Anna, Rieder, Dietmar, Weichberger, Amos, Sarg, Bettina, Grabherr, Felix, Mayr, Lisa, Moser, Patrizia, Nemati, Niloofar, Scholl-Bürgi, Sabine, Karall, Daniela, Vogel, Georg F., Welz, Lina, Aldrian, Denise, Koch, Robert, Pfister, Alexandra, Ran, Qitao, Kaser, Arthur, Blumberg, Richard S., Tancevski, Ivan, Sommer, Felix, Bacher, Petra, Schreiber, Stefan, Rosenstiel, Philip, Aden, Konrad, Baier, Gottfried, Bakiri, Latifa, Müller, Thomas, Weiss, Günter, Weersma, Rinse K., Trajanoski, Zlatko, Wagner, Erwin F., Tilg, Herbert and Adolph, Timon E.
Gastroenterology 170 (3): 523-538. March 2026

Structural and transduction patterns of human-specific polymorphic SVA insertions.
Kirby, Ashley E., Loftus, Mark, Golba, Emily C. and Konkel, Miriam K.
Mobile DNA 16 (1): 42. 6 November 2025

Integrated multimodel analysis of intestinal inflammation exposes key molecular features of preclinical and clinical IBD.
Gonzalez-Acera, Miguel, Patankar, Jay V. ORCID: https://orcid.org/0000-0002-1884-7424, Erkert, Lena, Cineus, Roodline, Gamez-Belmonte, Reyes, Leupold, Tamara, Bubeck, Marvin, Bao, Li-Li, Dinkel, Martin, Wang, Ru, Schickedanz, Laura, Limberger, Heidi, Stolzer, Iris, Gerlach, Katharina, Diemand, Leonard, Mascia, Fabrizio, Gupta, Pooja, Naschberger, Elisabeth ORCID: https://orcid.org/0000-0003-1291-622X, Koop, Kristina ORCID: https://orcid.org/0000-0002-1672-7234, Plattner, Christina, Sturm, Gregor, Weigmann, Benno ORCID: https://orcid.org/0000-0002-2398-0844, Günther, Claudia ORCID: https://orcid.org/0000-0001-8360-3525, Wirtz, Stefan, Stürzl, Michael ORCID: https://orcid.org/0000-0002-9276-2824, Hildner, Kai, Kühl, Anja A., Siegmund, Britta ORCID: https://orcid.org/0000-0002-0055-958X, Gießl, Andreas, Atreya, Raja ORCID: https://orcid.org/0000-0002-8556-8433, Hegazy, Ahmed N., Trajanoski, Zlatko, Neurath, Markus F. ORCID: https://orcid.org/0000-0003-4344-1474 and Becker, Christoph ORCID: https://orcid.org/0000-0002-1388-1041
Gut 74 (10): 1602-1615. 8 September 2025

IL-36 signaling as a drug target in Crohn's disease patients with IL36RN mutations.
Hecker, J. ORCID: https://orcid.org/0000-0002-4118-3961, Plattner, C. ORCID: https://orcid.org/0000-0002-3217-3278, Cancino, C.A., Löscher, B.S., Saurenbach, J., Letizia, M., Rieder, D., Freise, I., Koop, K., Neufert, C., Kunkel, D., Al Khatim, Z., Schaafs, L.A., Schütz, A. ORCID: https://orcid.org/0000-0002-0606-2574, Becker, C., Atreya, R., Trajanoski, Z. ORCID: https://orcid.org/0000-0002-0636-7351, Franke, A., Sonnenberg, E., Hegazy, A.N., Siegmund, B. ORCID: https://orcid.org/0000-0002-0055-958X and Weidinger, C. ORCID: https://orcid.org/0000-0002-9948-0088
EMBO Molecular Medicine 17 (7): 1539-1555. 11 July 2025

Pharmacological inhibitors of the gamma-secretase enzyme complex disrupt epithelial cell function triggering colitis in mice.
Erkert, Lena, Kabisch, Melanie, Gamez-Belmonte, Reyes, Gonzalez-Acera, Miguel, Patankar, Jay V, Schödel, Lena, Hofmann, Katharina, Wagner, Yara, Plattner, Christina, Spath, Eva-Maria, Distler, Ute, Tenzer, Stefan, Neufert, Clemens, Neurath, Markus F and Becker, Christoph
Journal of Crohn's & Colitis 19 (7): jjaf096. July 2025

ST6GAL1 promotes IBD B cell recruitment to the inflamed colon in a CD22-dependent mechanism.
Liu, Li-Juan, Müller, Tanja M., Dedden, Mark, Schramm, Sebastian, Leppkes, Moritz, Atreya, Raja ORCID: https://orcid.org/0000-0002-8556-8433, Atreya, Imke, Neurath, Markus F. and Zundler, Sebastian ORCID: https://orcid.org/0000-0003-0888-2784
Journal of Crohn's & Colitis 19 (7): jjaf097. July 2025

Mapping dihydropteroate synthase evolvability through identification of a novel evolutionarily critical substructure.
Sanyal, D., Shivram, A, Pandey, D., Banerjee, S. ORCID: https://orcid.org/0000-0002-3747-8425, Uversky, V.N., Muzata, D., Chivukula, A., Jasuja, R., Chattopadhyay, K. and Chowdhury, S.
International Journal of Biological Macromolecules 311 (Part 2): 143325. June 2025

