Monday, March 26, 2018 Ge Gao

Publications

Reverse chronological order, with * for (co-)corresponding and † for equal contribution.

Recent Publications

 

Research

  1. Chen Z.Y., Wei L., Gao G.* 2024. Foundation models for bioinformatics. Quant. Biol. (in press). [Journal Page]
  2. Liu X.†, Zhao X.M.†, Kang Y.J.†, Huang F., Liu S., Guo Y.X., Li Y.N., Yin C.C., Liu M.L., Han Q.M., Wang Q.W., Ye H., Yao H.H., Li C., Li J.H., P.C. W.Z., Zhang Y., Su Y., Gao G.*, Li Z.G.*, Sun X.L.* 2024. An autoantibody profile identified by human genome‐wide protein arrays in rheumatoid arthritis. Med Comm 5: e679. [PubMed][Website]
  3. Xia C.R.†, Cao Z.J.†*, Tu X.M., Gao G.* 2023. Spatial-linked alignment tool (SLAT) for aligning heterogenous slices. Nat Commun 14(1): 7236. (Featured as Editors’ Highlights) [PubMed][Website][Press]
  4. Wen Z.Y., Kang Y.J., Ke L., Yang D.C., Gao G.* 2023. Genome-Wide Identification of Gene Loss Events Suggests Loss Relics as a Potential Source of Functional lncRNAs in Humans. Mol Biol Evol 40(5).[PubMed][Website][Press]
  5. Cao Z.J. and Gao G.* 2022. Multi-omics single-cell data integration and regulatory inference with graph-linked embedding. Nat Biotechnol 40(10): 1458-1466. (Featured as Top 10 Bioinformatics Advances in China, 2022 as well as ESI Highly Cited (Top 1%) Paper)[PubMed][Website][Press]
  6. Tu X.M.†, Cao Z.J.†, Xia C.R., Mostafavi S.*, Gao G.* 2022. Cross-Linked Unified Embedding for cross-modality representation learning. In 36th Conference on Neural Information Processing Systems (NeurIPS 2022). (Featured as Oral/Top 5% Papers)[Paper][Website][Video Presentation/Poster]
  7. Shi F.Y., Wang Y., Huang D., Liang Y., Liang N., Chen X.W., Gao G.* 2022. Computational Assessment of the Expression-modulating Potential for Noncoding Variants. Genomics Proteomics Bioinformatics. (in press)[PubMed][Website]
  8. Kang Y.J., Li J.Y., Ke L., Jiang S., Yang D.C., Hou M., Gao G.* 2022. Quantitative model suggests both intrinsic and contextual features contribute to the transcript coding ability determination in cells. Brief Bioinform 23(1).[PubMed][Website][Press]
  9. Ding Y.†, Zheng Y.†, Wang J.†, Li H., Zhao C., Tao H., Li Y., Xu K., Huang X., Gao G.*, Chen H.*, Bo X.* 2022. Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance. Commun Biol 5(1): 1400.[PubMed][Website]
  10. Liu N.†, Xu Y.†, Li Q., Cao Y., Yang D., Liu S., Wang X., Mi Y., Liu Y., Ding C., Liu Y., Li Y., Yuan Y.W., Gao G., Chen J.*, Qian W.*, Zhang X.* 2022. A lncRNA fine-tunes salicylic acid biosynthesis to balance plant immunity and growth. Cell Host Microbe 30(8): 1124-1138 e1128.[PubMed]
  11. National Genomics Data Center Members and Partners. 2022. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Res 49(D1): D18-D28.[PubMed]
  12. Li J.Y.†, Jin S.†, Tu X.M., Ding Y.*, Gao G.* 2021. Identifying complex motifs in massive omics data with a variable-convolutional layer in deep neural network. Brief Bioinform 22(6).[PubMed][Website][Press]
  13. Wang Y.†, Shi F.Y.†, Liang Y., Gao G.* 2021. REVA as A Well-curated Database for Human Expression-modulating Variants. Genomics Proteomics Bioinformatics. 19(4):590-601.[PubMed][Website][Press]
  14. Cui Y.†, Lyu X.†, Ding L., Ke L., Yang D., Pirouz M., Qi Y., Ong J., Gao G., Du P.*, Gregory R.I.* 2021. Global miRNA dosage control of embryonic germ layer specification. Nature 593(7860): 602-606.[PubMed]
  15. Wang X.†, Wang H.†, Xu B.†, Huang D., Nie C., Pu L., Zajac G.J.M., Yan H., Zhao J., Shi F., Emmer B.T., Lu J., Wang R., Dong X., Dai J., Zhou W., Wang C., Gao G., Wang Y., Willer C., Lu X., Zhu Y., Chen X.W.* 2021. Receptor-Mediated ER Export of Lipoproteins Controls Lipid Homeostasis in Mice and Humans. Cell Metab 33(2): 350-366 e357.[PubMed]
