2023
- Kirk, J. S., Wang, J., Tracz, A., Long, M., Rosario, S. R., Ji, Y., Kumar, R., Liu, X., Singh, P. K., Puzanov, I., Chatta, G., Cheng, Q., Huang, J., Wrana, J. L., Lovell, J., Yu, H., Liu, S., Shen, M. M., Liu, T., and Tang, D. G. (2023). Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells. bioRxiv : the preprint server for biology, 2023.03.03.530998. link
- Ge, Y., Chen, X., Nan, N., Bard, J., Wu, F., Yergeau, D., Liu, T., Wang, J., and Mu, X. (2023) Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation. Nucleic Acids Res. 51 (5), 2151-2176
2022
- Wang, J., Morgan, W., Saini, A., Liu, T., Lough, J., and Han, L. (2022) Single-cell transcriptomic profiling reveals specific maturation signatures in human cardiomyocytes derived from LMNB2-inactivated induced pluripotent stem cells. Front Cell Dev Biol. Nov 28;10:895162. doi: 10.3389/fcell.2022.895162. eCollection 2022.
- Hagiwara, M., Fushimi, A., Bhattacharya, A., Yamashita, N., Morimoto, Y., Oya, M., Withers, HG., Hu, Q., Liu, T., Liu, S., Wong. KK., Long. MD., and Kufe. D. (2022) MUC1-C integrates type II interferon and chromatin remodeling pathways in immunosuppression of prostate cancer. Oncoimmunology.11(1):2029298.
- Bhattacharya, A., Fushimi, A., Yamashita, N., Hagiwara, M., Morimoto, Y., Rajabi, H., Long, M., Abdulla, M., Ahmad, R., Street, K., Liu, S., Liu, T., and Kufe, D. (2022) MUC1-C Dictates JUN and BAF-mediated Chromatin Remodeling at Enhancer Signatures in Cancer Stem Cells. Mol Cancer Res. link
2021
- Zhang, H., Song, L., Wang, X., Cheng, H., Wang, C., Meyer, C., Liu, T., Tang M., Aluru, S., Yue, F., Liu, XS., and Li, H. (2021) Fast Alignment and Preprocessing of Chromatin Profiles with Chromap. Nat Commu. 12(1):6566.
- Wu, F., Bard, J.E., Kann, J., Yergeau, D., Sapkota, D., Ge, Y., Hu, Z., Wang, J., Liu, T., and Mu, X. (2021) Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas. Nat Commun. 12(1):1465.
- Zhou, Y., Bastian, I.N., Long, M.D., Dow, M., Li, W.,Liu, T., Ngu, R.K., Antonucci, L., Huang, J.Y., Phung, Q.T., Zhao, X.H., Banerjee, S., Lin, X.J., Wang, H., Dang, B., Choi, S., Karin, D., Su, H., Ellisman, M.H., Jamieson, C., Bosenberg, M., Cheng, Z., Haybaeck, J., Kenner, L., Fisch, K.M., Bourgon, R., Hernandez, G., Lill, J.R., Liu, S., Carter, H., Mellman, I., Karin, M., and Shalapour, S. (2021) Activation of NF-κB and p300/CBP potentiates cancer chemoimmunotherapy through induction of MHC-I antigen presentation. Proc Natl Acad Sci U S A. 118(8).
