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Quantitative Single-Cell Transcript Assessment of Biomarkers Supports Cellular Heterogeneity in the Bovine IVD.

Li K, Kapper D, Mondal S, Lufkin T, Kraus P.

Vet Sci. 2019 May 12;6(2). pii: E42. doi: 10.3390/vetsci6020042.


Potential biomarkers of the mature intervertebral disc identified at the single cell level.

Li K, Kapper D, Youngs B, Kocsis V, Mondal S, Kraus P, Lufkin T.

J Anat. 2019 Jan;234(1):16-32. doi: 10.1111/joa.12904. Epub 2018 Nov 18.


Klhl14 Antisense RNA is a Target of Key Skeletogenic Transcription Factors in the Developing Intervertebral Disc.

Kraus P, Sivakamasundari V, Olsen V, Villeneuve V, Hinds A, Lufkin T.

Spine (Phila Pa 1976). 2019 Mar 1;44(5):E260-E268. doi: 10.1097/BRS.0000000000002827.


Isolation and 3D expansion of multipotent Sox9+ mouse lung progenitors.

Nichane M, Javed A, Sivakamasundari V, Ganesan M, Ang LT, Kraus P, Lufkin T, Loh KM, Lim B.

Nat Methods. 2017 Dec;14(12):1205-1212. doi: 10.1038/nmeth.4498. Epub 2017 Nov 6.


Ontogenic Identification and Analysis of Mesenchymal Stromal Cell Populations during Mouse Limb and Long Bone Development.

Nusspaumer G, Jaiswal S, Barbero A, Reinhardt R, Ishay Ronen D, Haumer A, Lufkin T, Martin I, Zeller R.

Stem Cell Reports. 2017 Oct 10;9(4):1124-1138. doi: 10.1016/j.stemcr.2017.08.007. Epub 2017 Sep 14.


A quantitative and qualitative RNA expression profiling assay for cell culture with single cell resolution.

Kraus P, Yerden R, Sipes D, Sur S, Lufkin T.

Cytotechnology. 2018 Feb;70(1):185-192. doi: 10.1007/s10616-017-0132-1. Epub 2017 Aug 10.


An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos.

Lee WJ, Chatterjee S, Yap SP, Lim SL, Xing X, Kraus P, Sun W, Hu X, Sivakamasundari V, Chan HY, Kolatkar PR, Prabhakar S, Lufkin T.

Biomed Res Int. 2017;2017:8932583. doi: 10.1155/2017/8932583. Epub 2017 May 28.


Implications for a Stem Cell Regenerative Medicine Based Approach to Human Intervertebral Disk Degeneration.

Kraus P, Lufkin T.

Front Cell Dev Biol. 2017 Mar 7;5:17. doi: 10.3389/fcell.2017.00017. eCollection 2017. Review.


RNA in situ hybridization characterization of non-enzymatic derived bovine intervertebral disc cell lineages suggests progenitor cell potential.

Kraus P, Yerden R, Kocsis V, Lufkin T.

Acta Histochem. 2017 Mar;119(2):150-160. doi: 10.1016/j.acthis.2016.12.004. Epub 2017 Jan 4.


A developmental transcriptomic analysis of Pax1 and Pax9 in embryonic intervertebral disc development.

Sivakamasundari V, Kraus P, Sun W, Hu X, Lim SL, Prabhakar S, Lufkin T.

Biol Open. 2017 Feb 15;6(2):187-199. doi: 10.1242/bio.023218.


Tetratricopeptide repeat domain 9A modulates anxiety-like behavior in female mice.

Lim LW, Shrestha S, Or YZ, Tan SZ, Chung HH, Sun Y, Lim CL, Khairuddin S, Lufkin T, Lin VC.

Sci Rep. 2016 Nov 21;6:37568. doi: 10.1038/srep37568.


Bovine annulus fibrosus cell lines isolated from intervertebral discs.

Kraus P, Lufkin T.

Genom Data. 2016 Oct 3;10:83-84. eCollection 2016 Dec.


Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro.

Chatterjee S, Kraus P, Sivakamasundari V, Yap SP, Kumar V, Prabhakar S, Lufkin T.

Genom Data. 2016 Sep 8;10:51-3. doi: 10.1016/j.gdata.2016.09.002. eCollection 2016 Dec.


Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters.

Kumar V, Rayan NA, Muratani M, Lim S, Elanggovan B, Xin L, Lu T, Makhija H, Poschmann J, Lufkin T, Ng HH, Prabhakar S.

Genome Res. 2016 May;26(5):612-23. doi: 10.1101/gr.201038.115. Epub 2016 Mar 8.


Gene expression profiles of Bapx1 expressing FACS sorted cells from wildtype and Bapx1-EGFP null mouse embryos.

Chatterjee S, Sivakamasundari V, Kraus P, Yap SP, Kumar V, Prabhakar S, Lufkin T.

Genom Data. 2015 Sep;5:103-105.


Plate in situ hybridization (PISH) as a time and cost effective RNA expression assay to study phenotypic heterogeneity in a population of cultured murine cells at single cell resolution.