  16. Cao Z.J.†, Wei L.†, Lu S., Yang D.C., Gao G.* 2020. Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST. Nat Commun 11(1): 3458.(Featured as Top 10 Bioinformatics Advances in China, 2020)[PubMed][Website][Press]
  17. Luo X.†, Tu X.†, Ding Y., Gao G.*, Deng M.* 2020. Expectation pooling: An effective and interpretable pooling method for predicting DNA-protein binding. Bioinformatics 36(5):1405. [PubMed][Website][Press]
  18. Tian F.†, Yang D. C.†, Meng Y. Q., Jin J.*, Gao G.* 2020. PlantRegMap: charting functional regulatory maps in plants. Nucleic Acids Res 48(D1):D1104. [PubMed][Website][Press]
  19. Ke L.†, Yang D.C.†, Wang Y., Ding Y., Gao G.* 2020. AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse. Nucleic Acids Res 48(W1):W230-W238. (Featured as Highly Accessed Paper) [PubMed][Website][Press]
  20. Lin Y.†, Luo Y.†, Sun Y.†, Guo W.†, Zhao X.†, Xi Y., Ma Y., Shao M., Tan W., Gao G.*, Wu C.*, Lin D.* 2020. Genomic and transcriptomic alterations associated with drug vulnerabilities and prognosis in adenocarcinoma at the gastroesophageal junction. Nat Commun 11(1): 6091. [PubMed]
  21. National Genomics Data Center Members and Partners. 2020. Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Res 48(D1): D24-D33. [PubMed]
  22. Jiang S.†, Cheng S. J.†, Ren L. C., Wang Q., Kang Y. J., Ding Y., Hou M., Yang X. X., Lin Y., Liang N., Gao G.* 2019. An expanded landscape of human long noncoding RNA. Nucleic Acids Res 47(15):7842. (Featured as China’s Top 10 Bioinformatics Database in China, 2019) [PubMed][Website][Press]
  23. Yang J.†, Lin Y.†, Huang Y., Jin J., Zou S., Zhang X., Li H., Feng T., Chen J., Zuo Z., Zheng J., Li Y., Gao G., Wu C.*, Tan W.*, Lin D.* 2019. Genome landscapes of rectal cancer before and after preoperative chemoradiotherapy. Theranostics 9(23): 6856-6866. [PubMed]
  24. Xiong L., Xu K., Tian K., Shao Y., Tang L., Gao G., Zhang M., Jiang T., Zhang Q. C. 2019. SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nat Commun 10(1): 4576. (Featured as Top 10 Bioinformatics Tools in China, 2019) [PubMed][Website]
  25. Shao Y.†, Chen C.†, Shen H., He B. Z., Yu D., Jiang S., Zhao S., Gao Z., Zhu Z., Chen X., Fu Y., Chen H., Gao G., Long M., Zhang Y. E.* 2019. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. Genome Res 29(4): 682-696. [PubMed][Website]
  26. Li W.†, Bai X.†, Li J.†, Zhao Y., Liu J., Zhao H., Liu L., Ding M., Wang Q., Shi F.Y., Hou M., Ji J., Gao G., Guo R., Sun Y., Liu Y., Xu D.* 2019. The nucleoskeleton protein IFFO1 immobilizes broken DNA and suppresses chromosome translocation during tumorigenesis. Nat Cell Biol 21(10): 1273-1285. [PubMed]
  27. Cheng S. J., Jiang S., Shi F. Y., Ding Y., Gao G.* 2018. Systematic identification and annotation of multiple-variant compound effects at transcription factor binding sites in human genome. J Genet Genomics 45(7): 373-379. [PubMed][Website][Press]
  28. Peng L.†, Cheng S. J.†, Lin Y.†, Cui Q., Luo Y., Chu J., Shao M., Fan W., Chen Y., Lin A., Xi Y., Sun Y., Zhang L., Zhang C., Tan W., Gao G.*, Wu C.*, Lin D. 2018. CCGD-ESCC: A Comprehensive Database for Genetic Variants Associated with Esophageal Squamous Cell Carcinoma in Chinese Population. Genomics Proteomics Bioinformatics 16(4): 262-268. [PubMed][Website][Press]
  29. Xu R.†, Xu Y.†, Huo W., Lv Z., Yuan J., Ning S., Wang Q., Hou M., Gao G., Ji J., Chen J., Guo R., Xu D.* 2018. Mitosis-specific MRN complex promotes a mitotic signaling cascade to regulate spindle dynamics and chromosome segregation. Proc Natl Acad Sci U S A 115(43): E10079-E10088. [PubMed]

