Moore Lab - Publications



Emerging Modeling Concepts and Solutions in Stem Cell Research.

Papatsenko D, Lemischka IR.

Curr Top Dev Biol. 2016;116:709-21. doi:

10.1016/bs.ctdb.2015.11.040. PubMed PMID: 26970649.

A dual molecular analogue tuner for dissecting protein function in mammalian cells.

Brosh R, Hrynyk I, Shen J, Waghray A, Zheng N, Lemischka IR.

Nat Commun. 2016 May 27;7:11742. doi: 10.1038/ncomms11742. PubMed PMID: 27230261; PubMed

Central PMCID: PMC4895048.

Identification of factors promoting ex vivo maintenance of mouse hematopoietic stem cells by long-term single-cell quantification.

Kokkaliaris KD, Drew E, Endele M, Loeffler D, Hoppe PS, Hilsenbeck O,

Schauberger B, Hinzen C, Skylaki S, Theodorou M, Kieslinger M, Lemischka I, Moore

K, Schroeder T.

Blood. 2016 Sep 1;128(9):1181-92. doi: 10.1182/blood-2016-03-705590. PubMed PMID: 27365423.

Modeling Cancer with Pluripotent Stem Cells.

Gingold J, Zhou R, Lemischka IR, Lee DF.
Trends Cancer. 2016 Sep;2(9):485-494. PubMed PMID: 27722205; PubMed

Central PMCID: PMC5050918.

Hematopoietic Stem Cells Count and Remember Self-Renewal Divisions.

Bernitz JM, Kim HS, MacArthur B, Sieburg H, Moore K.
Cell. 2016 Nov 17;167(5):1296-1309.e10. doi: 10.1016/j.cell.2016.10.022. PubMed PMID: 27839867.
Commented in Dev Cell. 2016 Nov 21;39(4):390-391. doi: 10.1016/j.devcel.2016.11.005.

Aging Hematopoietic Stem Cells Make Their History.

Fast EM1, Ira Zon L2.

Hematopoietic Reprogramming In Vitro Informs In Vivo Identification of Hemogenic Precursors to Definitive Hematopoietic Stem Cells.
Pereira CF, Chang B, Gomes A, Bernitz J, Papatsenko D, Niu X, Swiers G, Azzoni E, de Bruijn MF, Schaniel C, Lemischka IR, Moore KA.  Developmental Cell. 2016; 36(5):525-39,

Developmental Cell Previews:

Tracking HSC Origin: From Bench to Placenta. V. Calvanese and H.K.A. Mikkola, Dev Cell, .

Making a Hematopoietic Stem Cell.
Daniel MG, Pereira CF, Lemischka IR, Moore KA.

Trends in Cell Biology. 2016; 26(3):202-14. NIHMSID: NIHMS759629 PubMed [journal]

PMID: 26526106, PMCID: PMC4764442

Converting cell fates: generating hematopoietic stem cells de novo via transcription factor reprogramming.

Daniel MG, Lemischka IR, Moore K.  Annals of the New York

Academy of Sciences. 2016; PubMed [journal] PMID: 26748878

Emerging Modeling Concepts and Solutions in Stem Cell Research.

Papatsenko, D, Lemischka IR., Curr Top Dev Biol. 2016;116:709-21. doi: 10.1016/bs.ctdb.2015.11.040. Epub 2016 Feb 13. PMID:26970649


Modeling Familial Cancer with Induced Pluripotent Stem Cells.

Lee DF, Su J, Kim HS, Chang B, Papatsenko D, Zhao R, Yuan Y, Gingold J, Xia W, Darr H, Mirzayans R, Hung MC, Schaniel C, Lemischka IR.

Cell. 2015 Apr 9;161(2):240-54. doi:

PMID: 25860607

Video Abstract.  Download File (17.31 MB)

Myeloid Dysregulation in a Human Induced Pluripotent Stem Cell Model of PTPN11-Associated Juvenile Myelomonocytic Leukemia.