- Amobi-McCloud, A., Muthuswamy, R., Battaglia, S., Yu, H., Liu, T., Wang, J., Putluri, V., Singh, P., Qian, F., Huang, R.Y., Putluri, N., Takemasa, T., Lugade, A., Liu, S., and Odunsi, K. (2021) IDO1 expression in ovarian cancer induces PD-1 in T cells via aryl hydrocarbon receptor activation. Front Immunol. 12:678999
2020
- Wang, CF., Sun, DQ., Huang, X., Wan, CX., Li, ZY., Meyer, C., Liu, T., and Liu, XS. Integrative Analyses of Single-cell Transcriptome and Regulome using MAESTRO. Under revision at Genome Biology
- Humphrey, K.M., Zhu, L., Hickman, M.A., Hasan, S., Maria, H.,Liu, T., and Rusche, L.N. Evolution of Distinct Responses to Low NAD+ Stress by Rewiring the Sir2 Deacetylase Network in Yeasts. (2020) Genetics
2019
- Chen, H.M., Sackton, T., Wang, J., Mutlu B., Levine, E., Liu, T. and Mango, S.E. A heterochromatic histone methyltransferase lowers nucleosomeoccupancy at euchromatic promoters. Under peer-review at Development.
- Tarbell, E. and Liu, T. (2019) HMMRATAC, The Hidden Markov ModeleR for ATAC-seq. Nucleic Acid Research 47(16), e91}
- O’Brown, Z.K., Boulias, K., Wang, J., Wang, S.Y., O’Brown, N.M., Hao, Z., Shibuya, H., Fady, P.-E., Shi, Y., He, C., Megason, S.G., Liu, T., and Greer, E.L. (2019). Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA. BMC Genomics 20(1), 445
- Wang, Z.J., Zhong, P., Ma, K., Seo, J.S., Yang, F., Hu, Z., Zhang, F., Lin, L., Wang, J., Liu, T., Mata, E., Greengard, P., and Yan, Z. (2019). Amelioration of autism-like social deficits by targeting histone methyltransferases EHMT1/2 in Shank3-deficient mice. Mol Psychiatry doi:10.1038/s41380-019-0351-21. Daivs, RB., Likhite, N., Jackson, CA., Liu, T., Yu, MC. (2019) Robust repression of tRNA gene transcription during stress requires protein arginine methylation. Life Sci Alliance. 3;2(3). pii: e201800261.
Prior to 2019
- Zhang, P., He, D., Xu, Y., Hou, J., Pan, B.F., Wang, Y., Liu, T., Davis, C.M., Ehli, E.A., Tan, L., Zhou, F., Hu, J., Yu, Y., Chen, X., Nguyen, T.M., Rosen, J.M., Hawke, D.H., Ji, Z., Chen, Y. (2017). Genome-wide identification and differential analysis of translational initiation. Nature Communications 8(1), 1749.
- Zhu, L., Jiang, K., Webber, K., Wong, L., Liu, T., Chen, Y., Jarvis, J. (2017). Chromatin landscapes and genetic risk for juvenile idiopathic arthritis. Arthritis Research \& Therapy 19(1), 57. (first author Dr. Zhu is Liu’s postdoc)
- Mei, S., Qin, Q., Wu, Q., Sun, H., Zheng, R., Zang, C., Zhu, M., Wu, J., Shi, X., Taing, L., Liu, T., Brown, M., Meyer, C.A., Liu, X.S. (2017). Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Research 4;45(D1):D658-D662.
- Hui-Yuen, J.S., Zhu, L., Wong, L.P., Jiang, K., Chen, Y., Liu, T., Jarvis, J.N. (2016). Chromatin landscapes and genetic risk in systemic lupus. Arthritis Research \& Therapy 18:281. (co-first author Dr. Zhu is Liu’s postdoc)
- Qin, Q., Mei, S., Wu, Q., Sun, H., Li, L., Taing, L., Chen, S., Li, F., Liu, T., Zang, C., Xu, H., Chen, Y., Meyer, C.A., Zhang, Y., Brown, M., Long, H.W., Liu, X.S. (2016). ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. BMC bioinformatics 17, 404.
