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2020

Measuring the predictability of life outcomes with a scientific mass collaboration

Salganik, M. J., Lundberg, I., Kindel, A. T., Ahearn, C. E., Al-Ghoneim, K., Almaatouq, A., Altschul, D. M., Brand, J. E., Carnegie, N. B., Compton, R. J., Datta, D., Davidson, T., Filippova, A., Gilroy, C., Goode, B. J., Jahani, E., Kashyap, R., Kirchner, A., McKay, S., Morgan, A. C. & 92 others, Pentland, A., Polimis, K., Raes, L., Rigobon, D. E., Roberts, C. V., Stanescu, D. M., Suhara, Y., Usmani, A., Wang, E. H., Adem, M., Alhajri, A., AlShebli, B., Amin, R., Amos, R. B., Argyle, L. P., Baer-Bositis, L., Büchi, M., Chung, B. R., Eggert, W., Faletto, G., Fan, Z., Freese, J., Gadgil, T., Gagné, J., Gao, Y., Halpern-Manners, A., Hashim, S. P., Hausen, S., He, G., Higuera, K., Hogan, B., Horwitz, I. M., Hummel, L. M., Jain, N., Jin, K., Jurgens, D., Kaminski, P., Karapetyan, A., Kim, E. H., Leizman, B., Liu, N., Möser, M., Mack, A. E., Mahajan, M., Mandell, N., Marahrens, H., Mercado-Garcia, D., Mocz, V., Mueller-Gastell, K., Musse, A., Niu, Q., Nowak, W., Omidvar, H., Or, A., Ouyang, K., Pinto, K. M., Porter, E., Porter, K. E., Qian, C., Rauf, T., Sargsyan, A., Schaffner, T., Schnabel, L., Schonfeld, B., Sender, B., Tang, J. D., Tsurkov, E., van Loon, A., Varol, O., Wang, J., Wang, F., Weissman, S., Whitaker, K., Wolters, M. K., Woon, W. L., Wang, X., Wang, Z., Wu, J., Wu, C., Yang, K., Yin, J., Zhao, B., Zhu, C., Brooks-Gunn, J., Engelhardt, B. E., Hardt, M., Knox, D., Levy, K., Narayanan, A., Stewart, B. M., Watts, D. J. & McLanahan, S., Apr 14 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 15, p. 8398-8403 6 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

NetNMF-SC: Leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis

Elyanow, R., Dumitrascu, B., Engelhardt, B. E. & Raphael, B. J., Jan 1 2020, In : Genome Research. 30, 2, p. 195-204 10 p.

Research output: Contribution to journalArticle

Open Access
2019

Statistical tests for detecting variance effects in quantitative trait studies

Dumitrascu, B., Darnell, G., Ayroles, J. F. & Engelhardt Martin, B., Jan 15 2019, In : Bioinformatics. 35, 2, p. 200-210 11 p.

Research output: Contribution to journalArticle

4 Scopus citations
2018

Bayesian nonparametric discovery of isoforms and individual specific quantification

Aguiar, D., Cheng, L. F., Dumitrascu, B., Mordelet, F., Pai, A. A. & Engelhardt Martin, B., Dec 1 2018, In : Nature communications. 9, 1, 1681.

Research output: Contribution to journalArticle

2 Scopus citations

Clustering gene expression time series data using an infinite Gaussian process mixture model

McDowell, I. C., Manandhar, D., Vockley, C. M., Schmid, A. K., Reddy, T. E. & Engelhardt Martin, B., Jan 2018, In : PLoS computational biology. 14, 1, e1005896.