The IL-22–oncostatin M axis promotes intestinal inflammation and tumorigenesis.
Cineus, R. ORCID: https://orcid.org/0000-0003-4393-5757, Luo, Y. ORCID: https://orcid.org/0009-0003-0401-467X, Saliutina, M., Manna, S. ORCID: https://orcid.org/0000-0003-2360-0618, Cancino, C.A., Velasco Blázquez, L., Wang, L., Bösel, D., Abdelrahman, A., Klementowicz, J.E., Scherl, A., Hainbuch, S., Bréart, B., Kwon, G., Konopka, A., Guerra, G.M., von Coburg, E. ORCID: https://orcid.org/0009-0001-8546-8854, Gerbeth, Lo., Roels, J., Heinrich, F. ORCID: https://orcid.org/0000-0001-6097-5422, Müller, N. ORCID: https://orcid.org/0000-0003-1559-7711, Durek, P. ORCID: https://orcid.org/0000-0002-6179-0670, Deigendesch, N. ORCID: https://orcid.org/0000-0002-6036-3327, Ziai, J., Hung, J., Conrad, T. ORCID: https://orcid.org/0000-0001-5618-6295, Kühl, A.A. ORCID: https://orcid.org/0000-0003-2293-5387, Wirtz, S. ORCID: https://orcid.org/0000-0001-6936-7431, Löhning, M. ORCID: https://orcid.org/0000-0001-6382-7281, Keir, M. ORCID: https://orcid.org/0000-0002-0637-4092, Diefenbach, A. ORCID: https://orcid.org/0000-0002-9176-9530, Mashreghi, M.F. ORCID: https://orcid.org/0000-0002-8015-6907, Siegmund, B. ORCID: https://orcid.org/0000-0002-0055-958X, Schumann, M., Romagnani, C. ORCID: https://orcid.org/0000-0002-5167-7463, West, N.R. and Hegazy, A.N. ORCID: https://orcid.org/0000-0002-2946-8251
Nature Immunology 26 (6): 837-853. June 2025

A transcriptional atlas of gut-innervating neurons reveals activation of interferon signaling and ferroptosis during intestinal inflammation.
Forster, P.M., Jakob, M.O., Yusuf, D., Bubeck, M., Limberger, H., Luo, Y., Thieme, P., Polici, A., Sterczyk, N., Boulekou, S., Bartel, L., Cosovanu, C., Witkowski, M., González-Acera, M., Kühl, A.A., Weidinger, C., Backofen, R., Hegazy, A.N., Patankar, J.V. and Klose, C.S.N.
Neuron 113 (9): 1333-1351. 7 May 2025

Intestinal interstitial fluid isolation provides novel insight into the human host-microbiome interface.
Avery, E.G. ORCID: https://orcid.org/0000-0002-9094-1423, Haag, L.M., McParland, V. ORCID: https://orcid.org/0000-0003-0731-3272, Kedziora, S.M. ORCID: https://orcid.org/0000-0003-0124-2557, Zigra, G.J., Valdes, D.S. ORCID: https://orcid.org/0000-0002-1309-5147, Kirchner, M. ORCID: https://orcid.org/0000-0002-7049-534X, Popp, O. ORCID: https://orcid.org/0000-0001-6240-4666, Geisberger, S. ORCID: https://orcid.org/0000-0001-6477-1312, Nonn, O. ORCID: https://orcid.org/0000-0001-6385-2866, Karlsen, T.V., N'Diaye, G., Yarritu, A. ORCID: https://orcid.org/0000-0002-1724-0559, Bartolomaeus, H. ORCID: https://orcid.org/0000-0003-4288-3828, Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184, Tagiyeva, N.A. ORCID: https://orcid.org/0009-0006-7918-1220, Wimmer, M.I. ORCID: https://orcid.org/0009-0004-5793-0249, Haase, N. ORCID: https://orcid.org/0000-0003-0727-1738, Zhang, Y.D. ORCID: https://orcid.org/0009-0003-9465-2033, Wilhelm, A., Grütz, G., Tenstad, O., Wilck, N. ORCID: https://orcid.org/0000-0003-3189-5364, Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Klopfleisch, R., Kühl, A.A., Atreya, R., Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299, Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X, Siegmund, B., Wiig, H. ORCID: https://orcid.org/0000-0002-7740-8210 and Müller, D.N. ORCID: https://orcid.org/0000-0003-3650-5644
Cardiovascular Research 121 (5): 803-816. April 2025

TIFA renders intestinal epithelial cells responsive to microbial ADP-heptose and drives colonic inflammation in mice.
Erkert, L., Ruder, B., Kabisch, M., Gamez Belmonte, R., Patankar, J.V., Gonzalez Acera, M., Schödel, L., Chiriac, M.T., Cineus, R., Gnafakis, S., Leupold, T. ORCID: https://orcid.org/0000-0002-2026-4340, Thoma, O.M. ORCID: https://orcid.org/0000-0002-1665-9753, Stolzer, I., Taut, A., Thonn, V., Zundler, S., Günther, C., Diefenbach, A., Kühl, A.A., Hegazy, A.N., Waldner, M., Basic, M. ORCID: https://orcid.org/0000-0002-1995-618X, Bleich, A., Neurath, M.F., Wirtz, S. and Becker, C. ORCID: https://orcid.org/0000-0002-1388-1041
Mucosal Immunology 18 (2): 453-466. April 2025

Epithelial OPA1 links mitochondrial fusion to inflammatory bowel disease.
Bao, L.L. ORCID: https://orcid.org/0009-0003-3081-7062, Yu, Y.Q. ORCID: https://orcid.org/0000-0002-4847-8877, González-Acera, M. ORCID: https://orcid.org/0009-0008-9445-5650, Patankar, J.V. ORCID: https://orcid.org/0000-0002-1884-7424, Giessl, A. ORCID: https://orcid.org/0000-0002-9768-2049, Sturm, G. ORCID: https://orcid.org/0000-0001-9584-7842, Kühl, A.A. ORCID: https://orcid.org/0000-0003-2293-5387, Atreya, R. ORCID: https://orcid.org/0000-0002-8556-8433, Erkert, L., Gámez-Belmonte, R. ORCID: https://orcid.org/0000-0002-7159-8957, Krug, S.M. ORCID: https://orcid.org/0000-0002-1293-2484, Schmid, B. ORCID: https://orcid.org/0000-0002-9327-2296, Tripal, P., Chiriac, M.T., Hildner, K., Siegmund, B. ORCID: https://orcid.org/0000-0002-0055-958X, Wirtz, S. ORCID: https://orcid.org/0000-0001-6936-7431, Stürzl, M. ORCID: https://orcid.org/0000-0002-9276-2824, Mohamed Abdou, M. ORCID: https://orcid.org/0009-0002-7352-166X, Trajanoski, Z. ORCID: https://orcid.org/0000-0002-0636-7351, Neurath, M.F. ORCID: https://orcid.org/0000-0003-4344-1474, Zorzano, A. ORCID: https://orcid.org/0000-0002-1638-0306 and Becker, C. ORCID: https://orcid.org/0000-0002-1388-1041
Science Translational Medicine 17 (781): eadn8699. January 2025

Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype.
Leppä, A.M. ORCID: https://orcid.org/0000-0003-0849-1759, Grimes, K. ORCID: https://orcid.org/0000-0002-4805-2366, Jeong, H. ORCID: https://orcid.org/0000-0002-1526-3343, Huang, F.Y. ORCID: https://orcid.org/0000-0002-2163-9300, Andrades, A., Waclawiczek, A., Boch, T., Jauch, A., Renders, S., Stelmach, P. ORCID: https://orcid.org/0009-0000-5270-4761, Müller-Tidow, C. ORCID: https://orcid.org/0000-0002-7166-5232, Karpova, D., Sohn, M., Grünschläger, F., Hasenfeld, P., Benito Garagorri, E., Thiel, V., Dolnik, A. ORCID: https://orcid.org/0000-0003-4166-2900, Rodriguez-Martin, B., Bullinger, L. ORCID: https://orcid.org/0000-0002-5890-5510, Mrózek, K. ORCID: https://orcid.org/0000-0002-1408-5063, Eisfeld, A.K. ORCID: https://orcid.org/0000-0001-6442-1419, Krämer, A., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Korbel, J.O. ORCID: https://orcid.org/0000-0002-2798-3794 and Trumpp, A. ORCID: https://orcid.org/0000-0002-6212-3466
Nature Genetics 56 (12): 2790-2803. December 2024

p53 terminates the regenerative fetal-like state after colitis-associated injury.
Hartl, K. ORCID: https://orcid.org/0000-0002-2965-0512, Bayram, Ş. ORCID: https://orcid.org/0009-0009-5245-5473, Wetzel, A., Harnack, C., Lin, M. ORCID: https://orcid.org/0000-0003-4093-9277, Fischer, A.S. ORCID: https://orcid.org/0000-0002-2176-1779, Liu, L. ORCID: https://orcid.org/0000-0002-9553-5475, Beccacec, G. ORCID: https://orcid.org/0000-0002-6453-3725, Mastrobuoni, G. ORCID: https://orcid.org/0000-0003-4509-1295, Geisberger, S. ORCID: https://orcid.org/0000-0001-6477-1312, Forbes, M. ORCID: https://orcid.org/0000-0001-7775-8352, Monteiro, B.J.E. ORCID: https://orcid.org/0000-0001-9718-2776, Macino, M. ORCID: https://orcid.org/0000-0002-8730-9005, Flores, R.E. ORCID: https://orcid.org/0000-0001-6500-8407, Engelmann, C., Mollenkopf, H.J. ORCID: https://orcid.org/0000-0003-1167-4783, Schupp, M. ORCID: https://orcid.org/0000-0003-3720-1052, Tacke, F. ORCID: https://orcid.org/0000-0001-6206-0226, Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299, Berger, H. ORCID: https://orcid.org/0000-0002-6304-4946 and Sigal, M. ORCID: https://orcid.org/0000-0003-4772-0761
Science Advances 10 (43): eadp8783. 25 October 2024

Spatial single cell profiling using imaging mass cytometry: inflammatory versus penetrating Crohn's disease.
Lehmann, M. ORCID: https://orcid.org/0000-0002-3786-7375, Weixler, B., Elezkurtaj, S., Loddenkemper, C., Kühl, A.A. and Siegmund, B. ORCID: https://orcid.org/0000-0002-0055-958X
Journal of Crohn's & Colitis 18 (8): 1305-1318. August 2024

Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells.
Grimes, K. ORCID: https://orcid.org/0000-0002-4805-2366, Jeong, H. ORCID: https://orcid.org/0000-0002-1526-3343, Amoah, A., Xu, N., Niemann, J., Raeder, B. ORCID: https://orcid.org/0000-0002-9494-8884, Hasenfeld, P., Stober, C., Rausch, T. ORCID: https://orcid.org/0000-0001-5773-5620, Benito, E., Jann, J.C. ORCID: https://orcid.org/0000-0003-2200-0151, Nowak, D. ORCID: https://orcid.org/0000-0001-7130-7921, Emini, R., Hoenicka, M. ORCID: https://orcid.org/0000-0002-0986-6340, Liebold, A., Ho, A. ORCID: https://orcid.org/0000-0002-1656-0833, Shuai, S. ORCID: https://orcid.org/0000-0002-9527-8018, Geiger, H. ORCID: https://orcid.org/0000-0002-5794-5430, Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677 and Korbel, J.O. ORCID: https://orcid.org/0000-0002-2798-3794
Nature Genetics 56 (6): 1134-1146. June 2024

Unlocking the secrets of structural variants in a healthy tissue.
Korbel, J.O. and Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677
Nature Genetics 56 (6): 1047-1048. June 2024

Pangenome graph construction from genome alignments with Minigraph-Cactus.
Hickey, G. ORCID: https://orcid.org/0000-0002-2280-9404, Monlong, J., Ebler, J., Novak, A.M. ORCID: https://orcid.org/0000-0001-5828-047X, Eizenga, J.M., Gao, Y., Marschall, T. ORCID: https://orcid.org/0000-0002-9376-1030, Li, H. ORCID: https://orcid.org/0000-0003-4874-2874 and Paten, B. ORCID: https://orcid.org/0000-0001-8863-3539
Nature Biotechnology 42 (4): 663-673. April 2024

Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.
Lee, H., Greer, S.U., Pavlichin, D.S., Zhou, B., Urban, A.E., Weissman, T. and Ji, H.P.
Cell Reports Methods 3 (8): 100543. 28 August 2023

Functional analysis of structural variants in single cells using Strand-seq.
Jeong, H. ORCID: https://orcid.org/0000-0002-1526-3343, Grimes, K. ORCID: https://orcid.org/0000-0002-4805-2366, Rauwolf, K.K., Bruch, P.M. ORCID: https://orcid.org/0000-0002-9992-3109, Rausch, T. ORCID: https://orcid.org/0000-0001-5773-5620, Hasenfeld, P. ORCID: https://orcid.org/0000-0003-2319-2482, Benito, E., Roider, T. ORCID: https://orcid.org/0000-0002-6973-3531, Sabarinathan, R., Porubsky, D. ORCID: https://orcid.org/0000-0001-8414-8966, Herbst, S.A. ORCID: https://orcid.org/0000-0001-8502-0366, Erarslan-Uysal, B., Jann, J.C. ORCID: https://orcid.org/0000-0003-2200-0151, Marschall, T. ORCID: https://orcid.org/0000-0002-9376-1030, Nowak, D. ORCID: https://orcid.org/0000-0001-7130-7921, Bourquin, J.P., Kulozik, A.E. ORCID: https://orcid.org/0000-0003-1953-0848, Dietrich, S., Bornhauser, B. ORCID: https://orcid.org/0000-0003-2890-3191, Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677 and Korbel, J.O. ORCID: https://orcid.org/0000-0002-2798-3794
Nature Biotechnology 41 (6): 832-844. June 2023

A draft human pangenome reference.
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Nature 617 (7960): 312-324. 11 May 2023

Increased mutation and gene conversion within human segmental duplications.
Vollger, M.R., Dishuck, P.C., Harvey, W.T., DeWitt, W.S., Guitart, X., Goldberg, M.E., Rozanski, A.N., Lucas, J., Asri, M., Munson, K.M., Lewis, A.P., Hoekzema, K., Logsdon, G.A., Porubsky, D., Paten, B., Harris, K., Hsieh, P.H. and Eichler, E.E.
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Recombination between heterologous human acrocentric chromosomes.
Guarracino, A., Buonaiuto, S., de Lima, L.G., Potapova, T., Rhie, A., Koren, S., Rubinstein, B., Fischer, C., Gerton, J.L., Phillippy, A.M., Colonna, V. and Garrison, E.
Nature 617 (7960): 335-343. 11 May 2023

Inversion polymorphism in a complete human genome assembly.
Porubsky, D., Harvey, W.T., Rozanski, A.N., Ebler, J., Höps, W., Ashraf, H., Hasenfeld, P., Paten, B., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Marschall, T., Korbel, J.O. and Eichler, E.E. ORCID: https://orcid.org/0000-0002-8246-4014
Genome Biology 24 (1): 100. 30 April 2023

Gaps and complex structurally variant loci in phased genome assemblies.
Porubsky, D., Vollger, M.R., Harvey, W.T., Rozanski, A.N., Ebert, P., Hickey, G., Hasenfeld, P., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Stober, C., Korbel, J.O., Paten, B., Marschall, T. and Eichler, E.E.
Genome Research 33 (4): 496-510. April 2023

Semi-automated assembly of high-quality diploid human reference genomes.
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Nature 611 (7936): 519-531. 17 November 2022

A high-resolution map of small-scale inversions in the gibbon genome.
Mercuri, L. ORCID: https://orcid.org/0000-0002-3688-4501, Palmisano, D., L'Abbate, A. ORCID: https://orcid.org/0000-0002-5995-2001, D'Addabbo, P. ORCID: https://orcid.org/0000-0003-3325-4931, Montinaro, F. ORCID: https://orcid.org/0000-0002-4506-963X, Catacchio, C.R. ORCID: https://orcid.org/0000-0002-2166-723X, Hasenfeld, P. ORCID: https://orcid.org/0000-0003-2319-2482, Ventura, M. ORCID: https://orcid.org/0000-0001-7762-8777, Korbel, J.O. ORCID: https://orcid.org/0000-0002-2798-3794, Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Maggiolini, F.A.M. ORCID: https://orcid.org/0000-0001-6832-9388 and Antonacci, F. ORCID: https://orcid.org/0000-0002-5833-6186
Genome Research 32 (10): 1941-1951. October 2022

Store-operated calcium entry controls innate and adaptive immune cell function in inflammatory bowel disease.
Letizia, M. ORCID: https://orcid.org/0000-0002-8039-9415, Wang, Y.H. ORCID: https://orcid.org/0000-0002-3637-8852, Kaufmann, U. ORCID: https://orcid.org/0000-0003-4317-5794, Gerbeth, L. ORCID: https://orcid.org/0000-0001-6638-1959, Sand, A., Brunkhorst, M., Weidner, P. ORCID: https://orcid.org/0000-0003-2448-5981, Ziegler, J.F. ORCID: https://orcid.org/0000-0001-7445-541X, Böttcher, C. ORCID: https://orcid.org/0000-0002-6226-586X, Schlickeiser, S., Fernández, C., Yamashita, M., Stauderman, K. ORCID: https://orcid.org/0000-0002-8090-4549, Sun, K., Kunkel, D., Prakriya, M., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Siegmund, B., Feske, S. ORCID: https://orcid.org/0000-0001-5431-8178 and Weidinger, C. ORCID: https://orcid.org/0000-0002-9948-0088
EMBO Molecular Medicine 14 (9): e15687. 7 September 2022

Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders.
Porubsky, D., Höps, W., Ashraf, H., Hsieh, P.H., Rodriguez-Martin, B., Yilmaz, F., Ebler, J., Hallast, P., Maggiolini, F.A.M., Harvey, W.T., Henning, B., Audano, P.A., Gordon, D.S., Ebert, P., Hasenfeld, P., Benito, E., Zhu, Q., Lee, C., Antonacci, F., Steinrücken, M., Beck, C.R., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Marschall, T., Eichler, E.E. and Korbel, J.O. ORCID: https://orcid.org/0000-0002-2798-3794
Cell 185 (11): 1986-2005. 26 May 2022

Familial long-read sequencing increases yield of de novo mutations.
Noyes, M.D., Harvey, W.T., Porubsky, D., Sulovari, A., Li, R., Rose, N.R., Audano, P.A., Munson, K.M., Lewis, A.P., Hoekzema, K., Mantere, T., Graves-Lindsay, T.A., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Goodwin, S., Kramer, M., Mokrab, Y., Zody, M.C., Hoischen, A., Korbel, J.O., McCombie, W.R. and Eichler, E.E.
American Journal of Human Genetics 109 (4): 631-646. 7 April 2022

Mako: a graph-based pattern growth approach to detect complex structural variants.
Lin, J., Yang, X., Kosters, W., Xu, T., Jia, Y., Wang, S., Zhu, Q., Ryan, M., Guo, L., Zhang, C., Lee, C., Devine, S.E., Eichler, E.E. and Ye, K.
Genomics, Proteomics and Bioinformatics 20 (1): 205-218. February 2022

ASHLEYS: automated quality control for single-cell Strand-seq data.
Eimer, C. ORCID: https://orcid.org/0000-0001-6124-2669, Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Korbel, J.O., Marschall, T. ORCID: https://orcid.org/0000-0002-9376-1030 and Ebert, P. ORCID: https://orcid.org/0000-0001-7441-532X
Bioinformatics 37 (19): 3356-3357. 1 October 2021

Construction of whole genomes from scaffolds using single cell strand-seq data.
Hills, M., Falconer, E., O'Neill, K., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Howe, K. ORCID: https://orcid.org/0000-0003-2237-513X, Guryev, V. ORCID: https://orcid.org/0000-0002-5810-6022 and Lansdorp, P.M.
International Journal of Molecular Sciences 22 (7): 3617. 1 April 2021

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads.
Porubsky, D. ORCID: https://orcid.org/0000-0001-8414-8966, Ebert, P. ORCID: https://orcid.org/0000-0001-7441-532X, Audano, P.A., Vollger, M.R. ORCID: https://orcid.org/0000-0002-8651-1615, Harvey, W.T., Marijon, P. ORCID: https://orcid.org/0000-0002-6694-6873, Ebler, J., Munson, K.M. ORCID: https://orcid.org/0000-0001-8413-6498, Sorensen, M., Sulovari, A. ORCID: https://orcid.org/0000-0003-4354-9020, Haukness, M. ORCID: https://orcid.org/0000-0001-9991-8089, Ghareghani, M., Lansdorp, P.M., Paten, B., Devine, S.E., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Lee, C., Chaisson, M.J.P., Korbel, J.O. ORCID: https://orcid.org/0000-0002-2798-3794, Eichler, E.E. ORCID: https://orcid.org/0000-0002-8246-4014 and Marschall, T. ORCID: https://orcid.org/0000-0002-9376-1030
Nature Biotechnology 39 (3): 302-308. March 2021

Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M.J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., Yilmaz, F., Zhao, X., Hsieh, P.H., Lee, J., Kumar, S., Lin, J., Rausch, T., Chen, Y., Ren, J., Santamarina, M., Höps, W., Ashraf, H., Chuang, N.T., Yang, X., Munson, K.M., Lewis, A.P., Fairley, S., Tallon, L.J., Clarke, W.E., Basile, A.O., Byrska-Bishop, M., Corvelo, A., Evani, U.S., Lu, T.Y., Chaisson, M.J.P., Chen, J., Li, C., Brand, H., Wenger, A.M., Ghareghani, M., Harvey, W.T., Raeder, B., Hasenfeld, P., Regier, A.A., Abel, H.J., Hall, I.M., Flicek, P., Stegle, O., Gerstein, M.B, Tubio, J.M.C., Mu, Z., Li, Y.I., Shi, X., Hastie, A.R., Ye, K., Chong, Z., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Zody, M.C., Talkowski, M.E., Mills, R. E., Devine, S.E., Lee, C., Korbel, J.O., Marschall, T. and Eichler, E.E.
Science 372 (6537): eabf7117. 25 February 2021

Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.
Warren, W.C. ORCID: https://orcid.org/0000-0003-2255-2730, Harris, R.A. ORCID: https://orcid.org/0000-0002-7333-4752, Haukness, M. ORCID: https://orcid.org/0000-0001-9991-8089, Fiddes, I.T. ORCID: https://orcid.org/0000-0002-1580-7443, Murali, S.C., Fernandes, J. ORCID: https://orcid.org/0000-0002-8625-1796, Dishuck, P.C. ORCID: https://orcid.org/0000-0003-2223-9787, Storer, J.M ORCID: https://orcid.org/0000-0002-9619-5265, Raveendran, M. ORCID: https://orcid.org/0000-0001-6185-4059, Hillier, L.W., Porubsky, D., Mao, Y. ORCID: https://orcid.org/0000-0002-9648-4278, Gordon, D. ORCID: https://orcid.org/0000-0001-6552-4022, Vollger, M.R. ORCID: https://orcid.org/0000-0002-8651-1615, Lewis, A.P. ORCID: https://orcid.org/0000-0002-6195-4786, Munson, K.M. ORCID: https://orcid.org/0000-0001-8413-6498, DeVogelaere, E., Armstrong, J. ORCID: https://orcid.org/0000-0003-2077-4671, Diekhans, M. ORCID: https://orcid.org/0000-0002-0430-0989, Walker, J.A., Tomlinson, C. ORCID: https://orcid.org/0000-0001-9905-6159, Graves-Lindsay, T.A., Kremitzki, M., Salama, S.R. ORCID: https://orcid.org/0000-0001-6999-7193, Audano, P.A. ORCID: https://orcid.org/0000-0002-5187-0415, Escalona, M. ORCID: https://orcid.org/0000-0003-0213-4777, Maurer, N.W. ORCID: https://orcid.org/0000-0003-0007-7887, Antonacci, F. ORCID: https://orcid.org/0000-0002-5833-6186, Mercuri, L. ORCID: https://orcid.org/0000-0002-3688-4501, Maggiolini, F.A.M. ORCID: https://orcid.org/0000-0001-6832-9388, Catacchio, C.R. ORCID: https://orcid.org/0000-0002-2166-723X, Underwood, J.G., O'Connor, D.H. ORCID: https://orcid.org/0000-0003-2139-470X, Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Korbel, J.O., Ferguson, B. ORCID: https://orcid.org/0000-0002-6992-3538, Kubisch, H.M. ORCID: https://orcid.org/0000-0001-6281-8420, Picker, L. ORCID: https://orcid.org/0000-0003-0546-398X, Kalin, N.H., Rosene, D., Levine, J. ORCID: https://orcid.org/0000-0003-4177-6406, Abbott, D.H., Gray, S.B. ORCID: https://orcid.org/0000-0002-8816-0898, Sanchez, M.M. ORCID: https://orcid.org/0000-0001-7701-2892, Kovacs-Balint, Z.A., Kemnitz, J.W. ORCID: https://orcid.org/0000-0001-6511-404X, Thomasy, S.M. ORCID: https://orcid.org/0000-0001-5617-9677, Roberts, J.A. ORCID: https://orcid.org/0000-0002-0159-6112, Kinnally, E.L., Capitanio, J.P. ORCID: https://orcid.org/0000-0002-3680-1323, Skene, J.H.Pate ORCID: https://orcid.org/0000-0003-3205-0697, Platt, M. ORCID: https://orcid.org/0000-0003-3912-8821, Cole, S.A. ORCID: https://orcid.org/0000-0002-2651-0127, Green, R.E. ORCID: https://orcid.org/0000-0003-0516-5827, Ventura, M. ORCID: https://orcid.org/0000-0001-7762-8777, Wiseman, R.W. ORCID: https://orcid.org/0000-0002-7682-7085, Paten, B. ORCID: https://orcid.org/0000-0001-8863-3539, Batzer, M.A. ORCID: https://orcid.org/0000-0001-5699-863X, Rogers, J. ORCID: https://orcid.org/0000-0002-7374-6490 and Eichler, E.E.
Science 370 (6523): eabc6617. 18 December 2020

Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution.
Maggiolini, F.A.M., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Shew, C.J., Sulovari, A., Mao, Y., Puig, M., Catacchio, C.R., Dellino, M., Palmisano, D., Mercuri, L., Bitonto, M., Porubský, D., Cáceres, M., Eichler, E.E., Ventura, M., Dennis, M.Y., Korbel, J.O. and Antonacci, F.
Genome Research 30 (11): 1680-1693. November 2020

Recurrent inversion toggling and great ape genome evolution.
Porubsky, D., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Höps, W., Hsieh, P. ORCID: https://orcid.org/0000-0001-8294-6227, Sulovari, A. ORCID: https://orcid.org/0000-0003-4354-9020, Li, R., Mercuri, L., Sorensen, M., Murali, S.C., Gordon, D., Cantsilieris, S., Pollen, A.A., Ventura, M. ORCID: https://orcid.org/0000-0001-7762-8777, Antonacci, F. ORCID: https://orcid.org/0000-0002-5833-6186, Marschall, T. ORCID: https://orcid.org/0000-0002-9376-1030, Korbel, J.O. ORCID: https://orcid.org/0000-0002-2798-3794 and Eichler, E.E. ORCID: https://orcid.org/0000-0002-8246-4014
Nature Genetics 52 (8): 849-858. August 2020

Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads.
Vollger, M.R. ORCID: https://orcid.org/0000-0002-8651-1615, Logsdon, G.A. ORCID: https://orcid.org/0000-0003-2396-0656, Audano, P.A. ORCID: https://orcid.org/0000-0002-5187-0415, Sulovari, A., Porubsky, D., Peluso, P., Wenger, A.M., Concepcion, G.T., Kronenberg, Z.N., Munson, K.M. ORCID: https://orcid.org/0000-0001-8413-6498, Baker, C., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Spierings, D.C.J., Lansdorp, P.M., Surti, U., Hunkapiller, M.W. and Eichler, E.E. ORCID: https://orcid.org/0000-0002-8246-4014
Annals of Human Genetics 84 (2): 125-140. March 2020

Single-cell analysis of structural variations and complex rearrangements with tri-channel processing.
Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Meiers, S., Ghareghani, M., Porubsky, D., Jeong, H., van Vliet, M.A.C.C., Rausch, T. ORCID: https://orcid.org/0000-0001-5773-5620, Richter-Pechańska, P. ORCID: https://orcid.org/0000-0001-6727-6317, Kunz, J.B., Jenni, S., Bolognini, D. ORCID: https://orcid.org/0000-0002-8735-8093, Longo, G.M.C., Raeder, B. ORCID: https://orcid.org/0000-0002-9494-8884, Kinanen, V., Zimmermann, J., Benes, V. ORCID: https://orcid.org/0000-0002-0352-2547, Schrappe, M., Mardin, B.R. ORCID: https://orcid.org/0000-0002-3903-9354, Kulozik, A.E., Bornhauser, B., Bourquin, J.P., Marschall, T. ORCID: https://orcid.org/0000-0002-9376-1030 and Korbel, J.O. ORCID: https://orcid.org/0000-0002-2798-3794
Nature Biotechnology 38 (3): 343-354. March 2020

VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing.
Bolognini, D. ORCID: https://orcid.org/0000-0002-8735-8093, Sanders, A. ORCID: https://orcid.org/0000-0003-3945-0677, Korbel, J.O., Magi, A., Benes, V. and Rausch, T. ORCID: https://orcid.org/0000-0001-5773-5620
Bioinformatics 36 (4): 1267-1269. 15 February 2020

breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data.
Porubsky, D., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Taudt, A. ORCID: https://orcid.org/0000-0002-9639-2306, Colomé-Tatché, M., Lansdorp, P.M. and Guryev, V.
Bioinformatics 36 (4): 1260-1261. 15 February 2020

The effects of common structural variants on 3D chromatin structure.
Shanta, O., Noor, A. and Sebat, J. ORCID: https://orcid.org/0000-0002-9087-526X
BMC Genomics 21 (1): 95. 30 January 2020

Human-specific tandem repeat expansion and differential gene expression during primate evolution.
Sulovari, A. ORCID: https://orcid.org/0000-0003-4354-9020, Li, R., Audano, P.A., Porubsky, D., Vollger, M.R., Logsdon, G.A., Warren, W.C., Pollen, A.A. ORCID: https://orcid.org/0000-0003-3263-8634, Chaisson, M.J.P. and Eichler, E.E. ORCID: https://orcid.org/0000-0002-8246-4014
Proceedings of the National Academy of Sciences of the United States of America 116 (46): 23243-23253. 12 November 2019

Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Chaisson, M.J.P., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Zhao, X. ORCID: https://orcid.org/0000-0003-4036-9577, Malhotra, A., Porubsky, D., Rausch, T. ORCID: https://orcid.org/0000-0001-5773-5620, Gardner, E.J. ORCID: https://orcid.org/0000-0001-9671-1533, Rodriguez, O.L., Guo, L., Collins, R.L., Fan, X., Wen, J., Handsaker, R.E. ORCID: https://orcid.org/0000-0002-3128-3547, Fairley, S., Kronenberg, Z.N., Kong, X., Hormozdiari, F., Lee, D., Wenger, A.M. ORCID: https://orcid.org/0000-0003-1183-0432, Hastie, A.R., Antaki, D. ORCID: https://orcid.org/0000-0003-0381-7801, Anantharaman, T., Audano, P.A. ORCID: https://orcid.org/0000-0002-5187-0415, Brand, H., Cantsilieris, S., Cao, H., Cerveira, E., Chen, C., Chen, X. ORCID: https://orcid.org/0000-0002-2536-165X, Chin, C.S. ORCID: https://orcid.org/0000-0003-4394-2455, Chong, Z. ORCID: https://orcid.org/0000-0001-5750-1808, Chuang, N.T., Lambert, C.C., Church, D.M. ORCID: https://orcid.org/0000-0003-4264-1853, Clarke, L. ORCID: https://orcid.org/0000-0002-5989-6898, Farrell, A., Flores, J., Galeev, T., Gorkin, D.U. ORCID: https://orcid.org/0000-0003-4944-4107, Gujral, M., Guryev, V., Heaton, W.H., Korlach, J. ORCID: https://orcid.org/0000-0003-3047-4250, Kumar, S., Kwon, J.Y., Lam, E.T., Lee, J.E., Lee, J. ORCID: https://orcid.org/0000-0002-3492-1102, Lee, W.P., Lee, S.P., Li, S., Marks, P., Viaud-Martinez, K., Meiers, S., Munson, K.M. ORCID: https://orcid.org/0000-0001-8413-6498, Navarro, F.C.P. ORCID: https://orcid.org/0000-0002-5640-9070, Nelson, B.J., Nodzak, C., Noor, A., Kyriazopoulou-Panagiotopoulou, S., Pang, A.W.C., Qiu, Y. ORCID: https://orcid.org/0000-0002-0539-9714, Rosanio, G., Ryan, M., Stütz, A., Spierings, D.C.J., Ward, A., Welch, A.E., Xiao, M., Xu, W., Zhang, C., Zhu, Q., Zheng-Bradley, X., Lowy, E. ORCID: https://orcid.org/0000-0001-9312-1159, Yakneen, S. ORCID: https://orcid.org/0000-0001-7827-9839, McCarroll, S., Jun, G., Ding, L., Koh, C.L., Ren, B. ORCID: https://orcid.org/0000-0002-5435-1127, Flicek, P. ORCID: https://orcid.org/0000-0002-3897-7955, Chen, K. ORCID: https://orcid.org/0000-0003-4013-5279, Gerstein, M.B., Kwok, P.Y., Lansdorp, P.M., Marth, G.T., Sebat, J. ORCID: https://orcid.org/0000-0002-9087-526X, Shi, X. ORCID: https://orcid.org/0000-0003-4662-3177, Bashir, A., Ye, K., Devine, S.E., Talkowski, M.E., Mills, R.E., Marschall, T. ORCID: https://orcid.org/0000-0002-9376-1030, Korbel, J.O. ORCID: https://orcid.org/0000-0002-2798-3794, Eichler, E.E. ORCID: https://orcid.org/0000-0002-8246-4014 and Lee, C.
Nature Communications 10 (1): 1784. 16 April 2019

Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus.
Maggiolini, F.A.M. ORCID: https://orcid.org/0000-0001-6832-9388, Cantsilieris, S., D'Addabbo, P. ORCID: https://orcid.org/0000-0003-3325-4931, Manganelli, M. ORCID: https://orcid.org/0000-0002-8219-0252, Coe, B.P., Dumont, B.L. ORCID: https://orcid.org/0000-0003-0918-0389, Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Pang, A.W.C., Vollger, M.R. ORCID: https://orcid.org/0000-0002-8651-1615, Palumbo, O. ORCID: https://orcid.org/0000-0001-6583-3482, Palumbo, P. ORCID: https://orcid.org/0000-0001-9498-9902, Accadia, M. ORCID: https://orcid.org/0000-0001-5190-8834, Carella, M. ORCID: https://orcid.org/0000-0002-6830-6829, Eichler, E.E. ORCID: https://orcid.org/0000-0002-8246-4014 and Antonacci, F. ORCID: https://orcid.org/0000-0002-5833-6186
PLoS Genetics 15 (3): e1008075. 27 March 2019

Strand-seq enables reliable separation of long reads by chromosome via expectation maximization.
Ghareghani, M., Porubskỳ, D., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Meiers, S., Eichler, E.E., Korbel, J.O. and Marschall, T.
Bioinformatics 34 (13): i115-i123. 1 July 2018

Computational pan-genomics: status, promises and challenges.