- Kapoor, S., Zhu, L., Froyd, C., Liu, T., and Rusche, L.N. (2015). Regional centromeres in the yeast Candida lusitaniae lack pericentromeric heterochromatin. Proc Natl Acad Sci USA 112, 12139–12144. (co-first author Dr. Zhu is Liu’s postdoc)
- Jiang, K., Zhu, L., Buck, M.J., Chen, Y., Carrier, B., Liu, T., and Jarvis, J.N. (2015). Disease-Associated Single-Nucleotide Polymorphisms From Noncoding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells. Arthritis Rheumatol 67, 1966–1977. (Liu is a co-corresponding author, co-first author Dr. Zhu is Liu’s postdoc)
- Hsu, H.-T., Chen, H.-M., Yang, Z., Wang, J., Lee, N.K., Burger, A., Zaret, K., Liu, T., Levine, E., and Mango, S.E. (2015). Recruitment of RNA polymerase II by the pioneer transcription factor PHA-4. Science 348, 1372–1376.
- Ho, J.W.K., Jung, Y.L., Liu, T., Alver, B.H., Lee, S., Ikegami, K., Sohn, K.-A., Minoda, A., Tolstorukov, M.Y., Appert, A., et al. (2014). Comparative analysis of metazoan chromatin organization. Nature 512, 449–452. (co-first author)
- Meijer, D.H., Sun, Y., Liu, T., Kane, M.F., Alberta, J.A., Rowitch, D.H., Stiles, C.D., and Mehta, S. (2014). An amino terminal phosphorylation motif regulates intranuclear compartmentalization of Olig2 in neural progenitor cells. J. Neurosci. 34, 8507–8518.
- Liu, T. (2014). Use Model-Based Analysis of ChIP-Seq (MACS) to Analyze Short Reads Generated by Sequencing Protein-DNA Interactions in Embryonic Stem Cells. Methods Mol. Biol. 1150, 81–95.
- Catic, A., Suh, C.Y., Hill, C.T., Daheron, L., Henkel, T., Orford, K.W., Dombkowski, D.M., Liu, T., Liu, X.S., and Scadden, D.T. (2013). Genome-wide map of nuclear protein degradation shows NCoR1 turnover as a key to mitochondrial gene regulation. Cell 155, 1380–1395.
- Bailey, T., Krajewski, P., Ladunga, I., Lefebvre, C., Li, Q., Liu, T., Madrigal, P., Taslim, C., and Zhang, J. (2013). Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9, e1003326. (co-first author)
- Sun, H., Qin, B., Liu, T., Wang, Q., Liu, J., Wang, J., Lin, X., Yang, Y., Taing, L., Rao, P.K., et al. (2013). CistromeFinder for ChIP-seq and DNase-seq data reuse. Bioinformatics 29, 1352–1354.
- Shin, H., Liu, T., Duan, X., Zhang, Y., and Liu, X.S. (2013). Computational methodology for ChIP-seq analysis. Quantitative Biology 1–17.
- Feng, J., Liu, T., Qin, B., Zhang, Y., and Liu, X.S. (2012). Identifying ChIP-seq enrichment using MACS. Nat Protoc 7, 1728–1740. (co-first author)
- Landt, S.G., Marinov, G.K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B.E., Bickel, P., Brown, J.B., Cayting, P., et al. (2012). ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. 22, 1813–1831.
- Xu, K., Wu, Z.J., Groner, A.C., He, H.H., Cai, C., Lis, R.T., Wu, X., Stack, E.C., Loda, M., Liu, T., et al. (2012). EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science 338, 1465–1469
- Chen, Y., Negre, N., Li, Q., Mieczkowska, J.O., Slattery, M., Liu, T., Zhang, Y., Kim, T.-K., He, H.H., Zieba, J., et al. (2012). Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Meth 9, 609–614.
- Qin, B., Zhou, M., Ge, Y., Taing, L., Liu, T., Wang, Q., Wang, S., Chen, J., Shen, L., Duan, X., et al. (2012). CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. Bioinformatics 28, 1411–1412.
- Tang, Q., Chen, Y., Meyer, C., Geistlinger, T., Lupien, M., Wang, Q., Liu, T., Zhang, Y., Brown, M., and Liu, X.S. (2011). A comprehensive view of nuclear receptor cancer cistromes. Cancer Res. 71, 6940–6947.
