Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N and Tartaglia GG.
RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding.
(2024) Chem Reviews, 124:4734-4777.

Udani S, Langerman J, Koo D, Baghdasarian S, Cheng B, Kang S, Soemardy C, de Rutte J, Plath K* and Di Carlo D*. (2024).
Associating growth factor secretions and transcriptomes of single cells in nanovials using SEC-seq.
Nature Nanotechnology. 19:354-363. *corresponding authors.

Tang AA, Afasizheva A, Cano CT, Plath K, Black D and Franco E. (2024).
Optimization of RNA Pepper Sensors for the Detection of Arbitrary RNA Targets.
ACS Synth Biology, 13:498-508.

Dror I, Chitiashvili T, Tan SYX, Cano CT, Sahakyan A, Markaki Y, Chronis C, Collier A, Deng W, Liang G, Sun Y, Afasizheva A, Miller J, Xiao W, Black DL, Ding F and Plath K. (2024).
XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells.
Cell, 187:110-129.

Tu W, Christofk H* and Plath K* (2023).
Nutrient regulation of development and cell fate decisions.
Development, 150: dev199961. * corresponding authors.

Hoetker MS, Yagi M, Di Stefano B, Langerman J, Cristea S, Wong LP, Huebner AJ, Charlton J, Deng W, Haggerty C, Sadreyev RI, Meissner A, Michor F, Plath K and Hochedlinger K. (2023).
H3K36 methylation maintains cell identity by regulating opposing lineage programmes.
Nature Cell Biology, 25:1121-1134.

Cicchetto AC, Jacobson EC, Sunshine H, Wilde BR, Krall AS, Jarrett KE, Sedgeman L, Turner M, Plath K, Iruela-Arispe ML, de Aguiar Vallim TQ and Christofk HR. (2023).
ZFP36-mediated mRNA decay regulates metabolism.
Cell Reports, 42:112411.

Lo JH, Edwards M, Langerman J, Sridharan R, Plath K and Smale ST. (2022).
Essential roles for Oct4:Sox2 binding in establishing but not maintaining active and silent states of dynamically regulated genes in pluripotent cells.
Genes & Development, DOI: 10.1101/gad.350113.122.

Deng W, Sha J, Fanglei X; Yasaman JA, Plath K and Wohlschlegel J. (2022).
High-field asymmetric waveform ion mobility spectrometry interface enhances parallel reaction monitoring on an Orbitrap mass spectrometer.
Analytical Chemistry, 94:15939-15947.

Watanabe M, Buth JE, Haney JR, Vishlaghi N, Turcios F, Elahi LS, Gu W, Pearson CA, Kurdian A, Baliaouri NV, Collier AJ, Miranda OA, Dunn N, Chen D, Sabri S, Torre-Ubieta L, Clark AT, Plath K, Christofk HR, Kornblum HI, Gandal MJ, Novitch BG. (2022).
TGFβ superfamily signaling regulates the state of human stem cell pluripotency and capacity to create well-structured telencephalic organoids.
Stem Cell Reports. S2213-6711(22)00422-2. doi: 10.1016/j.stemcr.2022.08.013.

Jacobson EC, Pandya-Jones A, and Plath K. 2022.
A lifelong duty: how Xist maintains the inactive X chromosome.
Curr Opin Genet Dev, 75:101927. doi: 10.1016/j.gde.2022.101927.

Chitiashvili T, Hsu F, Dror I, Plath K & Clark A (2022).
FGFR3 is Expressed by Human Primordial Germ Cells and is Repressed after Meiotic Initiation to Form Primordial Oocytes.
Stem Cell Reports. 17(6):1268-1278. doi: 10.1016/j.stemcr.2022.04.015.

Collier AJ, Bendall A, Fabian C, Malcolm AA, Tilgner K, Semprich CI, WojdylaK, Nisi PS, Kishore K, Franklin VNR, Mirshekar-Syahkal B, D’Santos C, Plath K, Yusa K, and Rugg-Gunn PJ. (2022).
Genome-Wide Screening Identifies Polycomb Repressive Complex 1.3 as an Essential Regulator of Human Naïve Pluripotent Cell Reprogramming.
Science Advances, 8(12):eabk0013. doi: 10.1126/sciadv.abk0013.

Pezhouman A, Nguyen NB, Sercel AJ, Nguyen TL, Daraei A, Sabri S, Chapski DJ, Zheng M, Patananan AN, Ernst J, Plath K, Vondriska TM, Teitell MA, and Ardehali R. (2021).
Transcriptional, Electrophysiological, and Metabolic Characterizations of hESC-Derived First and Second Heart Fields Demonstrate a Potential Role of TBX5 in Cardiomyocyte Maturation.
Front Cell Dev Biol, 9:787684. doi: 10.3389/fcell.2021.787684.