Education

  1. Isik E.B., Brazas M.D., Schwartz R., Gaeta B., Palagi P.M., van Gelder C.W.G., Suravajhala P., Singh H., Morgan S.L., Zahroh H., Ling M., Satagopam V.P., McGrath A., Nakai K., Tan T.W., Gao G., Mulder N., Schonbach C., Zheng Y., De Las Rivas J., Khan A.M. 2023. Grand challenges in bioinformatics education and training. Nat Biotechnol 41(8): 1171-1174. [PubMed]

Invited Book Chapters

  1. Yang D.C., Ke L., Ding Y.*, Gao G.* 2021. AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Noncoding RNAs. Methods Mol Biol 2254: 111-131. [PubMed]

Preprints

  1. Wang Y., Liang N., Gao G.*. Quantify genetic variants’ regulatory potential via a hybrid sequence-oriented model. bioRxiv. [bioRxiv][Website]
  2. Tian F., Zhou F., Li X., Ma W., Wu H., Yang M., Chapman A.R., Lee D.F., Tan L., Xing D., Yin G., Semayel A., Wang J., Wang J., Sun W., He R., Zhang S., Cao Z., Wei L., Lu S., Yang D., Mao Y., Gao Y., Chen K., Zhang Y., Liu X., Yong J., Yan L., Huang Y., Qiao J.*, Tang F.*, Gao G.*, Xie X.S.* Genomic Architecture of Cells in Tissues (GeACT): Study of Human Mid-gestation Fetus. bioRxiv. [bioRxiv][Website]
  3. Ding Y., Li J.-Y., Wang M., Tu X., Gao G.* An exact transformation for CNN kernel enables accurate sequence motif identification and leads to a potentially full probabilistic interpretation of CNN. bioRxiv. [bioRxiv][Website]

Publications between 2006 and 2018

 