Briefings in Bioinformatics 19 (1): 118-135. January 2018

Dense and accurate whole-chromosome haplotyping of individual genomes.
Porubsky, D., Garg, S., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Korbel, J.O. ORCID: https://orcid.org/0000-0002-2798-3794, Guryev, V., Lansdorp, P.M. and Marschall, T. ORCID: https://orcid.org/0000-0002-9376-1030
Nature Communications 8 (1): 1293. 3 November 2017

Single-cell template strand sequencing by strand-seq enables the characterization of individual homologs.
Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Falconer, E., Hills, M., Spierings, D.C.J. and Lansdorp, P.M.
Nature Protocols 12 (6): 1151-1176. June 2017

Characterizing polymorphic inversions in human genomes by single-cell sequencing.
Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Hills, M., Porubský, D., Guryev, V., Falconer, E. and Lansdorp, P.M.
Genome Research 26 (11): 1575-1587. November 2016

Direct chromosome-length haplotyping by single-cell sequencing.
Porubský, D., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, van Wietmarschen, N., Falconer, E., Hills, M., Spierings, D.C.J., Bevova, M.R., Guryev, V. and Lansdorp, P.M.
Genome Research 26 (11): 1565-1574. November 2016

The prognostic impact of CD163-positive macrophages in follicular lymphoma: a study from the BC Cancer Agency and the Lymphoma Study Association.
Kridel, R., Xerri, L., Gelas-Dore, B., Tan, K., Feugier, P., Vawda, A., Canioni, D., Farinha, P., Boussetta, S., Moccia, A.A., Brice, P., Chavez, E.A., Kyle, A.H., Scott, D.W., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Fabiani, B., Slack, G.W., Minchinton, A.I., Haioun, C., Connors, J.M., Sehn, L.H., Steidl, C., Gascoyne, R.D. and Salles, G.
Clinical Cancer Research 21 (15): 3428-3435. August 2015

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.
Falconer, E., Hills, M., Naumann, U., Poon, S.S.S., Chavez, E.A., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Zhao, Y., Hirst, M. and Lansdorp, P.M.
Nature Methods 9 (11): 1107-1112. November 2012

Adult spinal cord radial glia display a unique progenitor phenotype.
Petit, A., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Kennedy, T.E., Tetzlaff, W., Glattfelder, K.J., Dalley, R.A., Puchalski, R.B., Jones, A.R. and Roskams, A.J.
PLoS ONE 6 (9): e24538. 12 September 2011

Essential role for Ptpn11 in survival of hematopoietic stem and progenitor cells.
Chan, G., Cheung, L.S., Yang, W., Milyavsky, M., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Gu, S., Hong, W.X., Liu, A.X., Wang, X., Barbara, M., Sharma, T., Gavin, J., Kutok, J.L., Iscove, N.N., Shannon, K.M., Dick, J.E., Neel, B.G. and Braun, B.S.
Blood 117 (16): 4253-4261. 21 April 2011

Letter

Engineering therapeutic regulatory T cells to overexpress G protein-coupled receptor 15 improves functional fitness for in vivo gut homing.
Müller, T.M., Liu, L.J., Wiesinger, M., Neurath, M.F., Voskens, C.J. and Zundler, S.
Gastroenterology 168 (2): 389-392. February 2025

Editorial

Single-cell multi-omics allows functional characterization of structural variants.
Korbel, J.O. and Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677
Nature Biotechnology 24 November 2022

Preprint

Interferon-independent STING enforces epithelial genome-integrity checkpoint to restrain tumor evolution.
Xiang, Hang, Macino, Martina ORCID: https://orcid.org/0000-0002-8730-9005, Woitaske-Proske, Clemens, Bodenstein, Nicholas, Bernardes, Joana P., Tran, Florian, Schmid, Nicole A., Martini, Gabriela Rios, Wotawa, Felix, Bornhaeuser, Johanna, Kakavand, Nassim, Dyck Dionisi, Oliver ORCID: https://orcid.org/0000-0002-0410-1736, van den Bossche, Silke, Yang, Guang, Wu, Qicong, Kugler, Julia, Welz, Lina, Konukiewitz, Bjorn, Fischer, Julius C., Peifer, Christian, Schreiber, Stefan, Rosenstiel, Philip, Tschurtschenthaler, Markus ORCID: https://orcid.org/0000-0002-0060-4790, Sanders, Ashley D. ORCID: https://orcid.org/0000-0003-3945-0677 and Aden, Konrad ORCID: https://orcid.org/0000-0003-3482-7316
bioRxiv : 2026.02.17.706442v2. 25 March 2026

Dataset

Transcriptomic profiling reveals substrate- and shear stress_x0002_dependent maturation of human small intestinal epithelial cells.
Alzain, N., Almalla, A., Sandu, K., Gerbeth, L., Ziegler, J., Gutwein, C., Weidner, P. ORCID: https://orcid.org/0000-0003-2448-5981, Glauben, R., Weinhart, M. and Siegmund, B.
[Dataset] 22 April 2026