Quinodoz SA, Jachowicz JW, Bhat P, Ollikainen N, Banerjee AK, Goronzy IN, Blanco MR, Chovanec P, Chow A, Markaki Y, Thai J, Plath K, and Guttman M. (2021).
RNA promotes the formation of spatial compartments in the nucleus.
Cell, 184:5775-5790.e30. doi: 10.1016/j.cell.2021.10.014.

Markaki Y, Chong JG, Wang Y, Jacobson EC, Luong C, Tan SYX, Jachowicz JW, Strehle M, Maestrini D, Banerjee AK, Mistry BA, Dror I, Dossin F, Schöneberg J, Heard E, Guttman M, Chou T*, and Plath K*. (2021).
Xist nucleates local protein gradients to propagate silencing across the X chromosome.
Cell,184:6174-6192. https://doi.org/10.1016/j.cell.2021.10.022. *corresponding authors.

Allison T, Langerman J, Sabri S, Otero-Garcia M, Lund A, Wei X, Samarasinghe R, Pouladakis, D, Langerman J, Mody I, Cobos I, Novitch BN, Geschwind DH, Plath K* and Lowry WE*. (2021).
Defining the nature of human pluripotent stem cell-derived interneurons via single cell analysis. Stem Cell Reports,
16:2548-2564. doi: 10.1016/j.stemcr.2021.08.006.

Deng W, Jacobson EC, Collier AJ and Plath K. 2021.
The transcription factor code in iPSC reprogramming.
Curr Opin Genet Dev, 70:89-96. doi: 10.1016/j.gde.2021.06.003.

Samarasinghe RA, Miranda OA, Buth JE, Mitchell S, Ferando I, Watanabe M, Allison TF, Kurdian A, Fotion NN, Gandal MJ, Golshani P, Plath K, Lowry WE, Parent JM, Mody I and Novitch BG. 2021.
Identification of neural oscillations and epileptiform changes in human brain organoids.
Nature Neuroscience, 24: 1488-1500. doi: 10.1038/s41593-021-00906-5.

Hancock GV, Liu W, Peretz L, Chen D, Gell JJ, Collier AJ, Zamudio JR, Plath K and Clark AT (2021).
Divergent roles for KLF4 and TFCP2L1 in naive ground state pluripotency and human primordial germ cell development.
Stem Cell Res. 55:102493. doi: 10.1016/j.scr.2021.102493.

Carraro G, Langerman J, Sabri S, Lorenzana Z, Purkayastha A, Zhang G, Konda B, Aros CJ, Calvert BA, Szymaniak A, Wilson E, Mulligan M, Bhatt P, Lu J, Vijayaraj P, Yao C, Shia DW, Lund AJ, Israely E, Rickabaugh TM, Ernst J, Mense M, Randell SH, Vladar EK, Ryan AL, Plath K*, Mahoney JE*, Stripp BR* and Gomperts BN*. (2021).
Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition.
Nature Medicine, 27:806-814. doi: 10.1038/s41591-021-01332-7. *corresponding authors.

Mullen PJ, Garcia G Jr, Purkayastha A, Matulionis N, Schmid EW, Momcilovic M, Sen C, Langerman J, Ramaiah A, Shackelford DB, Damoiseaux R, French SW, Plath K, Gomperts BN, Arumugaswami V, and Christofk HR. (2021).
SARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition.
Nature Communications, 12:1876. doi: 10.1038/s41467-021-22166-4.

Deng W, Sha J, Plath K, and Wohlschlegel JA. (2021).
Carboxylate-Modified Magnetic Bead (CMMB)-Based Isopropanol Gradient Peptide Fractionation (CIF) Enables Rapid and Robust Off-Line Peptide Mixture Fractionation in Bottom-Up Proteomics.
Mol Cell Proteomics, 20:100039. doi: 10.1074/mcp.RA120.002411.

Guo J, Sosa E, Chitiashvili T, Nie X, Rojas EJ, Oliver E; Plath K, Hotaling JM, Stukenborg JB, Clark AT, and Cairns BR. (2021).
Single-cell analysis of the developing human testis reveals somatic niche cell specification and fetal germline stem cell establishment.
Cell Stem Cell, 28:764-778.e4. doi: 10.1016/j.stem.2020.12.004.

Patananan AN, Sercel AJ, Wu TH, Ahsan FM, Torres A Jr, Kennedy SAL, Vandiver A, Collier AJ, Mehrabi A, Van Lew J, Zakin L, Rodriguez N, Sixto M, Tadros W, Lazar A, Sieling PA, Nguyen TL, Dawson ER, Braas D, Golovato J, Cisneros L, Vaske C, Plath K, Rabizadeh S, Niazi KR, Chiou PY, and Teitell MA. (2020).
Pressure-Driven Mitochondrial Transfer Pipeline Generates Mammalian Cells of Desired Genetic Combinations and Fates.
Cell Reports, 29;33(13):108562.