Kraus P, Kocsis V, Williams C, Youngs B, Lufkin T.

Biotechnol Lett. 2015 Aug;37(8):1573-7. doi: 10.1007/s10529-015-1833-1. Epub 2015 Apr 7.


Tetratricopeptide repeat domain 9A negatively regulates estrogen receptor alpha activity.

Shrestha S, Sun Y, Lufkin T, Kraus P, Or Y, Garcia YA, Guy N, Ramos P, Cox MB, Tay F, Lin VC.

Int J Biol Sci. 2015 Feb 27;11(4):434-47. doi: 10.7150/ijbs.9311. eCollection 2015.


In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column.

Chatterjee S, Sivakamasundari V, Yap SP, Kraus P, Kumar V, Xing X, Lim SL, Sng J, Prabhakar S, Lufkin T.

BMC Genomics. 2014 Dec 5;15:1072. doi: 10.1186/1471-2164-15-1072.


BAC transgenic zebrafish for transcriptional promoter and enhancer studies.

Kraus P, Winata CL, Lufkin T.

Methods Mol Biol. 2015;1227:245-58. doi: 10.1007/978-1-4939-1652-8_12.


Pleiotropic functions for transcription factor zscan10.

Kraus P, V S, Yu HB, Xing X, Lim SL, Adler T, Pimentel JA, Becker L, Bohla A, Garrett L, Hans W, Hölter SM, Janas E, Moreth K, Prehn C, Puk O, Rathkolb B, Rozman J, Adamski J, Bekeredjian R, Busch DH, Graw J, Klingenspor M, Klopstock T, Neff F, Ollert M, Stoeger T, Yildrim AÖ, Eickelberg O, Wolf E, Wurst W, Fuchs H, Gailus-Durner V, de Angelis MH, Lufkin T, Stanton LW.

PLoS One. 2014 Aug 11;9(8):e104568. doi: 10.1371/journal.pone.0104568. eCollection 2014. Erratum in: PLoS One. 2015;10(3):e0118766.


Generating mouse lines for lineage tracing and knockout studies.

Kraus P, Sivakamasundari V, Xing X, Lufkin T.

Methods Mol Biol. 2014;1194:37-62. doi: 10.1007/978-1-4939-1215-5_3.


Klf2 is an essential factor that sustains ground state pluripotency.

Yeo JC, Jiang J, Tan ZY, Yim GR, Ng JH, Göke J, Kraus P, Liang H, Gonzales KA, Chong HC, Tan CP, Lim YS, Tan NS, Lufkin T, Ng HH.

Cell Stem Cell. 2014 Jun 5;14(6):864-72. doi: 10.1016/j.stem.2014.04.015.


A conditional mouse line for lineage tracing of Sox9 loss-of-function cells using enhanced green fluorescent protein.

Chatterjee S, Kraus P, Sivakamasundari V, Xing X, Yap SP, Jie S, Lufkin T.

Biotechnol Lett. 2013 Dec;35(12):1991-6. doi: 10.1007/s10529-013-1303-6. Epub 2013 Aug 2.


Uniform, optimal signal processing of mapped deep-sequencing data.

Kumar V, Muratani M, Rayan NA, Kraus P, Lufkin T, Ng HH, Prabhakar S.

Nat Biotechnol. 2013 Jul;31(7):615-22. doi: 10.1038/nbt.2596. Epub 2013 Jun 16.


Regulatory genomics: Insights from the zebrafish.

Chatterjee S, Lufkin T.

Curr Top Genet. 2012;5:1-10.


Making sense of Dlx1 antisense RNA.

Kraus P, Sivakamasundari V, Lim SL, Xing X, Lipovich L, Lufkin T.

Dev Biol. 2013 Apr 15;376(2):224-35. doi: 10.1016/j.ydbio.2013.01.035. Epub 2013 Feb 8.


Pax1(EGFP): new wildtype and mutant EGFP mouse lines for molecular and fate mapping studies.

Sivakamasundari V, Kraus P, Jie S, Lufkin T.

Genesis. 2013 Jun;51(6):420-9. doi: 10.1002/dvg.22379. Epub 2013 Feb 25.


In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures.

Ng JH, Kumar V, Muratani M, Kraus P, Yeo JC, Yaw LP, Xue K, Lufkin T, Prabhakar S, Ng HH.

Dev Cell. 2013 Feb 11;24(3):324-33. doi: 10.1016/j.devcel.2012.12.011. Epub 2013 Jan 24.


Filling the silent void: genetic therapies for hearing impairment.

Sng J, Lufkin T.

Genet Res Int. 2012;2012:748698. doi: 10.1155/2012/748698. Epub 2012 Dec 4.


Bridging the Gap: Understanding Embryonic Intervertebral Disc Development.

Sivakamasundari V, Lufkin T.

Cell Dev Biol. 2012 May;1(2). pii: 103.


Emerging stem cell therapies: treatment, safety, and biology.

Sng J, Lufkin T.

