(Click for all publications)
2024
11. Zhe Liu#, Mingxia Zhai#, Weidi Wang#, An Gu, Weichen Song, Jisheng Liang, Shunying Yu*, Guan Ning Lin*
Comprehensive Analysis of Peripheral Transcriptomic and Epigenomic Profiles for Predicting Clinical High-Risk Psychosis Transitions: A Machine Learning Approach.
In submission. 2024
10. Zhe Liu#, Yihang Bao#, Weichen Song, An Gu, Guan Ning Lin*
EMO: Predicting Non-coding Mutation-induced Up-and Down-regulation of Risk Gene Expression using Deep Learning.
In submission. 2024
9. Weidi Wang, Weichen Song, Guan Ning Lin*, Zhen Wang*.
Genomic and genetic characterizations of infancy specifically expressed genes reveal their dominant roles in neuronal system.
In submission. 2024
8. Zhe Liu#, Yihang Bao#, Wenhaoi Li#, Weihao Li, Jinwei Wu, Weidi Wang*，Guan Ning Lin*.
MEMO-stab: Sequence-based Annotation of Mutation Effect on Transmembrane Protein Stability with Protein Language Model-Driven Machine Learning.
Current Research in Biotechnology，Under Review. 2024
7. Zhe Liu#, Yihang Bao#, Shuai Zeng#, Ruiyi Qian, Miaohan Deng, An Gu, Jianye Li, Weidi Wang, Wenxiang Cai，Wenhao Li, Han Wang*, Dong Xu*，Guan Ning Lin*.
Large Language Models in Psychiatry: Current Applications, Limitations, and Future Scope.
Big Data Mining and Analytics，Under Review. 2024
6. Mingxia Zhai，Zhe Liu，Weichen Song, Guan Ning Lin*.
Bidirectional two-sample Mendelian randomization analysis identifies causal associations between gut microbiome and sleep-related traits.
Nutrients, Under Review. 2024
5. Ying Cheng#, Xi Chen#, Xiao Qing Zhang#, Pei Jun Ju, Weidi Wang, Yu Fang, Guan Ning Lin*, Dong Hong Cui*.
The gene polymorphism models of RNF4 and SART3 are associated with the risk of schizophrenia.
Heliyon, In revision. 2024
4. Wenxiang Cai#，Weichen Song#, Shunying Yu, Min Zhao, Guan Ning Lin*.
A small number of human lineage mutations regulated RNA-protein binding of conserved genes and promoted human evolution.
General Psychiatry, Accepted. 2024
3. Weichen Song*, Yongyong Shi*, Guan Ning Lin*.
Haplotype Function Score improves biological interpretation and cross-ancestry polygenic prediction of human complex traits.
Elife, 2024 Apr 19:12:RP92574. doi: 10.7554/eLife.92574
2. Weihao Li#, Zhe Liu#, Yihang Bao, Guan Ning Lin*
Mutation-Drug Sensitivity Data Resource (MDSDR):A Comprehensive Resource for Studying and Addressing Drug Resistance.
ICBCB 2024. (EI).
1. Yihang Bao#, Wenjie Li#, Zehua Sun#, Yuanzhao Guo, Guan Ning Lin*, Han Wang*.
Probing Transmembrane Proteins Binding Domain via Multi-level Molecule Learning.
IEEE International Conference on Bioinformatics and Biomedicine(BIBM2023) (EI) CCF-B 类. 2024
2023
6. Rongwei Zhai, Geya Tong, Zheqin Li, Weichen Song, Yang Hu, Sha Xu, Qiqi Wei, Xiaocheng Zhang, Yi Li, Bingbing Liao, Chenyu Yuan,
Yinqing Fan, Ge Song, Yinyin Ouyang, Wenxuan Zhang, Yaqiu Tang, Minghui Jin, Yuxian Zhang, He Li, Zhi Yang, Guan Ning Lin, Dan J Stein, Zhi-Qi Xiong*, Zhen Wang*.