Mulero-Navarro S, Sevilla A, Roman AC, Lee DF, D'Souza SL, Pardo S, Riess I, Su J, Cohen N, Schaniel C, Rodriquez NA, Baccarini A, Brown BD, Cave H, Strullu M, Yalkcin S, Park CY, Dhandapany, PS, Yongchao G, Edelmann L, Bahieg S, Raynal R, Flex E, Tartaglia M, Moore KA, Lemischka IR, Gelb, BD. Cell Reports. 2015; 13(3):504-15. NIHMSID: NIHMS722789 PubMed [journal] PMID: 26456833, PMCID: PMC4618050

Identification of markers that functionally define a quiescent multiple myeloma cell sub-population surviving bortezomib treatment.

Adomako A, Calvo V, Biran N, Osman K, Chari A, Paton, JC, Moore K, Schewe DM, Aguirre-Ghiso JA.  BMC Cancer. 2015; 5:444. PubMed [journal] PMID: 26025442, PMCID: PMC4448210

Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal.

Papatsenko D, Darr H, Kulakovskiy IV, Waghray A, Makeev VJ, MacArthur BD, Lemischka IR.  Stem Cell Reports. 2015; 5(2):207-20.

Distribution Analyzer, a methodology for identifying and clustering outlier conditions from single-cell distributions, and its application to a Nanog reporter RNAi screen.

Gingold JA, Coakley ES, Su J, Lee DF, Lau Z, Zhou H, Felsenfeld DP, Schaniel C, Lemischka IR.  BMC Bioinformatics. 2015; 16:225. PubMed [journal] PMID: 26198214, PMCID: PMC4511455

Tbx3 Controls Dppa3 Levels and Exit from Pluripotency toward Mesoderm.

Waghray A, Saiz N, Jayaprakash AD, Freire AG, Papatsenko D, Pereira CF, Lee DF, BroshR, Chang B, Darr H, Gingold J, Kelley K, Schaniel C, Hadjantonakis AK, Lemischka IR.  Stem Cell Reports. 2015;5(1):97-110. PubMed [journal] PMID: 26095607, PMCID: PMC4618439

Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming.

Ding J, Huang X, Shao N, Zhou H, Lee DF, Faiola F, Fidalgo M, Guallar D, Saunders A, Shliaha PV, Wang H, Waghray A, Papatsenko D, Sánchez-Priego C, Li D, Yuan Y, Lemischka IR, Shen L, Kelley K, Deng H, Shen X, Wang J.  Cell Stem Cell. 2015 Jun 4;16(6):653-68. doi: 10.1016/j.stem.2015.04.001. Epub 2015 Apr 30. PMID:25936917


Papatsenko D, Lemischka IR.  2015 Jun 1;31(11):1860-2. doi: 10.1093/bioinformatics/btv058. Epub 2015 Jan 30. PMID:25637559

A genome-wide RNAi screen identifies opposing functions of Snai1 and Snai2 on the Nanog dependency in reprogramming.

Gingold JA, Fidalgo M, Guallar D, Lau Z, Sun Z, Zhou H, Faiola F, Huang X, Lee DF, Waghray A, Schaniel C, Felsenfeld DP, Lemischka IR, Wang J.

Mol Cell. 2014 Oct 2;56(1):140-52. doi: 10.1016/j.molcel.2014.08.014. Epub 2014 Sep 15.

PMID: 25240402 [PubMed - indexed for MEDLINE]

NetExplore: a web server for modeling small network motifs.

Papatsenko D, Lemischka IR.

Bioinformatics. 2015 Jan 30. pii: btv058. [Epub ahead of print]

PMID: 25637559

Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming.

Ding J, Huang X, Shao N, Zhou H, Lee DF, Faiola F, Fidalgo M, Guallar D, Saunders A, Shliaha PV, Wang H, Waghray A, Papatsenko D, Sánchez-Priego C, Li D, Yuan Y, Lemischka IR, Shen L, Kelley K, Deng H, Shen X, Wang J.

Cell Stem Cell. 2015 Apr 29. pii: S1934-5909(15)00159-9. doi: 10.1016/j.stem.2015.04.001. [Epub ahead of print]

PMID: 25936917


Uncovering the origins of a niche. 

Bernitz JM, Moore KA. 

Elife. 2014 Nov 11;3. doi: 10.7554/eLife.05041. PMID:  25387005

Out of the niche: exploring unknown pathways.

Moore K, Cossu G.

Development. 2014 Sep;141(18):3441-3444. doi: 10.1242/dev.110510..

PMID: 25183866

A genome-wide RNAi screen identifies opposing functions of Snai1 and Snai2 on the Nanog dependency in reprogramming.

