Publications
In preparation
51. Michael Boylan, Dale Maxwell, Wasay Mohiuddin Shaikh Qureshi, Fangfei Jiang, Gennadiy Tenin, Charlie F. Rowlands, Jingshu Liu, Karen Mitchell, Louise Stephen, Elton Rosas de Vasconcelos, Dapeng Wang, Meurig T. Gallagher, Dragos Leordean, Adam F. Hurlstone, Jamie Ellingford, David Smith, Colin A. Johnson, Ray O’Keefe, Sudipto Roy, Kathryn E. Hentges. pre-mRNA processing factor 8 (Prpf8) is required for laterality organ cilia function and left-right axis formation in mouse and zebrafish. In preparation.
50. Haidee Tinning, Alysha Taylor, Dapeng Wang, Anna Pullinger, Georgios Oikonomou, Miguel A. Velazquez, Paul Thompson, Achim Treumann, Peter T. Ruane, Mary J O’Connell, Niamh Forde. The embryo-derived protein PDI is highly conserved among placental mammals and alters the function of the endometrium in species with different implantation strategies. In preparation.
Under review
49. Tiago H. C. De Bem, Alessandra Bridi, Haidee Tinning, Rafael Vilar Sampaio, Irene Malo-Estepa, Dapeng Wang, Elton J. R. Vasconcelos, Ricardo Perecin Nociti, Ana C. F. C. M. de Avila, Juliano Rodrigues Sangalli, Igor Garcia Motta, Gilmar Arantes Ataide Jr., Julio C. B. da Silva, Yeda Fumie Watanabe, Angela Gonella-Diaza, Juliano C. da Silveira, Guilherme Pugliesi, Flavio Vieira Meirelles, Niamh Forde. Biosensor capability of the endometrium is mediated in part, by altered miRNA cargo from conceptus-derived extracellular vesicles. In preparation.
48. Gabriele Rizzuto, Dapeng Wang, Jinhui Chen, Tin Hang Hung, Anne Charlott Fitzky, Emily Flashman, John J. MacKay. Contrasted NCED gene expression across conifers with Rising and Peaking abscisic acid responses to drought. Under review.
47. Dapeng Wang, Sabina D Wiktor, Chew W Cheng, Katie J Simmons, Ashley Money, Lucia Pedicini, Asya Carlton, Alexander L Breeze, Lynn McKeown. EFCAB4B (CRACR2A) genetic variants associated with COVID-19 fatality. Under review.
2023
46. Rebecca J Brownlie#, Ruth Kennedy#, Erica B Wilson, Maja Milanovic, Claire F Taylor, Dapeng Wang, John R Davies, Heather Owston, Emma J Adams, Sophie Stephenson, Rebecca Caeser, Benjamin E Gewurz, Peter V Giannoudis, Claudio Scuoppo, Dennis McGonagle, Daniel J Hodson, Reuben M Tooze, Gina M Doody, Gordon Cook, David R Westhead, Ulf Klein*. Cytokine receptor IL27RA is an NF-kB-responsive gene involved in CD38 upregulation in multiple myeloma. Blood Advances. 2023 Aug 8;7(15):3874-3890. doi: 10.1182/bloodadvances.2022009044. PubMed PMID: 36867577.
45. Amy K. Stainthorp, Chi-Chuan Lin, Dapeng Wang, Ragini Medhi, Zamal Ahmed, Kin Man Suen, Eric A. Miska, Adrian Whitehouse, John E. Ladbury*. Regulation of microRNA expression by the adaptor protein GRB2. Scientific Reports. 2023 Jun 16;13(1):9784. doi: 10.1038/s41598-023-36996-3. PubMed PMID: 37328606.
44. Dapeng Wang*. Amplicon Sequencing Pipelines in Metagenomics. Methods in Molecular Biology. 2023;2649:69-83. doi: 10.1007/978-1-0716-3072-3_4. PubMed PMID: 37258858.
43. Dapeng Wang*. Metagenomics Databases for Bacteria. Methods in Molecular Biology. 2023;2649:55-67. doi: 10.1007/978-1-0716-3072-3_3. PubMed PMID: 37258857.
42. Barry Causier*, Mary McKay, Tayah Hopes, James Lloyd, Dapeng Wang, C. Jill Harrison, Brendan Davies. The TOPLESS corepressor regulates developmental switches in the bryophyte Physcomitrium patens that were critical for plant terrestrialisation. The Plant Journal. 2023 May 26. doi: 10.1111/tpj.16322. PubMed PMID: 37243383.
