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Article

Spatial single cell profiling using imaging mass cytometry: inflammatory versus penetrating Crohn's disease.
Lehmann, M., Weixler, B., Elezkurtaj, S., Loddenkemper, C., Kühl, A.A. and Siegmund, B.
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., Jeong, H., Amoah, A., Xu, N., Niemann, J., Raeder, B., Hasenfeld, P., Stober, C., Rausch, T., Benito, E., Jann, J.C., Nowak, D., Emini, R., Hoenicka, M., Liebold, A., Ho, A., Shuai, S., Geiger, H., Sanders, A.D. and Korbel, J.O.
Nature Genetics 56 (6): 1134-1146. June 2024

Pangenome graph construction from genome alignments with Minigraph-Cactus.
Hickey, G., Monlong, J., Ebler, J., Novak, A.M., Eizenga, J.M., Gao, Y., Marschall, T., Li, H. and Paten, B.
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., Grimes, K., Rauwolf, K.K., Bruch, P.M., Rausch, T., Hasenfeld, P., Benito, E., Roider, T., Sabarinathan, R., Porubsky, D., Herbst, S.A., Erarslan-Uysal, B., Jann, J.C., Marschall, T., Nowak, D., Bourquin, J.P., Kulozik, A.E., Dietrich, S., Bornhauser, B., Sanders, A.D. and Korbel, J.O.
Nature Biotechnology 41 (6): 832-844. June 2023

A draft human pangenome reference.
Liao, W.W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J.K., Monlong, J., Abel, H.J., Buonaiuto, S., Chang, X.H., Cheng, H., Chu, J., Colonna, V., Eizenga, J.M., Feng, X., Fischer, C., Fulton, R.S., Garg, S., Groza, C., Guarracino, A., Harvey, W.T., Heumos, S., Howe, K., Jain, M., Lu, T.Y., Markello, C., Martin, F.J., Mitchell, M.W., Munson, K.M., Mwaniki, M.N., Novak, A.M., Olsen, H.E., Pesout, T., Porubsky, D., Prins, P., Sibbesen, J.A., Sirén, J., Tomlinson, C., Villani, F., Vollger, M.R., Antonacci-Fulton, L.L., Baid, G., Baker, C.A., Belyaeva, A., Billis, K., Carroll, A., Chang, P.C., Cody, S., Cook, D.E., Cook-Deegan, R.M., Cornejo, O.E., Diekhans, M., Ebert, P., Fairley, S., Fedrigo, O., Felsenfeld, A.L., Formenti, G., Frankish, A., Gao, Yan, Garrison, N.A., Giron, C.G., Green, R.E., Haggerty, L., Hoekzema, K., Hourlier, T., Ji, H.P., Kenny, E.E., Koenig, B.A., Kolesnikov, A., Korbel, J.O., Kordosky, J., Koren, S., Lee, H.J., Lewis, A.P., Magalhães, H., Marco-Sola, S., Marijon, P., McCartney, A., McDaniel, J., Mountcastle, J., Nattestad, M., Nurk, S., Olson, N.D., Popejoy, A.B., Puiu, D., Rautiainen, M., Regier, A.A., Rhie, A., Sacco, S., Sanders, A.D., Schneider, V.A., Schultz, B.I., Shafin, K., Smith, M.W., Sofia, H.J., Abou Tayoun, A.N., Thibaud-Nissen, F., Tricomi, F.F., Wagner, J., Walenz, B., Wood, J.M.D., Zimin, A.V., Bourque, G., Chaisson, M.J P, Flicek, Paul, Phillippy, A.M., Zook, J.M., Eichler, E.E., Haussler, D., Wang, T., Jarvis, E.D., Miga, K.H., Garrison, E., Marschall, T., Hall, I.M., Li, H. and Paten, B.
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.
Nature 617 (7960): 325-334. 11 May 2023