Rhesus monkeys exhibiting spontaneous ritualistic behaviors resembling obsessive-compulsive disorder.
National Science Review , 08 December 2023, nwad312, https://doi.org/10.1093/nsr/nwad312
(Featured by 中国科学院脑科学与智能技术卓越创新中心、新浪)
5. Zhe Liu#, Yihang Bao#, Weidi Wang, Liangwei Pan, Han Wang*, Guan Ning Lin*.
Emden: A novel method Intergrating Graph and Transformer Representation for Predicting the Effect of Mutations on Clinical Drug Response.
Computers in Biology and Medicine, 10 Nov 2023, Volume 167, 107678.
4. Zhe Liu#, Wei Qian#, Wenxiang Cai#, Weichen Song，Weidi Wang, Dhruba Tara Maharjan, Wenhong Cheng, Jue Chen, Han Wang, Dong Xu*, Guan Ning Lin*.
MIPPI: Inferring the effects of protein variants on protein–protein interactions with interpretable transformer representations.
Research, 11 Sep 2023, Vol 6, Article ID: 0219, DOI: 10.34133/research.0219
3. Xue Jiang, Zhiqi Li, Aamir Mehmood, Heng Wang, Qiankun Wang, Yanyi Chu, Xueying Mao, Jing Zhao, Mingming Jiang, Bowen Zhao, Guan Ning Lin, Edwin Wang & Dongqing Wei.
A Self-attention Graph Convolutional Network for Precision Multi-tumor Early Diagnostics with DNA Methylation Data.
Interdisciplinary Sciences: Computational Life Sciences, 15, 405–418. 2023
2. Jisheng Liang, Zhe Liu, Yihang Bao, Wenxiang Cai and Guan Ning Lin*.
Transformers-RNP: Predicting the mutation effect on the stability of Protein-RNA complex with deep learning-based model.
ACM International Conference Proceeding Series (ICBBS 2023). (EI) CCF-B 类. 2023
1. Zhe Liu#, Mingxia Zhai#, Weichen Song, Yihang Bao, Wenxiang Cai and Guan Ning Lin*.
Assessing the Polygenic Risk between Anxiety and Gut Microbiota Using Machine Learning
ICBCB 2023. (EI)
2022
12. Dhruba Tara Maharjan, Weichen Song, Zhe Liu, Weidi Wang, Wenxiang Cai, Jue Chen, Fei Xu, Wei-hai Ying*, Guan Ning Lin*.
A Comprehensive Study of De Novo Mutations on the Protein-Protein Interaction Interfaces Provides New Insights into Developmental Delay.
Biomolecules 2022, 12(11), 1643c; https://doi.org/10.3390/biom12111643
11. Zhe Liu#, Weihao Pan#, Weihao Li#, Xuyang Zhen, Jisheng Liang, Wenxiang Cai, Fei Xu, Kai Yuan, Guan Ning Lin*.
Evaluation of the Effectiveness of Derived Features of AlphaFold2 on Single-Sequence Protein Binding Site Prediction.
Biology 2022, 11(10), 1454; https://doi.org/10.3390/biology11101454
10. Wenxiang Cai, Weichen Song, Zhe Liu, Dhruba Tara Maharjan, Jisheng Liang, Guan Ning Lin*.
An integrative analysis identified Schizophrenia-associated brain cell types and gene expression changes.
Int. J. Mol. Sci. 2022, 23(19), 11581
9. Kai Yuan, Weichen Song, Zhe Liu, Guan Ning Lin*, Shunying Yu*.
Mendelian Randomization and GWAS Meta Analysis Revealed the Risk-Increasing Effect of Schizophrenia on Cancers.
Biology. 2022 Sep 6, 11(9), 1345
8. Weichen Song, Kai Yuan, Zhe Liu, Wenxiang Cai, Jue Chen, Shunying Yu, Min Zhao*, Guan Ning Lin*.
Loci-level antagonistic selection shaped the polygenic architecture of human complex diseases.
