Publications – Laboratory for Statistical and Translational Genomics

2025

Coleman K.*, Schroeder A., Loth M., Zhang D., Park J.H., Blank N., Cowan A.J., Qian X., Chen J., Jiang J., Yan H., Samarah L.Z., Clemenceau J.R., Jang I., Kim M., Barnfather I., Rabinowitz J.D., Deng Y., Lee E.B., Lazar A., Gao J., Furth E.E., Hwang T.H., Wang L., Thaiss C.A., Hu J.*, Li M.*: Resolving tissue complexity by multi-modal spatial omics modeling with MISO. Nature Methods, 22(3):530-538, 2025 (* Co-corresponding authors).
Guo P., Mao L., Chen Y., Lee C.N., Cardilla A., Li M., Bartosovic M., Deng Y.: Multiplexed spatial mapping of chromatin features, transcriptome and proteins in tissues. Nature Methods, 22(3):520-529, 2025.
Moffitt J.R., Li M., Nie Q., Kanemaru K., Teichmann S.A., Dar D., Kagohara L.T., Itzkovitz S., Vento-Tormo R., Yanai I., Fertig E.J., Theis F.J.: What is the main bottleneck in deriving biological understanding from spatial transcriptomic profiling? Cell Systems, 16(2):101200, 2025.
Pei G., Min J., Rajapakshe K., Branchi V., Liu Y., Chellakkan B., Thege F., Sadeghian D., Zhang D., Cho K., Chu Y., Dai E., Han G., Li M., Yee C., Takahashi K., Garg B., Tiriac H., Bernard V., Semaan A., Grem J., Caffrey T., Burks J., Lowy A., Aguirre A., Grandgenett P., Hollingsworth M., Guerrero P., Wang L., Anirban M.: Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer. Nature, 642(8066):212-221, 2025.
Qian X.^#*, Coleman K.^#, Jiang S.^#, Kriz A.J., Marciano J.H., Luo C., Cai C., Manam M.D., Caglayan E., Otani A., Ghosh U., Shao D.D., Andersen R.E., Neil J.E., Johnson R., LeFevre A., Hecht J.L., Miller M.B., Sun L., Stringer C., Li M.*, Walsh C.*: Spatial single-cell analysis decodes cortical layer and area specification. Nature, 644(8075):153-163, 2025 (^# co-first authors; * Co-corresponding authors).
Litchevskiy L., Considine M., Gill J., Shandar V., Cox T.O., Descamps H.C., …., Li M., Thaiss C.A.: Gut metagenomes reveal interactions between dietary restriction, aging, and the microbiome in genetically diverse mice. Nature Microbiology, 10(5):1240-1257, 2025.
Liu Y., Sinjab A., Min J., Han G., Paradiso F., Zhang Y., Wang R., Pei G., Dai Y., Liu Y., Cho K.S., Dai E., Basi A., Burks J.K., Rajapakshe K.I., Chu Y., Jiang J., Zhang D., Yan X., Guerrero P.A., Serrano A., Li M., Hwang T.H., Futreal A., Ajani J.A., Solis Soto L.M., Jazaeri A.A., Kadara H., Maitra A., Wang L.: Conserved spatial subtypes and cellular neighborhoods of cancer-associated fibroblasts revealed by single-cell spatial multi-omics. Cancer Cell, 43(5):905-924, 2025.
Schroeder A., Loth M., Yao S., Luo C., Zhang D., Piya S., Plowey E., Hu W., Clemenceau J.R., Jang I., Kim M., Barnfather I., Chan S.J., Reynolds T.L., Carlile T., Cullen P., Tsai H.-H., Park J.H., Hwang T.H.*, Zhang B.*, Li M.*: Scaling up spatial transcriptomics for large-sized tissues: uncoverying cellular architecture beyond conventional platforms. Nature Methods, 22(9):1911-1922, 2025 (* co-corresponding authors).
Yuan M., Jin K., Schroeder A., Luo C., Yao S., Domoulin B., Levinsohn J., Luo T., Clemenceau J.R., Jang I., Kim M., Liu Y., Deng M., Furth E.E., Wilson P., Nayak A., Lubo I., Solis Soto L.M., Wang L., Park J.H., Susztak K., Hwang T.H., Li M.: Designing smart spatial omics experiments with S2Omics. Nature Cell Biology, accepted, 2025.

2024

Lee M.Y.Y. and Li M.: Integration of multi-modal single-cell data. Nature Biotechnology, 42(2):190-191, 2024.
Han G., Sinjab A., Rahal Z., Lynch A.M., Treekitkarnmongkol W., Liu Y., Serrano A.G., Feng J., Liang K., Khan K., Lu W., Hernandez S.D., Liu Y., Cao X., Dai E., Pei G., Hu J., Abaya C., Gomez-Bolanos L.I., Peng F., Chen M., Parra E.R., Cascone T., Sepesi B., Moghaddam S.J., Scheet P., Negrao M.V., Heymach J.V., Li M., Dubinett S.M., Stevenson C.S., Spira A.E., Fujimoto J., Solis L.M., Wistuba I.I., Chen J., Wang L., Kadara H.: An atlas of epithelial cell states and plasticity in lung adenocarcinoma. Nature, 627:656-663, 2024.
Zhang D., Schroeder A., Yan H., Yang H., Hu J., Lee M.Y.Y., Cho K.S., Susztak K., Xu G.X., Feldman M.D., Lee E.B., Furth E.E., Wang L., Li M. Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology. Nature Biotechnology, 42:1372-1377, 2024.
Bashore A.C., Chung A., Ibikunle C., Yan H., Xue C., Li M., Bauer R.C., Reilly M.P. Single-cell multimodal profiling of atherosclerosis identifies CD200 as a cell surface lineage marker of vascular smooth muscle cells and their derived cells. Circulation, 149:1231–1233, 2024.
Wang L., Li M., Hwang T.H. The 3D revolution in cancer discovery. Cancer Discovery, 14 (4): 625–629, 2024.
Bashore A.C., Yan H., Xue C., Zhu L.Y., Kim E., Mawson T., Coronel J., Chung A., Sachs N., Ho S., Ross L.S., Kissner M., Passegué E., Bauer R.C., Maegdefessel L., Li M., Reilly M.P. High-dimensional single-cell multimodal landscape of human carotid atherosclerosis. Atherosclerosis, Thrombosis, and Vascular Biology, 44:930–945, 2024.
Ho P.C., Yu W.H., Tee B.L., Lee W.P., Li C., Gu Y., Yokoyama J.S., Reyes-Dumeyer D., Choi Y.B., Yang H.S., Vardarajan B.N., Tzuang M., Lieu K., Lu A., Faber K.M., Potter Z.D., Revta C., Kirsch M., McCallum J., Mei D., Booth B., Cantwell L.B., Chen F., Chou S., Clark D., Deng M., Hong T.H., Hwang L.J., Jiang L., Joo Y., Kang Y., Kim E.S., Kim H., Kim K., Kuzma A.B., Lam E., Lanata S.C., Lee K., Li D., Li M., Li X., Liu C.L., Liu C., Liu L., Lupo J.L., Nguyen K., Pfleuger S.E., Qian J., Qian W., Ramirez V., Russ K.A., Seo E.H., Song Y.E., Tartaglia M.C., Tian L., Torres M., Vo N., Wong E.C., Xie Y., Yau E.B., Yi I., Yu V., Zeng X., St George-Hyslop P., Au R., Schellenberg G.D., Dage J.L., Varma R., Hsiung G.R., Rosen H., Henderson V.W., Foroud T., Kukull W.A., Peavy G.M., Lee H., Feldman H.H., Mayeux R., Chui H., Jun G.R., Ta Park V.M., Chow T.W., Wang L.S. Asian cohort for Alzheimer’s disease (ACAD) pilot study on genetic and non-genetic risk factors for Alzheimer’s disease among Asian Americans and Canadians. Alzheimer’s and Dementia, 20(3):2058-2071, 2024.
Weinstein S.M., Vandekar S.N., Li B., Alexander-Bloch A.F., Raznahan A., Li M., Gur R.E., Gur R.C., Roalf D.R., Park M.T.M., Chakravarty M., Baller E.B., Linn K.A., Satterthwaite T.D., Shinohara R.T.: Network enrichment significance testing in brain-phenotype association studies. Human Brain Mapping, 45(8):e26714, 2024.
Coleman K., Schroeder A., Li M.: Unlocking the power of spatial omics with AI. Nature Methods, 21:1378-1381, 2024.
Bashore A.C., Xue C., Kim E., Yan H., Zhu L.Y., Pan H., Kissner M., Ross L.S., Zhang H., Li M., Reilly M.P.: Monocyte single-cell multimodal profiling in cardiovascular disease risk states. Circulation Research, 135(6):685-700, 2024.
Hu F., Lucas A., Chen A.A., Coleman K., Horng H., Ng R.W.S., Tustison N.J., Davis K.A., Shou H., Li M., Shinohara R.T.: DeepComBat: a statistically motivated, hyperparameter-robust, deep learning approach to harmonization of neuroimaging data. Human Brain Mapping, 45(11):e26708, 2024.
Bai Z., Zhang D., Gao Y., Tao B., Zhang D., Bao S., Enninful A., Wang Y., Li H., Su G., Tian X., Zhang N., Xiao Y., Liu Y., Gerstein M., Li M.*, Xing Y.*, Lu J.*, Xu M.*, Fan R.*: Spatially exploring RNA biology in archival formalin-fixed prafiin-embedded tissues. Cell, 187(23):6760-6779, 2024 (* Co corresponding author).
Abedini A., Levinsohn J., Klotzer K.A., Dumoulin B., Ma Z., Frederick J., Dhillon P., Balzer B.S., Shrestha R., Liu H., Vitale S., Bergeson A.M., Devalaraja-Narashimha K., Grandi P., Bhattacharyya T., Hu E., Pullen S.S., Boustany-Kari C.M., Guarnieri P., Karihaloo A., Traum D., Yan H., Coleman K., Palmer M., Sarov-Blat L., Morton L., Hunter C.A., Kaestner K.H., Li M., Susztak K.: Single-cell multi-omic and spatial profiling of human kidneys implicates the fibrotic microenvironment in kidney disease progression. Nature Genetics, 56(8):1712-1724, 2024.
Yu H., Nagi S.S., Usoskin D., Hu Y., Kupari J., Bouchatta O., Yan H., Cranfill S.L., Gautam M., Su Y., Lu Y., Wymer J., Glanz M., Albrecht P., Song H., Ming G.-L., Prouty S., Seykora J., Wu H., Ma M., Marshall A., Rice F.L., Li M., Olausson H., Emfors P., Luo W.: Single-soma deep RNA sequencing of human dorsal root ganglion neurons reveals novel molecular and cellular mechansims underlying somatosensation. Nature Neuroscience, 27(12):2326-2340, 2024.

