We are a newly started computational biology lab at the Division of Biomedical Science and Biochemistry (BSB), Research School of Biological Science, ANU. My group is devoted to exploring diverse modes of gene regulatory networks, both post-transcriptional gene regulation by small RNAs, structural RNAs, and RNA binding proteins, and transcriptional regulation by transcription factors. In early 1960, Jacob and Monod proposed the first gene regulatory model that genes can be regulated at both transcriptional and post-transcriptional levels (see figure). These regulatory elements have shown to regulate a majority of animal transcripts and exert profound control of development and physiology. Thus, their dysfunction has enormous implications in diverse human disease mechanisms. We are particular interested in understanding how these regulatory elements are made, how they evolve, how they regulate their target gene expression, and what biological impact they have on animal development and disease. We work on organisms ranging from insects to vertebrates.
As a computational lab, our research projects are typically multi-disciplinary. We employ a variety of computational approaches, integrating computational machine learning and statistical method development, high-throughput genome-wide data analysis, and molecular genetics/biochemistry experimental validations in collaboration.
As a new lab, I am currently recruiting students. There are various possible projects for students, ranging from undergraduate term projects, summer scholar projects, to Honours and PhD projects (See “Projects” tab below). As a multi-disciplinary research group, I am interested in students with various backgrounds in science, such as bioinformatics, computer science, statistics, molecular biology, biochemistry, and other disciplines in science. If you would like to join, either to develop skills in computational biology or to tackle the proposed research questions, please email me at Jiayu.Wen@anu.edu.au.
Open to students
Discovery of genome-wide RNA-switches (Undergraduate, Honours, Graduate, Higher degree by research)
Explorations of evolution and adaptive regulation by testis-specific hairpin RNA-target interaction networks across insect genomes (Undergraduate, Honours, Graduate, Higher degree by research)
Gene regulation by cell-type specific TFs controlling neural cell fate specification. (Undergraduate, Honours, Graduate, Higher degree by research)
Roles of RNA-binding protein Elav family in regulating alternative polyadenylation in the central nervous system (Undergraduate, Honours, Graduate, Higher degree by research)
Jee D., Yang J., Park S., Farmer D., Wen J., Chou T., Chow A., Mcmanus M., Kharas M.,and Lai EC. Dual strategies for Argonaute2 mediated biogenesis of erythroid miRNAs underlie conserved requirements for slicing in mammals. Molecular Cell, (2018). 69(2) 265-278.e6. IF 15.05.
Sanfilippo P., Wen J., and Lai EC. Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species. Genome Biology (2017). 18 (1), 229. IF 11.9.
Lin CJ, Wen J, Bejarano F, Hu F, Bortolamiol-Becet D1, Kan L, Sanfilippo P, Kondo S, Lai EC. Characterization of a TUTase/RNase complex required for Drosophila gametogenesis. RNA (2017). 23(3):284-296. IF 4.94
Garaulet DL, SunK., Li W.,Wen J.,Panzarino A.O Ńeil J. Hiesinger R.,Young M.,and Lai EC. miR-124 Regulates Diverse Aspects of Rhythmic Behavior in Drosophila. The Journal of Neuroscience, (2016). 36(12):3414-21. IF 7.36. (This paper was co-authored with the 2017 Nobel Prize Laureate in Physiology or Medicine Prof. Michael Young on circadian rhythm in Drosophila.)
Wen J., Duan H., Bejarano F., Okamura K., Lacramioara F., Julie B., Bortolamiol-Becet D., Martin R., Ruby JG and Lai EC. Adaptive regulation of testis gene expression and control of male fertility by the Drosophila hairpin RNA pathway. Molecular Cell, (2015) 57(1):165-78. IF 15.05
Bortolamiol-Becet D., Hu F., Jee D., Wen J., Okamura K., Ching-Jung Lin, Stefan Ameres, and Lai EC. Selective suppression of the splicing-Mediated microRNA pathway by the terminal uridyltransferase Tailor. Molecular Cell. (2015). 59(2):217-28. IF 15.05
Wen J., Leucci, E., Lund, A, Krogh A. and Parker BJ. Transcriptome dynamics of the microRNA inhibition response. Nucleic Acids Research, (2015). 43(13):6207-21. IF 9.1.
