Laboratory for Genome Information Analysis

Main Publications List

  1. An atlas of human long non-coding RNAs with accurate 5’ ends.
    Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs AM, Noma S, Djebali S, Alam T, Medvedeva YA, Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez M, Hasegawa A, Tang D, Lassmann T, Heutink P, Babina M, Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO, de Hoon MJ, Arner E, Hayashizaki Y, Carninci P, Forrest AR.
    Nature., 543(7644):199-204. (2017)
  2. The Human Cell Atlas: Technical approaches and challenges.
    Hon CC, Shin JW, Carninci P, Stubbington MJT.
    Brief Funct Genomics., [Epub ahead of print] (2017)
  3. The FANTOM5 integrated expression atlas of miRNAs and their promoters.
    de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, Åström G, Babina M, Bertin N, Burroughs AM, Carlisle AJ, Daub CO, Detmar M, Deviatiiarov R, Fort A, Gebhard C, Goldowitz D, Guhl S, Ha TJ, Harshbarger J, Hasegawa A, Hashimoto K, Herlyn M, Heutink P, Hitchens KJ, Hon CC, Huang E, Ishizu Y, Kai C, Kasukawa T, Klinken P, Lassmann T, Lecellier CH, Lee W, Lizio M, Makeev V, Mathelier A, Medvedeva YA, Mejhert N, Mungall CJ, Noma S, Ohshima M, Okada-Hatakeyama M, Persson H, Rizzu P, Roudnicky F, Sætrom P, Sato H, Severin J, Shin JW, Swoboda RK, Tarui H, Toyoda H, Vitting-Seerup K, Winteringham L, Yamaguchi Y, Yasuzawa K, Yoneda M, Yumoto N, Zabierowski S, Zhang PG, Wells CA, Summers KM, Kawaji H, Sandelin A, Rehli M,; FANTOM Consortium, Hayashizaki Y, Carninci P, Forrest ARR, de Hoon MJL.
    Nat Biotechnol., 35(9):872-878. (2017)
  4. Exonuclease-mediated degradation of nascent RNA silences genes linked to severe malaria.
    Zhang Q, Siegel TN, Martins RM, Wang F, Cao J, Gao Q, Cheng X, Jiang L, Hon CC, Scheidig-Benatar C, Sakamoto H, Turner L, Jensen AT, Claes A, Guizetti J, Malmquist NA, Scherf A.
    Nature., 2014 Sep 18;513(7518):431-5. doi: 10.1038/nature13468. Epub 2014 Jun 29.: (2014)
  5. Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in Leishmania major and Trypanosoma brucei.
    Reynolds D, Cliffe L, Förstner KU, Hon CC, Siegel TN, Sabatini R.
    Nucleic Acids Res., 42(15):9717-29. (2014)
  6. Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica.
    Hon CC, Weber C, Sismeiro O, Proux C, Koutero M, Deloger M, Das S, Agrahari M, Dillies MA, Jagla B, Coppee JY, Bhattacharya A, Guillen N.
    Nucleic Acids Res., 41(3):1936-52. (2013)
  7. Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages.
    Vasquez JJ, Hon CC, Vanselow JT, Schlosser A, Siegel TN.
    Nucleic Acids Res., 42(6):3623-37. (2014)
  8. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.
    Janbon G, Ormerod KL, Paulet D, Byrnes EJ rd, Yadav V, Chatterjee G, Mullapudi N, Hon CC, Billmyre RB, Brunel F, Bahn YS, Chen W, Chen Y, Chow EW, Coppée JY, Floyd-Averette A, Gaillardin C, Gerik KJ, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh YP, Ianiri G, Jones S, Kodira CD, Kozubowski L, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wollschlaeger C, Wood IA, Zeng Q, Neuvéglise C, Newlon CS, Perfect JR, Lodge JK, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA, Cuomo CA, Dietrich FS.
    PLoS Genet., 2014 Apr 17;10(4):e1004261. doi: 10.1371/journal.pgen.1004261. eCollection 2014 Apr.: (2014)
  9. Identification of the virulence landscape essential for Entamoeba histolytica invasion of the human colon.
    Thibeaux R, Weber C, Hon CC, Dillies MA, Avé P, Coppée JY, Labruyère E, Guillén N.
    PLoS Pathog., 9(12):e1003824. (2013)
  10. Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum.
    Siegel TN, Hon CC, Zhang Q, Lopez-Rubio JJ, Scheidig-Benatar C, Martins RM, Sismeiro O, Coppée JY, Scherf A.
    BMC Genomics., 15:150 (2014)

 

 

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