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Article

Tracking rare single donor and recipient immune and leukemia cells after allogeneic hematopoietic cell transplantation using mitochondrial DNA mutations.
Penter, L., Cieri, N., Maurer, K., Kwok, M., Lyu, H., Lu, W.S., Oliveira, G., Gohil, S.H., Leshchiner, I., Lareau, C.A., Ludwig, L.S., Neuberg, D.S., Kim, H.T., Li, S., Bullinger, L., Ritz, J., Getz, G., Garcia, J.S., Soiffer, R.J., Livak, K.J. and Wu, C.J.
Blood Cancer Discovery 5 September 2024 (In Press)

Detection of Bombali virus in a Mops condylurus bat in Kyela, Tanzania.
Düx, A., Lwitiho, S.E., Ayouba, A., Röthemeier, C., Merkel, K., Weiss, S., Thaurignac, G., Lander, A., Kouadio, L., Nowak, K., Corman, V., Drosten, C., Couacy-Hymann, E., Krüger, D.H., Kurth, A., Calvignac-Spencer, S., Peeters, M., Ntinginya, N.E., Leendertz, F.H. and Mangu, C.
Viruses 16 (8): 1227. August 2024

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

Systematic benchmarking of single-cell ATAC-sequencing protocols.
De Rop, F.V., Hulselmans, G., Flerin, C., Soler-Vila, P., Rafels, A., Christiaens, V., González-Blas, C.B., Marchese, D., Caratù, G., Poovathingal, S., Rozenblatt-Rosen, O., Slyper, M., Luo, W., Muus, C., Duarte, F., Shrestha, R., Bagdatli, S.T., Corces, M.R., Mamanova, L., Knights, A., Meyer, K.B., Mulqueen, R., Taherinasab, A., Maschmeyer, P., Pezoldt, J., Lambert, C.L.G., Iglesias, M., Najle, S.R., Dossani, Z.Y., Martelotto, L.G., Burkett, Z., Lebofsky, R., Martin-Subero, J.I., Pillai, S., Sebé-Pedrós, A., Deplancke, B., Teichmann, S.A., Ludwig, L.S., Braun, T.P., Adey, A.C., Greenleaf, W.J., Buenrostro, J.D., Regev, A., Aerts, S. and Heyn, H.
Nature Biotechnology 42 (6): 916-926. June 2024

Latent human herpesvirus 6 is reactivated in CAR T cells.
Lareau, C.A., Yin, Y., Maurer, K., Sandor, K.D., Daniel, B., Yagnik, G., Peña, J., Crawford, J.C., Spanjaart, A.M., Gutierrez, J.C., Haradhvala, N.J., Riberdy, J.M., Abay, T., Stickels, R.R., Verboon, J.M., Liu, V., Buquicchio, F.A., Wang, F., Southard, J., Song, R., Li, W., Shrestha, A., Parida, L., Getz, G., Maus, M.V., Li, S., Moore, A., Roberts, Z.J., Ludwig, L.S., Talleur, A.C., Thomas, P.G., Dehghani, H., Pertel, T., Kundaje, A., Gottschalk, S., Roth, T.L., Kersten, M.J., Wu, C.J., Majzner, R.G. and Satpathy, A.T.
Nature 623 : 608-615. 16 November 2023

Clonally expanded PD-1-expressing T cells are enriched in synovial fluid of juvenile idiopathic arthritis patients.
Vanni, A., Mazzoni, A., Semeraro, R., Capone, M., Maschmeyer, P., Lamacchia, G., Salvati, L., Carnasciali, A., Farahvachi, P., Giani, T., Simonini, G., Filocamo, G., Romano, M., Liotta, F., Mashreghi, M.F., Cosmi, L., Cimaz, R., Magi, A., Maggi, L. and Annunziato, F.
European Journal of Immunology 53 (7): 2250162. July 2023

Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells.
Lareau, C.A., Dubois, S.M., Buquicchio, F.A., Hsieh, Y.H., Garg, K., Kautz, P., Nitsch, L., Praktiknjo, S.D., Maschmeyer, P., Verboon, J.M., Gutierrez, J.C., Yin, Y., Fiskin, E., Luo, W., Mimitou, E.P., Muus, C., Malhotra, R., Parikh, S., Fleming, M.D., Oevermann, L., Schulte, J., Eckert, C., Kundaje, A., Smibert, P., Vardhana, S.A., Satpathy, A.T., Regev, A., Sankaran, V.G., Agarwal, S. and Ludwig, L.S.
Nature Genetics 55 (7): 1198-1209. July 2023

Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility.
Lareau, C.A., Liu, V., Muus, C., Praktiknjo, S.D., Nitsch, L., Kautz, P., Sandor, K., Yin, Y., Gutierrez, J.C., Pelka, K., Satpathy, A.T., Regev, A., Sankaran, V.G. and Ludwig, L.S.
Nature Protocols 18 (5): 1416-1440. May 2023

Mitochondrial DNA mutations as natural barcodes for lineage tracing of murine tumor models.
Penter, L., Ten Hacken, E., Southard, J., Lareau, C., Ludwig, L.S., Li, S., Neuberg, D.S., Livak, K.J. and Wu, C.J.
Cancer Research 83 (5): 667-672. 1 March 2023

Concomitant sequencing of accessible chromatin and mitochondrial genomes in single cells using mtscATAC-seq.
Ludwig, L.S. and Lareau, C.A.
Methods in Molecular Biology 2611 : 269-282. 2023

Clonal expansion and epigenetic inheritance of long-lasting NK cell memory.
Rückert, T., Lareau, C.A., Mashreghi, M.F., Ludwig, L.S. and Romagnani, C.
Nature Immunology 23 (11): 1551-1563. November 2022

Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1.
Ludwig, L.S., Lareau, C.A., Bao, E.L., Liu, N., Utsugisawa, T., Tseng, A.M., Myers, S.A., Verboon, J.M., Ulirsch, J.C., Luo, W., Muus, C., Fiorini, C., Olive, M.E., Vockley, C.M., Munschauer, M., Hunter, A., Ogura, H., Yamamoto, T., Inada, H., Nakagawa, S., Ozono, S., Subramanian, V., Chiarle, R., Glader, B., Carr, S.A., Aryee, M.J., Kundaje, A., Orkin, S., Regev, A., McCavit, T., Kanno, H. and Sankaran, V.G.
Blood 139 (16): 2534-2546. 21 April 2022

Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC.
Fiskin, E., Lareau, C.A., Ludwig, L.S., Eraslan, G., Liu, F., Ring, A.M., Xavier, R.J. and Regev, A.
Nature Biotechnology 40 (3): 374-381. March 2022

Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations.
Miller, T.E., Lareau, C.A., Verga, J.A., DePasquale, E.A.K., Liu, V., Ssozi, D., Sandor, K., Yin, Y., Ludwig, L.S., El Farran, C.A., Morgan, D.M., Satpathy, A.T., Griffin, G.K., Lane, A.A., Love, J.C., Bernstein, B.E., Sankaran, V.G. and van Galen, P.
Nature Biotechnology 40 (7): 1030-1034. 24 February 2022

JAK inhibition in a patient with a STAT1 gain-of-function variant reveals STAT1 dysregulation as a common feature of aplastic anemia.
Rosenberg, J.M., Peters, J.M., Hughes, T., Lareau, C.A., Ludwig, L.S., Massoth, L.R., Austin-Tse, C., Rehm, H.L., Bryson, B., Chen, Y.B., Regev, A., Shalek, A.K., Fortune, S.M. and Sykes, D.B.
Med 3 (1): 42-57.e5. 14 January 2022

cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries.
Qi, M., Nayar, U., Ludwig, L.S., Wagle, N. and Rheinbay, E.
BMC Bioinformatics 22 (1): 611. 24 December 2021