2023

Lundgren P., Sharma P.V., Dohnalová L., Coleman K., Uhr G.T., Kircher S., Litichevskiy L., Bahnsen K., Descamps H.C., Demetriadou C., Chan J., Chellappa K., Cox T.O., Heyman Y., Pather S.R., Shoffler C., Petucci C., Shalem O., Raj A., Baur J.A., Snyder N.W., Wellen K.E., Levy M., Seale P., Li M., Thaiss C.A. A subpopulation of lipogenic brown adipocytes drives thermogenic memory. Nature Metabolism, 5:1691–1705, 2023.
Lee M.Y.Y., Kaestner K.H., Li M. Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data. Genome Biology, 24:244, 2023.
Dai D., Li M., Lee E.B. Human Alzheimer’s disease reactive astrocytes exhibit a loss of homeostatic gene expression. Acta Neuropathologica Communications 11(1):127, 2023.
Yanai I., Fertig E.J., Li M., Coscia F., Klughammer J., Nie Q., Chen J., Coskun A.F. What do you most hope spatial molecular profiling will help us understand? Cell Systems, 7:543-546, 2023.
Kim J., Nath K., Schmidlin K., Schaufelberger H., Quattropani C., Vannini S., Mossi S., Thumshirn M., Manz M., Litichevskiy L., Fan J., Dmitrieva-Posocco O., Li M., Levy M., Schär P., Zwahlen M., Thaiss C.A., Truninger K. Hierarchical contribution of individual lifestyle factors and their interactions on adenomatous and serrated polyp risk. Journal of Gastroenterology, 58(9):856-867, 2023.
Zhang Q.*, Jiang S.*, Schroeder A.*, Hu J., Li K., Zhang B., Dai D., Lee E.B., Xiao R., Li M. Leveraging spatial transcriptomics data to recover cell locations in single-cell RNA-seq with CeLEry. Nature Communications, 14(1):4050, 2023.
Chu Y., Dai E., Li Y., Han G., Pei G., Ingram D.R., Thakkar K., Qin J.-J., Dang M., Le X., Hu C., Deng Q., Siniab A., Gupta P., Wang R., Hao D., Peng F., Peng F., Yan X., Liu Y., Song S., Zhang S., Heymach J.V., Reuben A., Elamin Y.Y., Pizzi M.P., Lu Y., Lazcano R., Hu J., Li M., Curran M., Futreal A., Maitra A., Jazaeri A.A., Ajani J.A., Swanton C., Deng X.-D., Abbas H.A., Gillison M., Bhat K., Lazar A.J., Green M., Litchfield K., Kadara H., Yee C., Wang L. Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistence. Nature Medicine, 29(6):1550-1562, 2023.
Hu J., Coleman K., Lee E.B., Kadara H., Wang L.*, Li M.* Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA. Cell Systems, 14(5):404-417.e4, 2023.
Hu F., Chen A.A., Horng H., Bashyam V., Davatzikos C., Alexander-Bloch A., Li M., Shou H., Satterthwaite T.D., Yu M., Shinohara R.T. Image harmonization: a review of statistical and deep learning methods for removing batch effects and evaluation metrics for effective harmonization. Neuroimage, 274:120125, 2023.
Coleman K., Hu J., Schroeder A., Lee E.B., Li M. SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning. Communications Biology, 6(1):378, 2023.
Cynn E., Li D.Y., O’Reilly M.E., Wang Y., Bashore A.C., Jha A., Foulkes A.S., Zhang H., Winter H., Maegdefessel L., Yan H., Li M., Ross L., Xue C., Reilly M.P. Human macrophage long intergenic noncoding RNA, SIMALR, suppresses inflammatory macrophage apoptosis via NTN1 (Netrin-1). Arterioscler Thromb Vasc Biol, 43(2):286-299, 2023.

2022

Lakkis J, Schroeder A, Su K, Lee MYY, Bashore AC, Reilly MP, Li M. A multi-use deep learning method for CITE-seq and single-cell RNA-seq data integration with cell surface protein prediction and imputation. Nature Machine Intelligence, 4(11):940-952, 2022.
Auerbach BJ, FitzGerald GA, Li M. Tempo: an unsupervised Bayesian algorithm for circadian phase inference in single-cell transcriptomics. Nature Communications, 13(1):6580, 2022.
Fan J., Lyu Y., Zhang Q., Wang X., Li M.*, Xiao R.* MuSiC2: cell-type deconvolution for multi-condition bulk RNA-seq data. Briefings in Bioinformatics, 23(6):bbac430, 2022.
Dang M.., Wang R., Chu Y., Song X., Zhang J., Parra E.R., Wargo J.A., Swisher S.G., Cascone T., Sepesi B., Futreal A.P., Li M., Dubinett S.M., Fujimoto J., Solis Soto L.M., Wistuba I.I., Stevenson C.S., Spira A., Shalapour S., Kadara H., Wang L. The Single-cell immunogenomic landscape of B and plasma cells in early-stage lung adenocarcinoma. Cancer Discovery, 12(11):2626-2645, 2022.
Chen C., Leung Y.Y., Ionita M., Wang L.S.*, Li M.* Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge. Bioinformatics, 38(19):4530-4536, 2022.
Zauhar R., Biber J., Jabri Y., Kim M., Hu J., Kaplan L., Pfaller A.M., Schäfer N., Enzmann V., Schlötzer-Schrehardt U., Straub T., Hauck S.M., Gamlin P.D., McFerrin M.B., Messinger J., Strang C.E., Curcio C.A., Dana N., Pauly D.*, Grosche A.*, Li M.*, Stambolian D.* As in real estate, location matters: cellular expression of complement varies between macular and peripheral regions of the retina and supporting tissues. Frontiers Immunology, 13:895519, 2022.
Sterling J.K., Baumann B., Foshe S., Voigt A., Guttha S., Alnemri A., McCright S.J., Li M., Zauhar R.J., Montezuma S.R., Kapphahn R.J., Chavali V.R.M., Hill D.A., Ferrington D.A., Stambolian D., Mullins R.F., Merrick D., Dunaief J.L. Inflammatory adipose activates a nutritional immunity pathway leading to retinal dysfunction. Cell Reports, 39(11):110942, 2022.
Dmitrieva-Posocco O., Wong A.C., Lundgren P., Golos A.M., Descamps H.C., Dohnalová L., Cramer Z., Tian Y., Yueh B., Eskiocak O., Egervari G., Lan Y., Liu J., Fan J., Kim J., Madhu B., Schneider K.M., Khoziainova S., Andreeva N., Wang Q., Li N., Furth E.E., Bailis W., Kelsen J.R., Hamilton K.E., Kaestner K.H., Berger S.L., Epstein J.A., Jain R., Li M., Beyaz S., Lengner C.J., Katona B.W., Grivennikov S.I., Thaiss C.A., Levy M. β-Hydroxybutyrate suppresses colorectal cancer Nature, 605(7908):160-165, 2022.
Zhong L., Yao L., Holdreith N., Yu W., Rui T., Miao Z., Elkaim Y., Li M., Gong Y., Pacifici M., Maity A., Busch T.M., Joeng K.S., Cengel K., Seale P., Tong W., Qin L. Transient expansion and myofibroblast conversion of adipogenic lineage precursors mediate bone marrow repair after radiation. JCI Insight, 87(7):e150323, 2022.
Bellenguez C., Kuçukali F., Jansen I., Kleineidam L., Moreno-Grau S., Amin N., Naj A., Campos-Martin R., …, Li M., …, Schellenberg G., van Duijn C., Sims R., van der Flier W., Ruiz A., Ramirez A., Lambert J.C.. New insights into the genetic etiology of Alzheimer’s disease and related dementias. Nature Genetics, 54:412–436, 2022.
Ma W.F., Hodonsky C.J., Turner A.W., Wong D., Song Y., Mosquera J.V., Ligay A.V., Slenders L., Gancayco C., Pan H., Barrientos N.B., Mai D., Alencar G.F., Owsiany K., Owens G.K., Reilly M.P., Li M., Pasterkamp G., Mokry M., van der Laan S.W., Khomtchouk, B.B., Clint C.L. Enhanced single-cell RNA-seq workflow reveals coronary artery disease cellular cross-talk and candidate drug targets. Atherosclerosis, 340:12-22, 2022.

