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View full publication list on PubMed | Google Scholar

2025

A cellular and spatial atlas of TP53-associated tissue remodeling defines a multicellular tumour ecosystem in lung adenocarcinoma. Zhao W, Nguyen T, Bhagwat A, Kumar A, Giotti B, Kepecs B, Weirather JL, Mahadevan NR, Segerstolpe A, Dolasia K, … , Regev A, Johnson BE, Tsankov AM. Nature Cancer. 2025 Oct 7. doi: 10.1038/s43018-025-01053-7. PMID: 41057692

Learning the cellular origins across cancers using single-cell chromatin landscapes. Bairakdar MD, Lee W, Giotti B, Kumar A, Stancl P, Wagenblast E, Hambardzumyan D, Polak P, Karlic R†, Tsankov AM†. Nature Commun. 2025 Sep 17;16(1):8301. doi: 10.1038/s41467-025-63957-3. PMID: 40962882

Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumours. Hegde S, Giotti B, Soong BY, …, Tsankov AM, Marron TU, Ma S, Brown BD, Merad M. Nature. 2025 Sep 10. doi: 10.1038/s41586-025-09493-y. PMID: 40931076

Single cell profiling of human airway identifies tuft-ionocyte progenitor cells displaying cytokine-dependent differentiation bias in vitro. Shah VS, Waghray A, Lin B, Bhagwat A, Monga I, Slyper M, Giotti B, Kim S, Sun D, Xu K, Park E, Bairakdar M, … , Regev A†, Rajagopal J†, Tsankov AM†. Nat Commun. 2025 Jun 4;16(1):5180. PMID: 40467553. doi: 10.1038/s41467-025-60441-w

Single-cell dissection of the genotype-immunophenotype relationship in glioblastoma. Soni N, Rawat K, Chen Z, DiMauro A, Giotti B, Hambardzumyan D†, Tsankov AM†. Brain. 2025 Apr 11:awaf129. doi: 10.1093/brain/awaf129. PMID: 40215269

Mismatch repair deficiency drives malignant progression and alters the tumor immune microenvironment in glioblastoma models. Puigdelloses Vallcorba M, Soni N, … , Tsankov AM, Bindra RS, Rabadan R, Vasquez JC, Hambardzumyan D. J Clin Invest. 2025 Dec 23:e195189. doi: 10.1172/JCI195189. PMID: 41433099

Glioblastoma shift from bulk to infiltrative growth is guided by plexin-B2-mediated microglia alignment in invasive niches. Kang S, Ughetta ME, Zhang JY, Marallano VJ, Sattiraju A, Hannah T, Wahane S, Ramakrishnan A, Estill M, Tsankova NM, Shen L, Tsankov AM, Friedel RH, Zou H. Nat Cancer. 2025 May 29. doi: 10.1038/s43018-025-00985-4. PMID: 40442367

Oncofetal reprogramming drives phenotypic plasticity in WNT-dependent colorectal cancer. Mzoughi S, Schwarz M, Wang X, Demircioglu D, … , Giotti B, … , Tsankov AM, Sansom OJ, Marine JC, Barker N, Gargiulo G, Guccione E. Nat Genet. 2025 Feb;57(2):402-412. doi: 10.1038/s41588-024-02058-1. PMID: 39930084

Insights, opportunities, and challenges provided by large cell atlases. Hemberg M, Marini F, … , Tsankov A, van der Laan SW, Yajima M, Yang J, Zanini F, Jelic I. Genome Biol. 2025 Oct 20;26(1):358. doi: 10.1186/s13059-025-03771-8. PMID: 41116172

2024

Single cell view of tumor microenvironment gradients in pleural mesothelioma. Giotti B*, Dolasia K*, Zhao W*, Cai P*, … , Miriam Merad, Raja Flores, Sebra R, Horowitz A, Marron TU, Tocheva A, Wolf A, Tsankov AM. Cancer Discovery 2024 July 5. doi: 10.1158/2159-8290.CD-23-0017 PMID: 38959428

NOTCH1 drives sexually dimorphic immune responses in hepatocellular carcinoma. Lindblad KE, Donne R, Liebling I, Barcena-Varela M, Lozano A, Ruiz de Galarreta M, Dhainaut M, Param NJ, Giotti B, … , Kamphorst AO, Tsankov AM, Lujambio A. Cancer Discovery 2024 Nov 19. doi: 10.1158/2159-8290.CD-24-1215. Epub ahead of print. PMID: 39560425.