Longitudinal single-cell dynamics of chromatin accessibility and mitochondrial mutations in chronic lymphocytic leukemia mirror disease history.
Penter, L., Gohil, S.H., Lareau, C., Ludwig, L.S., Parry, E.M., Huang, T., Li, S., Zhang, W., Livitz, D., Leshchiner, I., Parida, L., Getz, G., Rassenti, L.Z., Kipps, T.J., Brown, J.R., Davids, M.S., Neuberg, D.S., Livak, K.J., Sankaran, V.G. and Wu, C.J.
Cancer Discovery 11 (12): 3048-3063. December 2021

Induction of antigen-specific tolerance by nanobody-antigen adducts that target class-II major histocompatibility complexes.
Pishesha, N., Harmand, T., Smeding, L.Y., Ma, W., Ludwig, L.S., Janssen, R., Islam, A., Xie, Y.J., Fang, T., McCaul, N., Pinney, W., Sugito, H.R., Rossotti, M.A., Gonzalez-Sapienza, G. and Ploegh, H.L.
Nature Biomedical Engineering 5 (11): 1389-1401. November 2021

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.
Mimitou, E.P., Lareau, C.A., Chen, K.Y., Zorzetto-Fernandes, A.L., Hao, Y., Takeshima, Y., Luo, W., Huang, T.S., Yeung, B.Z., Papalexi, E., Thakore, P.I., Kibayashi, T., Wing, J.B., Hata, M., Satija, R., Nazor, K.L., Sakaguchi, S., Ludwig, L.S., Sankaran, V.G., Regev, A. and Smibert, P.
Nature Biotechnology 39 (10): 1246-1258. October 2021

Familial thrombocytopenia due to a complex structural variant resulting in a WAC-ANKRD26 fusion transcript.
Wahlster, L., Verboon, J.M., Ludwig, L.S., Black, S.C., Luo, W., Garg, K., Voit, R.A., Collins, R.L., Garimella, K., Costello, M., Chao, K.R., Goodrich, J.K., DiTroia, S.P., O’Donnell-Luria, A., Talkowski, M.E., Michelson, A.D., Cantor, A.B. and Sankaran, V.G.
Journal of Experimental Medicine 218 (6): e20210444. 7 June 2021

Skin-resident innate lymphoid cells converge on a pathogenic effector state.
Bielecki, P., Riesenfeld, S.J., Hütter, J.C., Torlai Triglia, E., Kowalczyk, M.S., Ricardo-Gonzalez, R.R., Lian, M., Amezcua Vesely, M.C., Kroehling, L., Xu, H., Slyper, M., Muus, C., Ludwig, L.S., Christian, E., Tao, L., Kedaigle, A.J., Steach, H.R., York, A.G., Skadow, M.H., Yaghoubi, P., Dionne, D., Jarret, A., McGee, H.M., Porter, C.B.M., Licona-Limón, P., Bailis, W., Jackson, R., Gagliani, N., Gasteiger, G., Locksley, R.M., Regev, A. and Flavell, R.A.
Nature 592 (7852): 128-132. 1 April 2021

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling.
Lareau, C.A., Ludwig, L.S., Muus, C., Gohil, S.H., Zhao, T., Chiang, Z., Pelka, K., Verboon, J.M., Luo, W., Christian, E., Rosebrock, D., Getz, G., Boland, G.M., Chen, F., Buenrostro, J.D., Hacohen, N., Wu, C.J., Aryee, M.J., Regev, A. and Sankaran, V.G.
Nature Biotechnology 39 (4): 451-461. April 2021