Research

  1. Kang Y. J., Yang D. C., Kong L., Hou M., Meng Y. Q., Wei L., Gao G.* 2017. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Res 45(W1): W12-W16. (Featured as ESI Highly Cited (Top 1%) Paper) [PubMed][Website]
  2. Cheng S. J., Shi F. Y., Liu H., Ding Y., Jiang S., Liang N., Gao G.* 2017. Accurately annotate compound effects of genetic variants using a context-sensitive framework. Nucleic Acids Res 45(10): e82. (Featured as Highly Accessed Paper) [PubMed][Website]
  3. Jin J.†, Tian F.†, Yang D. C., Meng Y. Q., Kong L., Luo J.*, Gao G.* 2017. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res 45(D1): D1040-D1045. (Featured as ESI Highly Cited (Top 1%) Paper) [PubMed][Website]
  4. Zhou Y.†, Wang P.†, Tian F.†, Gao G., Huang L.*, Wei W.*, Xie X. S.* 2017. Painting a specific chromosome with CRISPR/Cas9 for live-cell imaging. Cell Res 27(2): 298-301. [PubMed][Website]
  5. Tang Z.†, Li C.†, Kang B., Gao G., Li C., Zhang Z.* 2017. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res 45(W1): W98-W102. (Featured as ESI Highly Cited (Top 1%) Paper) [PubMed][Website]
  6. Chen Z. X.*, Oliver B., Zhang Y. E., Gao G., Long M.* 2017. Expressed Structurally-stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements. Genome Biol Evol 9(4): 981-992. [PubMed]
  7. Hou M., Tian F., Jiang S., Kong L., Yang D., Gao G.* 2016. LocExpress: a web server for efficiently estimating expression of novel transcripts. BMC Genomics 17(13): 175-179. (Featured as “Best Paper” at InCoB’16) [PubMed][Website]
  8. Hou M., Tang X., Tian F., Shi F., Liu F., Gao G.* 2016. AnnoLnc: a web server for systematically annotating novel human lncRNAs. BMC Genomics 17(1): 931. (Featured as Highly Accessed Paper) [PubMed][Website]
  9. Feng S., Zhao Y., Xu Y., Ning S., Huo W., Hou M., Gao G., Ji J., Guo R.*, Xu D.* 2016. Ewing Tumor-associated Antigen 1 Interacts with Replication Protein A to Promote Restart of Stalled Replication Forks. J Biol Chem 291(42): 21956-21962. (Featured as “Highlights of 2016” by J. Biol. Chem.) [PubMed]
  10. Xue Y., Lameijer E. W., Ye K., Zhang K., Chang S., Wang X., Wu J., Gao G., Zhao F., Li J., Han C., Xu S., Xiao J., Yang X., Ying X., Zhang X., Chen W. H., Liu Y., Zhang Z., Huang K., Yu J.* 2016. Precision Medicine: What Challenges Are We Facing? Genomics Proteomics Bioinformatics 14(5): 253-261. [PubMed]
  11. Hu B.†, Jin J.†, Guo A. Y., Zhang H., Luo J., Gao G.* 2015. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31(8): 1296-1297. (Featured as ESI Highly Cited (Top 1%) Paper) [PubMed][Website]
  12. Jin J., He K., Tang X., Li Z., Lv L., Zhao Y., Luo J., Gao G.* 2015. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol Biol Evol 32(7): 1767-1773. [PubMed][Website]
  13. Zhao Y., Tang L., Li Z., Jin J., Luo J., Gao G.* 2015. Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics. BMC Evol Biol 15: 66. (Featured as “Very Good (being of special significance in its field)” by Faculty of 1000) [PubMed][Website]
  14. Xing M., Yang M., Huo W., Feng F., Wei L., Jiang W., Ning S., Yan Z., Li W., Wang Q., Hou M., Dong C., Guo R., Gao G., Ji J., Zha S., Lan L., Liang H., Xu D.* 2015. Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway. Nat Commun 6: 6233. [PubMed]
  15. Gao G.†, Vibranovski M. D.†, Zhang L., Li Z., Liu M., Zhang Y. E., Li X., Zhang W., Fan Q., VanKuren N. W., Long M.*, Wei L.* 2014. A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster. Genome Res 24(4): 629-638. [PubMed]
  16. Xiao A.†, Cheng Z.†, Kong L., Zhu Z., Lin S., Gao G.*, Zhang B.* 2014. CasOT: a genome-wide Cas9/gRNA off-target searching tool. Bioinformatics 30(8): 1180-1182. (Featured as ESI Highly Cited (Top 1%) Paper) [PubMed][Website]