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., Marschall, T., Korbel, J.O. and Eichler, E.E.
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., 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.
Jarvis, E.D., Formenti, G., Rhie, A., Guarracino, A., Yang, C., Wood, J., Tracey, A., Thibaud-Nissen, F., Vollger, M.R., Porubsky, D., Cheng, H., Asri, M., Logsdon, G.A., Carnevali, P., Chaisson, M.J.P., Chin, C.S., Cody, S., Collins, J., Ebert, P., Escalona, M., Fedrigo, O., Fulton, R.S., Fulton, L.L., Garg, S., Gerton, J.L., Ghurye, J., Granat, A., Green, R.E., Harvey, W., Hasenfeld, P., Hastie, A., Haukness, M., Jaeger, E.B., Jain, M., Kirsche, M., Kolmogorov, M., Korbel, J.O., Koren, S., Korlach, J., Lee, J., Li, D., Lindsay, T., Lucas, J., Luo, F., Marschall, T., Mitchell, M.W., McDaniel, J., Nie, F., Olsen, H.E., Olson, N.D., Pesout, T., Potapova, T., Puiu, D., Regier, A., Ruan, J., Salzberg, S.L., Sanders, A.D., Schatz, M.C., Schmitt, A., Schneider, V.A., Selvaraj, S., Shafin, K., Shumate, A., Stitziel, N.O., Stober, C., Torrance, J., Wagner, J., Wang, J., Wenger, A., Xiao, C., Zimin, A.V., Zhang, G., Wang, T., Li, H., Garrison, E., Haussler, D., Hall, I., Zook, J.M., Eichler, E.E., Phillippy, A.M., Paten, B., Howe, K. and Miga, K.H.
Nature 611 (7936): 519-531. 17 November 2022

A high-resolution map of small-scale inversions in the gibbon genome.
Mercuri, L., Palmisano, D., L'Abbate, A., D'Addabbo, P., Montinaro, F., Catacchio, C.R., Hasenfeld, P., Ventura, M., Korbel, J.O., Sanders, A.D., Maggiolini, F.A.M. and Antonacci, F.
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., Wang, Y.H., Kaufmann, U., Gerbeth, L., Sand, A., Brunkhorst, M., Weidner, P., Ziegler, J.F., Böttcher, C., Schlickeiser, S., Fernández, C., Yamashita, M., Stauderman, K., Sun, K., Kunkel, D., Prakriya, M., Sanders, A.D., Siegmund, B., Feske, S. and Weidinger, C.
EMBO Molecular Medicine : e15687. 2 August 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., Marschall, T., Eichler, E.E. and Korbel, J.O.
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., 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., Sanders, A.D., Korbel, J.O., Marschall, T. and Ebert, P.
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., Howe, K., Guryev, V. 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., Ebert, P., Audano, P.A., Vollger, M.R., Harvey, W.T., Marijon, P., Ebler, J., Munson, K.M., Sorensen, M., Sulovari, A., Haukness, M., Ghareghani, M., Lansdorp, P.M., Paten, B., Devine, S.E., Sanders, A.D., Lee, C., Chaisson, M.J.P., Korbel, J.O., Eichler, E.E. and Marschall, T.
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., 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., Harris, R.A., Haukness, M., Fiddes, I.T., Murali, S.C., Fernandes, J., Dishuck, P.C., Storer, J.M, Raveendran, M., Hillier, L.W., Porubsky, D., Mao, Y., Gordon, D., Vollger, M.R., Lewis, A.P., Munson, K.M., DeVogelaere, E., Armstrong, J., Diekhans, M., Walker, J.A., Tomlinson, C., Graves-Lindsay, T.A., Kremitzki, M., Salama, S.R., Audano, P.A., Escalona, M., Maurer, N.W., Antonacci, F., Mercuri, L., Maggiolini, F.A.M., Catacchio, C.R., Underwood, J.G., O'Connor, D.H., Sanders, A.D., Korbel, J.O., Ferguson, B., Kubisch, H.M., Picker, L., Kalin, N.H., Rosene, D., Levine, J., Abbott, D.H., Gray, S.B., Sanchez, M.M., Kovacs-Balint, Z.A., Kemnitz, J.W., Thomasy, S.M., Roberts, J.A., Kinnally, E.L., Capitanio, J.P., Skene, J.H.Pate, Platt, M., Cole, S.A., Green, R.E., Ventura, M., Wiseman, R.W., Paten, B., Batzer, M.A., Rogers, J. 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., 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., Höps, W., Hsieh, P., Sulovari, A., Li, R., Mercuri, L., Sorensen, M., Murali, S.C., Gordon, D., Cantsilieris, S., Pollen, A.A., Ventura, M., Antonacci, F., Marschall, T., Korbel, J.O. and Eichler, E.E.
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., Logsdon, G.A., Audano, P.A., Sulovari, A., Porubsky, D., Peluso, P., Wenger, A.M., Concepcion, G.T., Kronenberg, Z.N., Munson, K.M., Baker, C., Sanders, A.D., Spierings, D.C.J., Lansdorp, P.M., Surti, U., Hunkapiller, M.W. and Eichler, E.E.
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., Meiers, S., Ghareghani, M., Porubsky, D., Jeong, H., van Vliet, M.A.C.C., Rausch, T., Richter-Pechańska, P., Kunz, J.B., Jenni, S., Bolognini, D., Longo, G.M.C., Raeder, B., Kinanen, V., Zimmermann, J., Benes, V., Schrappe, M., Mardin, B.R., Kulozik, A.E., Bornhauser, B., Bourquin, J.P., Marschall, T. and Korbel, J.O.
Nature Biotechnology 38 (3): 343-354. March 2020

VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing.
Bolognini, D., Sanders, A., Korbel, J.O., Magi, A., Benes, V. and Rausch, T.
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., Taudt, A., 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.
BMC Genomics 21 (1): 95. 30 January 2020

Human-specific tandem repeat expansion and differential gene expression during primate evolution.
Sulovari, A., Li, R., Audano, P.A., Porubsky, D., Vollger, M.R., Logsdon, G.A., Warren, W.C., Pollen, A.A., Chaisson, M.J.P. and Eichler, E.E.
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., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E.J., Rodriguez, O.L., Guo, L., Collins, R.L., Fan, X., Wen, J., Handsaker, R.E., Fairley, S., Kronenberg, Z.N., Kong, X., Hormozdiari, F., Lee, D., Wenger, A.M., Hastie, A.R., Antaki, D., Anantharaman, T., Audano, P.A., Brand, H., Cantsilieris, S., Cao, H., Cerveira, E., Chen, C., Chen, X., Chin, C.S., Chong, Z., Chuang, N.T., Lambert, C.C., Church, D.M., Clarke, L., Farrell, A., Flores, J., Galeev, T., Gorkin, D.U., Gujral, M., Guryev, V., Heaton, W.H., Korlach, J., Kumar, S., Kwon, J.Y., Lam, E.T., Lee, J.E., Lee, J., Lee, W.P., Lee, S.P., Li, S., Marks, P., Viaud-Martinez, K., Meiers, S., Munson, K.M., Navarro, F.C.P., Nelson, B.J., Nodzak, C., Noor, A., Kyriazopoulou-Panagiotopoulou, S., Pang, A.W.C., Qiu, Y., 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., Yakneen, S., McCarroll, S., Jun, G., Ding, L., Koh, C.L., Ren, B., Flicek, P., Chen, K., Gerstein, M.B., Kwok, P.Y., Lansdorp, P.M., Marth, G.T., Sebat, J., Shi, X., Bashir, A., Ye, K., Devine, S.E., Talkowski, M.E., Mills, R.E., Marschall, T., Korbel, J.O., Eichler, E.E. 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., Cantsilieris, S., D'Addabbo, P., Manganelli, M., Coe, B.P., Dumont, B.L., Sanders, A.D., Pang, A.W.C., Vollger, M.R., Palumbo, O., Palumbo, P., Accadia, M., Carella, M., Eichler, E.E. and Antonacci, F.
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., 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., Korbel, J.O., Guryev, V., Lansdorp, P.M. and Marschall, T.
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., 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., 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., 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., 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., 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., 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., 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

Editorial

Single-cell multi-omics allows functional characterization of structural variants.
Korbel, J.O. and Sanders, A.D.
Nature Biotechnology 24 November 2022

Preprint

A fully phased accurate assembly of an individual human genome.
Porubsky, D., Ebert, P., Audano, P.A., Vollger, M.R., Harvey, W.T., Munson, K.M., Sorensen, M., Sulovari, A., Haukness, M., Ghareghani, M., Lansdorp, P.M., Paten, B., Devine, S.E., Sanders, A.D., Lee, C., Chaisson, M.J.P., Korbel, J.O., Eichler, E.E. and Marschall, T.
bioRxiv : 855049. 26 November 2019

Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes.
Sanders, A.D., Meiers, S., Ghareghani, M., Porubsky, D., Jeong, H., van Vliet, M.A.C.C., Rausch, T., Richter-Pechańska, P., Kunz, J.B., Jenni, S., Raeder, B., Kinanen, V., Zimmermann, J., Benes, V., Schrappe, M., Mardin, B.R., Kulozik, A., Bornhauser, B., Bourquin, J.P., Marschall, T. and Korbel, J.O.
bioRxiv : 849604. 21 November 2019