Gingold JA, Fidalgo M, Guallar D, Lau Z, Sun Z, Zhou H, Faiola F, Huang X, Lee DF, Waghray A, Schaniel C, Felsenfeld DP, Lemischka IR, Wang J.

Mol Cell. 2014 Oct 2;56(1):140-52. doi: 10.1016/j.molcel.2014.08.014. Epub 2014 Sep 15.

PMID: 25240402

'From blood to blood': de-differentiation of hematopoietic progenitors to stem cells.

Pereira CF, Lemischka IR, Moore K.

EMBO J. 2014 Jul 17;33(14):1511-3. doi: 10.15252/embj.201488980. Epub 2014 Jun 6.

PMID:  24907133

Construction and validation of a regulatory network for pluripotency and self-renewal of mouse embryonic stem cells.

Xu H, Ang YS, Sevilla A, Lemischka IR, Ma'ayan A.

PLoS Comput Biol. 2014 Aug 14;10(8):e1003777. doi: 10.1371/journal.pcbi.1003777. eCollection 2014 Aug.

PMID: 25122140

Genomic editing tools to model human diseases with isogenic pluripotent stem cells.

Kim HS, Bernitz J, Lee DF, Lemischka IR.

Stem Cells Dev. 2014 Jul 30. [Epub ahead of print]

PMID: 25075441

Divisional History and Hematopoietic Stem Cell Function during Homeostasis.

Qiu J, Papatsenko D, Niu X, Schaniel C, Moore K.

Stem Cell Reports. 2014 Mar 20;2(4):473-90. doi: 10.1016/j.stemcr.2014.01.016. eCollection 2014 Apr 8.  PMID:  24749072

"There will be blood" from fibroblasts.

Pereira CF, Lemischka IR, Moore K.

Cell Cycle. 2014 Feb 1;13(3):335-6. doi: 10.4161/cc.27507. Epub 2013 Dec 13. No abstract available.  PMID:  24335410


Epigenetic roles of MLL oncoproteins are dependent on NF-κB.

Kuo HP, Wang Z, Lee DF, Iwasaki M, Duque-Afonso J, Wong SH, Lin CH, Figueroa ME, Su J,Lemischka IR, Cleary ML.

Cancer Cell. 2013 Oct 14;24(4):423-37. doi: 10.1016/j.ccr.2013.08.019. Epub 2013 Sep 19.  PMID: 24054986

Expression of podocalyxin separates the hematopoietic and vascular potentials of mouse embryonic stem cell-derived mesoderm.

Zhang H, Nieves JL, Fraser ST, Isern J, Douvaras P, Papatsenko D, D'Souza SL, Lemischka IR, Dyer MA, Baron MH.

Stem Cells. 2014 Jan;32(1):191-203. doi: 10.1002/stem.1536.  PMID: 24022884

Statistical mechanics of pluripotency.

MacArthur BD, Lemischka IR.

Cell. 2013 Aug 1;154(3):484-9. doi: 10.1016/j.cell.2013.07.024.  PMID: 23911316


Patterning pluripotency in embryonic stem cells.

Zhang YS, Sevilla A, Wan LQ, Lemischka IR, Vunjak-Novakovic G.

Stem Cells. 2013 Sep;31(9):1806-15. doi: 10.1002/stem.1468.  PMID: 23843329

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.

Xu H, Baroukh C, Dannenfelser R, Chen EY, Tan CM, Kou Y, Kim YE, Lemischka IR, Ma'ayan A.

Database (Oxford). 2013 Jun 21;2013:bat045. doi: 10.1093/database/bat045. Print 2013. PMID: 23794736

Induction of a hemogenic program in mouse fibroblasts.

Pereira CF, Chang B, Qiu J, Niu X, Papatsenko D, Hendry CE, Clark NR, Nomura-Kitabayashi A, Kovacic JC, Ma'ayan A, Schaniel C, Lemischka IR, Moore K.

Cell Stem Cell. 2013 Aug 1;13(2):205-18. doi: 10.1016/j.stem.2013.05.024. Epub 2013 Jun 13.  PMID: 23770078

MacroH2A histone variants act as a barrier upon reprogramming towards pluripotency.