Research output: Contribution to journalArticle

10 Scopus citations

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Barbeira, A. N., Dickinson, S. P., Bonazzola, R., Zheng, J., Wheeler, H. E., Torres, J. M., Torstenson, E. S., Shah, K. P., Garcia, T., Edwards, T. L., Stahl, E. A., Huckins, L. M., Aguet, F., Ardlie, K. G., Cummings, B. B., Gelfand, E. T., Getz, G., Hadley, K., Handsaker, R. E., Huang, K. H. & 225 others, Kashin, S., Karczewski, K. J., Lek, M., Li, X., MacArthur, D. G., Nedzel, J. L., Nguyen, D. T., Noble, M. S., Segrè, A. V., Trowbridge, C. A., Tukiainen, T., Abell, N. S., Balliu, B., Barshir, R., Basha, O., Battle, A., Bogu, G. K., Brown, A., Brown, C. D., Castel, S. E., Chen, L. S., Chiang, C., Conrad, D. F., Damani, F. N., Davis, J. R., Delaneau, O., Dermitzakis, E. T., Engelhardt Martin, B., Eskin, E., Ferreira, P. G., Frésard, L., Gamazon, E. R., Garrido-Martín, D., Gewirtz, A. D. H., Gliner, G., Gloudemans, M. J., Guigo, R., Hall, I. M., Han, B., He, Y., Hormozdiari, F., Howald, C., Jo, B., Kang, E. Y., Kim, Y., Kim-Hellmuth, S., Lappalainen, T., Li, G., Li, X., Liu, B., Mangul, S., McCarthy, M. I., McDowell, I. C., Mohammadi, P., Monlong, J., Montgomery, S. B., Muñoz-Aguirre, M., Ndungu, A. W., Nobel, A. B., Oliva, M., Ongen, H., Palowitch, J. J., Panousis, N., Papasaikas, P., Park, Y. S., Parsana, P., Payne, A. J., Peterson, C. B., Quan, J., Reverter, F., Sabatti, C., Saha, A., Sammeth, M., Scott, A. J., Shabalin, A. A., Sodaei, R., Stephens, M., Stranger, B. E., Strober, B. J., Sul, J. H., Tsang, E. K., Urbut, S., Van De Bunt, M., Wang, G., Wen, X., Wright, F. A., Xi, H. S., Yeger-Lotem, E., Zappala, Z., Zaugg, J. B., Zhou, Y. H., Akey, J., Bates, D., Chan, J., Claussnitzer, M., Demanelis, K., Diegel, M., Doherty, J. A., Feinberg, A. P., Fernando, M. S., Halow, J., Hansen, K. D., Haugen, E., Hickey, P. F., Hou, L., Jasmine, F., Jian, R., Jiang, L., Johnson, A., Kaul, R., Kellis, M., Kibriya, M. G., Lee, K., Li, J. B., Li, Q., Lin, J., Lin, S., Linder, S., Linke, C., Liu, Y., Maurano, M. T., Molinie, B., Nelson, J., Neri, F. J., Park, Y., Pierce, B. L., Rinaldi, N. J., Rizzardi, L. F., Sandstrom, R., Skol, A., Smith, K. S., Snyder, M. P., Stamatoyannopoulos, J., Tang, H., Wang, L., Wang, M., Van Wittenberghe, N., Wu, F., Zhang, R., Nierras, C. R., Branton, P. A., Carithers, L. J., Guan, P., Moore, H. M., Rao, A., Vaught, J. B., Gould, S. E., Lockart, N. C., Martin, C., Struewing, J. P., Volpi, S., Addington, A. M., Koester, S. E., Little, A. R., Brigham, L. E., Hasz, R., Hunter, M., Johns, C., Johnson, M., Kopen, G., Leinweber, W. F., Lonsdale, J. T., McDonald, A., Mestichelli, B., Myer, K., Roe, B., Salvatore, M., Shad, S., Thomas, J. A., Walters, G., Washington, M., Wheeler, J., Bridge, J., Foster, B. A., Gillard, B. M., Karasik, E., Kumar, R., Miklos, M., Moser, M. T., Jewell, S. D., Montroy, R. G., Rohrer, D. C., Valley, D. R., Davis, D. A., Mash, D. C., Undale, A. H., Smith, A. M., Tabor, D. E., Roche, N. V., McLean, J. A., Vatanian, N., Robinson, K. L., Sobin, L., Barcus, M. E., Valentino, K. M., Qi, L., Hunter, S., Hariharan, P., Singh, S., Um, K. S., Matose, T., Tomaszewski, M. M., Barker, L. K., Mosavel, M., Siminoff, L. A., Traino, H. M., Flicek, P., Juettemann, T., Ruffier, M., Sheppard, D., Taylor, K., Trevanion, S. J., Zerbino, D. R., Craft, B., Goldman, M., Haeussler, M., Kent, W. J., Lee, C. M., Paten, B., Rosenbloom, K. R., Vivian, J., Zhu, J., Nicolae, D. L., Cox, N. J. & Im, H. K., Dec 1 2018, In : Nature communications. 9, 1, 1825.

Research output: Contribution to journalArticle

92 Scopus citations

Fast Moment Estimation for Generalized Latent Dirichlet Models

Zhao, S., Engelhardt Martin, B., Mukherjee, S. & Dunson, D. B., Oct 2 2018, In : Journal of the American Statistical Association. 113, 524, p. 1528-1540 13 p.

