30 Publications (Page 1 of 2)
2021
MOGONET integrates multi-omics data using graph convolutional networks allowing patient classification and biomarker identification.
Wang, TongxinShao, WeiHuang, ZhiTang, HaixuZhang, JieDing, Zhengming and Huang, Kun
Nature communications, vol. 12, (no. 1), pp. 3445, June 8, 2021. | Journal Article
 
ParsVNN: parsimony visible neural networks for uncovering cancer-specific and drug-sensitive genes and pathways.
Huang, XiaoqingHuang, KunJohnson, TravisRadovich, MilanZhang, JieMa, Jianzhu and Wang, Yijie
NAR genomics and bioinformatics, vol. 3, (no. 4), pp. lqab097, December 2021. | Journal Article
 
TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery.
Liu, YusongYe, XiufenYu, Christina YShao, WeiHou, JieFeng, WeixingZhang, Jie and Huang, Kun
BMC bioinformatics, vol. 22, pp. 111, October 25, 2021. | Journal Article
 
TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.
Huang, ZhiHan, ZhiWang Resource, TongxinShao, WeiXiang, ShunianSalama, PaulRizkalla, MaherHuang, Kun and Zhang, Jie
Genomics, proteomics & bioinformatics, March 8, 2021. | Journal Article
 
Weakly Supervised Deep Ordinal Cox Model for Survival Prediction from Whole-slide Pathological Images.
Shao, WeiWang, TongxinHuang, ZhiHan, ZhiZhang, Jie and Huang, Kun
IEEE transactions on medical imaging, vol. PP, July 15, 2021. | Journal Article
2020
A pan-kidney cancer study identifies subtype specific perturbations on pathways with potential drivers in renal cell carcinoma.
Zhan, XiaohuiLiu, YusongYu, Christina YWang, Tian-FuZhang, JieNi, Dong and Huang, Kun
BMC medical genomics, vol. 13, pp. 190, December 28, 2020. | Journal Article
 
Deep learning-based cancer survival prognosis from RNA-seq data: approaches and evaluations
Huang, ZhiHuang, ZhiHuang, ZhiHuang, ZhiZ, HuangHuang, ZhiHuang, ZhiHuang, ZhiJohnson, Travis SJohnson, Travis SJohnson, Travis SJohnson, Travis SJohnson, Travis STS, JohnsonJohnson, Travis SJohnson, Travis SHan, ZhiHan, ZhiHan, ZhiHan, ZhiZ, HanHan, ZhiHan, ZhiHan, ZhiHelm, BryanHelm, BryanHelm, BryanHelm, BryanHelm, BryanHelm, BryanB, HelmHelm, BryanCao, ShaS, CaoCao, ShaCao, ShaCao, ShaCao, ShaCao, ShaCao, ShaZhang, ChiZhang, ChiZhang, ChiZhang, ChiZhang, ChiZhang, ChiC, ZhangZhang, ChiSalama, PaulSalama, PaulSalama, PaulSalama, PaulSalama, PaulSalama, PaulP, SalamaSalama, PaulRizkalla, MaherRizkalla, MaherRizkalla, MaherRizkalla, MaherRizkalla, MaherM, RizkallaRizkalla, MaherRizkalla, MaherCY, YuYu, Christina YYu, Christina YYu, Christina YYu, Christina YYu, Christina YYu, Christina YYu, Christina YCheng, JunJ, ChengCheng, JunCheng, JunCheng, JunCheng, JunCheng, JunCheng, JunXiang, ShunianXiang, ShunianXiang, ShunianXiang, ShunianS, XiangXiang, ShunianXiang, ShunianXiang, ShunianZhan, XiaohuiZhan, XiaohuiZhan, XiaohuiZhan, XiaohuiZhan, XiaohuiX, ZhanZhan, XiaohuiZhan, XiaohuiZhang, JieZhang, JieZhang, JieZhang, JieZhang, JieZhang, JieJ, ZhangZhang, JieHuang, KunHuang, KunHuang, KunHuang, KunHuang, KunHuang, KunHuang, Kun and K, Huang
BMC Medical Genomics, vol. 13, pp. 1-12, 2020. | Journal Article
 
Deep-Learning-Based Characterization of Tumor-Infiltrating Lymphocytes in Breast Cancers From Histopathology Images and Multiomics Data.
Lu, ZixiaoXu, SiwenShao, WeiWu, YiZhang, JieHan, ZhiFeng, Qianjin and Huang, Kun
JCO clinical cancer informatics, vol. 4, pp. 480-490, May 2020. | Journal Article
 