2021

Lu C., Glisovic-Aplenc T., Bernt K.M., Nestler K., Cesare J., Cao L., Lee H., Fazelinia H., Chinwalla A., Xu Y., Shestova O., Xing Y., Gill S., Li M., Garcia B., Aplenc R.J. Longitudinal large-scale semiquantitative proteomic data stability across multiple instrument platforms. Journal of Proteome Research, 20(11):5203-5211, 2021.
Hu J., Li X., Coleman K., Schroeder A., Irwin D.J., Lee E.B., Shinohara R.T., Li M. SpaGCN: integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network. Nature Methods, 18: 1342–1351, 2021.
Auerbach B.J., Hu J., Reilly M.P., Li M. Applications of single-cell genomics and computational strategies to study common disease and population-level variation. Genome Research, 31: 1719–1727, 2021.
Lakkis J., Wang D., Zhang Y., Hu G., Wang K., Pan H., Ungar L., Reilly M.P., Li X., Li M. A joint deep learning model enables simultaneous denoising, batch effect correction and clustering in single-cell transcriptomics. Genome Research, 31: 1753–1766, 2021.
Sheng X., Guan Y., Ma Z., Wu J., Liu H., Qiu C., Vitale S., Miao Z., Seasock M.J., Palmer M., Shin M.K., Duffin K.L., Pullen S.S., Edwards T., Hellwege J.N., Hung A.M., Li M., Voight B.F., Coffman T.M., Brown C.D., Susztak K. Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments. Nature Genetics, doi: 10.1038/s41588-021-00909-9, 2021.
Lyu Y., Zauhar R., Dana N., Strang C.E., Wang K., Liu S., Pan N., Gamlin P., Kimble J.A., Messinger J.D., Curcio C.A., Stambolian D., Li M. Implications of specific retinal cell-type involvement and gene expression changes in AMD progression using integrative analysis of single-cell and bulk RNA-seq profiling. Scientific Reports, 11: 15612, 2021.
Choa R., Tohyama J., Wada S., Meng H., Hu J., Okumura M., May R.M., Robertson T.F., Pai R.-A. L., Nace A., Hopkins C., Jacobsen E.A., Haldar M., FitzGerald G.A., Behrens E.M., Minn A.J., Seale P., Cotsarelis G., Kim B., Sekyora J.T., Li M., Arany Z., Kambayashi T. Thymic stromal lymphopoietin induces adipose loss through sebum hyper secretion. Science, 373(6554):eabd2893, 2021.
Pluta J., Pyle L.C., Nead K.T., Wilf R., Li M., Mitra N., Weathers B., D’Andrea K., …, Kanetsky P.A., Nathanson K.L.. Testicular Cancer Consortium. Identification of 22 susceptibility loci associated with testicular germ cell tumors. Nature Communications, 12(1):4487, 2021.
Hu J., Schroeder A., Coleman K., Chen C., Auerbach B.J., Li M. Statistical and machine learning methods for spatially resolved transcriptomics with histology. Computational and Structural Biotechnology Journal, 19: 3829-3841, 2021.
Hu J., Li M. Discussion of “Exponential-Family Embedding With Application to Cell Developmental Trajectories for Single-Cell RNA-Seq Data”. Journal of the American Statistical Association, 116(534):475-477, 2021.
Hu Y., Fang L., Chen X., Zhong J.F., Li M., Wang K. LIQA: long-read isoform quantification and analysis. Genome Biology, 22(1):182, 2021.
Miao Z., Balzer M.S., Ma Z., Liu H., Wu J., Shrestha R., Aranyi T., Kwan A., Kondo A., Pontoglio M., Kim J., Li M., Kaestner K.H., Susztak K. Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. Nature Communications, 12(1):2277, 2021.
Fan J., Wang X., Xiao R.*, Li M.* Detecting cell-type-specific allelic expression imbalance by integrative analysis of bulk and single-cell RNA sequencing data. PLOS Genetics, 17(3):e1009080, 2021.
Wang L., Breton C., Warzecha C.C., Bell P., Yan H., He Z., White J., Zhu Y., Li M., Buza E.L., Jantz D., Wilson J.M. Long-term stable reduction of low-density lipoprotein in nonhuman primates following in vivo genome editing of PCSK9. Molecular Therapy, S1525-0016(21)00087-3, 2021.
Dhillon P., Park J., Hurtado Del Pozo C., Li L., Doke T., Huang S., Zhao J., Kang H.M., Shrestra R., Balzer M.S., Chatterjee S., Prado P., Han S.Y., Liu H., Sheng X., Dierickx P., Batmanov K., Romero J.P., Prósper F., Li M., Pei L., Kim J., Montserrat N., Susztak K. The nuclear receptor ESRRA protects from kidney disease by coupling metabolism and differentiation. Cell Metabolism, 33(2):379-394, 2021.
Wang R., Dang M., Harada K., Han G., Wang F., Pizzi M.P., Zhao M., Tatlonghari G., Zhang S., Hao D., Lu Y., Zhao S., Badgwell B.D., Murphy M.B., Shanbhag N., Estrella J.S., Roy-Chowdhuri S., Abdelhakeen A.A.F., Wang Y., Peng G., Hanash S., Calin G.A., Song X., Chu Y., Zhang J., Li M., Chen K., Lazar A.J., Futreal A., Song S., Ajanı J.A., Wang L. Single-cell dissection of intratumoral heterogeneity and lineage diversity in metastatic gastric adenocarcinoma. Nature Medicine, 27(1):141-151, 2021.

2020

Hordeaux J., Buza E.L., Jeffrey B., Song C., Jahan T., Yuan Y., Zhu Y., Bell P., Li M., Chichester J.A., Calcedo R., Wilson J.M. MicroRNA-mediated inhibition of transgene expression reduces dorsal root ganglion toxicity by AAV vectors in primates. Science Translational Medicine 12(569):eaba9188, 2020.
Palumbo S.A., Adamson K.M., Krishnamurthy S., Manoharan S., Beiler D., Seiwell A., Young C., Metpally R., Crist R.C., Doyle G.A., Ferraro T.N., Li M., Berrettini W.H., Robishaw J.D., Troiani V. Assessment of probable opioid use disorder using Electronic Health Record documentation. JAMA Network Open 3(9):e2015909, 2020.
Hu J., Li X., Hu G., Lyu Y., Susztak K., Li M. Iterative transfer learning with neural network for clustering and cell type classification in single-cell RNA-seq analysis. Nature Machine Intelligence 2:607-618, 2020.
Nguyen A.T.*, Wang K.*, Hu G.*, Wang X., Miao Z., Azevedo J.A., Sua E.R., Van Deerlin V.M., Choi D., Roeder K., Li M.*, Lee E.* APOE and TREM2 regulate amyloid responsive microglia in Alzheimer’s disease. Acta Neuropathologica 140:477-493, 2020.
Pan H.*, Xue C.*, Auerbach B.J.*, Fan J., Bashore A.C., Cui J., Yang D.Y., Trignano S.B., Liu W., She J., Ihuegbu C.O., Bush E.C., Worley J., Vlahos L., Laos P., Solomon R.A., Connolly E.S., Califano A., Sims P.A., Zhang H., Li M.*, Reilly M.P.* Single-cell genomics reveals a novel cell state during smooth muscle cell phenotypic switching and potential therapeutic targets for atherosclerosis in mouse and human. Circulation 142(21):2060-2075, 2020.
Hordeaux J., Buza E.L., Dyer C., Goode T., Mitchell T.W., Richman L., Denton N., Hinderer C., Katz N., Schmid R., Miller R., Choudhury G.R., Horiuchi M., Nambiar K., Yan H., Li M., Wilson J.M. AAV-induced dorsal root ganglia pathology. Human Gene Therapy 31(15-16):808-818, 2020.
Liu E., Radmanesh B., Yi D., Dadi A., Himmelfarb J., Li M., Freedman B.S., Lin J. Modeling APOL1 Nephropathy Risk Variants with Genome-Edited Kidney Organoids and Single-Cell Transcriptomics. Kidney360, 1(3):203-215, 2020.
Hua X., Hu G., Gao L., Chang Y., Hu Y., Hu Q., Chen X., Yang P., Zhang Y., Li M., Song J. Single-cell RNA-sequencing for dissecting the immunological network in myocarditis. Circulation 142(4):384-400, 2020.
Fan J., Hu J., Xue C., Zhang H., Susztak K., Reilly M.P., Xiao R.*, Li M.* ASEP: gene-based detection of allele-specific expression in a population by RNA-seq. PLOS Genetics. 2020. https://doi.org/10.1371/journal.pgen.1008786
Hu Y., Wang K., Li M. Detecting differential alternative splicing events in scRNA-seq with or without unique molecular identifiers. PLOS Computational Biology. 2020. https://doi.org/10.1371/journal.pcbi.1007925.
Li X., Wang K., Lyu Y., Pan H., Zhang J., Stambolian D., Susztak K., Reilly M.P., Hu G.*, Li M.* Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis. Nature Communications 11:2338, 2020.
Zhong L., Yao L., Tower R.J., Wei Y., Miao Z., Park J., Shrestha R., Wang L., Yu W., Holdreith N., Huang X., Zhang Y., Tong W., Gong Y., Ahn J., Susztak K., Dyment N., Li M., Long F., Chen C., Seale P., Qin L. Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment. eLife e54695, 2020.
Provoost L., Siracusa C., Stefanovski D., Che Y., Li M., Casal M. Cognitive Abilities of Dogs with Mucopolysaccharidosis I: Learning and Memory. Animals 10(3);e397, 2020.
Wang L., Yang Y., Breton C., Bell P., Li M., Zhang J., Che Y., Saveliev A., He Z., White J., Latshaw C., Xu C., McMenamin D., Yu H., Morizono H., Batshaw M.L., Wilson J.M. A mutation-independent CRISPR-Cas9-mediated gene targeting approach to treat a murine model of ornithine transcarbamylase deficiency. Science Advances 6(7):eaax5701, 2020.
Li Y.R., Glessner J.T., Coe B.P., Li J., Mohebnasab M., Chang X., Connolly J., Kao C., Wei Z., Bradfield J., Kim C., Hou C., Khan M., Mentch F., Qiu H., Bakay M., Cardinale C., Lemma M., Abrams D., Bridglall-Jhingoor A., Behr M., Harrison S., Otieno G., Thomas A., Wang F., Chiavacci R., Wu L., Hadley D., Goldmuntz E., Elia J., Maris J., Grundmeier R., Devoto M., Keating B., March M., Pellagrino R., Grant S.F.A., Sleiman P.M.A., Li M., Eichler E.E., Hakonarson H. Rare copy number variants in over 100,000 European ancestry subjects reveal multiple disease association. Nature Communications 11(1): 255, 2020.

2019

Gupta V., Cadieux C.L., McMenamin D., Medina-Jaszek C.A., Arif M., Ahonkhai O., Wielechowski E., Taheri M., Che Y., Goode T., Limberis M.P., Li M., Cerasoli D.M., Tretiakova A.P., Wilson J.M. Adeno-associated virus-mediated expression of human butyrylcholinesterase to treat organophosphate poisoning. PLOS ONE 14(11): e0225188, 2019.
Cordero P., Parikh1 V.N., Chin E., Erbilgin A., Gloudemans M., Huang Y., Chang A.C., Smith K.S., Dewey F., Zaleta K., Morley M., Brandimarto J., Glazer N., Pavlovic A., Zhao M., Moravec C., Tang W.H., Viterna J., Malloy1 C., Hannenhalli S., Li H., Ritter S., Li M., Bernstein D., Connolly A., Hakonarson H., Lusis A.J., Margulies K.B., Depaoli-Roach A., Montgomery S.B., Wheeler M.P., Cappola T., Ashley E.A. Pathologic gene network rewiring implicates PPP1R3A as a central regulator in pressure overload heart failure. Nature Communications 10(1):2760, 2019.
Fu J., Wang Y., Li G., Han L., Li Y., Li L., Feng D., Wu Y., Xiao X., Li M., Grant S.F.A., Li M., Gao S. Childhood sleep duration modifies the polygenic risk for obesity in youth through leptin pathway: the Beijing Child and Adolescent Metabolic Syndrome cohort study. International Journal of Obesity 43(8):1556-1567, 2019.
Fang L., Kao C., Gonzalez M.V., Mafra F.A., Pellegrino da Silva R., Li M., Wenzel S.S., Wimmer K., Hakonarson H., Wang K. LinkedSV for detection of mosaic structural variants from linked read exome and genome sequencing data. Nature Communications 10(1):5585, 2019.
Pauly D., Agarwal D., Dana N., Schafer N., Biber J., Wunderlich K.A., Jabri Y., Straub T., Zhang N.R., Gautam A.K., Weber B.H.F., Hauck S.M., Kim M., Curcio C.A., Stambolian D., Li M., Grosche A. Cell-type-specific complement expression in the healthy and diseased retina. Cell Reports, 29(9):2835-2848, 2019.
Wang L., Yang Y., Breton C.A., White J., Zhang J., Che Y., Saveliev A., McMenamin D., He Z., Latshaw C., Li M., Wilson J.M. CRISPR/Cas9-mediated in vivo gene targeting corrects hemostasis in newborn and adult factor IX knockout mice. Blood, 133(26):2745-2752, 2019.
Xie G., Dong C., Kong Y., Zhong J.F, Li M., Wang K. Group lasso regularized deep learning for cancer prognosis from multi-omics and clinical features. Genes 21;10(3). pii: E240.
Schwartz G.W., Manning B., Zhou Y., Velu P., Bigdeli A., Astles R., Lehman A.W., Morrissette J.J.D., Perl A.E., Li M., Carroll M., Faryabi R.B. Classes of ITD Predict Outcomes in AML Patients Treated with FLT3 Inhibitors. Clinical Cancer Research 25(2): 573-583, 2019.
Wang X., Park J., Susztak J., Zhang N.*, Li M.* Bulk tissue cell type deconvolution with multi-subject single-cell expression reference. Nature Communications 10(1):380, 2019.