Meshorer E, Plath K. (2020).
Chromatin and Nuclear Architecture in Stem Cells.
Stem Cell Reports. 15(6):1155-1157.

Purkayastha A, Sen C, Garcia G Jr, Langerman J, Shia DW, Meneses LK, Vijayaraj P, Durra A, Koloff CR, Freund DR, Chi J, Rickabaugh TM, Mulay A, Konda B, Sim MS, Stripp BR, Plath K*, Arumugaswami V*, and Gomperts BN*. (2020).
Direct Exposure to SARS-CoV-2 and Cigarette Smoke Increases Infection Severity and Alters the Stem Cell-Derived Airway Repair Response.
Cell Stem Cell, 27(6):869-875.e4. *corresponding authors.

Chitiashvili T, Dror I, Kim R, Hsu FM, Chaudhari R, Pandolfi E, Chen D, Liebscher S, Schenke-Layland K, Plath K*, and Clark A*. (2020).
Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation.
Nature Cell Biology, 22(12):1436-1446. *corresponding authors.

Pandya-Jones A, Markaki Y, Serizay J, Chitiashvili T, Mancia Leon WR, Damianov A, Chronis C, Papp B, Chen CK, McKee R, Wang XJ, Chau A, Sabri S, Leonhardt H, Zheng S, Guttman M, Black DL*, and Plath K*. (2020).
A protein assembly mediates Xist localization and gene silencing.
Nature, 587(7832):145-151. *corresponding authors.

Xi H, Langerman J, Sabri S, Chien P, Young CS, Younesi S, Hicks M, Gonzalez K, Fujiwara W, Marzi J, Liebscher S, Spencer M, Van Handel B, Evseenko D, Schenke-Layland K, Plath K*, and Pyle AD*. (2020).
A Human Skeletal Muscle Atlas Identifies the Trajectories of Stem and Progenitor Cells across Development and from Human Pluripotent Stem Cells.
Cell Stem Cell, 27(1):181-185. *corresponding authors.

Takahashi R, Grzenda A, Allison TF, Rawnsley J, Balin SJ, Sabri S, Plath K, and Lowry WE. (2019).
Defining transcriptional signatures of human hair follicle cell states.
Journal of Investigative Dermatology.

Polioudakis D, de la Torre-Ubieta L, Langerman J, Elkins AG, Shi X, Stein JL, Vuong CK, Nichterwitz S, Gevorgian M, Opland CK, Lu D, Connell W, Ruzzo EK, Lowe JK, Hadzic T, Hinz FI, Sabri S, Lowry WE, Gerstein MB, Plath K, Geschwind DH.
A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation.
Neuron. 2019 Jul 3. pii: S0896-6273(19)30561-6.
PMID:31303374

Bonora G, Rubbi L, Morselli M, Ma F, Chronis C, Plath K, Pellegrini M
DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS)
PLoS One. 2019 Apr 4;14(4):e0214368.
PMID:30946758

Fei Sun, Constantinos Chronis, Michael Kronenberg, Xiao-Fen Chen, Trent Su, Fides D. Lay, Kathrin Plath, Siavash K. Kurdistani, Michael F. Carey
Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods
Cell Stem Cell. 2019 Jan 3;24(1):138-152.e8.
PMID:30609396

Zhang W, Chronis C, Chen X, Zhang H, Spalinskas R, Pardo M, Chen L, Wu G, Zhu Z, Yu Y, Yu L, Choudhary J, Nichols J, Parast M, Greber B, Sahlén P, and Plath K. (2019).
The BAF and PRC2 complex subunits Dpf2 and Eed antagonistically converge on Tbx3 to control ESC differentiation.
Cell Stem Cell. 24:138-152.

Kai Fu, Constantinos Chronis, Abdenour Soufi, Giancarlo Bonora, Miguel Edwards, Stephen T Smale, Kenneth S. Zaret, Kathrin Plath, and Matteo Pellegrini
Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPSC reprogramming
BMC Genomics. 2018 Dec 22;19(1):956.

Bruno Di Stefano, Mai Ueda, Shan Sabri, Justin Brumbaugh, Aaron J. Huebner, Anna Sahakyan, Kendall Clement, Katie J. Clowers, Alison R. Erickson, Keiko Shioda, Steven P. Gygi, Hongcang Gu, Toshi Shioda, Alexander Meissner, Yasuhiro Takashima, Kathrin Plath, and Konrad Hochedlinger |
Reduced MEK inhibition preserves genomic stability in naïve human ES cells
Nat Methods. 2018 Sep;15(9):732-740

Jelinek D, Flores A, Uebelhoer M, Pasque V, Plath K, Iruela-Arispe ML, Christofk HR, Lowry WE, Coller HA.
Mapping Metabolism: Monitoring Lactate Dehydrogenase Activity Directly in Tissue.
J Vis Exp. doi: 10.3791/57760.