41. Soo Young Baik#, Alisha Maini#, Haidee Tinning, Dapeng Wang, Daman J Adlam, Peter T Ruane, Niamh Forde*. Transcriptional response of endometrial cells to Insulin, cultured using microfluidics. Reproduction and Fertility. 2023 May 1:RAF-21-0120. doi: 10.1530/RAF-21-0120. PubMed PMID: 37200206.
40. Alysha S. Taylor, Haidee Tinning, Vladimir Ovchinnikov, Jessica Edge, William Smith, Anna L. Pullinger, Ruth A. Sutton, Bede Constantinides, Dapeng Wang, Karen Forbes, Niamh Forde*, Mary J. O’Connell*. A burst of genomic innovation at the origin of placental mammals mediated embryo implantation. Communications Biology. 2023 Apr 26;6(1):459. doi: 10.1038/s42003-023-04809-y. PubMed PMID: 37100852.
39. Laura Hume#, Jessica C. Edge#, Haidee Tinning, Dapeng Wang, Alysha S. Taylor, Vladimir Ovchinnikov, Annika V. Geijer-Simpson, Pavle Vrljicak, Jan J. Brosens, Emma S. Lucas, Nigel A.B. Simpson, Jayne Shillito, Karen Forbes, Mary J. O’Connell, Niamh Forde*. MicroRNAs emerging coordinate with placental mammals alter pathways in endometrial epithelia important for endometrial function. iScience. 2023 Mar 4;26(4):106339. doi: 10.1016/j.isci.2023.106339. PubMed PMID: 36968081.
38. Dapeng Wang, Vinod Kumar, Katie L Burnham, Alexander J Mentzer, Brian D Marsden*, Julian C Knight*. COMBATdb: a database for the COVID-19 Multi-Omics Blood ATlas. Nucleic Acids Research. 2023 Jan 6;51(D1):D896-D905. doi: 10.1093/nar/gkac1019. PubMed PMID: 36353986.
2022
37. Nunzio D'Agostino*, Wenli Li*, Dapeng Wang*. High-throughput transcriptomics. Scientific Reports. 2022 Nov 29;12(1):20313. doi: 10.1038/s41598-022-23985-1. PubMed PMID: 36446824.
36. Christos P Kotanidis, Cheng Xie, Donna Alexander, Jonathan C L Rodrigues, Katie Burnham, Alexander Mentzer, Daniel O'Connor, Julian Knight, Muhammad Siddique, Helen Lockstone, Sheena Thomas, Rafail Kotronias, Evangelos K Oikonomou, Ileana Badi, Maria Lyasheva, Cheerag Shirodaria, Sheila F Lumley, Bede Constantinides, Nicholas Sanderson, Gillian Rodger, Kevin K Chau, Archie Lodge, Maria Tsakok, Fergus Gleeson, David Adlam, Praveen Rao, Das Indrajeet, Aparna Deshpande, Amrita Bajaj, Benjamin J Hudson, Vivek Srivastava, Shakil Farid, George Krasopoulos, Rana Sayeed, Ling-Pei Ho, Stefan Neubauer, David E Newby, Keith M Channon, John Deanfield, Charalambos Antoniades*; COMBAT Consortium; ORFAN investigators. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19. The Lancet Digital Health. 2022 Aug 26;4(10):e705–16. PubMed PMID: 36038496. (Member of the COMBAT Consortium)
35. Wanda M Waterworth, Rosalind Latham, Dapeng Wang, Mona Alsharif, Christopher E West*. Seed DNA damage responses promote germination and growth in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America. 2022 Jul 26;119(30):e2202172119. doi: 10.1073/pnas.2202172119. PubMed PMID: 35858436.
34. Louise Richardson, Dapeng Wang, Ruth Hughes, Colin A Johnson, Michelle Peckham*. RNA-Seq analysis of a Pax3-expressing myoblast clone in-vitro and effect of culture surface stiffness on differentiation. Scientific Reports. 2022 Feb 18;12(1):2841. doi: 10.1038/s41598-022-06795-3. PubMed PMID: 35181706.
33. COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. Cell. 2022 Mar 3;185(5):916-938.e58. doi: 10.1016/j.cell.2022.01.012. PubMed PMID: 35216673. (Member of the COMBAT Consortium)
32. Yanchun Peng#, Suet Ling Felce#, Danning Dong#, Frank Penkava#, Alexander J Mentzer#, Xuan Yao#, Guihai Liu#, Zixi Yin#, Ji-Li Chen#, Yongxu Lu, Dannielle Wellington, Peter A C Wing, Delaney C C Dominey-Foy, Chen Jin, Wenbo Wang, Megat Abd Hamid, Ricardo A Fernandes, Beibei Wang, Anastasia Fries, Xiaodong Zhuang, Neil Ashley, Timothy Rostron, Craig Waugh, Paul Sopp, Philip Hublitz, Ryan Beveridge, Tiong Kit Tan, Christina Dold, Andrew J Kwok, Charlotte Rich-Griffin, Wanwisa Dejnirattisa, Chang Liu, Prathiba Kurupati, Isar Nassiri, Robert A Watson, Orion Tong, Chelsea A Taylor, Piyush Kumar Sharma, Bo Sun, Fabiola Curion, Santiago Revale, Lucy C Garner, Kathrin Jansen, Ricardo C Ferreira, Moustafa Attar, Jeremy W Fry, Rebecca A Russell; COMBAT Consortium; Hans J Stauss, William James, Alain Townsend, Ling-Pei Ho, Paul Klenerman, Juthathip Mongkolsapaya, Gavin R Screaton, Calliope Dendrou, Stephen N Sansom, Rachael Bashford-Rogers, Benny Chain, Geoffrey L Smith, Jane A McKeating, Benjamin P Fairfax, Paul Bowness, Andrew J McMichael, Graham Ogg, Julian C Knight*, Tao Dong*. An immunodominant NP105-113-B*07:02 cytotoxic T cell response controls viral replication and is associated with less severe COVID-19 disease. Nature Immunology. 2022 Jan;23(1):50-61. doi: 10.1038/s41590-021-01084-z. PubMed PMID: 34853448. (Member of the COMBAT Consortium)
2021
31. Damien J Downes, Amy R Cross, Peng Hua, Nigel Roberts, Ron Schwessinger, Antony J Cutler, Altar M Munis, Jill Brown, Olga Mielczarek, Carlos E de Andrea, Ignacio Melero; COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium; Deborah R Gill, Stephen C Hyde, Julian C Knight, John A Todd, Stephen N Sansom, Fadi Issa, James O J Davies*, Jim R Hughes*. Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus. Nature Genetics. 2021 Nov;53(11):1606-1615. doi: 10.1038/s41588-021-00955-3. PubMed PMID: 34737427. (Member of the COMBAT Consortium)
30. Anthony M Buckley*, Ines B Moura, Norie Arai, William Spittal, Emma Clark, Yoshihiro Nishida, Hannah C Harris, Karen Bentley, Georgina Davis, Dapeng Wang, Suparna Mitra, Takanobu Higashiyama, Mark H Wilcox*. Trehalose-Induced Remodelling of the Human Microbiota Affects Clostridioides difficile Infection Outcome in an In Vitro Colonic Model: A Pilot Study. Frontiers in Cellular and Infection Microbiology. 2021;11:670935. doi: 10.3389/fcimb.2021.670935. eCollection 2021. PubMed PMID: 34277467.
29. Katerina Douka, Isabel Birds, Dapeng Wang, Andreas Kosteletos, Sophie Clayton, Abigail Byford, Elton J R Vasconcelos, Mary J O'Connell, Jim Deuchars, Adrian Whitehouse, Julie L Aspden*. Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation. RNA. 2021 Sep;27(9):1082-1101. doi: 10.1261/rna.078782.121. PubMed PMID: 34193551.
28. Tiago H C De Bem, Haidee Tinning, Elton J R Vasconcelos, Dapeng Wang, Niamh Forde*. Endometrium On-a-Chip Reveals Insulin- and Glucose-induced Alterations in the Transcriptome and Proteomic Secretome. Endocrinology. 2021 Jun 1;162(6). doi: 10.1210/endocr/bqab054. PubMed PMID: 33693651.
2020
27. Mingrui Wang, Dapeng Wang, Jun Yu, Shi Huang*. Enrichment in conservative amino acid changes among fixed and standing missense variations in slowly evolving proteins. PeerJ. 2020;8:e9983. doi: 10.7717/peerj.9983. eCollection 2020. PubMed PMID: 32995099.
26. Haidee Tinning, Alysha Taylor, Dapeng Wang, Bede Constantinides, Ruth Sutton, Georgios Oikonomou, Miguel A Velazquez, Paul Thompson, Achim Treumann, Mary J O'Connell, Niamh Forde*. The role of CAPG in molecular communication between the embryo and the uterine endometrium: Is its function conserved in species with different implantation strategies?. The FASEB Journal. 2020 Aug;34(8):11015-11029. doi: 10.1096/fj.202000882RR. PubMed PMID: 32619075.