2018

Fu J., Li Y., Esangbedo I.C., Li G., Feng D., Li L., Xu L., Han L., Li M., Li C., Gao S., Li M., Willi S.M. Circulating Osteonectin and Adipokine Profiles in Relation to Metabolically Healthy Obesity in Chinese Children: Findings From BCAMS. Journal of American Heart Association 7(23): e009169, 2018.
Rothwell W.T., Bell P., Richman L.K., Limberis M.P., Tretiakova A.P., Li M., Wilson J.M. Intrathecal Viral Vector Delivery of Trastuzumab Prevents or Inhibits Tumor Growth of Human HER2-Positive Xenografts in Mice. Cancer Research 78(21): 6171-6182, 2018.
Ferguson J.F., Xue C., Gao Y., Tian T., Shi J., Zhang X., Wang Y., Li Y.D., Wei Z., Li M., Zhang H., Reilly M.P. Tissue-Specific Differential Expression of Novel Genes and Long Intergenic Noncoding RNAs in Humans With Extreme Response to Evoked Endotoxemia. Circulation Genomics Precision Medicine 11(11): e001907, 2018.
Saveliev A., Liu J., Li M., Hirata L., Latshaw C., Zhang J., Wilson J.M. Accurate and Rapid Sequence Analysis of Adeno-Associated Virus Plasmids by Illumina Next-Generation Sequencing. Human Gene Therapy Methods 29(5): 201-211, 2018.
Rothwell W.T., Bell P., Richman L.K., Limberis M.P., Tretiakova A.P., Li M., Wilson J.M. Intrathecal viral vector delivery of trastuzumab prevents or inhibits tumor growth of human HER2-positive Xenografts in mice. Cancer Research 78(21):6171-6182, 2018.
Wang J., Huang M., Torre E., Dueck H., Shaffer S., Murray J., Raj A., Li M., Zhang N.R. Gene expression distribution deconvolution in single-cell RNA sequencing. Proceedings of National Academy of Science 115(28):E6437-E6446, 2018.
Wang L., Smith J., Breton C., Clark P., Zhang J., Ying L., Che Y., Lape J., Bell P., Calcedo R., Buza E.L., Saveliev A., Bartsevich V., He Z., White J., Li M., Jantz D., Wilson J.M. Meganuclease targeting of PCSK9 in macaque liver leads to stable reduction in serum cholesterol. Nature Biotechnology. 2018 Sep;36(8):717-725.
Huang M., Wang J., Torre E., Dueck H., Shaffer S., Bonasio R., Murray J., Raj A., Li M., Zhang N.R. SAVER: gene expression recovery for single-cell RNA sequencing. Nature Methods 15(7):539-542, 2018.
Li G., Esangbedo I.C., Xu L., Fu J., Li L., Feng D., Han L., Xiao X., Li M., Mi J., Li M., Gao S., Willi S.M. Childhood retinol-binding protein 4 (RBP4) levels predicting the 10-year risk of insulin resistance and metabolic syndrome: the BCAMS study. Cardiovascular Diabetologia 17(1): 69, 2018.
Zhang X., Xue C., Lin J., Ferguson J.F., Weiner A., Liu W., Han Y., Hinkle C., Li W., Jiang H., Gosai S., Hachet M., Garcia B.A., Gregory B.D., Soccio R.E., Hogenesch J.B., Seale P., Li M., Reilly M.P. Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of linc-ADAL in adipocyte metabolism. Science Translational Medicine 20;10(446). pii: eaar5987, 2018.
Li G., Feng D., Wang Y., Fu J., Han L., Li L., Grant S.F.A., Li M., Li M., Gao S. Loss of Cardio-Protective Effects at the CDH13 Locus Due to Gene-Sleep Interaction: The BCAMS Study. EBioMedicine 32: 164-171, 2018.
Zhang H., Zhang N.R., Li M., Reilly M.P. First giant steps toward a cell atlas of atherosclerosis. Circulation Research. 122(12):1632-1634, 2018.
Park J., Shrestha R., Qiu C., Kondo A., Huang S., Werth M., Li M., Barasch J., Susztak K., Li M. Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease. Science 18;360(6390):758-763, 2018.
Hu Y., Lin J., Hu J., Hu G., Wang K., Zhang H., Reilly M.P., Li M. PennDiff: detecting differential alternative splicing and transcription by RNA sequencing. Bioinformatics 15;34(14):2384-2391, 2018.

2017

Zhang H., Xue C., Wang Y., Shi J., Zhang X., Li W., Nunez S., Foulkes A.S., Lin J., Hinkle C.C., Yang W., Morrisey E.E., Rader D.J., Li M., Reilly M.P. Deep RNA sequencing uncovers a repertoire of human macrophage long intergenic noncoding RNAs modulated by macrophage activation and associated with cardiometabolic diseases. Journal of American Heart Association 6: e007431, 2017.
DeAngelis M.M., Owen L.A., Morrison M.A., Morgan D.J., Li M., Shakoor A., Vitale A., Iyengar S., Stambolian D., Kim I.K., Farrer L.A. Genetics of age-related macular degeneration (AMD). Human Molecular Genetics 26: R246, 2017.
Li M., Zauhar R.J., Grazal C., Curcio C.A., DeAngelis M.M., Stambolian D. RNA expression in human retina. Human Molecular Genetics. 2017 Aug 1;26(R1):R68-R74.
Fu J, Li G, Li L, Yin J, Cheng H, Han L, Zhang Q, Li N, Xiao X, Grant SFA, Li M, Gao S, Mi J, Li M. The role of established East Asian obesity-related loci on pediatric leptin levels highlights a neuronal influence on body weight regulation in Chinese children and adolescents: the BCAMS study. Oncotarget 8(55):93593-93607, 2017.
Wang X., Xiao R., Zhu X., Li M. Gene mapping in admixed families: a cautionary note on the interpretation of the transmission disequilibrium test and a possible solution. Human Heredity 81(2):106-116, 2017.
Jiang Y., Zhang N.R.*, Li M.* SCALE: modeling allele-specific gene expression by single-cell RNA sequencing. Genome Biology. 2017 Apr 26;18(1):74.
Xue C., Zhang X., Zhang H., Ferguson J.F., Wang Y., Hinkle C., Li M., Reilly M.P. De novo RNA sequence assembly during in vivo inflammatory stress reveals hundreds of unannotated lincRNAs in human blood CD14+ monocytes and in adipose tissue. Physiology Genomics 49:287-309, 2017.
Jia C., Hu Y., Kelly D., Kim J., Li M.*, Zhang N.R.* Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data. Nucleic Acids Research. 2017 Nov 2;45(19):10978-10988.
Li L., Fu J., Yu X.T., Li G., Xu L., Yin J., Cheng H., Hou D., Zhao X., Gao S., Li W., Li C., Grant S.F., Li M., Xiao Y., Mi J., Li M. Sleep duration and cardiometabolic risk among Chinese school-aged children: do adipokines play a mediating role? Sleep 40:zsx042, 2017.
Shah R.D., Xue C., ZhangH., Tuteja S., Li M., Reilly M.P., Ferguson J.F. Expression of Calgranulin genes S100A8, S100A9 and S100A12 is modulated by n-3 PUFA during inflammation in adipose tissue and mononuclear cells. PLOS ONE 12(1):e0169614, 2017.

2016

Fu J., Hou C., Li L., Feng D., Li G., Li M., Li C., Gao S., Li M. Vitamin D modifies the associations between circulating betatrophin and cardiometabolic risk factors among youths at risk for metabolic syndrome. Cardiovascular Diabetology 15(1):142, 2016.
Lin J., Hu Y., Nunez S., Foulkes A.S., Cieply B., Xue C., Gerelus M., Li W., Zhang H., Rader D.J., Musunuru K., Li M., Reilly M.P. Transcriptome-wide analysis reveals modulation of human macrophage inflammatory phenotype through alternative splicing. Arteriosclerosis, Thrombosis, and Vascular Biology 36(7):1434-47, 2016.
Ballantyne R.L., Zhang X., Nunez S., Xue C., Zhao W., Reed E., Salaheen D., Foulkes A.S., Li M.*, Reilly M.P.* Genome-wide interrogation reveals hundreds of long intergenic noncoding RNAs that associate with cardiometabolic traits. Human Molecular Genetics 25(14):3125-3141, 2016.
Hu M., Li M., Li W., Liang H. Joint analysis of spikes and local field potentials using copula. Neuroimage 133:457-67, 2016.
Murillo G.H., You N., Su X., Cui W., Reilly M.P., Li M., Ning K., Cui X. MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data. Bioinformatics 32(10):1486-92, 2016.
Hughes A.E., Bridgett S., Meng W., Li M., Curcio C.A., Stambolian D., Bradley D.T. Sequence and expression of Complement Factor H gene cluster variants and their roles in age-related macular degeneration risk. Investigative Ophthalmology and Vision Science 57(6): 2763-9, 2016.
Li L., Yin J., Cheng H., Wang Y., Gao S., Li M., Grant S.F., Li C., Mi J., Li M. Identification of genetic and environmental factors predicting metabolically healthy obesity in children: data from the BCAMS study. Journal of Clinical Endocrinology and Metabolism 101(4):1816-25, 2016.
Ferguson J.F., Xue C., Hu Y., Li M., Reilly M.P. Adipose tissue RNASeq reveals novel gene-nutrient interactions following n-3 PUFA supplementation and evoked inflammation in humans. Journal of Nutritional Biochemistry 30:126-32, 2016.
Fritsche L.G., Igl W., Bailey J.N., Grassmann F., …, Li M., Curcio C.A., …, Stambolian D., Haines J.L., Iyengar S.K., Weber B.H., Abecasis G.R., Heid I.M. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. Nature Genetics 48(2):134-43, 2016.