Gaspar-Maia A, Qadeer ZA, Hasson D, Ratnakumar K, Leu NA, Leroy G, Liu S, Costanzi C, Valle-Garcia D, Schaniel C, Lemischka I, Garcia B, Pehrson JR, Bernstein E.

Nat Commun. 2013;4:1565. doi: 10.1038/ncomms2582. Erratum in: Nat Commun. 2013;4:2090.  PMID: 23463008

SETD6 monomethylates H2AZ on lysine 7 and is required for the maintenance of embryonic stem cell self-renewal.

Binda O, Sevilla A, LeRoy G, Lemischka IR, Garcia BA, Richard S.

Epigenetics. 2013 Feb;8(2):177-83. doi: 10.4161/epi.23416. Epub 2013 Jan 16.  PMID: 23324626


Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity.

MacArthur BD, Sevilla A, Lenz M, Müller FJ, Schuldt BM, Schuppert AA, Ridden SJ, Stumpf PS, Fidalgo M, Ma'ayan A, Wang J, Lemischka IR.

Nat Cell Biol. 2012 Nov;14(11):1139-47. doi: 10.1038/ncb2603. Epub 2012 Oct 28.  PMID: 23103910

Zfp281 mediates Nanog autorepression through recruitment of the NuRD complex and inhibits somatic cell reprogramming.

Fidalgo M, Faiola F, Pereira CF, Ding J, Saunders A, Gingold J, Schaniel C, Lemischka IR, Silva JC, Wang J.

Proc Natl Acad Sci USA. 2012 Oct 2;109(40):16202-7. doi: 10.1073/pnas.1208533109. Epub 2012 Sep 17. PMID: 22988117

Reprogramming cell fates: insights from combinatorial approaches.

Pereira CF, Lemischka IR, Moore K.

Ann N Y Acad Sci. 2012 Aug;1266:7-17. doi: 10.1111/j.1749-6632.2012.06508.x. Review.  PMID: 22901251

Regulation of embryonic and induced pluripotency by aurora kinase-p53 signaling.

Lee DF, Su J, Ang YS, Carvajal-Vergara X, Mulero-Navarro S, Pereira CF, Gingold J, Wang HL, Zhao R, Sevilla A, Darr H, Williamson AJ, Chang B, Niu X, Aguilo F, Flores ER, Sher YP, Hung MC, Whetton AD, Gelb BD, Moore KA, Snoeck HW, Ma'ayan A, Schaniel C, Lemischka IR.

Cell Stem Cell. 2012 Aug 3;11(2):179-94. doi: 10.1016/j.stem.2012.05.020.  PMID: 22862944

Combining competition assays with genetic complementation strategies to dissect mouse embryonic stem cell self-renewal and pluripotency.

Lee DF, Su J, Sevilla A, Gingold J, Schaniel C, Lemischka IR.

Nat Protoc. 2012 Mar 22;7(4):729-48. doi: 10.1038/nprot.2012.018.  PMID: 22441292

Ling J, Kang Y, Zhao R, Xia Q, Lee DF, Chang Z, Li J, Peng B, Fleming JB, Wang H, Liu J, Lemischka IR, Hung MC, Chiao PJ. (2012) KrasG12D-induced IKK2/ß/NF-?B activation by IL-1a and p62 feedforward loops is required for development of pancreatic ductal adenocarcinoma. Cancer Cell. Jan 17;21(1):105-20.


Honda H, Takubo K, Oda H, Kosaki K, Tazaki T, Yamasaki N, Miyazaki K, Moore KA, Honda Z, Suda T, Lemischka IR. (2011) Hemp, an mbt domain-containing protein, plays essential roles in hematopoietic stem cell function and skeletal formation. Proc Natl Acad Sci. Feb 8;108(6):2468-73.

Green MD, Chen A, Nostro MC, d'Souza SL, Schaniel C, Lemischka IR, Gouon-Evans V, Keller G, Snoeck HW. (2011) Generation of anterior foregut endoderm from human embryonic and induced pluripotent stem cells. Nat Biotechnol. Mar;29(3):267-72.

Ang YS, Tsai SY, Lee DF, Monk J, Su J, Ratnakumar K, Ding J, Ge Y, Darr H, Chang B, Wang J, Rendl M, Bernstein E, Schaniel C, Lemischka IR. (2011) Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell. Apr 15;145(2):183-97.