Human Genetics. 2022 Aug, https://link.springer.com/article/10.1007/s00439-022-02471-8
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7. Yueqi Shi, Shaoyi Wang, Shunying Yu, Guan Ning Lin, Weichen Song.
Psychological factors as the risk factor of mouth ulcers: A two-sample Mendelian randomization study.
Journal of Health Psychology. 2022 Jun;27(7):1556-1568.
6. Zhe Liu, Weihao Pan, Xuyang Zhen, Jisheng Liang, Wenxiang Cai, Guan Ning Lin*.
Will AlphaFold2 be Helpful in Improving the Accuracy of Single-sequence PPI Site Prediction?
ICBCB 2022. (EI)
5. Kai Yuan, Weichen Song and Shijie Tang, Guan Ning Lin*, Shunying Yu*.
Two-sample Mendelian randomization study for Schizophrenia and cancers.
ICBCB 2022. (EI)
4. Weichen Song#, Lihua Xu#, Tianhong Zhang, Weidi Wang, Yingmei Fu, Qingqing Xu, Ruixue Yuan, Ailing Ning, Jijun Wang*, Guan Ning Lin*, Shunying Yu*.
Peripheral transcriptome of clinical high-risk psychosis reflects symptom alteration and helps prognosis prediction.
Psychiatry and Clinical Neurosciences. 2022 March 6, https://doi.org/10.1111/pcn.13346 (PMID: 35253315)
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3. Weihao Pan#, Zhe Liu#, Weichen Song, Xuyang Zhen, Kai Yuan, Fei Xu*, Guan Ning Lin*.
An Integrative Segmentation Framework for Cell Nucleus of Fluorescence Microscopy.
Genes. 2022 Feb, 13(3), 431.
2. Weichen Song, Guan Ning Lin, Shunying Yu, Min Zhao*.
Genome-wide identification of the shared genetic basis of cannabis and cigarette smoking and schizophrenia implicates NCAM1 and neuronal abnormality.
Psychiatry Research. 2022 Feb, 310, 114453; https://doi.org/10.1016/j.psychres.2022.114453 （PMID: 35235886）
1. Guan Ning Lin#,*, Weichen Song#, Weidi Wang#, Pei Wang#, Huan Yu, Wenxiang Cai, Xue Jiang, Wu Huang, Wei Qian, Yucan Chen,
Miao Chen, Shunying Yu, Tingting Xu, Yumei Jiao, Qiang Liu, Chen Zhang, Zhenghui Yi, Qing Fan, Jue Chen, Zhen Wang*.
De novo mutations identified by whole-genome sequencing implicate chromatin modifications in obsessive-compulsive disorder.
Science Advances. 2022 Jan, 8(2), eabi6180. DOI: 10.1126/sciadv.abi6180
（全文中文翻译）通过全基因组测序揭示DNM突变与强迫症中的染色质修饰有关
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2021
20. Weichen Song, Weidi Wang, Zhe Liu, Wenxiang Cai, Shunying Yu, Min Zhao, Guan Ning Lin*.
A Comprehensive Evaluation of Cross-Omics Blood-Based Biomarkers for Neuropsychiatric Disorders.
Journal of Personalized Medicine. 2021 Nov, 11(12), 1247; https://doi.org/10.3390/jpm11121247
19. Weichen Song#, Yueqi Shi#, Weidi Wang, Wei Qian, Shunying Yu, Min Zhao, Guan Ning Lin*.
A selection pressure landscape for 870 human polygenic traits.
Nature Human Behaviour. 2021 Nov, 5(12), 1731-1743; https://doi.org/10.1038/s41562-021-01231-4
News & Views from Nature Human Behaviour （同行评价）：Selection still shapes our genome
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18. Xuyang Zhen, Guan Ning Lin*.