2015

Lin J.J., Zhang X., Xue C., Zhang H., Shashaty M.G., Gosai S., Meyer N.J., Grazioli A., Hinkle C., Caughey J., Li W., Susztak K., Gregory B.D., Li M., Reilly M.P. The long noncoding RNA landscape in hypoxic and inflammatory renal epithelial injury. American Journal of Physiology and Renal Physiology 309(11):F901-13, 2015.
Chen H.Y., Rader D.J., Li M. Likelihood inferences on semi-parametric odds ratio model. Journal of the American Statistical Association 110(511):1125-35, 2015.
Xu Z., Duan Q., Yan S., Chen W., Li M., Lange E., Li Y. DISSCO: direct imputation of summary statistics allowing covariates. Bioinformatics 31(15):2434-42, 2015.
Christofidou P., Nelson C.P., Nikpay M., Qu L., Li M., Loley C., Debiec R., Braund P.S., Denniff M., Charchar F.J., Arjo A.R., Trégouët D.A., Goodall A.H., Cambien F., Ouwehand W.H., Roberts R., Schunkert H., Hengstenberg C., Reilly M.P., Erdmann J., McPherson R., König I.R., Thompson J.R., Samani N.J., Tomaszewski M. Runs of homozygosity: association with coronary artery disease and gene expression in monocytes and macrophages. American Journal of Human Genetics 97(2):228-37, 2015.
Jia C., Guan W., Yang A., Xiao R., Tang W.H., Moravec C.S., Margulies K.B., Cappola T.P., Li C., Li M. MetaDiff: differential isoform expression analysis using random-effects meta-regression. BMC Bioinformatics 16(1):208, 2015.
Zhang H., Xue C., Shah R., Bermingham K., Hinkle C.C., Li W., Rodrigues A., Tabita-Martinez J., Millar J., Cuchel M., Pashos E.E., Liu Y., Yan R., Yang W., Gosai S.J., VanDorn D., Chou S.T., Gregory B.D., Morrisey E.E., Li M., Rader D.J., Reilly M.P. Functional analysis and transcriptomic profiling of iPSC-derived macrophages and their application in modeling Mendelian disease. Circulation Research 117(1):17-28, 2015.
Hu M., Clark K., Gong X., Noudoost B., Li M., Moore T., Liang H. Copula regression analysis of simultaneously recorded frontal eye field and inferotemporal spiking activity during object-based working memory. Journal of Neuroscience 35(23):8745-57, 2015.
Wang X., Zhang S., Li Y., Li M., Sha Q. A powerful approach to test an optimally weighted combination of rare variants in admixed populations. Genetic Epidemiology 39(4):294-305, 2015.
Tian L., Kazmierkiewicz K.L., Bowman A.S., Li M., Curcio C.A., Stambolian D.E. Transcriptome of the human retina, retinal pigmented epithelium and choroid. Genomics 105(5-6):253-64, 2015.
Ferguson J.F., Meyer N.J., Qu L., Xue C., Liu Y., DerOhannessian S.L., Rushefski M., Paschos G.K., Tang S., Schadt E.E., Li M., Christie J.D., Reilly M.P. Integrative genomics identifies 7p11.2 as a novel locus for fever and clinical stress response in humans. Human Molecular Genetics 24(6):1801-12, 2015.
Liu Y., Morley M., Brandimarto J., Hannenhalli S., Hu Y., Ashley E.A., Tang W.H., Moravec C.S., Margulies K.B., Cappola T.P., Li M. RNA-Seq identifies novel myocardial gene expression signatures of heart failure. Genomics 105(2):83-9, 2015.
Do R., Stitziel N.O., Won H.H., Jørgensen A.B., …, Li M., …, Abecasis G.R., Watkins H., Nickerson D.A., Ardissino D., Sunyaev S.R., O’Donnell C.J., Altshuler D., Gabriel S., Kathiresan S. Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction. Nature 518(7537):102-6, 2015.

2014

Meyer N.J., Ferguson J.F., Feng R., Wang F., Patel P.N., Li M., Xue C., Qu L., Liu Y., Boyd J.H., Russell J.A., Christie J.D., Walley K.R., Reilly M.P. A functional synonymous coding variant in the IL1RN gene is associated with survival in septic shock. American Journal of Respiratory and Critical Care Medicine 190(6): 656-64, 2014.
Jia C., Hu Y., Liu Y., Li M. Mapping splicing quantitative trait loci using RNA-Seq. Cancer Informatics 14(Suppl 1):45-53, 2015.
Li M., Jia C., Kazmierkiewicz K.L., Bowman A.S., Tian L., Liu Y., Gupta N.A., Gudsieva H.V., Yee S.S., Kim M., Dentchev T., Kimble J.A., Parker J.S., Messinger J.D., Curcio C.A., Stambolian D. Comprehensive analysis of gene expression in human retina and supporting tissues. Human Molecular Genetics 23(15):4001-14, 2014.
Liu Y., Ferguson J.F., Xue C., Ballantyne R.L., Silverman I.M., Gosai S.J., Serfecz J., Morley M.P., Gregory B.D., Li M.*, Reilly M.P.* Tissue-specific RNA-Seq in human evoked inflammation identifies blood and adipose lincRNA signatures of cardiometabolic diseases. Arteriosclerosis Thrombosis Vascular Biology 34(4):902-12, 2014.
Peloso G.M., Auer P.L., Bis J.C., Voorman A., Morrison A.C., Stitziel N.O., …, Li M., Rader D.J., Reilly M.P., …, Kathiresan S., Cupples L.A. Association of low-frequency and rare coding-sequence variants with blood lipids and coronary heart disease in 56,000 whites and blacks. American Journal of Human Genetics 94(2):223-32, 2014.
Hu Y., Lin J., Hu J., Hu G., Wang K., Zhang H., Reilly M.P., Li M. PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Nucleic Acids Research 42(3):e20, 2014.

2013

Baldwin D.A., Sarnowski C.P., Reddy S.A., Blair I.A., Clapper M., Lazarus P., Li M., Muscat J.E., Penning T.M., Vachani A., Whitehead A.S. Development of a genotyping microarray for studying the role of gene-environment interactions in risk for lung cancer. Journal of Biomolecular Techniques 24(4):198-217, 2013.
Holmes M.V., Simon T., Exeter H.J., Folkersen L., Asselbergs F.W., Guardiola M., Cooper J.A., Palmen J., Hubacek J.A., Carruthers K.F., Horne B.D., Brunisholz K.D., Mega J.L., van Iperen E.P., Li M., …, Talmud P.J. Secretory Phospholipase A2-IIA and Cardiovascular Disease: a Mendelian randomization study. Journal of the American College of Cardiology 62(21):1966-76, 2013.
Byrnes A.E., Wu M.C., Wright F.A., Li M., Li Y. The value of statistical or bioinformatics annotation for rare variant association with quantitative trait. Genetic Epidemiology 37(7):666-74, 2013.
Ferguson J.F., Matthews G.J., Townsend R.R., Raj D.S., Kanetsky P.A., Budoff M., Fischer M.J., Rosas S.E., Kanthety R., Rahman M., Master S.R., Qasim A., Li M., Mehta N.N., Shen H., Mitchell B.D., O’Connell J.R., Shuldiner A.R., Ho W.K., Young R., Rasheed A., Danesh J., He J., Kusek J.W., Ojo A.O., Flack J., Go A.S., Gadegbeku C.A., Wright J.T., Saleheen D., Feldman H.I., Rader D.J., Foulkes A.S., Reilly M.P. Candidate gene association study of coronary artery calcification in chronic kidney disease: findings from the chronic renal insufficiency cohort study. Journal of American College of Cardiology 62(9):789-98, 2013.
Chen H.Y., Reilly M.P., Li M. Semiparametric odds ratio model for case-control and matched case-control designs. Statistics in Medicine 32(18): 3126-42, Aug 2013.
Wojczynski M.K., Li M., Bielak L.F., Kerr K.F., Reiner A.P., …, Reilly M.P. Genetics of coronary artery calcification among African Americans, a meta-analysis. BMC Medical Genetics 19:75, 2013.
Liu Y., Ferguson J.F., Xue C., Silverman I.M., Gregory B.S., Reilly M.P., Li M. Evaluating the impact of sequencing depth on transcriptome profiling in human adipose. PLoS ONE 8(6):e66883, 2013.
Vardhanabhuti S., Li M., Li H. A hierarchical Bayesian model for estimating and inferring differential isoform expression for multi-sample RNA-Seq data. Statistics in Biosciences 5(1):119-137, 2013.
Meyer N.J., Feng R., Li M., Zhao Y., Sheu C.C., Tejera P., Gallop R., Bellamy S., Rushefski M., Lanken P.N., Aplenc R., O’Keefe G.E., Wurfel M.M., Christiani D.C. and Christie J.D. IL1RN Coding Variant Is Associated with Lower Risk of Acute Respiratory Distress Syndrome and Increased Plasma IL1RA. American Journal of Respiratory and Critical Care Medicine 187(9):950-9, 2013.
Ng M.C., Saxena R., Li J., Palmer N.D., Dimitrov L., Xu J., Rasmussen-Torvik L.J., Zmuda J.M., Siscovick D.S., Patel S.R., Crook E.D., Sims M., Chen Y.D., Bertoni A.G., Li M., Grant S.F., Dupuis J., Meigs J.B., Psaty B.M., Pankow J.S., Langefeld C.D., Freedman B.I., Rotter J.I., Wilson J.G. and Bowden DW. Transferability and fine mapping of type 2 diabetes Loci in african americans: the candidate gene association resource plus study. Diabetes 62(3):965-76, 2013.
Mao X., Li Y., Liu Y., Lange L. and Li M. Testing genetic association with rare variants in admixed populations. Genetic Epidemiology 37(1): 38-47, Jan 2013.
Liu E.Y., Li M., Wang W. and Li Y. MaCH-admix: genotype imputation for admixed populations. Genetic Epidemiology 37(1):25-37, 2013.