David Jenlinek, Aimee Flores, Melanie Uebelhoer, Vincent Pasque, Kathrin Plath, M. Luisa Iruela-Arispe, Heather R. Christofk, William E. Lowry, Hilary A. Coller
Mapping Metabolism: Monitoring Lactate Dehydrogenase Activity Directly in Tissue
J Vis Exp. 2018 Jun 21;(136). doi: 10.3791/57760.

Sahakyan A, Yang Y and Plath K.
The Role of Xist in X-Chromosome Dosage Compensation.
Trends Cell Biology, 28: 999-1013.

Allison TF, Smith AJH, Anastassiadis K, Sloane-Stanley J, Biga V, Stavish D, Hackland J, Sabri S, Langerman J, Jones M, Plath K, Coca D, Barbaric I, Gokhale P, Andrews PW.
Identification and Single-Cell Functional Characterization of an Endodermally Biased Pluripotent Substrate in Human Embryonic Stem Cells.
Stem Cell Reports, 10: 1895-1907.

Ohashi M, Korsakova E, Allen D, Lee P, Fu K, Vargas BS, Cinkornpumin J, Salas C, Park JC, Germanguz I, Langerman J, Chronis C, Kuoy E, Tran S, Xiao X, Pellegrini M, Plath K*, and Lowry WE*.
Loss of MECP2 Leads to Activation of P53 and Neuronal Senescence.
Stem Cell Reports, 10: 1453-1463. *corresponding authors.

Pasque V, Karnik R, Chronis C, Petrella P, Langerman J, Bonora G, Song J, Vanheer L, Sadhu Dimashkie A, Meissner A, Plath K.
X Chromosome Dosage Influences DNA Methylation Dynamics during Reprogramming to Mouse iPSCs.
Stem Cell Reports, 10: 1537-1550.

Sereti KI, Nguyen NB, Kamran P, Zhao P, Ranjbarvaziri S, Park S, Sabri S, Engel JL, Sung K, Kulkarni RP, Ding Y, Hsiai TK, Plath K, Ernst J, Sahoo D, Mikkola HKA, Iruela-Arispe ML, Ardehali R.
Analysis of cardiomyocyte clonal expansion during mouse heart development and injury.
Nature Communication, 9 :754.

Keegan A, Plath K, Damoiseaux R.
High-Throughput Screening of a Luciferase Reporter of Gene Silencing on the Inactive X Chromosome.
Methods Mol Biol, 1755: 75-87.

Sahakyan A, Plath K, Rougeulle C.
Regulation of X-chromosome dosage compensation in human: mechanisms and model systems.
Philos Trans R Soc Lond B Biol Sci. 2017 Nov 5;372(1733). pii: 20160363. doi: 10.1098/rstb.2016.0363. Review.

Guo G, von Meyenn F, Rostovskaya M, Clarke J, Dietmann S, Baker D, Sahakyan A, Myers S, Bertone P, Reik W, Plath K, Smith A.
Epigenetic resetting of human pluripotency.
2017 Aug 1;144(15):2748-2763. doi: 10.1242/dev.146811.

Huang C, Su T, Xue Y, Cheng C, Lay F, McKee R, Li M., Vashisht A, Wohlschlegel J, Novitch B, Plath K, Kurdistani S, Carey M
Cbx3 maintains lineage specificity during neural differentiation
Genes Dev. 2017 31: 241-246. 10.1101/gad.292169.116

Chronis C, Fiziev P, Papp B, Butz S, Bonora G, Sabri S, Ernst J, Plath K
Cooperating Binding of Transcription Factors Orchestrates Reprogramming
Cell. 2017 Jan 19; 168; 1-18. doi: 10.1016/j.cell.2016.12.016

Sahakyan A, Kim R, Chronis C, Sabri S, Bonora G, Theunissen T, Kuoy E, Langerman J, Clark AT, Jaenisch R, Plath K.
Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation
Cell Stem Cell. 2016 Dec 15; 20: 1-15. doi: 10.1016/j.stem.2016.10.006

Patel S, Bonora G, Sahakyan A, Kim R, Chronis C, Langerman J, Fitz-Gibbon S, Rubbi L, Skelton RJP, Ardehali R, Pellegrini M, Lowry WE, Clark AT, Plath K.
Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during Differentiation
Cell Reports. 2016 Dec 15; 18:1-14. doi: 10.1016/j.celrep.2016.11.054

Gu W, Gaeta X, Sahakyan A, Chan AB, Hong CS, Kim R, Braas D, Plath K, Lowry WE, Christofk HR.
Glycolytic Metabolism Plays a functional Role in Regulating Human Pluripotent Stem Cell State.
Cell Stem Cell. 2016 Oct 6; 19(4):476-490. doi: 10.1016/j.stem.2016.08.008

Sahakyan A, Plath K.
Transcriptome Encyclopedia of Early Human Development
Cell. 2016 May 5; 165(4):777-9. doi: 10.1016/j.cell.2016.04.042

Pandya-Jones A, Plath K.
The Inc between 3D Chromatin Structure and X Chromosome Inactivation.
Semin Cell Dev Biol. 2016 Apr 5. pii: S1084-9521(16)30087-8. doi: 10.1016/j.semcdb.2016.04.002.