Liquid biopsy in the clinical management of bladder cancer: current status and future developments.
Kouba, ErikKouba, ErikLopez-Beltran, AntonioLopez-Beltran, AntonioMontironi, RodolfoMontironi, RodolfoMassari, FrancescoMassari, FrancescoHuang, KunHuang, KunSantoni, MatteoSantoni, MatteoChovanec, MichalChovanec, MichalCheng, MichaelCheng, MichaelScarpelli, MarinaScarpelli, MarinaZhang, JieZhang, JieCimadamore, AlessiaCimadamore, AlessiaCheng, Liang and Cheng, Liang
Expert review of molecular diagnostics, vol. 20, (no. 2), pp. 255-264, February 2020. | Journal Article
 
Multi-task multi-modal learning for joint diagnosis and prognosis of human cancers
Shao, WeiShao, WeiWang, TongxinWang, TongxinSun, LiangSun, LiangDong, TianhanDong, TianhanHan, ZhiHan, ZhiHuang, ZhiHuang, ZhiZhang, JieZhang, JieZhang, DaoqiangZhang, DaoqiangHuang, Kun and Huang, Kun
Medical Image Analysis, vol. 65, Oct 2020. | Journal Article
 
Vascular amyloid accumulation alters the gabaergic synapse and induces hyperactivity in a model of cerebral amyloid angiopathy.
Cisternas, P.Cisternas, PabloTaylor, X.Taylor, XavierPerkins, A.Perkins, AbigailMaldonado, O.Maldonado, OrlandoAllman, ElysabethAllman, E.Cordova, RicardoCordova, R.Marambio, Y.Marambio, YamilMunoz, B.Munoz, BraulioPennington, TaylorPennington, T.Xiang, ShunianXiang, S.Zhang, JieZhang, J.Vidal, RubenVidal, R.Atwood, B.Atwood, BradyLasagna-Reeves, Cristian A and Lasagna-Reeves, C.A.
Aging cell, vol. 19, (no. 10), pp. e13233, October 2020. | Journal Article
2019
BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes
Wang, TongxinJohnson, TravisShao, WeiLu, ZixiaoHelm, BryanZhang, Jie and Huang, Kun
Genome Biology (Online Edition), vol. 20, (no. 1), pp. 165, 2019-12-00. | Journal Article
 
Correlation Analysis of Histopathology and Proteogenomics Data for Breast Cancer.
Zhan, XiaohuiZhan, XiaohuiCheng, JunCheng, JunHuang, ZhiHuang, ZhiHan, ZhiHan, ZhiHelm, BryanHelm, BryanLiu, XiaowenLiu, XiaowenZhang, JieZhang, JieWang, Tian-FuWang, Tian-FuNi, DongNi, DongHuang, Kun and Huang, Kun
Molecular & cellular proteomics : MCP, vol. 18, (no. 8S1), pp. S37-S51, August 9, 2019. | Journal Article
 
Generalized gene co-expression analysis via subspace clustering using low-rank representation
Wang, TongxinZhang, Jie and Huang, Kun
BMC bioinformatics, vol. 20, (no. Suppl 7), pp. 196, 2019-May-01. | Journal Article
2018
Mutational Mechanisms That Activate Wnt Signaling and Predict Outcomes in Colorectal Cancer Patients
Hankey, WilliamHankey, WilliamMcIlhatton, Michael AMcIlhatton, Michael AKenechi, EbedeEbede, KenechiKennedy, BrianKennedy, BrianHancioglu, BarisZhang, JieZhang, JieBrock, Guy NBrock, Guy NHuang, KunHuang, KunGroden, Joanna and Groden, Joanna
Cancer Research, vol. 78, (no. 3), pp. 617-630, Feb 1, 2018. | Journal Article
2017
Pan-cancer analysis of frequent DNA co-methylation patterns reveals consistent epigenetic landscape changes in multiple cancers
Zhang, JieZhang, JieHuang, Kun and Huang, Kun
BMC Genomics, vol. 18, pp. 1-14, 2017. | Journal Article
2016
Exome‐wide single‐base substitutions in tissues and derived cell lines of the constitutive Fhit knockout mouse
Paisie, Carolyn APaisie, Carolyn ASchrock, Morgan SSchrock, Morgan SKarras, Jenna RKarras, Jenna RZhang, JieZhang, JieMiuma, SatoshiMiuma, SatoshiOuda, Iman MOuda, Iman MWaters, Catherine EWaters, Catherine ESaldivar, Joshua CSaldivar, Joshua CDruck, TeresaDruck, TeresaHuebner, Kay and Huebner, Kay
Cancer Science, vol. 107, (no. 4), pp. 535, April 2016. | Journal Article
 