Wen J., Ladewig E., and Lai EC. Analysis of nearly one thousand mammalian mirtrons reveals novel features of Dicer substrates. PLOS Computational Biology, (2015). 11(9):e1004441. IF 5.28
Wen J., Mohammed J, Tsai H, Robine N, Westholm JO, Ladewig E, Bortolamiol-Becet D, Dai Q, Okamura K, Flynt AS, Zhang D, Andrews J, Cherbas L, Kaufman TC, Cherbas P, Siepel A and Lai EC. Diversity of miRNAs, siRNAs and piRNAs across 25 Drosophila cell lines. Genome Research, (2014) 24(7), 1236-1250. IF 15.57.
Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J., Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE. Diversity and dynamics of the Drosophila transcriptome. Nature (2014) 512(7515), 393–399. IF 41.30.
The modENCODE Consortium. Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigo R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J., Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Comparative analysis of the transcriptome across distant species. Nature (2014) 512(7515):445-8. IF 41.30
Frankel LB, Di Malta C., Wen J., Eskelinen E., Ballabio A. and Lund, AH. A non-conserved miRNA regulates lysosomal function and impacts on a human lysosomal storage disorder. Nature Communication, (2014) 5:5840. current IF 11.47
Simola DF, Wissler L, Donahue G, Waterhouse RM, Helmkampf M, Roux J, Nygaard S, Glastad KM, Hagen DE, Viljakainen L, Reese JT, Hunt BG, Graur D, Elhaik E, Kriventseva EV, Wen J., Parker BJ, Cash E, Privman E, Childers CP, Munoz-Torres MC, Boomsma JJ, Bornberg-Bauer E, Currie CR, Elsik CG, Suen G, Goodisman MA, Keller L, Liebig J, Rawls A, Reinberg D, Smith CD, Smith CR, Tsutsui N, Wurm Y, Zdobnov EM, Berger SL, Gadau J. Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Research. (2013) 23(8):1235-47. IF 15.57
Stadthagen G, Tehler D, Hoyland-Kroghsbo NM, Wen J, Krogh A, Jensen KT, Santoni-Rugiu E, En-gelholm LH, Lund AH. Loss of miR-10a activates lpo and collaborates with activated Wnt signaling in inducing intestinal neoplasia in female mice. PLoS Genetics. (2013) 9(10):e1003913. IF 8.56
Patella F., Leucci E., Evangelista M.,Parker BJ, Wen J., Mercatanti A., Lund A.,and Rainaldi G. MiR-492 impairs the angiogenic potential of endothelial cells. J Cell Mol Med, (2013) 17(8):1006- 15. IF 5.81
Gregersen LH,Jacobsen A.,Frankel LB, Wen J, Krogh A.,and Lund AH. microRNA-143down-regulates Hexokinase 2 in colon cancer cells. BMC Cancer, (2012) 12:232. IF 3.77
Wen J., Parker BJ., Jacobsen A., and Krogh A. MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. RNA, (2011) 17(5):820-34. IF 4.94
Parker BJ., Moltke I., RothA.,Washietl S.,Wen J.,Kellis M.,Breaker R.,and Pedersen JS. New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Research (2011) 21(11):1929-43. IF 15.57
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alfoldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome As- sembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 478(7370):476-82. IF 41.30
Frankel LB., Wen J., Lees M., Høyer-Hansen M., Farkas T., Krogh A., Jäättelä,M., Lund AH. microRNA-101 is a potent inhibitor of autophagy. The EMBO journal (2011) 30(22):4628-41. IF 9.84
Chen Y., Jørgensen M., Kolde R., Zhao X., Parker BJ., Valen E., Wen J., Sandelin A., Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data. BMC Genomics, (2011) 12:544. IF 4.36
Jacobson A., Wen J., Marks DS., and Krogh A. Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Research (2010) 20(8):1010-9. IF 15.57
Gregersen, LH, Jacobsen, A., Frankel, LB, Wen J., Krogh, A. and Lund, A. microRNA-145 targets YES and STAT1 in colon cancer cells. PLoS One, (2010) 5(1):e8836. IF 3.23
Parker BJ.*, and Wen J. * Predicting microRNA targets in time-series microarray experiments via functional data analysis. BMC Bioinformatics, (2009) 10:S32. (*equal first authors.) IF 3.45
Wen J., FrickeyT., and WeillerGF. Computational prediction of candidate miRNAs and their targets from Medicago truncatula non-protein-coding transcripts. In Silico Biology, (2008) 8: 0024.
Wen J., Parker BJ., and Weiller GF. In silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula. In Silico Biology, (2007) 7: 0034.
Steele EJ., Lindley RA., Wen J., and Weiller GF. Computational analyses how A-to-G mutations correlate with nascent mRNA hairpins at somatic hypermutation hotspots. DNA Repair (2006) 5(11):1346-63. IF 3.455