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Muus, C., Luecken, M.D., Eraslan, G., Sikkema, L., Waghray, A., Heimberg, G., Kobayashi, Y., Vaishnav, E.D., Subramanian, A., Smillie, C., Jagadeesh, K.A., Duong, E.T., Fiskin, E., Triglia, E.T., Ansari, M., Cai, P., Lin, B., Buchanan, J., Chen, S., Shu, J., Haber, A.L., Chung, H., Montoro, D.T., Adams, T., Aliee, H., Allon, S.J., Andrusivova, Z., Angelidis, I., Ashenberg, O., Bassler, K., Bécavin, C., Benhar, I., Bergenstråhle, J., Bergenstråhle, L., Bolt, L., Braun, E., Bui, L.T., Callori, S., Chaffin, M., Chichelnitskiy, E., Chiou, J., Conlon, T.M., Cuoco, M.S., Cuomo, A.S.E., Deprez, M., Duclos, G., Fine, D., Fischer, D.S., Ghazanfar, S., Gillich, A., Giotti, B., Gould, J., Guo, M., Gutierrez, A.J., Habermann, A.C., Harvey, T., He, P., Hou, X., Hu, L., Hu, Y., Jaiswal, A., Ji, L., Jiang, P., Kapellos, T.S., Kuo, C.S., Larsson, L., Leney-Greene, M.A., Lim, K., Litviňuková, M., Ludwig, L.S., Lukassen, S., Luo, W., Maatz, H., Madissoon, E., Mamanova, L., Manakongtreecheep, K., Leroy, S., Mayr, C.H., Mbano, I.M., McAdams, A.M., Nabhan, A.N., Nyquist, S.K., Penland, L., Poirion, O.B., Poli, S., Qi, C.C., Queen, R., Reichart, D., Rosas, I., Schupp, J.C., Shea, C.V., Shi, X., Sinha, R., Sit, R.V., Slowikowski, K., Slyper, M., Smith, N.P., Sountoulidis, A., Strunz, M., Sullivan, T.B., Sun, D., Talavera-López, C., Tan, P., Tantivit, J., Travaglini, K.J., Tucker, N.R., Vernon, K.A., Wadsworth, M.H., Waldman, J., Wang, X., Xu, K., Yan, W., Zhao, W. and Ziegler, C.G.K.
Nature Medicine 27 (3): 546-559. 2 March 2021

Purifying selection against pathogenic mitochondrial DNA in human T cells.
Walker, M.A., Lareau, C.A., Ludwig, L.S., Karaa, A., Sankaran, V.G., Regev, A. and Mootha, V.K.
New England Journal of Medicine 383 (16): 1556-1563. 15 October 2020

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features.
Ray, J.P., de Boer, C.G., Fulco, C.P., Lareau, C.A., Kanai, M., Ulirsch, J.C., Tewhey, R., Ludwig, L.S., Reilly, S.K., Bergman, D.T., Engreitz, J.M., Issner, R., Finucane, H.K., Lander, E.S., Regev, A. and Hacohen, N.
Nature Communications 11 (1): 1237. 6 March 2020

Longitudinal assessment of clonal mosaicism in human hematopoiesis via mitochondrial mutation tracking.
Lareau, C.A., Ludwig, L.S. and Sankaran, V.G.
Blood Advances 3 (24): 4161-4165. 23 December 2019

Transcriptional states and chromatin accessibility underlying human erythropoiesis.
Ludwig, L.S., Lareau, C.A., Bao, E.L., Nandakumar, S.K., Muus, C., Ulirsch, J.C., Chowdhary, K., Buenrostro, J.D., Mohandas, N., An, X., Aryee, M.J., Regev, A. and Sankaran, V.G.
Cell Reports 27 (11): 3228-3240. 11 June 2019

Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis.
Nandakumar, S.K., McFarland, S.K., Mateyka, L.M., Lareau, C.A., Ulirsch, J.C., Ludwig, L.S., Agarwal, G., Engreitz, J.M., Przychodzen, B., McConkey, M., Cowley, G.S., Doench, J.G., Maciejewski, J.P., Ebert, B.L., Root, D.E. and Sankaran, V.G.
eLife 8 : e44080. 9 May 2019