2012

Moberg P.J., Li M., Kanes S.J., Gur R.E., Kamath V., Turetsky B.I. Association of schizophrenia with the phenylthiocarbamide (PTC) taste receptor haplotype on chromosome 7q. Psychiatric Genetics 22(6):286-9, 2012.
Christie J.D., Wurfel M.M., Feng R., O’Keefe G.E., Bradfield J., Ware L.B., Christiani D.C., Calfee C.S., Cohen M.J., Matthay M., Meyer N.J., Kim C., Li M., Akey J., Barnes K.C., Sevransky J., Lanken P.N., May A.K., Aplenc R., Maloney J.P., Hakonarson H; Trauma ALI SNP Consortium (TASC) investigators. Genome-wide association identifies PPFIA1 as a candidate gene for acute lung injury risk following major trauma. PLoS ONE 7(1):e28268, 2012.
Voight B.F., Peloso G.M., Orho-Melander M., Frikke-Schmidt R., Barbalic M., Jensen M.K., Hindy G., Holm H., Ding E.L., Johnson T., Schunkert H., Samani N.J., Clarke R., Hopewell J., Thompson J.F., Li M., …, Rader D.J., Peltonen L., Schwartz S.M., Altshuler D., Kathiresan S. Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study. The Lancet 380(9841):572-80, 2012.
Wassel C.L., Lamina C., Nambi V., Coassin S., Mukamal K.J., Ganesh S.K., Jacobs D.R. Jr, Franceschini N., Papanicolaou G.J., Gibson Q., Yanek L.R., van der Harst P., Ferguson J.F., Crawford D.C., Waite L.L., Allison M.A., Criqui M.H., McDermott M.M., Mehra R., Cupples L.A., Hwang S.J., Redline S., Kaplan R.C., Heiss G., Rotter J.I., Boerwinkle E., Taylor H.A., Eraso L.H., Haun M., Li M., …, Murabito J.M. Genetic determinants of the ankle-brachial index: a meta-analysis of a cardiovascular candidate gene 50K SNP panel in the candidate gene association resource (CARe) consortium. Atherosclerosis 222(1):138-47, 2012.
The Early Growth Genetics (EGG) Consortium, Bradfield J.P., Taal H.R., Timpson N.J., Scherag A., Lecoeur C., Warrington N.M., Hypponen E., Holst C., Valcarcel B., Thiering E., Salem R.M., Schumacher F.R., Cousminer D.L., Sleiman P.M., Zhao J., Berkowitz R.I., Vimaleswaran K.S., Jarick I., Pennell C.E., Evans D.M., St Pourcain B., Berry D.J., Mook-Kanamori D.O., Hofman A., Rivadeneira F., Uitterlinden A.G., van Duijn C.M., van der Valk R.J., de Jongste J.C., Postma D.S., Boomsma D.I., Gauderman W.J., Hassanein M.T., Lindgren C.M., Mägi R., Boreham C.A., Neville C.E., Moreno L.A., Elliott P., Pouta A., Hartikainen A.L., Li M., …, Hakonarson H., Grant S.F. A genome-wide association meta-analysis identifies new childhood obesity loci. Nature Genetics 44(5):526-31, 2012.
Saxena R., Elbers C.C., Guo Y., Peter I., Gaunt T.R., Mega J.L., Lanktree M.B., Tare A., Castillo B.A., Li Y.R., Johnson T., Bruinenberg M., Gilbert-Diamond D., Rajagopalan R., Voight B.F., Balasubramanyam A., Barnard J., Bauer F., Baumert J., Bhangale T., Böhm B.O., Braund P.S., Burton P.R., Chandrupatla H.R., Clarke R., Cooper-DeHoff R.M., Crook E.D., Davey-Smith G., Day I.N., de Boer A., de Groot M.C., Drenos F., Ferguson J., Fox C.S., Furlong C.E., Gibson Q., Gieger C., Gilhuijs-Pederson L.A., Glessner J.T., Goel A., Gong Y., Grant S.F., Grobbee D.E., Hastie C., Humphries S.E., Kim C.E., Kivimaki M., Kleber M., Meisinger C., Kumari M., Langaee T.Y., Lawlor D.A., Li M., …, Hakonarson H., Siscovick D.S., Keating B.J. Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci. American Journal of Human Genetics 90(3):410-25, 2012.
Ferguson J.F., Hinkle C.C., Mehta N.N., Bagheri R., DerOhannessian S.L., Shah R., Wolfe M., Bradfield J.P., Hakonarson H., Wang X., Master S., Rader D.J., Li M., Reilly M. Translational studies of lipoprotein-associated phospholipase A2 in inflammation and atherosclerosis. Journal of the American College of Cardiology 59(8): 763-72, 2012.
He J., Li H., Edmondson A.C., Rader D.J., Li M. A Gaussian copula approach for the analysis of secondary phenotypes in case-control genetic association studies. Biostatistics 13(3):497-508, 2012.

2011

Zhao J., Bradfield J.P., Zhang H., Sleiman P.M., Kim C., Glessner J.T., Deliard S., Thomas K.A., Frackelton E.C., Li M., Chiavacci R.M., Berkowitz R.I., Hakonarson H., Grant S.F.A. Role of BMI-associated loci identified in GWAS meta-analyses in the context of common childhood obesity in European Americans. Obesity 19(12): 2436-9, 2011.
Khetarpal S.A., Edmondson A.C., Raghavan A., Neeli H., Jin W., Badellino K.O., Demissie S., Manning A.K., DerOhannessian S., Wolfe M., Cupples A., Li M., Kathiresan S., Rader D.J.: Mining the LIPG allelic spectrum reveals the contribution of rare and common regulatory variants to HDL cholesterol. PLoS Genetics 7(12): e1002393, 2011.
Chen H.-Y., Li M. Improving power and robustness for detecting genetic association with extreme-value sampling design. Genetic Epidemiology 35(8): 823-30, 2011.
Song P.X.-K., Li M., Yuan Y.: Rejoinder: Joint regression analysis for discrete longitudinal data. Biometrics 67(3):1175-6, 2011.
Bhatia G., Patterson N., Pasanius B., Zaitlen N., Genovese G., Pollack S., Mallick S., Mayers S., Tandon A., Spence C., Palmer C.D., Adeyemo A.A., Akylbekova E.L., Cupples L.A., Divers J., Fornage M., Kao W.H.L., Lange L., Li M., Musani S., Mychaleckyj J.C., Ogunniyi A., Papanicolaou G., Rotimi C.N., Rotter J.I., Ruczinski I., Salako B., Siscovick D.S., Tayo B.O., Yang Q., McCarroll S., Sabeti P., Lettre G., De Jager P., Hirschhorn J., Zhu X., Cooper R., Reich D., Wilson J.G., Price A.L.: Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection. American Journal of Human Genetics 89(3):368-81, 2011.
Wild P.S., Zeller T., Schillert A., Szymczak S., Sinning C.R., Deiseroth A., Schnabel R.B., Lubos E., Keller T., Eleftheriadis M.S., Bickel C., Rupprecht H.J., Wilde S., Rossmann H., Diemert P., Cupples L.A., Perret C., Erdmann J., Stark K., Kleber M.E., Epstein S.E., Voight B.F., Kuulaasma K., Li M., …, Blankenberg S.: A genome-wide association study identifies LIPA as a susceptibility gene for coronary artery disease. Circulation Cardiovascular Genetics 4(4):403-12, 2011.
Kanetsky P.A., Mitra N., Vardhanabhuti S., Vaughn D.J., Li M., Ciosek S.L., Letrero R., D’Andrea K., Vaddi M., Roddy D.R., Reilly M.P., Schwartz S.M., Nathanson K.L.: A second independent locus within DMRT1 is associated with testicular germ cell tumor susceptibility. Human Molecular Genetics 20(15):3109-17, 2011.
Wang K., Edmondson A.C., Li M., Gao F., Qasim A.N., Devaney J.M., Burnett M.S., Waterworth D.M., Mooser V., Grant S.F.A., Epstein S.E., Reilly M.P., Hakonarson H., Rader D.J.: Pathway-wide association study implicates multiple sterol transport metabolism genes in HDL cholesterol regulation. Frontiers in Genetics 2:41, 2011.
Li M., Wang I.X., Li Y., Bruzel A., Richards A., Toung J.M., Cheung V.G.: Widespread RNA and DNA sequence differences in the human transcriptome. Science 333(6038):53-8, 2011.
Zhao J., Bradfield J.P., Li M., Zhang H., Mentch F.D., Wang K., Sleiman P.M., Kim C.E., Glessner J.T., Frackelton E.C., Chiavacci R.M., Berkowitz R.I., Zemel B.S., Hakonarson H., Grant S.F.A.: BMD-associated variation at the Osterix locus is correlated with pediatric BMI in females. Obesity 19(6):1311-4, 2011.
Toung J., Morley M., Li M., Cheung V.G.: RNA-Sequence analysis of human B cells. Genome Research 21(6):991-8, 2011.
Shah R., Hinkle C.C., Ferguson J.F., Mehta N.N., Li M., Qu L., Lu Y., Putt M.E., Ahima R.S., Reilly M.P.: Fractalkine is a novel human adipochemokine associated with type 2 diabetes. Diabetes 60(5):1512-28, 2011.
Rushefski M., Aplenc R., Meyer N., Li M., Feng R., Lanken P.N., Gallop R., Bellamy S., Localio R.A., Feinstein S.I., Fisher A.B., Albelda S.M., Christie J.D.: Novel variants in the PRDX6 gene and the risk of acute lung injury following major trauma. BMC Medical Genetics 12:77, 2011.
Meyer N.J., Li M., Feng R., Bradfield J., Gallop R., Bellamy S., Fuchs B.D., Lanken P.N., Albelda S.M., Rushefski M., Aplenc R., Abramova H., Atochina-Vasserman E.N., Beer M.F., Calfee C.S., Cohen M.J., Pittet J.F., Christiani D.C., O’Keefe G.E., Ware L.B., May A.K., Wurfel M.M., Hakonarson H., Christie J.D. ANGPT2 genetic variant is associated with trauma-associated acute lung injury and altered plasma Angiopoietin-2 isoform ratio. American Journal of Respiratory and Critical Care Medicine 83(10):1344-53, 2011.
Chikkagoudar S., Wang K., Li M.: GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores. BMC Research Notes 4(1):158, 2011.
Pasaniuc B., Zaitlen N., Lettre G., Chen G., Tandon A., Kao L., Ruczinski I., Fornage M., Siscovick D., Zhu X., Larkin E., Lange L., Cupples L.A., Yang Q., Akylbekova M., Musani S., Divers J., Mychaleckjy J., Li M., …, Price A.L.: Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and breast cancer consortium. PLoS Genetics 7(4):e1001371, 2011.
Mehta N.N., Li M., William D., Khera A., DerOhannessian S., Qu L., Ferguson J., McLaughlin C., Shaikh L.H., Shah R., Patel P., He J., Stylianou I., Hakonarson H., Rader D.J., Reilly M.P. The novel atherosclerosis locus at 10q11 regulates plasma CXCL12 levels. European Heart Journal 32(8):963-71, 2011.
Edmondson A.C., Braund P.S., Stylianou I.M., Khera A.V., Nelson C.P., Wolfe M.L., Derohannessian S.L., Keating B.J., Qu L., He J., Tobin M.D., Tomaszewski M., Baumert J., Klopp N., Doering A., Thorand B., Li M., Reilly M.P., Koenig W., Samani N.J., Rader D.J. Dense genotyping of candidate gene loci identifies variants associated with high-density lipoprotein cholesterol. Circulation Cardiovascular Genetics 4(2):145-55, 2011.
Wang X., Zhu X., Qin H., Cooper R., Ewens W., Li C., Li M. Adjustment for local ancestry in genetic association analysis of admixed populations. Bioinformatics 27(5): 670-7, 2011.
Schunkert H, König IR, Kathiresan S, Reilly MP, Assimes TL, Holm H, Preuss M, Stewart AF, Barbalic M, Gieger C, Absher D, Aherrahrou Z, Allayee H, …, Li M.,…, CARDIoGRAM Consortium, Samani NJ: Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nature Genetics 43(4):333-8, 2011.
Lettre G., Palmer C.D., Young T., Ejebe K., Allayee H., Benjamin E.J., Bennett F., Bowden D.W., Chakravarti A., Dreisbach A., Farlow D.N., Folsom A.R., Fornage M., Forrester T., Fox E., Haiman C.A., Hartiala J., Hazen S.L., Heckbert S.R., Henderson B.E., Hirschhorn J.N., Keating B., Kritchevsky S.B., Larkin E., Li M., …, Kathiresan S., Boerwinkle E.: Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: The NHLBI CARe Project. PLoS Genetics 7(2):e1001300, 2011.
He J., Wang K., Edmondson A.C., Rader D.J., Li C., Li M. Gene-based interaction analysis by incorporating external linkage disequilibrium information. European Journal of Human Genetics 19(2):164-172, 2011.
Cappola T.P., Matkovich S.J., Wang W., Van Booven D., Li M., Wang X., Qu L., Reilly M.P., Hakonarson H., Nerbonne J.M., Dorn G.W. 2nd. Loss-of-function DNA sequence variant in the CLCNKA chloride channel implicates the cardio-renal axis in interindividual heart failure risk variation. Proceedings of the National Academy of Sciences 108(6):2456-61, 2011.
Reilly M.*, Li M.*, He J., Ferguson J.F., Stylianou I.M.,Mehta N.N., Burnett M.S., Devaney J.M., Knouff C.W., Thompson J.R., Horne, B.D., Stewart A.F., Assimes T.L., Wild P.S., Allayee H., Linsel-Nitschke P., Patel R.S., Myocardial Infarction Genetics Consortium, Wellcome Trust Case Control Consortium, Martinelli N., Girelli D., Quyyumi A.A., Anderson J.L., Erdmann J., Hall A.S., Schunkert H., Quertermous T., Blankenberg S., Hazen S.L., Roberts R., Kathiresan S, Samani N.J., Epstein S.E., Rader D.J. Identification of ADAMTS7 as a novel locus for coronary atherosclerosis and association of ABO with myocardial infarction in the presence of coronary atherosclerosis: two genome-wide association studies. The Lancet 377(9763): 383-92, Jan 2011.
Lanktree M.B., Guo Y., Murtaza M., Glessner J.T., Bailey S.D., Onland-Moret N.C., Lettre G., Li M., Soranzo N., FitzGerald G.A., Reiner A., Hegele R.A., Hakonarson H., Keating B.J. Meta-analysis of dense genecentric association studies reveals common and uncommon variants associated with height. American Journal of Human Genetics 88(1): 6-18, Jan 2011.