2019
25. Wanda M Waterworth, Michael Wilson, Dapeng Wang, Thomas Nuhse, Stacey Warward, Julian Selley, Christopher E West*. Phosphoproteomic analysis reveals plant DNA damage signalling pathways with a functional role for histone H2AX phosphorylation in plant growth under genotoxic stress. The Plant Journal. 2019 Dec;100(5):1007-1021. doi: 10.1111/tpj.14495. PubMed PMID: 31410901.
24. Dapeng Wang*. IntronDB: a database for eukaryotic intron features. Bioinformatics. 2019 Nov 1;35(21):4400-4401. doi: 10.1093/bioinformatics/btz242. PubMed PMID: 30949679.
2018
23. Dapeng Wang*. hppRNA-a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples. Briefings in Bioinformatics. 2018 Jul 20;19(4):622-626. doi: 10.1093/bib/bbw143. PubMed PMID: 28096075.
22. Dapeng Wang*. GCevobase: an evolution-based database for GC content in eukaryotic genomes. Bioinformatics. 2018 Jun 15;34(12):2129-2131. doi: 10.1093/bioinformatics/bty068. PubMed PMID: 29420682.
21. Charlotta Böiers#, Simon E Richardson#, Emma Laycock, Alya Zriwil, Virginia A Turati, John Brown, Jason P Wray, Dapeng Wang, Chela James, Javier Herrero, Ewa Sitnicka, Stefan Karlsson, Andrew J H Smith, Sten Erik W Jacobsen, Tariq Enver*. A Human IPS Model Implicates Embryonic B-Myeloid Fate Restriction as Developmental Susceptibility to B Acute Lymphoblastic Leukemia-Associated ETV6-RUNX1. Developmental Cell. 2018 Feb 5;44(3):362-377.e7. doi: 10.1016/j.devcel.2017.12.005. PubMed PMID: 29290585.
2017
20. Itaru Kato, Yoko Nishinaka, Masahiro Nakamura, Ayse U Akarca, Akira Niwa, Hiroki Ozawa, Kenichi Yoshida, Makiko Mori, Dapeng Wang, Makiko Morita, Hiroo Ueno, Yusuke Shiozawa, Yuichi Shiraishi, Satoru Miyano, Rajeev Gupta, Katsutsugu Umeda, Kenichiro Watanabe, Katsuyoshi Koh, Souichi Adachi, Toshio Heike, Megumu K Saito, Masashi Sanada, Seishi Ogawa, Teresa Marafioti, Akira Watanabe, Tatsutoshi Nakahata*, Tariq Enver*. Hypoxic adaptation of leukemic cells infiltrating the CNS affords a therapeutic strategy targeting VEGFA. Blood. 2017 Jun 8;129(23):3126-3129. doi: 10.1182/blood-2016-06-721712. PubMed PMID: 28424164.
2015
19. Dapeng Wang*. DLGP: A database for lineage-conserved and lineage-specific gene pairs in animal and plant genomes. Biochemical and Biophysical Research Communications. 2016 Jan 15;469(3):542-5. doi: 10.1016/j.bbrc.2015.12.039. PubMed PMID: 26697753.
18. Dapeng Wang#,*, Jiayue Xu#, Jun Yu*. KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation. Biology Direct. 2015 Sep 16;10:53. doi: 10.1186/s13062-015-0083-4. PubMed PMID: 26376976.
17. Dapeng Wang*, Jun Yu*. LCGserver: A Webserver for Exploring Evolutionary Trajectory of Gene Orders in a Large Number of Genomes. OMICS: A Journal of Integrative Biology. 2015 Sep;19(9):574-7. doi: 10.1089/omi.2015.0060. PubMed PMID: 26258441.
16. Cristina Pina#, José Teles#, Cristina Fugazza#, Gillian May, Dapeng Wang, Yanping Guo, Shamit Soneji, John Brown, Patrik Edén, Mattias Ohlsson, Carsten Peterson, Tariq Enver*. Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis. Cell Reports. 2015 Jun 16;11(10):1503-10. doi: 10.1016/j.celrep.2015.05.016. PubMed PMID: 26051941.
2014
15. Dapeng Wang*, Jun Yu*. Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs. Nucleic Acids Research. 2015 Jan;43(Database issue):D990-5. doi: 10.1093/nar/gku1070. PubMed PMID: 25378306.
2013
14. Lei Wang#, Xiao-Wei Zhang#, Lin-Lin Pan, Wan-Fei Liu, Da-Peng Wang, Guang-Yu Zhang, Yu-Xin Yin, An Yin, Shan-Gang Jia, Xiao-Guang Yu, Gao-Yuan Sun, Song-Nian Hu, Ibrahim S Al-Mssallem*, Jun Yu*. A large-scale gene discovery for the red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae). Insect Science. 2013 Dec;20(6):689-702. doi: 10.1111/j.1744-7917.2012.01561.x. PubMed PMID: 23955844.