Hypoxia drives shared and distinct transcriptomic changes in two invasive glioma stem cell lines. Marallano V*, Ughetta M*, ... , Zou H, Tsankov AM†, Friedel RH†. Sci Rep. 2024 Mar 27;14(1):7246. PMID: 38538643 †Corresponding

Microglia and monocyte-derived macrophages drive progression of pediatric high-grade gliomas and are transcriptionally shaped by histone mutations. Ross JL*, Piñero G*, Puigdelloses-Vallcorba M*, Soni N*, … , Tsankov AM, Hambardzumyan D. Immunity. 2024 Nov 12;57(11):2669-2687.e6. doi: 10.1016/j.immuni.2024.09.007. Epub 2024 Oct 11. PMID: 39395421

Class IIa HDAC4 and HDAC7 cooperatively regulate gene transcription in Th17 cell differentiation. Cheung KL, Zhao L, Sharma R, … , Wang X, Zhang F, Ren C, Walsh MJ, Xiong H, Tsankov A, Zhou MM. Proc Natl Acad Sci U S A. 2024 Apr 30;121(18):e2312111121. Epub 2024 Apr 24. PMID: 38657041

An essential role for Cmtr2 in mammalian embryonic development. Yermalovich AV, Mohsenin Z, Cowdin M, Giotti B, Gupta A, Feng A, Golomb L, Wheeler DB, Xu K, Tsankov A, Cleaver O, Meyerson M. Dev Biol. 2024 Jul 31:S0012-1606(24)00199-4. doi: 10.1016/j.ydbio.2024.07.019. Online ahead of print. PMID: 39094818

NOTCH1 drives tumor plasticity and metastasis in hepatocellular carcinoma. Lindblad KE, Donne R, Liebling I, Bresnahan E, Barcena-Varela M, Lozano A, Park E, Giotti B, Burn O, Fiel MI, Bravo-Cordero JJ, Tsankov AM, Lujambio A. bioRxiv [Preprint]. 2024 Oct 27:2024.10.23.619856. doi: 10.1101/2024.10.23.619856. PMID: 39484457; PMCID: PMC11527037.

2023

A paracrine circuit of IL-1B/IL-1R1 between myeloid and tumor cells drives genotype-dependent glioblastoma progression. Chen Z*, Giotti B*, Kaluzova M, … , Tsankov AM†, Hambardzumyan D†. J. Clin. Invest. 2023 Sep 21;e163802. PMID: 37733448 †Corresponding

An integrated cell atlas of the lung in health and disease. Sikkema L, Strobl D, … , Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe’er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis F. Nature Med. 2023. Jun;29(6):1563-1577. PMID: 37291214

Hypoxic niches attract and sequester tumor-associated macrophages and cytotoxic T cells and reprogram them for immunosuppression. Sattiraju A, Kang S, Giotti B, Chen Z, … , Tsankov AM, Hambardzumyan D, Friedel RH, Zou H. Immunity 2023 Jul 7:S1074-7613(23)00274-1. PMID: 37451265

Monocyte depletion enhances neutrophil influx and proneural to mesenchymal transition in glioblastoma. Chen Z, Soni N, Pinero G, Giotti B, … , Tsankov AM, Hambardzumyan D. Nature Communications, 2023 Apr 3;14(1):1839. PMID: 37012245

Intratumoral dendritic cell-CD4+ T helper cell niches enable CD8+ T cell differentiation following PD-1 blockade in hepatocellular carcinoma. Magen A, Hamon P, … , Tsankov AM, … , Marron TU, Thurston G, Kamphorst AO, Merad M. Nature Med. 2023. Jun;29(6):1389-1399. PMID: 37322116

2022

An atlas of late prenatal human neurodevelopment resolved by single-nucleus transcriptomics. Ramos SI,

Mussa ZM, Falk EN, Pai B, Giotti B, Allette K, Cai P, Dekio F., Sebra R., Beaumont KG, Tsankov AM†, and Tsankova NM†. Nature Communications, 2022. †Corresponding

Novel microenvironment-based classification of intrahepatic cholangiocarcinoma with therapeutic implications.
Martin-Serrano MA, Kepecs B, Torres-Martin M, … , Villanueva A, Guccione E, Friedman SL, Lujambio A, Tocheva A, Llovet JM, Thung SN, Tsankov AM, Sia D. Gut. 2022 May 18:gutjnl-2021-326514. PMID: 35584893