2005 - 2010

2010

Wang K., Li M., Hakonarson H.: Analysing biological pathways in genome-wide association studies. Nature Review Genetics 11(12): 843-54, Dec 2010.
Soranzo N., Sanna S., Wheeler E., Gieger C., Radke D., Dupuis J., Bouatia-Naji N., Langenberg C., Prokopenko I., Stolerman E., Sandhu M.S., Heeney M.M., Devaney J.M., Reilly M.P., Ricketts S.L., Stewart A.F., Voight B.F., …, Li M., …, Meigs J.B.: Common variants at 10 genomic loci influence hemoglobin A1(C) levels via glycemic and nonglycemic pathways. Diabetes 59(12): 3229-39, Dec 2010.
Shen H., Bielak L.F., Ferguson J.F., Streeten E.A., Yerges-Armstrong L.M., Liu J., Post W., O’Connell J.R., Hixson J.E., Kardia S.L.R., Sun Y.V., Jhun M.A., Wang X., Mehta N.N., Li M., Koller K.L., Hakonarson H., Keating B.J., Rader D.J., Shuldiner A.R., Peyser P.A., Reilly M.P., Mitchell B.D. Association of the vitamin D metabolism gene CYP24A1 with coronary artery calcification. Arteriosclerosis, Thrombosis, and Vascular Biology 30(12): 2648-54, Dec 2010.
Qin H., Morris N., Kang S.J., Li M., Tayo B., Lyon H., Hirschhorn J., Cooper R.S., Zhu X.: Interrogating local population structure for fine mapping in genome-wide association studies. Bioinformatics 26(23): 2961-8, Dec 2010.
Zhao J., Schug J., Li M., Kaestner K., Grant S.F.A.: Disease-associated loci are significantly over-represented among genes bound by TCF7L2 in vivo. Diabetologia 53(11): 2340-6, Nov 2010.
Li Y., Byrnes A.E., Li M.: To identify associations with rare variants, just WHaIT: Weighted haplotype and imputation-based tests. American Journal of Human Genetics 87(5): 728-35, Nov 2010.
Glessner J.T., Bradfield J.P., Wang K., Takahashi N., Zhang H., Sleiman P.M., Mentch F.D., Kim C.E., Hou C., Thomas K.A., Garris M.L., Deliard S., Frackelton E.C., Otieno F.G., Zhao J., Chiavacci R.M., Li M., Buxbaum J.D., Berkowitz R.I., Hakonarson H., Grant S.F.A.: A Genome-wide Study Reveals Copy Number Variants Exclusive to Childhood Obesity Cases. American Journal of Human Genetics 87(5): 661-6, Nov 2010.
Assimes T.L., Holm H., Kathiresan S., Reilly M.P., Thorleifsson G., Voight B.F., Erdmann J., Willenborg C., Vaidya D., Xie C., Patterson C.C., Morgan T.M., Burnett M.-S., Li M., Stefansson K., Schunkert H., Samani N.J., Quertermous T.: Lack of association between the Tr719Arg polymorphism in kinesin-like protein 6 and coronary artery disease in 19 case-control studies. Journal of the American College of Cardiology 56(19): 1552-63, Nov 2010.
Preuss M., Konig I.R., Thompson J., Erdmann J., Absher D., Assimes T.L., Blankenberg S., Boerwinkle E., Chen L., Cupples A., Epstein S., Hall A., Halperin E., Hengstenberg C., Laaksonen R., Li M., …, Rader D., Reilly M., Roberts R., Schillert A., Stewart A., Thorleifsson G., Ziegler A., Kathiresan S., Thorsteinsdottir U., Samani N.J., Schunkert H.: Design of the Coronary ARtery DIsease Genome-Wide Replication And Meta-Analysis (CARDIoGRAM) Study. A Genome-wide association meta-analysis involving more than 22 000 cases and 60 000 controls. Circulation Cardiovascular Genetics 3(5): 475-83, Oct 2010.
Wang K., Li M., Hakonarson H.: ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 38(16): e164, Sep 2010.
Teslovich T.M., Musunuru K., Smith A.V., Edmondson A.C., Stylianou I.M., Koseki M., Pirruccello J.P., Ripatti S., Chasman D.I., Willer C.J.,…, Li M., …, Abecasis G.R., Boehnke M., Kathiresan S.: Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466(7307): 707-713, Aug 2010.
Haas E.J., Zaoutis T.E., Prasad P., Li M., Coffin S.E.: Risk factors and outcomes for vancomycin-resistant enterococcus bloodstream infection in children. Infection Control and Hospital Epidemiology 31(10): 1038-42, Aug 2010.
Raychaudhuri S., Ripke S., Li M., Neale B.M., Fagerness J., Reynolds R., Sobrin L., Swaroop A., Abecasis G.R., Seddon J.M., Daly M.J.: Associations of a CFHR1/CFHR3 deletion and a CFH SNP to age related macular degeneration are not independent. Nature Genetics 42(7): 553-5, Jul 2010.
Zhao J.*, Li M.*, Bradfield J.P., Zhang H., Mentch F.D., Wang K., Sleiman P.M., Kim C.E., Glessner J.T., Hou C., Keating B.J., Thomas K.A., Garris M.L., Deliard S., Frackelton E.C., Otieno F.G., Chiavacci R.M., Berkowitz R.I., Hakonarson H., Grant S.F.A.: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. BMC Medical Genetics 11: 96, Jun 2010.
Liu J.Z., Tozzi F., Waterworth D.M., Pillai S.G., Muglia P., Middleton L., Berrettini W., …, Li M., …, Marchini J.: Meta-analysis and imputation refines the association of 15q25 with smoking quantity. Nature Genetics 42(5): 436-40, May 2010.
Cappola T.P., Li M., He J., Ky B., Gilmore J., Qu L., Keating B., Reilly M., Kim C.E., Glessner J., Frackelton E., Hakonarson H., Syed,F., Hindes A., Matkovich S.J., Cresci S., Dorn G.W. 2nd.: Common variants in HSPB7 and FRMD4B associated with advanced heart failure. Circulation Cardiovascular Genetics 3(2): 147-54, Apr 2010.
Zhao J., Li M., Bradfield J.P, Wang K., Zhang H., Sleiman P, Kim C.E, Annaiah K., Glaberson W., Glessner J.T., Otieno F.G., Thomas- Kelly A,, Garris M., Hou C., Frackelton E.C., Chiavacci R.,M, Berkowitz R.I., Hakonarson H., Grant Struan F.A.: Examination of type 2 diabetes GWAS loci reveals HHEX-IDE as a locus influencing pediatric BMI. Diabetes 59(3): 751-5, Mar 2010.
Li M., Reilly M.P., Rader D.J., Wang L.S.: Correcting population stratification in genetic association studies using a phylogenetic approach. Bioinformatics 26(6): 798-806, Mar 2010.