Stem Cells Int. 2012;2012:521343. doi: 10.1155/2012/521343. Epub 2012 Aug 2.


Embryonic stem cells: protein interaction networks.

Ng PM, Lufkin T.

Biomol Concepts. 2011 Apr;2(1-2):13-25. Epub 2012 May 3.


Mouse strain specific gene expression differences for illumina microarray expression profiling in embryos.

Kraus P, Xing X, Lim SL, Fun ME, Sivakamasundari V, Yap SP, Lee H, Karuturi RK, Lufkin T.

BMC Res Notes. 2012 May 14;5:232. doi: 10.1186/1756-0500-5-232.


Comparison of IRES and F2A-based locus-specific multicistronic expression in stable mouse lines.

Chan HY, V S, Xing X, Kraus P, Yap SP, Ng P, Lim SL, Lufkin T.

PLoS One. 2011;6(12):e28885. doi: 10.1371/journal.pone.0028885. Epub 2011 Dec 21.


Making no bones about it: Transcription factors in vertebrate skeletogenesis and disease.

Chatterjee S, Sivakamasundari V, Lee WJ, Chan HY, Lufkin T.

Trends Dev Biol. 2012;6:45-52.


Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes.

Chatterjee S, Bourque G, Lufkin T.

BMC Dev Biol. 2011 Oct 20;11:63. doi: 10.1186/1471-213X-11-63.


Nuclear accumulation of an uncapped RNA produced by Drosha cleavage of a transcript encoding miR-10b and HOXD4.

Phua SL, Sivakamasundari V, Shao Y, Cai X, Zhang LF, Lufkin T, Featherstone M.

PLoS One. 2011;6(10):e25689. doi: 10.1371/journal.pone.0025689. Epub 2011 Oct 3.


New Bapx1(Cre-EGFP) mouse lines for lineage tracing and conditional knockout studies.

Sivakamasundari V, Chan HY, Yap SP, Xing X, Kraus P, Lufkin T.

Genesis. 2012 Apr;50(4):375-83. doi: 10.1002/dvg.20802. Epub 2012 Jan 6.


Alternative splicing in self-renewal of embryonic stem cells.

Cheong CY, Lufkin T.

Stem Cells Int. 2011;2011:560261. doi: 10.4061/2011/560261. Epub 2011 Jun 9.


Endogenous tagging of the murine transcription factor Sox5 with hemaglutinin for functional studies.

Lee WJ, Kraus P, Lufkin T.

Transgenic Res. 2012 Apr;21(2):293-301. doi: 10.1007/s11248-011-9531-9. Epub 2011 Jul 6.


Fishing for function: zebrafish BAC transgenics for functional genomics.

Chatterjee S, Lufkin T.

Mol Biosyst. 2011 Aug;7(8):2345-51. doi: 10.1039/c1mb05116d. Epub 2011 Jun 7. Review.


Molecular conservation of estrogen-response associated with cell cycle regulation, hormonal carcinogenesis and cancer in zebrafish and human cancer cell lines.

Lam SH, Lee SG, Lin CY, Thomsen JS, Fu PY, Murthy KR, Li H, Govindarajan KR, Nick LC, Bourque G, Gong Z, Lufkin T, Liu ET, Mathavan S.

BMC Med Genomics. 2011 May 16;4:41. doi: 10.1186/1755-8794-4-41.


In silico tandem affinity purification refines an Oct4 interaction list.

Cheong CY, Lon Ng PM, Ponnampalam R, Tsai HH, Bourque G, Lufkin T.

Stem Cell Res Ther. 2011 May 13;2(3):26. doi: 10.1186/scrt67.


Generation of mice with a novel conditional null allele of the Sox9 gene.

Yap SP, Xing X, Kraus P, Sivakamasundari V, Chan HY, Lufkin T.

Biotechnol Lett. 2011 Aug;33(8):1551-8. doi: 10.1007/s10529-011-0608-6. Epub 2011 Apr 12.


Dlx6 regulates molecular properties of the striatum and central nucleus of the amygdala.

Wang B, Lufkin T, Rubenstein JL.

J Comp Neurol. 2011 Aug 15;519(12):2320-34. doi: 10.1002/cne.22618.


Determinants of generic drug substitution in Switzerland.

Decollogny A, Eggli Y, Halfon P, Lufkin TM.

BMC Health Serv Res. 2011 Jan 26;11:17. doi: 10.1186/1472-6963-11-17.


The sound of silence: mouse models for hearing loss.

Chatterjee S, Lufkin T.

Genet Res Int. 2011;2011:416450. doi: 10.4061/2011/416450. Epub 2011 Oct 9.


A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity.

Chia NY, Chan YS, Feng B, Lu X, Orlov YL, Moreau D, Kumar P, Yang L, Jiang J, Lau MS, Huss M, Soh BS, Kraus P, Li P, Lufkin T, Lim B, Clarke ND, Bard F, Ng HH.

Nature. 2010 Nov 11;468(7321):316-20. doi: 10.1038/nature09531. Epub 2010 Oct 17.


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