- Liu, T., Ortiz, J.A., Taing, L., Meyer, C.A., Lee, B., Zhang, Y., Shin, H., Wong, S.S., Ma, J., Lei, Y., et al. (2011). Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol 12, R83.
- Feng, J., Liu, T., and Zhang, Y. (2011). Using MACS to Identify Peaks from ChIP-Seq Data. Curr Protoc Bioinformatics Chapter 2, Unit2.14.
- Wang, X., Laurie, J.D., Liu, T., Wentz, J., and Liu, X.S. (2011). Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites. Genomics 97, 235–243.
- Feng, D., Liu, T., Sun, Z., Bugge, A., Mullican, S.E., Alenghat, T., Liu, X.S., and Lazar, M.A. (2011). A Circadian Rhythm Orchestrated by Histone Deacetylase 3 Controls Hepatic Lipid Metabolism. Science 331, 1315–1319. (co-first author)
- Chen, Y., Meyer, C.A., Liu, T., Li, W., Liu, J.S., and Liu, X.S. (2011). MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. Genome Biol 12, R11.
- Liu, T., Rechtsteiner, A., Egelhofer, T.A., Vielle, A., Latorre, I., Cheung, M.-S., Ercan, S., Ikegami, K., Jensen, M., Kolasinska-Zwierz, P., et al. (2011). Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res 21, 227–236.
- Gerstein, M., Lu, Z.J., Nostrand, E.L.V., Cheng, C., Arshinoff, B.I., Liu, T., and etc. (the worm modENCODE consortium). (2010). Integrative Analysis of Functional Elements in the Caenorhabditis elegans Genome by the modENCODE Project. Science 330(6012): 1775-1787. (co-first author)
- Shin, H., Liu, T., Manrai, A.K., Liu, X.S. (2009). CEAS: cis-regulatory element annotation system. Bioinformatics 25 (19):2605-6
- Kolasinska-Zwierz, P., Down, T., Latorre, I., Liu, T., Liu, X.S., Ahringer, J. (2009). Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41 (3):376-81
- Deng, L., Zhang, Y., Kang, J., Liu, T., Zhao, H., Gao, Y., Li, C., Pan, H., Tang, X., Wang, D., Niu, T., Yang, H., Zeng, C. (2008). An unusual haplotype structure on human chromosome 8p23 derived from the inversion polymorphism. Hum Mutat 29(10):1209-16.
- He, S., Liu, C., Skogerbø, G., Zhao, H., Wang, J., Liu, T., Bai, B., Zhao, Y., Chen, R. (2008). NONCODE v2.0: decoding the non-coding. Nucleic Acids Res 36(Database issue):D170-2.
- Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nussbaum, C., Myers, R.M., Brown, M., Li, W., Liu, X.S.. (2008). Model-based analysis of ChiP-Seq (MACS). Genome Biology 9:R137. (co-first author)
- He, S., Su, H., Liu, C., Skogerbø, G., He, H., He, D., Zhu, X., Liu, T., Zhao, Y., Chen, R. (2008). MicroRNA-encoding long non-coding RNAs. BMC Genomics 9:236.
- He, H., Wang, J., Liu, T., Liu, X.S., Li, T., Wang, Y., Qian, Z., Zheng, H., Zhu, X., Wu, T., Shi, B., Deng, W., Zhou, W., Skogerbø, G., Chen, R. (2007). Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray. Genome Res 17(10):1471-7. (co-first author)
- The DNA sequence, annotation and analysis of human chromosome 3. Nature 440(7088):1194-8. (list author)
- He, H., Cai, L., Skogerbø, G., Deng, W., Liu, T., Zhu, X., Wang, Y., Jia, D., Zhang, Z., Tao, Y., Zeng, H., Aftab, M.N., Cui, Y., Liu, G., Chen, R. (2006). Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray. Nucleic Acids Res 34(10):2976-83.