  17. Jin J., Zhang H., Kong L., Gao G.*, Luo J.* 2014. PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res 42(1): D1182-1187. (Featured as ESI Highly Cited (Top 1%) Paper) [PubMed][Website]
  18. Li H., Yue R., Wei B., Gao G., Du J., Pei G.* 2014. Lysophosphatidic acid acts as a nutrient-derived developmental cue to regulate early hematopoiesis. EMBO J 33(12): 1383-1396. [PubMed]
  19. Huang A. Y., Xu X., Ye A. Y., Wu Q., Yan L., Zhao B., Yang X., He Y., Wang S., Zhang Z., Gu B., Zhao H. Q., Wang M., Gao H., Gao G., Zhang Z., Yang X., Wu X., Zhang Y., Wei L.* 2014. Postzygotic single-nucleotide mosaicisms in whole-genome sequences of clinically unremarkable individuals. Cell Res 24(11): 1311-1327. [PubMed]
  20. Tang X., Hou M., Ding Y., Li Z., Ren L., Gao G.* 2013. Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell. BMC Genomics 14(Suppl 5): S3. [PubMed]
  21. Shu J.†, Wu C.†, Wu Y.†, Li Z.†, Shao S., Zhao W., Tang X., Yang H., Shen L., Zuo X., Yang W., Shi Y., Chi X., Zhang H., Gao G., Shu Y., Yuan K., He W., Tang C.*, Zhao Y., Deng H.* 2013. Induction of pluripotency in mouse somatic cells with lineage specifiers. Cell 153(5): 963-975. [PubMed]
  22. Wang J., Kong L., Gao G., Luo J.* 2013. A brief introduction to web-based genome browsers. Brief Bioinform 14(2): 131-143. [PubMed]
  23. Xiao A., Wu Y., Yang Z., Hu Y., Wang W., Zhang Y., Kong L., Gao G., Zhu Z., Lin S.*, Zhang B.* 2013. EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering. Nucleic Acids Res 41(Database issue): D415-422. [PubMed]
  24. Kong L.†, Wang J.†, Zhao S., Gu X., Luo J.*, Gao G.* 2012. ABrowse – a customizable next-generation genome browser framework. BMC Bioinformatics 13: 2. (Featured as Highly Accessed Paper) [PubMed]
  25. Yue R.†, Li H.†, Liu H., Li Y., Wei B., Gao G., Jin Y., Liu T., Wei L., Du J., Pei G.* 2012. Thrombin receptor regulates hematopoiesis and endothelial-to-hematopoietic transition. Dev Cell 22(5): 1092-1100. [PubMed]
  26. Wang J.†, Kong L.†, Zhao S., Zhang H., Tang L., Li Z., Gu X., Luo J.*, Gao G.* 2011. Rice-Map: a new-generation rice genome browser. BMC Genomics 12: 165. (Featured as Highly Accessed Paper) [PubMed]
  27. Chen Z. X., Zhang Y. E., Vibranovski M., Luo J., Gao G.*, Long M.* 2011. Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome. Mol Biol Evol 28(10): 2823-2832. [PubMed]
  28. Zhang J., Gao G., Chen J. J., Taylor G., Cui K. M., He X. Q.* 2011. Molecular features of secondary vascular tissue regeneration after bark girdling in Populus. New Phytol 192(4): 869-884. [PubMed]
  29. Xie C., Mao X., Huang J., Ding Y., Wu J., Dong S., Kong L., Gao G., Li C. Y., Wei L.* 2011. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39(Web Server issue): W316-322. (Featured as ESI Highly Cited (Top 1%) Paper) [PubMed][Website]
  30. Liu M., Liu P., Zhang L., Cai Q., Gao G., Zhang W., Zhu Z., Liu D.*, Fan Q.* 2011. mir-35 is involved in intestine cell G1/S transition and germ cell proliferation in C. elegans. Cell Res 21(11): 1605-1618. [PubMed]
  31. Du P., Wu J., Zhang J., Zhao S., Zheng H., Gao G., Wei L., Li Y.* 2011. Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors. PLoS Pathog 7(8): e1002176. [PubMed]
  32. Zhang H., Jin J., Tang L., Zhao Y., Gu X., Gao G.*, Luo J.* 2011. PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res 39(Database issue): D1114-1117. (Featured as ESI Highly Cited (Top 1%) Paper) [PubMed][Website]
  33. Shen L., Gao G.*, Zhang Y., Zhang H., Ye Z., Huang S., Huang J., Kang J.* 2010. A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA. Nucleic Acids Res 38(18): 6054-6064. [PubMed]