Research output: Contribution to journalArticle

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

McDowell, I. C., Barrera, A., D’Ippolito, A. M., Vockley, C. M., Hong, L. K., Leichter, S. M., Bartelt, L. C., Majoros, W. H., Song, L., Safi, A., Koçak, D. D., Gersbach, C. A., Hartemink, A. J., Crawford, G. E., Engelhardt, B. E. & Reddy, T. E., Sep 2018, In : Genome Research. 28, 9, p. 1272-1284 13 p.

Research output: Contribution to journalArticle

8 Scopus citations

GPCR-specific autoantibody signatures are associated with physiological and pathological immune homeostasis

Cabral-Marques, O., Marques, A., Giil, L. M., De Vito, R., Rademacher, J., Günther, J., Lange, T., Humrich, J. Y., Klapa, S., Schinke, S., Schimke, L. F., Marschner, G., Pitann, S., Adler, S., Dechend, R., Müller, D. N., Braicu, I., Sehouli, J., Schulze-Forster, K., Trippel, T. & 16 others, Scheibenbogen, C., Staff, A., Mertens, P. R., Löbel, M., Mastroianni, J., Plattfaut, C., Gieseler, F., Dragun, D., Engelhardt Martin, B., Fernandez-Cabezudo, M. J., Ochs, H. D., al-Ramadi, B. K., Lamprecht, P., Mueller, A., Heidecke, H. & Riemekasten, G., Dec 1 2018, In : Nature communications. 9, 1, 5224.

Research output: Contribution to journalArticle

17 Scopus citations
2017

Adaptive randomized dimension reduction on massive data

Darnell, G., Georgiev, S., Mukherjee, S. & Engelhardt, B. E., Nov 1 2017, In : Journal of Machine Learning Research. 18

Research output: Contribution to journalArticle

5 Scopus citations

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

Saha, A., Kim, Y., Gewirtz, A. D. H., Jo, B., Gao, C., McDowell, I. C., Engelhardt Martin, B. & Battle, A., Jan 1 2017, In : Genome Research. 27, 11, p. 1843-1858 16 p.

Research output: Contribution to journalArticle

43 Scopus citations

Detecting differential growth of microbial populations with Gaussian process regression

Tonner, P. D., Darnell, C. L., Engelhardt Martin, B. & Schmid, A. K., Feb 2017, In : Genome Research. 27, 2, p. 320-333 14 p.

Research output: Contribution to journalArticle

16 Scopus citations

Dynamic landscape and regulation of RNA editing in mammals

GTEx Consortium, Oct 11 2017, In : Nature. 550, 7675, p. 249-254 6 p.

Research output: Contribution to journalArticle

125 Scopus citations

Expandable factor analysis

Srivastava, S., Engelhardt Martin, B. & Dunson, D. B., Sep 1 2017, In : Biometrika. 104, 3, p. 649-663 15 p.

Research output: Contribution to journalArticle

3 Scopus citations

Genetic effects on gene expression across human tissues

GTEx Consortium, Oct 11 2017, In : Nature. 550, 7675, p. 204-213 10 p.

Research output: Contribution to journalArticle

774 Scopus citations

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing

Genotype-Tissue Expression Consortium, National Institutes of Health (NIH) Common Fund, iospecimen Collection Source Site-National Disease Research Interchange, Biospecimen Collection Source Site-Roswell Park Cancer Institute, Biospecimen Core Resource-Van Andel Research Institute, Brain Bank Repository-University of Miami, Leidos Biomedical Project Management, Ethical, Legal, and Social Implications Study, Genome Browser Data Integration, and Visualization-European Bioinformatics Institute, Genome Browser Data Integration and Visualization-Genomics Institute, University of California, Santa Cruz:, LDACC-Analysis Working Group (AWG), Funded Statistical Methods groups-AWG, Enhancing GTEx funded Group, NIH/NHGRI, NIH/NCI, NIH/NIMH, NIH/NIDA & Other members of the AWG, Apr 19 2017, In : Science Translational Medicine. 9, 386, eaal5209.

Research output: Contribution to journalArticle

162 Scopus citations

Landscape of X chromosome inactivation across human tissues

GTEx Consortium, Oct 11 2017, In : Nature. 550, 7675, p. 244-248 5 p.