13. Bin Xie#, Dapeng Wang#, Yong Duan, Jun Yu*, Hongxing Lei*. Functional networking of human divergently paired genes (DPGs). PLoS ONE. 2013;8(10):e78896. doi: 10.1371/journal.pone.0078896. eCollection 2013. PubMed PMID: 24205343.
12. Yunbo Li#, Dapeng Wang#,*, Lei Wang#, Jinhai Yu, Danhua Du, Ye Chen, Peng Gao, Duen-Mei Wang, Jun Yu, Feng Zhang*, Shuanglin Fu*. Distinct genomic aberrations between low-grade and high-grade gliomas of Chinese patients. PLoS ONE. 2013;8(2):e57168. doi: 10.1371/journal.pone.0057168. PubMed PMID: 23451178.
11. Dapeng Wang#, Yan Xia#, Xinna Li, Lixia Hou, Jun Yu*. The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. Nucleic Acids Research. 2013 Jan;41(Database issue):D1199-205. doi: 10.1093/nar/gks1225. PubMed PMID: 23193278.
2012
10. Dapeng Wang#, Yao Su#, Xumin Wang, Hongxing Lei*, Jun Yu*. Transposon-derived and satellite-derived repetitive sequences play distinct functional roles in Mammalian intron size expansion. Evolutionary Bioinformatics. 2012;8:301-19. doi: 10.4137/EBO.S9758. PubMed PMID: 22807622.
9. Dapeng Wang#, Yubin Zhang#, Zhonghua Fan#, Guiming Liu, Jun Yu*. LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes. Evolutionary Bioinformatics. 2012;8:39-46. doi: 10.4137/EBO.S8540. PubMed PMID: 22267903.
2011
8. Dapeng Wang, Jun Yu#. Both size and GC-content of minimal introns are selected in human populations. PLoS ONE. 2011 Mar 17;6(3):e17945. doi: 10.1371/journal.pone.0017945. PubMed PMID: 21437290.
7. Dapeng Wang#, Fei Liu#, Lei Wang, Shi Huang, Jun Yu*. Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes. Biology Direct. 2011 Feb 22;6:13. doi: 10.1186/1745-6150-6-13. PubMed PMID: 21342519.
6. Y-H Zhao#, D-P Wang#, L-L Zhang#, F Zhang, D-M Wang, W-Y Zhang*. Genomic expression profiles of blood and placenta reveal significant immune-related pathways and categories in Chinese women with gestational diabetes mellitus. Diabetic Medicine. 2011 Feb;28(2):237-46. doi: 10.1111/j.1464-5491.2010.03140.x. PubMed PMID: 21219437.
2010
5. Feng Liu#, Dapeng Wang#, Jianjun Fu, Gaoyuan Sun, Yubang Shen, Lingli Dong, Bing Zhang, Songnian Hu*, Jiale Li*. Identification of immune-relevant genes by expressed sequence tag analysis of head kidney from grass carp (Ctenopharyngodon idella). Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. 2010 Jun;5(2):116-23. doi: 10.1016/j.cbd.2010.02.003. PubMed PMID: 20403773.
4. Jiang Zhu, Fuhong He, Dapeng Wang, Kan Liu, Dawei Huang, Jingfa Xiao, Jiayan Wu, Songnian Hu, Jun Yu*. A novel role for minimal introns: routing mRNAs to the cytosol. PLoS ONE. 2010 Apr 12;5(4):e10144. doi: 10.1371/journal.pone.0010144. PubMed PMID: 20419085.
3. Dapeng Wang#, Yubin Zhang#, Zhang Zhang, Jiang Zhu, Jun Yu*. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics. 2010 Mar;8(1):77-80. doi: 10.1016/S1672-0229(10)60008-3. PubMed PMID: 20451164.
2009
2. Dapeng Wang, Song Zhang, Fuhong He, Jiang Zhu, Songnian Hu, Jun Yu*. How do variable substitution rates influence Ka and Ks calculations?. Genomics Proteomics Bioinformatics. 2009 Sep;7(3):116-27. doi: 10.1016/S1672-0229(08)60040-6. PubMed PMID: 19944384.
1. Da-Peng Wang#, Hao-Lei Wan#, Song Zhang#, Jun Yu*. Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates. Biology Direct. 2009 Jun 16;4:20. doi: 10.1186/1745-6150-4-20. PubMed PMID: 19531225.