Pastor WA, Chen D, Liu W, Kim R, Sahakyan A, Lukianchikov A, Plath K, Jacobsen SE, Clark AT
Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory
Cell Stem Cell. 2016 Feb 2. pii: S1934-5909(16)00020-5. doi: 10.1016/j.stem.2016.01.019

Pasque V, Plath K.
X chromosome reactivation in reprogramming and in development
Curr Opin Cell Biol. 2015 Dec; 37: 75-83. doi: 10.1016/j.ceb.2015.10.006. Epub 2015 Nov 11.

Minkovsky A, Sahakyan A, Bonora G, Damoiseaux R, Dimitrova E, Rubbi L, Pellegrini M, Radu C, Plath K.
A high-throughput screen of inactive X chromosome reactivation identifies the enhancement of DNA demethylation by 5-aza-2?-dC upon inhibition of ribonucleotide reductase.
Epigenetics & Chromatin. 2015, 8:42.

McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco MR, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, Lander ES, Hess S, Plath K, and Guttman M
The Xist lncRNA directly interacts with SHARP to silence transcription through HDAC3
Nature doi:10.1038/nature14443

Pasque V*, Tchieu J*, Karnik R, Uyeda M, Sadhu Dimashkie A, Case D, Papp B, Bonora G, Patel S, Ho R, Schmidt R, McKee R, Sado T, Tada T, Meissner A, Plath K.
X Chromosome Reactivation Dynamics Reveal Stages of Reprogramming to Pluripotency
Cell. 2014 Dec 18; 159(7); 1681-97. *authors contributed equally

Bonora G, Plath K**, Denholtz M**.
A mechanistic link between gene regulation and genome architecture in mammalian development.
Curr Opin Genet Dev. 2014 Aug;27:92-101.** Corresponding authors.

Minkovsky A, Sahakyan A, Rankin-Gee E, Bonora G, Patel S, Plath K.
The Mbd1-Atf7ip-Setdb1 pathway contributes to the maintenance of X chromosome inactivation.
Epigenetics & Chromatin. 2014 Jun 26;7:12.

Denholtz M*, Bonora G*, Chronis C, Splinter E, de Laat W, Ernst J, Pellegrini M**, Plath K**.
Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization.
Cell Stem Cell. 2013 Nov 7;13(5):602-16. *authors contributed equally; ** Corresponding authors.

Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES**, Plath K**, Guttman M**.
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome.
Science. 2013 Aug 16;341(6147):1237973.** Corresponding authors. (also see Perspective in Science)

Britton, L.P., Newhart, A., Bhanu, N.V., Sridharan, R., Gonzales-Cope, M., Plath, K., Janicki, S.M., and Garcia, B.A.
Initial Characterization of Histone H3 Serine 10 O-Acetylation
Epigenetics. 2013 8:1101-1113.

Trounson A, Daley GQ, Pasque V, Plath K.
A new route to human embryonic stem cells.
Nature Medicine. 2013 19(7):820-821.

Ho R*, Papp B*, Hoffman JA, Merrill BJ**, Plath K**.
Stage-specific regulation of reprogramming to induced pluripotent stem cells by Wnt signaling and T cell factor proteins.
Cell Rep. 2013 Jun 27;3(6):2113-26. *authors contributed equally; ** Corresponding authors.

Sridharan R, Gonzales-Cope M*, Chronis C*, Bonora G, McKee R, Huang C, Patel S, Lopez D, Mishra N, Pellegrini M, Carey M, Garcia BA**, Plath K**.
Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1? in reprogramming to pluripotency.
Nat Cell Biol. 2013 Jul;15(7):872-82. *authors contributed equally; ** Corresponding authors.

Minkovsky A, Barakat TS, Sellami N, Chin MH, Gunhanlar N, Gribnau J, Plath K.
The pluripotency factor-bound intron 1 of Xist is dispensable for X chromosome inactivation and reactivation in vitro and in vivo.
Cell Rep. 2013 Mar 28;3(3):905-18.

Papp, B. and Plath, K.
Epigenetics of Reprogramming to Induced Pluripotency.
Cell. 2013 152:1324-1343.

Denholtz M, Plath K.
Pluripotency in 3D: genome organization in pluripotent cells.
Curr Opin Cell Biol. 2012 Dec;24(6):793-801.