Josowitz R, Carvajal-Vergara X, Lemischka IR, Gelb BD. (2011) Induced pluripotent stem cell-derived cardiomyocytes as models for genetic cardiovascular disorders. Curr Opin Cardiol. May;26(3):223-9.

Aguilo F, Avagyan S, Labar A, Sevilla A, Lee DF, Kumar P, Lemischka IR, Zhou BY, Snoeck HW. (2011) Prdm16 is a physiologic regulator of hematopoietic stem cells. Blood. May 12;117(19):5057-66.

Tsai SY, Bouwman BA, Ang YS, Kim SJ, Lee DF, Lemischka IR, Rendl M. (2011) Single transcription factor reprogramming of hair follicle dermal papilla cells to induced pluripotent stem cells. Stem Cells. Jun;29(6):964-71.

Ang YS, Gaspar-Maia A, Lemischka IR, Bernstein E. (2011) Stem cells and reprogramming: breaking the epigenetic barrier? Trends Pharmacol Sci. Jul;32(7):394-401.

Schaniel C, Sirabella D, Qiu J, Niu X, Lemischka IR, Moore KA. (2011) Wnt-inhibitory factor 1 dysregulation of the bone marrow niche exhausts hematopoietic stem cells. Blood. Sep 1;118(9):2420-9.


Patient-specific induced pluripotent stem-cell-derived models of LEOPARD syndrome.

Carvajal-Vergara X, Sevilla A, D'Souza SL, Ang YS, Schaniel C, Lee DF, Yang L, Kaplan AD, Adler ED, Rozov R, Ge Y, Cohen N, Edelmann LJ, Chang B, Waghray A, Su J, Pardo S, Lichtenbelt KD, Tartaglia M, Gelb BD, Lemischka IR.

Nature. 2010 Jun 10;465(7299):808-12. doi: 10.1038/nature09005.  PMID: 20535210

Huilei Xu, Christoph Schaniel, Lemischka IR, Avi Ma'ayan. (2010) Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdisciplinary Reviews: Systems Biology and Medicine. Online: 24 March 2010

Tarleton HP, Lemischka IR. (2010) Delayed differentiation in embryonic stem cells and mesodermal progenitors in the absence of CtBP2. Mech Dev. 127(1-2): 107-19.


Rong Lu, Florian Markowetz, Richard D. Unwin, Jeffrey T. Leek, Edoardo M. Airoldi, Ben D. MacArthur, Alexander Lachmann, Roye Rozov, Avi Ma'ayan, Laurie A. Boyer, Olga G. Troyanskaya, Anthony D. Whetton, Ihor R. Lemischka. (2009) Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature. 462: 358 - 362

Macarthur BD, Ma'ayan A, Lemischka IR. (2009) Toward Stem Cell Systems Biology: From Molecules to Networks and Landscapes. Cold Spring Harb Symp Quant Biol. 2009 Mar 27.

Glauche I, Moore K, Thielecke L, Horn K, Loeffler M, Roeder I. (2009) Stem cell proliferation and quiescence - two sides of the same coin. PLOS Comput Biol. 5: e1000447.

Schaniel, Christoph and Moore, Kateri. (2009) Genetic Models to Study Quiescent Stem Cells and Their Niches. Ann NY Acad Sci. 1176: 26-35.


Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG. (2008) A genomewide functional network for the laboratory mouse. PLoS Comput Biol. 4:e1000165.

Krasnov P, Michurina T, Packer MA, Stasiv Y, Nakaya N, Moore KA, Drazan KE, Enikolopov G. (2008) Neuronal nitric oxide synthase contributes to the regulation of hematopoiesis. Mol Med. 14: 141-149.


Fasano CA, Dimos JT, Ivanova NB, Lowry N, Lemischka IR, Temple S. (2007) shRNA knockdown of Bmi-1 reveals a critical role for p21-Rb pathway in NSC self-renewal during development. Cell Stem Cell. 1:87-99.

Chateauvieux S, Ichante JL, Delorme B, Frouin V, Pietu G, Langonne A, Gallay N, Sensebe L, Martin MT, Moore KA, Charbord P. (2007) The Molecular Profile of Mouse Stromal Mesenchymal Stem Cells. Physiological Genomics. 29: 128-138.