PPSNV: A Novel Predictor for Pathogenicity of Nonsynonymous SNV based on Ensemble Learning.
ACM International Conference Proceeding Series (ICBBS 2021). (EI) CCF-B 类
17. Weihao Pan, Zhe Liu, Guan Ning Lin*.
ASW-Net: A Deep Learning-based Tool for Cell Nucleus Segmentation of Fluorescence Microscopy.
ACM International Conference Proceeding Series (ICBBS 2021). (EI) CCF-B 类
16. Huadong Lai, Xiaomu Cheng, Qiang Liu, Wenqin Luo, Mengyao Liu, Man Zhang, Juju Miao,
Zhongzhong Ji, Guan Ning Lin, Weichen Song, Lianhua Zhang; Juanjie Bo, Guoliang Yang, Jia Wang*, Wei-Qiang Gao*.
Single-cell RNA sequencing reveals the epithelial cell heterogeneity and invasive subpopulation in human bladder cancer.
International Journal of Cancer. 2021 Sep 3. 149 (12), 2099-2115.
15. Xue Jiang, Miao Chen, Weichen Song, Guan Ning Lin*.
Label propagation-based semi-supervised feature selection on decoding clinical phenotypes with RNA-seq data.
BMC Medical Genomics. 2021 Aug. 14:141.
14. Kevin Chau, Pan Zhang, Jorge Urresti, Megha Amar, Akula Bala Pramod, Amy Thomas, Roser Corominas, Guan Ning Lin, Lilia M. Iakoucheva.
Full-length isoform transcriptome of the developing human brain provides further insights into autism.
Cell Reports. 2021 Aug. 36(9):109631.
13. Xue Jiang*, Weihao Pan, Miao Chen, Weidi Wang, Weichen Song, Guan Ning Lin*.
Integrative enrichment analysis of gene expression based on an artificial neuron.
BMC Medical Genomics. 2021 Aug. 14:173.
12. Wenqin Luo#, Guan Ning Lin#, Weichen Song#, Yu Zhang, Huadong Lai, Man Zhang, Juju Miao, Xiaomu Cheng, Yongjie Wang,
Wenxiang Wei, Wei-Qiang Gao*, Ru Yang*, Jia Wang*.
Combined single-cell and spatial transcriptomics reveal the precise cellular status of postnatal cerebellar granule cells and connecton with medulloblastoma.
BMC Biology. 2021 July 01.
11. Weichen Song#, Wei Qian#, Weidi Wang, Shunying Yu, Guan Ning Lin*.
Mendelian randomization studies of brain MRI yield insights into the pathogenesis of neuropsychiatric disorders.
BMC Genomics. 2021 June 02.
10. Liang Chen, Wenxiang Cai, Weidi Wang, Zhe Liu, Guan Ning Lin*.
Spatiotemporal 22q11.21 protein network implicates DGCR8-dependent microRNA biogenesis as a risk for late-fetal cortical development in psychiatric diseases.
Life. 2021 May 31.
9. Yucan Chen, Min Liu, Weidi Wang, Li Li*, Guan Ning Lin*.
Loss of Setd2 enhances inflammatory bowel disease through interfering microRNA expression in mice.
Genomics. 2021 May 28.
8. Liang Chen, Weidi Wang, Wenxiang Cai, Weichen Song, Guan Ning Lin*.
Spatiotemporal 7q11.23 protein network analysis reveals DNA repair pathway during early-fetal brain development in psychiatric diseases.
Scientific Reports. 2021 April 15.
7. Weichen Song, Weidi Wang, Shunying Yu, Guan Ning Lin*.
Dissection of the Genetic Association between Anorexia Nervosa and Obsessive–Compulsive Disorder at the Network and Cellular Levels.
Genes. 2021 March 27. (PDF)
6. Dhruba Tara Maharjan, Ali Alamdar Shah Syed*, Guan Ning Lin, Weihai Ying*.
Testosterone in Female Depression: A Meta-Analysis and Mendelian Randomization Study.