Fhit loss‐associated initiation and progression of neoplasia in vitro
Karras, Jenna RKarras, Jenna RSchrock, Morgan SSchrock, Morgan SBatar, BahadirBatar, BahadirZhang, JieZhang, JieLa Perle, KristaLa Perle, KristaDruck, TeresaDruck, TeresaHuebner, Kay and Huebner, Kay
Cancer Science, vol. 107, (no. 11), pp. 1598, November 2016. | Journal Article
 
Normalized lmQCM: An Algorithm for Detecting Weak Quasi-Cliques in Weighted Graph with Applications in Gene Co-Expression Module Discovery in Cancers
Zhang, Jie and Huang, Kun
Cancer Informatics, vol. 2014, (no. Suppl. 3), pp. 146, 2016-07-24. | Journal Article
 
Visceral Adipose MicroRNA 223 Is Upregulated in Human and Murine Obesity and Modulates the Inflammatory Phenotype of Macrophages
Deiuliis, Jeffrey ADeiuliis, Jeffrey ADeiuliis, Jeffrey ASyed, RafayDuggineni, DheerajDuggineni, DheerajDuggineni, DheerajRutsky, JessicaRutsky, JessicaRutsky, JessicaRengasamy, PalanivelZhang, JieZhang, JieZhang, JieHuang, KunHuang, KunHuang, KunNeedleman, BradleyNeedleman, BradleyNeedleman, BradleyMikami, DeanMikami, DeanMikami, DeanPerry, KylePerry, KylePerry, KyleHazey, JeffreyHazey, JeffreyHazey, JeffreyRajagopalan, SanjayRajagopalan, Sanjay and Rajagopalan, Sanjay
PLoS One, vol. 11, (no. 11), Nov 2016. | Journal Article
2013
Analysis of BRCA1 variants in double-strand break repair by homologous recombination and single-strand annealing.
Towler, William ITowler, William IZhang, JieZhang, JieRansburgh, Derek JRansburgh, Derek J RToland, Amanda EToland, Amanda EIshioka, ChikashiIshioka, ChikashiChiba, NatsukoChiba, NatsukoParvin, Jeff and Parvin, Jeffrey D
Human mutation, vol. 34, (no. 3), pp. 439-445, March 2013. | Journal Article
 
Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
Bailey, TimothyBailey, TimothyKrajewski, PawelKrajewski, PawelLadunga, SteveLadunga, IstvanLefebvre, CelineLefebvre, CelineLi, QunhuaLi, QunhuaLiu, TaoLiu, TaoMadrigal, PedroMadrigal, PedroTaslim, CennyTaslim, CennyZhang, Jie and Zhang, Jie
PLoS computational biology, vol. 9, (no. 11), pp. e1003326, 2013-00-00. | Journal Article
2012
Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes.
Liu, Hui-wenLiu, Hui-wenZhang, JieZhang, JieHeine, George FHeine, GeorgeArora, MansiArora, MansiGulcin Ozer, HaticeGulcin Ozer, HaticeOnti-Srinivasan, RaghuramOnti-Srinivasan, RaghuramHuang, KunHuang, KunParvin, Jeffrey D and Parvin, Jeffrey D
Nucleic acids research, vol. 40, (no. 20), pp. 10172-10186, November 1, 2012. | Journal Article
 
Identifying common genes and networks in multi-organ fibrosis.
Wenzke, Kevin EWenzke, Kevin ECantemir-Stone, CarmenCantemir-Stone, CarmenZhang, JieZhang, JieMarsh, Clay BMarsh, Clay BHuang, Kun and Huang, Kun
AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science, vol. 2012, pp. 106-115, 2012. | Journal Article
 
Promoters active in interphase are bookmarked during mitosis by ubiquitination.
Arora, MansiArora, MansiZhang, JieZhang, JieHeine, GeorgeHeine, George FOzer, GulcinOzer, GulcinLiu, Hui-wenLiu, Hui-wenHuang, KunHuang, KunParvin, Jeffrey D and Parvin, Jeffrey D
Nucleic acids research, vol. 40, (no. 20), pp. 10187-10202, November 1, 2012. | Journal Article