2009

Zhao J., Bradfield J.P., Li M., Wang K., Zhang H., Kim C.E., Annaiah K., Glessner J.T., Thomas K., Garris M., Frackelton E.C., Otieno F.G., Shaner J.L., Smith R.M., Chiavacci R.M., Berkowitz R.I., Hakonarson H., Grant S.F.: The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI. Obesity 17(12): 2254-7, Dec 2009.
Li M., Wang K., Grant S.F.A., Hakonarson H., Li C.: ATOM: a powerful gene-based association test by combining optimally weighted markers. Bioinformatics 25(4): 497-503, 2009.
Soranzo N., Spector T.D., Mangino M., Kühnel B., Rendon A., Teumer A., Willenborg C., Wright B., Chen L., Li M., …, Reilly M.P., Stewart A.F., Erdmann J., Samani N.J., Meisinger C., Greinacher A., Deloukas P., Ouwehand W.H., Gieger, C.: A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. Nature Genetics 41(11): 1182-90, Nov 2009.
Zhao J., Li M., Bradfield J.P., Wang K., Zhang H., Sleiman P., Kim C.E., Annaiah K., Glaberson W., Glessner J.T., Otieno G.F., Thomas K.A., Garris M., Hou C., Frackelton E.C., Chiavacci R.M., Berkowitz R.I., Hakonarson H., Grant S.F.: Examination of type 2 diabetes loci implicates CDKAL1 as a birth weight gene. Diabetes 58(10): 2414-8, Oct 2009.
Brown R.J., Edmondson A.C., Griffon N., Hill T.B., Fuki I.V., Badellino K.O., Li M., Wolfe M.L., Reilly M.P., Rader D.J.: A naturally occurring variant of endothelial lipase associated with elevated HDL exhibits impaired synthesis. Journal of Lipids Research 50(9): 1910-6, Sep 2009.
Kanetsky P., Mitra N., Vardhanabhuti S., Li M., Vaughn D., Letrero R., Ciosek S., Doody D., Smit, L., Weaver J., Albano A., Chen C., Starr J., Rader D.J., Godwin A.K., Reilly M., Hakonarson H., Schwartz S., Nathanson K.: Common variation in KITLG and at 5q31.3 proximate to testicular germ cell cancer. Nature Genetics 41(7): 811-5, Jul 2009.
Grant S.F.A., Bradfield J.P., Zhang H., Wang, K., Kim C.E., Annaiah K., Santa E., Glessner J.T., Thomas K., Garris M., Frackelton E.C., Otieno F.G., Shane J.L., Smith R.M., Imielinski M., Chiavacci R.M., Li M., Berkowitz R.I., Hakonarson H.: Investigation of the locus near MC4R with childhood obesity in Americans of European and African ancestry. Obesity 17(7): 1461-5, Jul 2009.
Bucan M., Abrahams B.S., Wang K., Glessner J., Herman E.I., Sonnenblick L.I., Alvarez R.A.I., Imielinski M., Hadley D., Bradfield J.P., Kim C., Gidaya N.B., Lindquist I., Hutman T., Sigman M., Kustanovich V., Lajonchere C., Singleton A., Kim J., Wassink T.H., McMahon W.M., Owley T., Sweeney J.A., Coon H., Nurnberger J.I., Li M., Cantor R.M., Minshew N.J., Sutcliffe J.S., Cook E.H., Dawson G., Buxbaum J.D., Grant S.F.A., Schellenberg G.D., Geschwind D.H., Hakonarson H.: Genome-wide analyses of exonic copy number variants in a family-based study point to novel autism susceptibility genes. PLoS Genetics 5(6): e1000536, Jun 2009.
Edmonson A.C., Brown R.J., Kathiresan S., Cupples L.A., Demissie S., Manning A., Jensen M., Rimm E.B., Wang J., Wolfe M.L., Derohannessian S., Li M., Reilly M., Evens D., Hegele R.A., Rader D.J.: Loss-of-function variants in endothelial lipase are a cause of elevated HDL cholesterol in humans. Journal of Clinical Investigation 119(4): 1042-50, Apr 2009.
Wang K., Zhang H., Kugathasan S., Annese V., Bradfield J., Russell R.K., Sleiman P.M.A., Imielinski M., Glessner J., Hou C., Wilson D.C., Walters T., Kim C., Cucchiara S., Frackelton E.C., Limbergen J.V., Guthery S., Denson L., Piccoli D., Li M., Dubinsky M., Silverberg M., Griffiths A., Grant S.F.A., Sansangi J., Baldassano R., Hakonarson H.: Diverse genome-wide association studies associate the IL12/IL23 pathway with Crohns Disease. American Journal of Human Genetics 84(3): 399-405, Mar 2009.
Song P.X., Li M., Yuan Y.: Joint regression analysis of correlated data using Gaussian copulas. Biometrics 65(1): 60-68, Mar 2009.

2008

Wang K., Chen Z., Tadesse M.G., Glessner J., Grant S.F.A., Hakonarson H., Bucan M., Li M.: Modeling genetic inheritance of copy number variations. Nucleic Acids Research 36(21): e138, Dec 2008.
Li C.*, Li M.*, Lange E.M., Watanabe R.M.: Prioritized subset analysis: improving power in genome-wide association studies. Human Heredity 65(3): 129-41, 2008.
Keating B.J., Tischfield S., Murrary S.S., Bhangale T., Price T.S., Glessner J.T., Galver L., Barrett J.C., Grant S.F., Farlow D.N., Chandrupatla H.R., Hansen M., Ajmal S., Papanicolaou G.J., Guo Y., Li M., …, Rader D.J., Hirschhorn J.N., Fitzgerald G.A.: Concept, design and implementation of a cardiovascular gene-centric 50K SNP array for large-scale genomic association studies. PLoS ONE 3(10): e3583, 2008.
Grant S.F.A., Li M., Bradfield J.P., Kim C.E., Annaiah K., Santa E., Glessner J.T., Casalunovo T., Frackelton E.C., Otieno F.G., Shaner J.L., Smith R.M., Eckert A.W., Imielinski M., Chiavacci R.M., Berkowitz R.I., Hakonarson H.: Association of HMGA2 gene variation with height in specific pediatric age categories. Genomics Insights 1: 13-6, 2008.
Wei Z., Li M., Rebbeck T., Li H.: U-statistics-based tests for multiple genes in genetic association studies. Annals of Human Genetics 72(Pt 6): 821-33, Nov 2008.
Li M., Li C.: Assessing departure from Hardy-Weinberg equilibrium in the presence of disease association. Genetic Epidemiology 32(7): 589-99, Nov 2008.
Diskin S.J., Li M., Hou C., Yang S., Glessner J., Hakonarson H., Bucan M., Maris J.M., Wang K.: Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Research 36(19): e126, Nov 2008.
Christie J.D., Ma S.F., Aplenc R., Li M., Lanken P.N., Fuchs B., Albelda S.M., Flores C., Garcia J.G.N.: Variation in the myosin light chain kinase gene is associated with development of acute lung injury after major trauma. Critical Care Medicine 36(10): 2794-800, Oct 2008.
Ewens W.J., Li M., Spielman R.S.: A review of family-based tests for linkage disequilibrium between a quantitative trait and a genetic marker. PLoS Genetics 4(9): e1000180, Sep 2008.
Li C., Li M., Long J., Cai Q., Zheng W.: Evaluating cost efficiency of SNP chips in genome-wide association studies. Genetic Epidemiology 32(5): 387-95, Jul 2008.
Becker D.J., Gordon R.Y., Morris P., Yorko J., Gordon Y.J., Li M., Iqbal N.: Simvastatin vs therapeutic lifestyle changes and supplements: randomized primary prevention trial. Mayo Clinic Proceedings 83(7): 758-64, Jul 2008.
Vorovich E., Chuai S., Li M., Averna J., Marwin V., Wolfe D., Reilly M.P., Cappola T.P.: Comparison of matrix metalloproteinase 9 and brain natriuretic peptide as clinical biomarkers in chronic heart failure. American Heart Journal 155(6): 992-7, Jun 2008.
Li M., Li C., Guan W.: Evaluation of coverage variation of SNP chips for genome-wide association studies. European Journal of Human Genetics 16(5): 635-43, May 2008.
Grant S.F.A., Li M., Bradfield J.P., Kim C.E., Annaiah K., Santa E., Glessner J.T., Casalunovo T., Frackelton E.C., Otieno F.G., Shaner J.L., Smith R.M., Eckert A.W., Chiavaccci R.M., Berkowitz R.I., Hakonarson H.: Association analysis of the FTO gene with obesity in children of Caucasian and African ancestry reveals a common tagging SNP. PLoS ONE 3(3): e1746, Mar 2008.
Ewens W.J., Li M.: Comments on entropy-based transmission/disequilibrium test. Human Genetics 123(1): 97-100, Feb 2008.
Li C., Li M.: GWA simulator: a rapid whole-genome simulation program. Bioinformatics 24(1): 140-2, Jan 2008.

2007

Wilcox M.A., Li Z., Tapper W., Browning S., Curtin K., Ding J., Ding Y., Gagnon F., Li M., Matthew G., Mei L., Rao S., Shaw J., Wei Z., Yu Z., Zhang W., Zheng T., Zhu G.G.: Genetic association with rheumatoid arthritis-Genetic Analysis Workshop 15: summary of contributions from Group 2. Genetic Epidemiology 31(Suppl 1): S12-21, 2007.
Wei Z., Li M.: Genome-wide linkage and association analysis of rheumatoid arthritis in a Canadian population. BMC Proceedings 1(Suppl 1): S19, Dec 2007.
Wang K., Li M., Bucan M.: Pathway-based approaches for analysis of genome-wide association studies. American Journal of Human Genetics 81(6): 1278-83, Dec 2007.
Wang K., Li M., Hadley D., Liu R., Glessner J., Grant S.F.A., Hakonarson H., Bucan M.: PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Research 17(11): 1665-74, Nov 2007.

2006

Li M., Atmaca-Sonmez P., Othman M., Branham K.E.H., Wade M.S., Li Y., Liang L., Zareparsi S., Swaroop A., Abecasis G.R.: CFH haplotypes without Y402H coding variant show strong association with susceptibility to age-related macular degeneration. Nature Genetics 38(9): 1049-54, Sep 2006.
Li M., Boehnke M., Abecasis G.R., Song- P X-K.: Quantitative trait linkage analysis using Gaussian copulas. Genetics173(4): 2317-27, Aug 2006.
Li M., Boehnke M., Abecasis G.R.: Efficient study designs for test of genetic association using subship data and unrelated cases and controls. American Journal of Human Genetics 78(5): 778-92, May 2006.

2005

Zareparsi S., Branham K.E.H., Li M., Klein R.J., Ott J., Hoh J., Abecasis G.R., Swaroop A.: Strong association of Y402H variation in complement factor H at 1q32 with susceptibility for age-related macular degeneration. American Journal of Human Genetics 77(1): 149-53, Jul 2005.
Zareparsi S., Buraczynski M., Branham K.E.H., Shah S., Eng D., Li M., Pawar H., Yashar B.M., Moroi S., Lichter P.R., Petty H.R., Richards J.E., Abecasis G.R., Elner V.M., Swaroop A.: Toll-like receptor 4 variant D299G is associated with susceptibility to age-related macular degeneration. Human Molecular Genetics 14(11): 1449-55, Jun 2005.
Li M., Boehnke M., Abecasis G.R.: Joint modeling of linkage and association: identifying SNPs responsible for a linkage signal. American Journal of Human Genetics 76(6): 934-49, Jun 2005.