Impaired human hematopoiesis due to a cryptic intronic splicing mutation.
Abdulhay, N.J., Fiorini, C., Verboon, J.M., Ludwig, L.S., Ulirsch, J.C., Zieger, B., Lareau, C.A., Mi, X., Roy, A., Obeng, E.A., Erlacher, M., Gupta, N., Gabriel, S.B., Ebert, B.L., Niemeyer, C.M., Khoriaty, R.N., Ancliff, P., Gazda, H.T., Wlodarski, M.W. and Sankaran, V.G.
Journal of Experimental Medicine 216 (5): 1050-1060. 6 May 2019

Interrogation of human hematopoiesis at single-cell and single-variant resolution.
Ulirsch, J.C., Lareau, C.A., Bao, E.L., Ludwig, L.S., Guo, M.H., Benner, C., Satpathy, A.T., Kartha, V.K., Salem, R.M., Hirschhorn, J.N., Finucane, H.K., Aryee, M.J., Buenrostro, J.D. and Sankaran, V.G.
Nature Genetics 51 (4): 683-693. April 2019

Lineage tracing in humans enabled by mitochondrial mutations and single-cell genomics.
Ludwig, L.S., Lareau, C.A., Ulirsch, J.C., Christian, E., Muus, C., Li, L.H., Pelka, K., Ge, W., Oren, Y., Brack, A., Law, T., Rodman, C., Chen, J.H., Boland, G.M., Hacohen, N., Rozenblatt-Rosen, O., Aryee, M.J., Buenrostro, J.D., Regev, A. and Sankaran, V.G.
Cell 176 (6): 1325-1339. 7 March 2019

The genetic landscape of diamond-blackfan anemia.
Ulirsch, J.C., Verboon, J.M., Kazerounian, S., Guo, M.H., Yuan, D., Ludwig, L.S., Handsaker, R.E., Abdulhay, N.J., Fiorini, C., Genovese, G., Lim, E.T., Cheng, A., Cummings, B.B., Chao, K.R., Beggs, A.H., Genetti, C.A., Sieff, C.A., Newburger, P.E., Niewiadomska, E., Matysiak, M., Vlachos, A., Lipton, J.M., Atsidaftos, E., Glader, B., Narla, A., Gleizes, P.E., O'Donohue, M.F., Montel-Lehry, N., Amor, D.J., McCarroll, S.A., O'Donnell-Luria, A.H., Gupta, N., Gabriel, S.B., MacArthur, D.G., Lander, E.S., Lek, M., Da Costa, L., Nathan, D.G., Korostelev, A.A., Do, R., Sankaran, V.G. and Gazda, H.T.
American Journal of Human Genetics 103 (6): 930-947. 6 December 2018

Ribosome levels selectively regulate translation and lineage commitment in human hematopoiesis.
Khajuria, R.K., Munschauer, M., Ulirsch, J.C., Fiorini, C., Ludwig, L.S., McFarland, S.K., Abdulhay, N.J., Specht, H., Keshishian, H., Mani, D.R., Jovanovic, M., Ellis, S.R., Fulco, C.P., Engreitz, J.M., Schütz, S., Lian, J., Gripp, K.W., Weinberg, O.K., Pinkus, G.S., Gehrke, L., Regev, A., Lander, E.S., Gazda, H.T., Lee, W.Y., Panse, V.G., Carr, S.A. and Sankaran, V.G.
Cell 173 (1): 90-103. 22 March 2018

Einfluss genetischer Varianten auf die humane Erythropoese [Influence of genetic variants on human erythropoiesis].
Ludwig, L.S.
BIOspektrum 22 (7): 768-769. November 2016

Insight into GATA1 transcriptional activity through interrogation of cis elements disrupted in human erythroid disorders.
Wakabayashi, A., Ulirsch, J.C., Ludwig, L.S., Fiorini, C., Yasuda, M., Choudhuri, A., McDonel, P., Zon, L.I. and Sankaran, V.G.
Proceedings of the National Academy of Sciences of the United States of America 113 (16): 4434-4439. 19 April 2016