A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma. Zhou R. W., Xu J., Martin T. C., Zachem A. L., He J., Ozturk S., Demircioglu D., Bansal A., Trotta A. P., Giotti B, ... , Tsankov A, ... , Bernstein E, Parsons RE. Nat Commun. 2022 Oct 17; 13(1):6041. PMID: 36253360

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment. Hwang WL, Jagadeesh KA, Guo JA, ... , Tsankov A, ... , Jacks T, Regev A. Nat Genet. 2022 Jul 28. PMID: 35902743

Single-nucleus cross-tissue molecular reference maps towards understanding disease gene function. Eraslan G, Drokhlyansky E, Anand S, ... , Tsankov AM, Branton PA, Marshall JL, Greka A, Getz G, Segrè AV, Aguet F, Rozenblatt-Rosen O, Ardlie KG, Regev A. Science. 2022 May 13;376(6594):eabl4290. PMID: 35549429.

2020-2021
Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity. Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, ... , Tsankov AM, ... et al. Nat Commun. 2021 Jul 14;12(1):4314. PMID: 34262047

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Triglia ET, Ansari M, Cai P,…,Giotti B,…,Wang X, Xu K, Yan W, Zhao W, ... , Tsankov AM, ... et al. Nature Medicine. 2021 Mar 2. PMID: 33654293.

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19. Bernardes JP, Mishra N, Tran F, Bahmer T, Best L, Blase JI, ... , Tsankov AM, ... et al. Immunity. 2020 Dec 15. PMID: 33296687.

Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2-Mediated Myoarditis. Tucker NR, Chaffin M, Bedi KC Jr, Papangeli I, Akkad AD, Arduini A, ... , Tsankov AM, ... et al. Circulation. 2020 Aug 18. PMID: 32795091

Emergence of a High-Plasticity Cell State during Lung Cancer Evolution. Marjanovic ND, Hofree M, Chan JE, Canner D, Wu K, Trakala M, Hartmann GG, Smith OC, Kim JY, Evans KV, Hudson A, Ashenberg O, Porter CBM, Bejnood A, Subramanian A, Pitter K, Yan Y, Delorey T, Phillips DR, Shah N, Chaudhary O, Tsankov A, ... et al. Cancer Cell. 2020 Jul 23. PMID: 32707077.

SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues. Ziegler CG*, Allon SJ*, Nyquist SK*, Mbano IM*, ... , Tsankov AM, ... et al. Cell. 2020 Apr 27. PMID: 32413319

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Sungnak W, Huang N, Becavin C, Berg M, Queen R, Litvinukova M, ... , Tsankov AM, ... et al. Nature Medicine 2020 Apr 23. PMID: 32327758

A single-cell and single-nucleus RNA-Seq toobox for fresh and frozen human tumors. Slyper M*, Porter CBM*, Ashenberg O*, ... , Tsankov AM, ... , Rozenblatt-Rosen O, Regev A. Nature Medicine 2020 May;26(5):792-802. PMID: 32405060.

2019 and prior

Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression. Tsankov AM§, Wadsworth MH, Akopian A, Charlton J, Allon S, Arczewska A, Mead B, Drake RS, Smith ZD, Mikkelsen TS, Shalek AK§, Meissner A§. Development. 2019 Sep 12;146(19). PMID:31515224. §-corresponding authors

Transcription factor binding dynamics during human ES cell differentiation. Tsankov AM, Gu H, Akopian V, Ziller MJ, Donaghey J, Amit I, Gnirke A, Meissner A. Nature. 2015 Feb 19; 518(7539):344-9. PMID: 25693565; PMCID: PMC4499331.

A qPCR ScoreCard quantifies the differentiation potential of human pluripotent stem cells. Tsankov AM, Akopian V, Pop R, Chetty S, Gifford CA, Daheron L, Tsankova NM, Meissner A. Nature Biotechnol. 2015 Nov; 33(11):1182-92. PMID: 26501952; PMCID: PMC4636964.

Analysis of chromatin accessibility uncovers TEAD1 as a regulator of migration in human glioblastoma. Tome-Garcia J, Erfani P, Nudelman G, Tsankov AM, Katsyv I, Tejero R, Walsh M, Friedel RH, Zaslavsky E, Tsankova NM. Nature Communication. 2018 10 01; 9(1):4020. PMID: 30275445.