Chen, X.F., Lehmann, L., Lin, J.J., Vashisht, A., Schmidt, R., Ferrari, R., Huang, C., McKee, R., Mosley, A., Plath, K., Kurdistani, S.K., Wohlschlegel, J., and Carey, M.
Mediator and SAGA have distinct roles in Pol II preinitiation complex assembly and function.
Cell Reports. 2012 2:1061-1067.

Papp B, Plath K.
Pluripotency re-centered around Esrrb.
EMBO J. 2012, Nov 14;31(22):4255-7.

Plath, K., Srivastava, D., Alvarez-Buylla, A., Tanaka, E.M., Kriegstein, A.R.
Stem cells in the land of the rising sun: ISSCR 2012.
Cell Stem Cell. 2012, 11(5):607-614.

Schmidt R, Plath K.
The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation.
Genome Biol. 2012, Oct 22;13(10):251.

Pera, M.F., and Plath, K.
Cell reprogramming.
Current Opinion Genet Dev. 2012, 22(5):401-402.

Nsair, A., Schenke-Layland, K., Van Handel, B., Evseenko, D., Kahn, M., Zhao, P., Mendelis, J., Heydarkhan, S., Awaji, O., Vottler, M., Geist, S., Chyu, J., Gago-Lopez, N., Crooks, G.M., Plath, K., Goldhaber, J., Mikkola, H.K., and MacLellan, W.R.
Characterization and therapeutic potential of induced pluripotent stem cell-derived cardiovascular progenitor cells.
Plos One. 2012, 7(10):e45603.

Diaz-Perez, S.V., Kim, R., Li, Z., Marquez, V.E., Patel, S., Plath, K., Clark, A.T.
Derivation of new human embryonic stem cell lines reveals rapid epigenetic progression in vitro that can be prevented by chemical modification of chromatin.
Hum Mol Genet. 2012, 21(4):751-764.

Karumbayaram, S., Lee, P., Azghadi, S.F., Cooper, A.R., Patterson, M., Kohn, D.B., Pyle, A., Clark, A., Byrne, J., Zack, J.A., Plath, K., and Lowry, W.E.
From skin biopsy to neurons through a pluripotent intermediate under Good Manufacturing Practice protocols.
Stem Cells Transl Med. 2012, 1(1):36-43.

Minkovsky A, Patel S, Plath K.
Concise review: Pluripotency and the transcriptional inactivation of the female Mammalian X chromosome.
Stem Cells. 2012, Jan;30(1):48-54.

Lin JJ, Lehmann LW, Bonora G, Sridharan R, Vashisht AA, Tran N, Plath K, Wohlschlegel JA, Carey M.
Mediator coordinates PIC assembly with recruitment of CHD1.
Genes Dev. 2011 Oct 15;25(20):2198-209.

Cooper, A.R., Patel, S., Senadheera, S., Plath, K., Kohn, D.B., and Hollis, R.P.
Highly efficient large-scale lentiviral vector concentration by tandem tangential flow filtration.
J Virol Methods. 2011 177:1-9.

Sridharan R, Plath K.
Small RNAs loom large during reprogramming.
Cell Stem Cell. 2011 Jun 3;8(6):599-601.

Plath, K. and Lowry, W.E.
Progress in understanding reprogramming to the induced pluripotent state.
Nature Reviews Genetics. 2011 12:253-265.

Papp, B. and Plath, K.
Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape.
Cell Research. 2011 21:486-501.

Ho R*, Chronis C*, Plath K.
Mechanistic insights into reprogramming to induced pluripotency.
J Cell Physiol. 2010 Oct 13. * Authors contributed equally to this work.

Mayshar Y, Ben-David U, Lavon N, Biancotti JC, Yakir B, Clark AT, Plath K, Lowry WE, Benvenisty N.
Identification and classification of chromosomal aberrations in human induced pluripotent stem cells.
Cell Stem Cell. 2010 Oct 8;7(4):521-31.

Mason MJ, Plath K, Zhou Q.
Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data.
Bioinformatics. 2010 Nov 15;26(22):2826-32.

Tchieu J*, Kuoy E*, Chin MH, Trinh H, Patterson M, Sherman SP, Aimiuwu O, Lindgren A, Hakimian S, Zack JA, Clark AT, Pyle AD, Lowry WE, Plath K.
Female human iPSCs retain an inactive X chromosome.
Cell Stem Cell. 2010 Sep 3;7(3):329-42. * Authors contributed equally to this work.

Chin MH, Pellegrini M, Plath K**, Lowry WE**.
Molecular analyses of human induced pluripotent stem cells and embryonic stem cells.
Cell Stem Cell. 2010 Aug 6;7(2):263-9. ** Corresponding authors.

Xu J, Watts JA, Pope SD, Gadue P, Kamps M, Plath K, Zaret KS, Smale ST.
Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells.
Genes Dev. 2009 Dec 15;23(24):2824-38.

Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B, Fussner E, Bazett-Jones DP, Plath K, Dalton S, Rathjen PD, Gilbert DM.
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis.
Genes Dev. 2009 Dec 15;23(24):2824-38.

Mason MJ, Fan G, Plath K, Zhou Q, Horvath S.
Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells.
BMC Genomics. 2009 Jul 20;10:327.

Gaspar-Maia A, Alajem A, Polesso F, Sridharan R, Mason MJ, Heidersbach A, Ramalho-Santos J, McManus MT, Plath K, Meshorer E, Ramalho-Santos M.
Chd1 regulates open chromatin and pluripotency of embryonic stem cells.
Nature. 2009 Aug 13;460(7257):863-8.

Chin MH, Mason MJ, Xie W, Volinia S, Singer M, Peterson C, Ambartsumyan G, Aimiuwu O, Richter L, Zhang J, Khvorostov I, Ott V, Grunstein M, Lavon N, Benvenisty N, Croce CM, Clark AT, Baxter T, Pyle AD, Teitell MA, Pelegrini M, Plath K**, Lowry WE**.
Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures.
Cell Stem Cell. 2009 Jul 2;5(1):111-23. ** Corresponding authors.

Daley GQ, Lensch MW, Jaenisch R, Meissner A, Plath K, Yamanaka S.
Broader implications of defining standards for the pluripotency of iPSCs.
Cell Stem Cell. 2009 Mar 6;4(3):200-1

Xie W, Song C, Young NL, Sperling AS, Xu F, Sridharan R, Conway AE, Garcia BA, Plath K, Clark AT, Grunstein M.
Histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells.
Mol Cell. 2009 Feb 27;33(4):417-27.

Karumbayaram S, Novitch BG, Patterson M, Umbach JA, Richter L, Lindgren A, Conway AE, Clark AT, Goldman SA, Plath K, Wiedau-Pazos M, Kornblum HI, Lowry WE.
Directed differentiation of human-induced pluripotent stem cells generates active motor neurons.
Stem Cells. 2009 Apr;27(4):806-11.

Saxe JP, Tomilin A, Schöler HR, Plath K, Huang J.
Post-translational regulation of Oct4 transcriptional activity.
PLoS ONE. 2009;4(2):e4467.

Hochedlinger K, Plath K.
Epigenetic reprogramming and induced pluripotency.
Development. 2009 Feb;136(4):509-23.

Kanellopoulou C, Muljo SA, Dimitrov SD, Chen X, Colin C, Plath K**, Livingston DM**.
X chromosome inactivation in the absence of Dicer.
Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1122-7. ** Corresponding authors.

Sridharan R*, Tchieu J*, Mason MJ*, Yachechko R, Kuoy E, Horvath S, Zhou Q and Plath K.
Role of the murine reprogramming factors in inducing pluripotency.
Cell 2009 Jan 23;136(2):364-77. * Authors contributed equally to this work.

Park TS, Galic Z, Conway AE, Lindgren A, van Handel BJ, Magnusson M, Richter L, Teitell MA, Mikkola HK, Lowry WE, Plath K, Clark AT.
Derivation of primordial germ cells from human embryonic and induced pluripotent stem cells is significantly improved by coculture with human fetal gonadal cells.
Stem Cells. 2009 Apr;27(4):783-95.

Lowry WE, Plath K.
The many ways to make an iPS cell.
Nat Biotechnol. 2008 Nov;26(11):1246-8.

Schenke-Layland K, Rhodes K, Angelis E, Butylkova Y, Heydarkhan-Hagvall S, Gekas C, Zhang R, Goldhaber J, Mikkola HK, Plath K and MacLellan WR.
Reprogrammed fibroblasts differentiate into cells of the cardiovascular and hematopoietic lineages.
Stem Cells 2008 Jun;26(6):1537-46.

Sridharan, R. and Plath, K.
Illuminating the black box of reprogramming.
Cell Stem Cell. 2008 2:295-297

Lowry WE**, Richter L*, Yachechko R*, Pyle AD, Tchieu J, Sridharan R, Clark AT, Plath K**.
Generation of human induced pluripotent stem cells from dermal fibroblasts.
Proc Natl Acad Sci USA. 2008 Feb 26;105(8):2883-8. * Both authors contributed equally to this work. ** Corresponding authors.

Nusinow DA, Sharp JA, Morris A, Salas S, Plath K, Panning B.
The histone domain of macroH2A1 contains several dispersed elements that are each sufficient to direct enrichment on the inactive X chromosome.
J Mol Biol. 2007 Aug 3;271(1):11-8.