Targeted application of human genetic variation can improve red blood cell production from stem cells.
Giani, F.C., Fiorini, C., Wakabayashi, A., Ludwig, L.S., Salem, R.M., Jobaliya, C.D., Regan, S.N., Ulirsch, J.C., Liang, G., Steinberg-Shemer, O., Guo, M.H., Esko, T., Tong, W., Brugnara, C., Hirschhorn, J.N., Weiss, M.J., Zon, L.I., Chou, S.T., French, D.L., Musunuru, K. and Sankaran, V.G.
Cell Stem Cell 18 (1): 73-78. 7 January 2016

Genome-wide association study follow-up identifies cyclin A2 as a regulator of the transition through cytokinesis during terminal erythropoiesis.
Ludwig, L.S., Cho, H., Wakabayashi, A., Eng, J.C., Ulirsch, J.C., Fleming, M.D., Lodish, H.F. and Sankaran, V.G.
American Journal of Hematology 90 (5): 386-91. May 2015

X-linked macrocytic dyserythropoietic anemia in females with an ALAS2 mutation.
Sankaran, V.G., Ulirsch, J.C., Tchaikovskii, V., Ludwig, L.S., Wakabayashi, A., Kadirvel, S., Lindsley, R.C., Bejar, R., Shi, J., Lovitch, S.B., Bishop, D.F. and Steensma, D.P.
Journal of Clinical Investigation 125 (4): 1665-1669. 1 April 2015

Altered translation of GATA1 in Diamond-Blackfan anemia.
Ludwig, L.S., Gazda, H.T., Eng, J.C., Eichhorn, S.W., Thiru, P., Ghazvinian, R., George, T.I., Gotlib, J.R., Beggs, A.H., Sieff, C.A., Lodish, H.F., Lander, E.S. and Sankaran, V.G.
Nature Medicine 20 (7): 748-753. July 2014

Cyclin D3 coordinates the cell cycle during differentiation to regulate erythrocyte size and number.
Sankaran, V.G., Ludwig, L.S., Sicinska, E., Xu, J., Bauer, D.E., Eng, J.C., Patterson, H.C., Metcalf, R.A., Natkunam, Y., Orkin, S.H., Sicinski, P., Lander, E.S. and Lodish, H.F.
Genes & Development 26 (18): 2075-2087. 15 September 2012

Methylation matters: binding of Ets-1 to the demethylated Foxp3 gene contributes to the stabilization of Foxp3 expression in regulatory T cells.
Polansky, J.K., Schreiber, L., Thelemann, C., Ludwig, L., Krüger, M., Baumgrass, R., Cording, S., Floess, S., Hamann, A. and Huehn, J.
Journal of Molecular Medicine 88 (10): 1029-1040. October 2010

Review

Mitochondrial genetics through the lens of single-cell multi-omics.
Nitsch, L., Lareau, C.A. and Ludwig, L.S.
Nature Genetics 56 (7): 1355-1365. July 2024

Single-cell genomics-based immune and disease monitoring in blood malignancies.
Rathgeber, A.C., Ludwig, L.S. and Penter, L.
Clinical Hematology International 6 (2): 62-84. 14 June 2024

Single-cell multi-omics and lineage tracing to dissect cell fate decision-making.
Haghverdi, L. and Ludwig, L.S.
Stem Cell Reports 18 (1): 13-25. 10 January 2023

Emerging cellular and gene therapies for congenital anemias.
Ludwig, L.S., Khajuria, R.K. and Sankaran, V.G.
American Journal of Medical Genetics C 172C (4): 332-348. 12 December 2016

Letter

Confounding in ex vivo models of Diamond-Blackfan anemia.
Ulirsch, J.C., Lareau, C., Ludwig, L.S., Mohandas, N., Nathan, D.G. and Sankaran, V.G.
Blood 130 (9): 1165-1168. 31 August 2017

Editorial

Editorial: Lineage tracing, hematopoietic stem cell and immune cell dynamics.
Lareau, C.A., Romagnani, C. and Ludwig, L.S.
Frontiers in Immunology 13 : 1062415. 18 October 2022