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Montoro DT, Haber AL, Biton M, Vinarsky V, Lin B, Birket SE, Yuan F, Chen S, Leung HM, Villoria J, Rogel N, Burgin G, Tsankov AM, Waghray A, Slyper M, Waldman J, Nguyen L, Dionne D, Rozenblatt-Rosen O, Tata PR, Mou H, Shivaraju M, Bihler H, Mense M, Tearney GJ, Rowe SM, Engelhardt JF, Regev A, Rajagopal J. Nature. 2018 08; 560(7718):319-324. PMID: 30069044.

Global delay in nascent strand DNA methylation. Charlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A. Nat Struct Mol Biol. 2018 Apr; 25(4):327-332. PMID: 29531288.

Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease. Warren CR, O'Sullivan JF, Friesen M, Becker CE, Zhang X, Liu P, Wakabayashi Y, Morningstar JE, Shi X, Choi J, Xia F, Peters DT, Florido MHC, Tsankov AM, Duberow E, Comisar L, Shay J, Jiang X, Meissner A, Musunuru K, Kathiresan S, Daheron L, Zhu J, Gerszten RE, Deo RC, Vasan RS, O'Donnell CJ, Cowan CA. Cell Stem Cell. 2017 04 06; 20(4):547-557.e7. PMID: 28388431.

A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Choi J, Lee S, Mallard W, Clement K, Tagliazucchi GM, Lim H, Choi IY, Ferrari F, Tsankov AM, Pop R, Lee G, Rinn JL, Meissner A, Park PJ, Hochedlinger K. Nature Biotechnol. 2015 Nov; 33(11):1173-81. PMID: 26501951; PMCID: PMC4847940.

Automated, high-throughput derivation, characterization and differentiation of induced pluripotent stem cells. Paull D, Sevilla A, Zhou H, Hahn AK, Kim H, Napolitano C, Tsankov A, Shang L, Krumholz K, Jagadeesan P, Woodard CM, Sun B, Vilboux T, Zimmer M, Forero E, Moroziewicz DN, Martinez H, Malicdan MC, Weiss KA, Vensand LB, Dusenberry CR, Polus H, Sy KT, Kahler DJ, Gahl WA, Solomon SL, Chang S, Meissner A, Eggan K, Noggle SA. Nature Methods. 2015 Sep; 12(9):885-92. PMID: 26237226.

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A. Nature Genetics. 2015 May; 47(5):469-78. PMID: 25822089; PMCID: PMC4414868.

Dissecting neural differentiation regulatory networks through epigenetic footprinting. Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cachiarelli D, Tsankov A, Epstein C, Rinn JR, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A. Nature. 2015 Feb 19; 518(7539):355-359. PMID: 25533951; PMCID: PMC4336237.

A comparison of non-integrating reprogramming methods. Schlaeger TM, Daheron L, Brickler TR, Entwisle S, Chan K, Cianci A, DeVine A, Ettenger A, Fitzgerald K, Godfrey M, Gupta D, McPherson J, Malwadkar P, Gupta M, Bell B, Doi A, Jung N, Li X, Lynes MS, Brookes E, Cherry AB, Demirbas D, Tsankov AM, Zon LI, Rubin LL, Feinberg AP, Meissner A, Cowan CA, Daley GQ. Nature Biotechnol. 2015 Jan; 33(1):58-63. PMID: 25437882.

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A. Cell. 2013 May 23; 153(5):1149-63. PMID: 23664763; PMCID: PMC3709577.

Toward a unified physical model of nucleosome patterns flanking transcription start sites. Möbius W, Osberg B, Tsankov AM, Rando OJ, Gerland U. Proc Natl Acad Sci U S A. 2013 Apr 02; 110(14):5719-24. PMID: 23509245; PMCID: PMC3619296.

Genome-wide identification and characterization of replication origins by deep sequencing. Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P, Weng Z, Rhind N. Genome Biology. 2012 Apr 24; 13(4):R27. PMID: 22531001; PMCID: PMC3446301.

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Tsankov A, Yanagisawa Y, Rhind N, Regev A, Rando OJ. Genome Research. 2011 Nov; 21(11):1851-62. PMID: 21914852; PMCID: PMC3205570.

The role of nucleosome positioning in the evolution of gene regulation. Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ. PLoS Biology. 2010 Jul 06; 8(7):e1000414. PMID: 20625544; PMCID: PMC2897762.

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