Biomolecules. 2021 March 10.
5. Weidi Wang#，Yucan Chen#, Jingjing Zhao, Liang Chen, Weichen Song, Li Li*, Guan Ning Lin*.
Alternatively splicing interactomes identify novel isoform-specific partners for NSD2.
Frontiers in Cell and Developmental Biology. 2021 February 25; 9:612019.
4. Miao Chen, Weidi Wang, Weichen Song, Wei Qian, Guan Ning Lin*.
Integrative Analysis Identified Key Schizophrenia Risk Factors from Abnormal Behavior Mouse Gene Set.
Life. 2021 February 23; 11(2):172. https://doi.org/10.3390/life11020172
3. Zhe Liu, Yingli Gong, Yihang Bao, Yuanzhao Guo, Han Wang*, Guan Ning Lin*.
TMPSS: A Deep Learning-Based Predictor for Secondary Structure and Topology Structure Prediction of Alpha-helical Transmembrane Proteins.
Frontiers in Bioengineering and Biotechnology. 2021 Jan 25
2. Yousong Su, Lu Yang, Zezhi Li, Weidi Wang, Mengjuan Xing, Yu Fang, Ying Cheng, Guan Ning Lin, Donghong Cui.
The interaction of ASAH1 and NGF gene involving in neurotrophin signaling pathway contributes to schizophrenia susceptibility and psychopathology.
Progress in Neuro-Psychopharmacology and Biological Psychiatry. 2021 01 10，104:110015
1. Shi-Yu Peng, Zhe Shi, Dong-Sheng Zhou, Xin-Yue Wang, Xing-Xing Li, Xiao-Li Liu, Wei-Di Wang, Guan Ning Lin, Bing-Xing Pan, Valerie Voon, Anthony A. Grace, Markus Heilig, Ma-Li Wong & Ti-Fei Yuan.
Reduced motor cortex GABABR function following chronic alcohol exposure.
Molecular Psychiatry. 2021-01. https://doi.org/10.1038/s41380-020-01009-6
2020
3. Vikas Pejaver, Jorge Urresti, Jose Lugo-Martinez, Kymberleigh A. Pagel, Guan Ning Lin, Hyun-Jun Nam, Matthew Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney & Predrag Radivojac.
Inferring the molecular and phenotypic impact of amino acid variants with MutPred2.
Nature Communication. 2020 Nov 20. doi.org/10.1038/s41467-020-19669-x
2. Lu Ji, Wei Qian, Liming Gui, Zhongzhong Ji, Pan Yin, Guan Ning Lin, You Wang, Bin Ma, Wei Qiang Gao.
Blockade of β-catenin-induced CCL28 suppresses gastric cancer progression via inhibition of Treg cell infiltration.
Cancer Research. 2020 Mar 10. doi: 10.1158/0008-5472.CAN-19-3074.
1. Xue Jiang#，Jingjing Zhao#，Wei Qian，Weichen Song, Guan Ning Lin*.
A Generative Adversarial Network Model for Disease Gene Prediction with RNA-seq Data.
IEEE Access. 2020 Feb 21. DOI: 10.1109/ACCESS.2020.2975585
2019
9. Xiao Liu#, Weichen Song#, Brandon Y. Wong, Ting Zhang, Shunying Yu, Guan Ning Lin* and Xianting Ding*.
A Comparison and Guideline of Clustering Methods for Mass Cytometry Data.
Genome Biology. 2019 Dec;20:297.
8. Weichen Song#, Yifeng Shen#, Yanhua Zhang, Sufang Peng, Ran Zhang, Ailing Ning, Huafang Li, Xia Li, Guan Ning Lin*, Shunying Yu*.
Expression Alteration of microRNAs in Nucleus Accumbens is Associated with Chronic Stress and Antidepressant Treatment in Rats.
BMC Medical Informatics and Decision Making. 2019 Dec 19;19(Suppl 6):271.