Research output: Contribution to journalArticle

127 Scopus citations

The impact of rare variation on gene expression across tissues

GTEx Consortium, Oct 11 2017, In : Nature. 550, 7675, p. 239-243 5 p.

Research output: Contribution to journalArticle

60 Scopus citations
2016

Bayesian group factor analysis with structured sparsity

Zhao, S., Gao, C., Mukherjee, S. & Engelhardt Martin, B., Apr 1 2016, In : Journal of Machine Learning Research. 17, p. 1-47 47 p.

Research output: Contribution to journalArticle

10 Scopus citations

Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering

Gao, C., McDowell, I. C., Zhao, S., Brown, C. D. & Engelhardt Martin, B., Jul 2016, In : PLoS computational biology. 12, 7, e1004791.

Research output: Contribution to journalArticle

21 Scopus citations

Meta-analysis of Genome-Wide Association Studies for Extraversion: Findings from the Genetics of Personality Consortium

van den Berg, S. M., de Moor, M. H. M., Verweij, K. J. H., Krueger, R. F., Luciano, M., Arias Vasquez, A., Matteson, L. K., Derringer, J., Esko, T., Amin, N., Gordon, S. D., Hansell, N. K., Hart, A. B., Seppälä, I., Huffman, J. E., Konte, B., Lahti, J., Lee, M., Miller, M., Nutile, T. & 102 others, Tanaka, T., Teumer, A., Viktorin, A., Wedenoja, J., Abdellaoui, A., Abecasis, G. R., Adkins, D. E., Agrawal, A., Allik, J., Appel, K., Bigdeli, T. B., Busonero, F., Campbell, H., Costa, P. T., Smith, G. D., Davies, G., de Wit, H., Ding, J., Engelhardt Martin, B., Eriksson, J. G., Fedko, I. O., Ferrucci, L., Franke, B., Giegling, I., Grucza, R., Hartmann, A. M., Heath, A. C., Heinonen, K., Henders, A. K., Homuth, G., Hottenga, J. J., Iacono, W. G., Janzing, J., Jokela, M., Karlsson, R., Kemp, J. P., Kirkpatrick, M. G., Latvala, A., Lehtimäki, T., Liewald, D. C., Madden, P. A. F., Magri, C., Magnusson, P. K. E., Marten, J., Maschio, A., Mbarek, H., Medland, S. E., Mihailov, E., Milaneschi, Y., Montgomery, G. W., Nauck, M., Nivard, M. G., Ouwens, K. G., Palotie, A., Pettersson, E., Polasek, O., Qian, Y., Pulkki-Råback, L., Raitakari, O. T., Realo, A., Rose, R. J., Ruggiero, D., Schmidt, C. O., Slutske, W. S., Sorice, R., Starr, J. M., St Pourcain, B., Sutin, A. R., Timpson, N. J., Trochet, H., Vermeulen, S., Vuoksimaa, E., Widen, E., Wouda, J., Wright, M. J., Zgaga, L., Generation Scotland, S., Porteous, D., Minelli, A., Palmer, A. A., Rujescu, D., Ciullo, M., Hayward, C., Rudan, I., Metspalu, A., Kaprio, J., Deary, I. J., Räikkönen, K., Wilson, J. F., Keltikangas-Järvinen, L., Bierut, L. J., Hettema, J. M., Grabe, H. J., Penninx, B. W. J. H., van Duijn, C. M., Evans, D. M., Schlessinger, D., Pedersen, N. L., Terracciano, A., McGue, M., Martin, N. G. & Boomsma, D. I., Mar 1 2016, In : Behavior Genetics. 46, 2, p. 170-182 13 p.

Research output: Contribution to journalArticle

48 Scopus citations
2015

Meta-analysis of genome-wide association studies for neuroticism, and the polygenic association with major depressive disorder