Maherali N*, Sridharan R*, Xie W, Utikal J, Eminli S, Arnold K, Stadtfeld K, Yachechko R, Tchieu J, Jaenisch R, Plath K**, Hochedlinger K**.
Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution.
Cell Stem Cell 2007 June 7;1(1):55-70 * Authors contributed equally to this work. ** Corresponding authors

Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Waqschal A, Feil R, Schreiber SL, Lander ES.
A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
Cell 2006, Apr 21;125(2):315-26

Boyer LA*, Plath K*, Zeitlinger J, Brambrink T, Medeiros L, Lee TI, Levine SS, Wernig M, Tajonar A, Ray MK, Bell GW, Otte AP, Vidal M, Gifford DK, Young RA and Jaenisch R.
Polycomb complexes repress developmental regulators in murine embryonic stem cells.
Nature 2006, May 18;441(7091):349-53 * Authors contributed equally to this work.

Chu F, Nusinow DA, Chalkley RJ, Plath K, Panning B, Burlingame AL.
Mapping post-translational modifications of the histone variant MacroH2A1 using tandem mass spectrometry.
Mol Cell Proteomics 2006, Jan;5(1):194-203.

Beard C, Hochedlinger K, Plath K, Wutz A and Jaenisch R.
An efficient method to generate single-copy transgenic mice by site specific integrationin embryonic stem cells.
Genesis 2006, Jan;44(1):23-8.

de la Cruz CC, Fang J, Plath K, Worringer KA, Nusinow DA, Zhang Y and Panning B.
Developmental regulation of Suz12 localization.
Chromosoma 2005;114(3):183-92.

Plath K, Talbot D, Hamer KM, Otte AP, Yang TP, Jaenisch R and Panning B.
Developmentally regulated alterations in polycomb repressive complex 1 proteins on the inactive X chromosome.
J. Cell Biol. 2004;167(6):1025-35.

Plath K, Wilkinson BM, Stirling CJ and Rapoport TA.
Interactions between Sec-complex and perpro-a-factor during posttranslational protein transport into the ER.
Mol. Biol. Cell, 2004;15(1):1-10.

Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B and Zhang Y.
Role of histone H3 lysine 27 methylation in X inactivation.
Science 2003;300(1):131-135.

Plath K, Mlynarczyk-Evans SK, Nusinow DA and Panning B.
Xist RNA and the mechanism of X chromosome inactivation.
Annu. Rev. Genet. 2002;36(1):233-78.

Plath K, Rapoport TA.
Spontaneous release of cytosolic proteins from posttranslational substrates before their transport into the endoplasmic reticulum.
J. Cell Biol. 2000;151(1):167-178.

Menetret JF, Neuhof A, Morgan DG, Plath K, Radermacher M, Rapoport TA and Akey CW.
The structure of ribosome-channel complexes engaged in protein translocation.
Mol. Cell. 2000;6:1219-1232.

Plath K.
Protein transport into the endoplasmic reticulum.
Biospektrum. 2000;6:466-467.

Rapoport TA, Matlack KES, Plath K, Misselwitz B and Staeck O.
Posttranslational protein translocations across the membrane of the endoplasmic reticulum.
Biol. Chem 1999;380:1143-1150.

Matlack KES, Misselwitz B, Plath K and Rapoport TA.
BiP acts as a molecular ratchet during posttranslational transport of prepro-factor across the ER membrane.
Cell 1999;97:553-564.

Plath, K., Mothes, W., Wilkinson, B.M., Stirling, C.J., Rapoport, T.A.
Signal sequence recognition in posttranslational protein transport across the yeast ER membrane.
Cell 1998;94:795-807.

Matlack, K.E., Plath, K., Misselwitz, B., Rapoport, T.A.
Protein transport by purified yeast Sec complex and Kar2p without membranes.
Science 1997; 277:938-941.

Hanein D, Matlack KE, Jungnickel B, Plath K, Kalies KU, Miller KR, Rapoport TA and Akey CW.
Oligomeric rings of the Sec61p complex induced by ligands required for protein translocation.
Cell 1996;87:721-732.

Finke K*, Plath K*, Panzer S, Prehn S, Rapoport TA, Hartmann and Sommer T.
A second trimeric complex containing homologs of the Sec61p complex functions in protein transport across the ER membrane of S. cerevisiae.
EMBO J. 1996;15:1482-1494. * Authors contributed equally to this work.

Engel K, Schultz H, Martin F, Kotlyarov A, Plath K, Hahn M, Heinemann U and Gaestel M.
Constitutive activation of mitogen-activated protein kinase-activated protein kinase 2 by mutation of phosphorylation sites and an A-helix motif.
J. Biol. Chem. 1995;270:27213-21.

Plath K, Engel K, Schwedersky G and Gaestel M.
Characterization of the proline-rich region of mouse MAPKAP kinase 2: influence on catalytic properties and binding to the c-abl SH3 domain in vitro.
Biochem. Biophys. Res. Commun. 1994;203:1188-1194.

Engel K, Plath K and Gaestel M.
The MAP kinase-activated protein kinase 2 contains a proline-rich SH3-binding domain.
FEBS Lett. 1993;336:143-147.