7. Guan Ning Lin#,*, Sijia Guo#, Xian Tan, Weidi Wang, Wei Qian, Weichen Song, Jingru Wang, Shunying Yu, Zhen Wang, Donghong Cui*, Han Wang*.
PsyMuKB: An Integrative Knowledge Base of De Novo Variants in Developmental Disorders.
Genomics Proteomics & Bioinformatics. 2019 Dec 04. https://doi.org/10.1016/j.gpb.2019.10.002
weblink: https://www.psymukb.net/
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6. Xue Jiang, Miao Chen, Weichen Song, Guan Ning Lin*.
Label Propagation Based Semi-supervised Feature Selection to Decode Clinical Phenotype of Huntington’s Disease.
Intelligent Computing Theories and Application. pp 529-542. 2019. (EI)
5. Xue Jiang*, Weihao Pan, Miao Chen, Weidi Wang, Weichen Song, Guan Ning Lin*.
Integrative Enrichment Analysis of Intra- and Inter- Tissues’ Differentially Expressed Genes Based on Perceptron.
Intelligent Computing Theories and Application. pp 93-104. 2019. (EI)
4. Pei wang, Qing Zhao, Tingting Xu, Qiu-meng Gu, Qiang Liu, Yong Wang, Guan Ning Lin, Zhen Wang.
Interaction between PGRN gene and the early trauma on clinical characteristics in patients with obsessive-compulsive disorder.
Journal of Affective Disorders. 23 November 2019.
3. Hai-Long Zhang, Jia-Wen Long, Wei Han, Jiuzhou Wang, Weichen Song, Guan Ning Lin & Dong-Min Yin.
Comparative analysis of cellular expression pattern of schizophrenia risk genes in human versus mouse cortex.
Cell & Bioscience. 2019 Nov, volume 9, Article number: 89
2. Yu Fang, Weidi Wang, Cuizhen Zhu, Guan Ning Lin, Ying Cheng, Junhui Zou, Donghong Cui.
Use of tobacco in schizophrenia: a double-edged sword.
Brain and Behavior. 2019 Oct 11:e01433. doi: 10.1002/brb3.1433.
1. Weidi Wang, Roser Corominas, Guan Ning Lin*.
De novo mutations from whole exome sequencing in neurodevelopmental and psychiatric disorders: from discovery to application.
Frontiers in Genetics. 2019. doi: 10.3389/fgene.2019.00258.
upto - 2018
Pagel KA, Pejaver V, Guan Ning Lin, Nam HJ, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P.
When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants.
Bioinformatics. 2017 Jul 15;33(14):i389-i398. doi: 10.1093/bioinformatics/btx272.
Guan Ning Lin, Corominas R, Nam HJ, Urresti J, Iakoucheva LM.
Comprehensive Analyses of Tissue-Specific Networks with Implications to Psychiatric Diseases.
Methods Mol Biol. 2017;1613:371-402. doi: 10.1007/978-1-4939-7027-8_15.
Brandler WM, Antaki D, Gujral M, Noor A, Rosanio G, Chapman TR, Barrera DJ, Lin GN, Malhotra D, Watts AC, Wong LC, Estabillo JA, Gadomski TE, Hong O, Fajardo KV, Bhandari A, Owen R, Baughn M, Yuan J, Solomon T, Moyzis AG, Maile MS, Sanders SJ, Reiner GE, Vaux KK, Strom CM, Zhang K, Muotri AR, Akshoomoff N, Leal SM, Pierce K, Courchesne E, Iakoucheva LM, Corsello C, Sebat J*.
Frequency and Complexity of De Novo Structural Mutation in Autism.
Am J Hum Genet. 2016 Apr 7;98(4):667-79. doi: 10.1016/j.ajhg.2016.02.018.
(Featured by SFARI)
Guan Ning Lin#, Corominas R#, Lemmens I, Yang X, Tavernier J, Hill DE, Vidal M, Sebat J, Iakoucheva LM.