  34. Gao G., Li J. T., Kong L., Tao L., Wei L.* 2009. Human herpesvirus miRNAs statistically preferentially target host genes involved in cell signaling and adhesion/junction pathways. Cell Res 19(5): 665-667. [PubMed]
  35. Zhao S. Q., Wang J., Zhang L., Li J. T., Gu X., Gao G.*, Wei L.* 2009. BOAT: Basic Oligonucleotide Alignment Tool. BMC Genomics 10 Suppl 3: S2. [PubMed]
  36. Liu X.†, Wu J.†, Wang J., Liu X., Zhao S., Li Z., Kong L., Gu X., Luo J.*, Gao G.* 2009. WebLab: a data-centric, knowledge-sharing bioinformatic platform. Nucleic Acids Res 37(Web Server issue): W33-39. [PubMed][Website]
  37. Li Z., Zhang H., Ge S., Gu X., Gao G.*, Luo J.* 2009. Expression pattern divergence of duplicated genes in rice. BMC Bioinformatics 10(Suppl 6): S8. [PubMed]
  38. Li Z.†, Liu M.†, Zhang L.†, Zhang W., Gao G., Zhu Z., Wei L., Fan Q.*, Long M.* 2009. Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster. Nucleic Acids Res 37(13): 4308-4314. [PubMed]
  39. Zhao M., Chen X., Gao G., Tao L., Wei L.* 2009. RLEdb: a database of rate-limiting enzymes and their regulation in human, rat, mouse, yeast and E. coli. Cell Res 19(6): 793-795. [PubMed]
  40. Guo A. Y.†, Chen X.†, Gao G., Zhang H., Zhu Q. H., Liu X. C., Zhong Y. F., Gu X., He K.*, Luo J.* 2008. PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Res 36(Database issue): D966-969. [PubMed][Website]
  41. Liu H.†, Zhu F.†, Yong J.†, Zhang P., Hou P., Li H., Jiang W., Cai J., Liu M., Cui K., Qu X., Xiang T., Lu D., Chi X., Gao G., Ji W., Ding M., Deng H.* 2008. Generation of induced pluripotent stem cells from adult rhesus monkey fibroblasts. Cell Stem Cell 3(6): 587-590. [PubMed]
  42. Kong L., Zhang Y., Ye Z. Q., Liu X. Q., Zhao S. Q., Wei L.*, Gao G.* 2007. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35(Web Server issue): W345-349. (Featured as ESI Highly Cited (Top 1%) Paper) [PubMed][Website]
  43. Ren L., Gao G., Zhao D., Ding M., Luo J., Deng H. 2007. Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation. Genome Biol 8(3): R35. [PubMed]
  44. Zhu Q. H., Guo A. Y., Gao G., Zhong Y. F., Xu M., Huang M., Luo J.* 2007. DPTF: a database of poplar transcription factors. Bioinformatics 23(10): 1307-1308. [PubMed][Website]
  45. Sun Y., Zhao S., Yu H., Gao G.*, Luo J.* 2007. ABCGrid: Application for Bioinformatics Computing Grid. Bioinformatics 23(9): 1175-1177. [PubMed]
  46. Ye Z. Q., Zhao S. Q., Gao G., Liu X. Q., Langlois R. E., Lu H., Wei L.* 2007. Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP). Bioinformatics 23(12): 1444-1450. [PubMed]
  47. Zhang Y., Li J., Kong L., Gao G., Liu Q. R., Wei L.* 2007. NATsDB: Natural Antisense Transcripts DataBase. Nucleic Acids Res 35(Database issue): D156-161. [PubMed]
  48. Gao G., Zhong Y., Guo A., Zhu Q., Tang W., Zheng W., Gu X., Wei L.*, Luo J.* 2006. DRTF: a database of rice transcription factors. Bioinformatics 22(10): 1286-1287. (Featured as ESI Highly Cited (Top 1%) Paper) [PubMed][Website]

Education

  1. Ding Y., Wang M., He Y., Ye A. Y., Yang X., Liu F., Meng Y., Gao G.*, Wei L.* 2014. “Bioinformatics: Introduction and Methods,” a Bilingual Massive Open Online Course (MOOC) as a New Example for Global Bioinformatics Education. PLoS Comput Biol 10(12): e1003955. (The very first Education paper from China mainland at PLoS Comput Biol) [PubMed]

Invited Book Chapters

  1. He K., Guo A. Y., Gao G., Zhu Q. H., Liu X. C., Zhang H., Chen X., Gu X., Luo J.* 2010. Computational identification of plant transcription factors and the construction of the PlantTFDB database. Methods Mol Biol 674: 351-368. [PubMed]

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