Spatio-temporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases.
Neuron. 2015 Feb 18;85(4):742-54. doi: 10.1016/j.neuron.2015.01.010. (Issue Highlights).
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Rolland T, Tasan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian S, Yang X, Ghamsari L,
Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis A-R, Convery-Zupan D, Corominas R, Hardy M, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C,
Franzosa E, Gebreab F, Gutierrez BJ, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J,
Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere J, Vega K, Walsh J,
Cusick ME, Xia Y, Barabasi A-L, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M.
A proteome-scale map of the human interactome network.
Cell. 2014 Nov 20;159(5):1212-26.
Corominas R#, Yang X#, Lin GN#, Kang S#, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Trigg SA, Fan C, Yi S, Tasan M, Lemmens I, Kuang X, Zhao N, Malhotra D, Michaelson JJ, Vacic V, Calderwood MA, Roth FP, Tavernier J, Horvath S, Salehi-Ashtiani K, Korkin D, Sebat J, Hill DE, Hao T, Vidal M, Iakoucheva LM.
Protein interaction network of alternativelyspliced isoforms from brain links genetic risk factors for autism.
Nat. Commun. 2014 April 11;5:3650 doi: 10.1038/ncomms4650.
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Michaelson JJ, Shi Y, Gujral M, Zheng H, Malhotra D, Jin X, Jian M, Liu G, Greer D, Bhandari A, Wu W, Corominas R, Peoples A, Koren A, Gore A, Kang S, Lin GN, Estabillo J, Gadomski T, Singh B, Zhang K, Akshoomoff N, Corsello C, McCarroll S, Iakoucheva LM, Li Y, Wang J, Sebat J.
Whole-genome sequencing in autism identifies hot spots for de novo germline mutation.
Cell. 2012 Dec 21;151(7):1431-42.
Lin GN, Zhang C, and Xu D.
Polytomy identification in microbial phylogenetic reconstruction.
BMC System Biology. 2011;5 Suppl 3:S2. doi: 10.1186/1752-0509-5-S3-S2.
Lin GN, Wang Z, Xu D, and Cheng J.
SeqRate: sequence-based protein folding type classification and rates prediction.
BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S1. doi: 10.1186/1471-2105-11-S3-S1.
Lin GN, Cai Z, Lin G, Chakraborty S, and Xu D.
ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets.
BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S5. doi: 10.1186/1471-2105-10-S1-S5.
GP Srivastava, T Joshi, Z Song, C Zhang, Lin GN, P Li, A Ross, M Popescu, J Liu, J Qiu, and D Xu.
GO-based Gene Function and Network Characterization.
Ontology-Based Data Mining in Biomedical Research. Mihail Popescu and Dong Xu eds. Artech House, Norwood, MA, USA. 83-111, 2009.
Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP..
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.
Genome Biol. 2008;9 Suppl 1:S2. doi: 10.1186/gb-2008-9-s1-s2.
Zhang C, Joshi T, Lin GN, Xu D.
An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data.
Int J Comput Biol Drug Des. 2008;1(3):254-74.
Joshi T, Zhang C, Lin GN, Song Z, Xu D.
An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data.
Methods Mol Bio. 2008;439:369-86. doi: 10.1007/978-1-59745-188-8_25.
Allen JO, Fauron CM, Minx P, Roark L, Oddiraju S, Lin GN, Meyer L, Sun H, Kim K, Wang C, Du F, Xu D, Gibson M, Cifrese J, Clifton SW, Newton KJ.
Comparisons among two fertile and three male-sterile mitochondrial genomes of maize.
Genetics. 2007 Oct;177(2):1173-92.
Baker EJ*, Lin GN*, Liu H, Kosuri R.
NFU-Enabled FASTA: moving bioinformatics applications onto wide area networks.
Source Code Biol Med. 2007 Nov 26;2:8. doi: 10.1186/1751-0473-2-8.