De Moor, M. H. M., Van Den Berg, S. M., Verweij, K. J. H., Krueger, R. F., Luciano, M., Arias Vasquez, A., Matteson, L. K., Derringer, J., Esko, T., Amin, N., Gordon, S. D., Hansell, N. K., Hart, A. B., Seppälä, I., Huffman, J. E., Konte, B., Lahti, J., Lee, M., Miller, M., Nutile, T. & 98 others, Tanaka, T., Teumer, A., Viktorin, A., Wedenoja, J., Abecasis, G. R., Adkins, D. E., Agrawal, A., Allik, J., Appel, K., Bigdeli, T. B., Busonero, F., Campbell, H., Costa, P. T., Davey Smith, G., Davies, G., De Wit, H., Ding, J., Engelhardt Martin, B., Eriksson, J. G., Fedko, I. O., Ferrucci, L., Franke, B., Giegling, I., Grucza, R., Hartmann, A. M., Heath, A. C., Heinonen, K., Henders, A. K., Homuth, G., Hottenga, J. J., Iacono, W. G., Janzing, J., Jokela, M., Karlsson, R., Kemp, J. P., Kirkpatrick, M. G., Latvala, A., Lehtimäki, T., Liewald, D. C., Madden, P. A. F., Magri, C., Magnusson, P. K. E., Marten, J., Maschio, A., Medland, S. E., Mihailov, E., Milaneschi, Y., Montgomery, G. W., Nauck, M., Ouwens, K. G., Palotie, A., Pettersson, E., Polasek, O., Qian, Y., Pulkki-Råback, L., Raitakari, O. T., Realo, A., Rose, R. J., Ruggiero, D., Schmidt, C. O., Slutske, W. S., Sorice, R., Starr, J. M., St Pourcain, B., Sutin, A. R., Timpson, N. J., Trochet, H., Vermeulen, S., Vuoksimaa, E., Widen, E., Wouda, J., Wright, M. J., Zgaga, L., Porteous, D., Minelli, A., Palmer, A. A., Rujescu, D., Ciullo, M., Hayward, C., Rudan, I., Metspalu, A., Kaprio, J., Deary, I. J., Räikkönen, K., Wilson, J. F., Keltikangas-Järvinen, L., Bierut, L. J., Hettema, J. M., Grabe, H. J., Van Duijn, C. M., Evans, D. M., Schlessinger, D., Pedersen, N. L., Terracciano, A., McGue, M., Penninx, B. W. J. H., Martin, N. G. & Boomsma, D. I., Jul 1 2015, In : JAMA Psychiatry. 72, 7, p. 642-650 9 p.

Research output: Contribution to journalArticle

132 Scopus citations
5 Scopus citations

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

Zhang, W., Spector, T. D., Deloukas, P., Bell, J. T. & Engelhardt Martin, B., Jan 24 2015, In : Genome biology. 16, 1, 14.

Research output: Contribution to journalArticle

64 Scopus citations
2014

Genetic variation associated with euphorigenic effects of d-amphetamine is associated with diminished risk for schizophrenia and attention deficit hyperactivity disorder

Hart, A. B., Gamazon, E. R., Engelhardt Martin, B., Sklar, P., Kähler, A. K., Hultman, C. M., Sullivan, P. F., Neale, B. M., Faraone, S. V., De Wit, H., Cox, N. J. & Palmer, A. A., Apr 22 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 16, p. 5968-5973 6 p.

Research output: Contribution to journalArticle

10 Scopus citations

Mangravite et al. reply

Mangravite, L. M., Engelhardt Martin, B., Stephens, M. & Krauss, R. M., Oct 2 2014, In : Nature. 513, 7518, p. E3

Research output: Contribution to journalArticle

4 Scopus citations
2013

A statin-dependent QTL for GATM expression is associated with statin-induced myopathy

Mangravite, L. M., Engelhardt Martin, B., Medina, M. W., Smith, J. D., Brown, C. D., Chasman, D. I., Mecham, B. H., Howie, B., Shim, H., Naidoo, D., Feng, Q., Rieder, M. J., Chen, Y. D. I., Rotter, J. I., Ridker, P. M., Hopewell, J. C., Parish, S., Armitage, J., Collins, R., Wilke, R. A. & 3 others, Nickerson, D. A., Stephens, M. & Krauss, R. M., Sep 3 2013, In : Nature. 502, 7471, p. 377-380 4 p.

Research output: Contribution to journalArticle

132 Scopus citations

Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

Brown, C. D., Mangravite, L. M. & Engelhardt Martin, B., Aug 1 2013, In : PLoS genetics. 9, 8, e1003649.

Research output: Contribution to journalArticle

79 Scopus citations

Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: Recurrence of tyrosine aminotransferase activity in the Iα subfamily

Muratore, K. E., Engelhardt, B. E., Srouji, J. R., Jordan, M. I., Brenner, S. E. & Kirsch, J. F., Sep 1 2013, In : Proteins: Structure, Function and Bioinformatics. 81, 9, p. 1593-1609 17 p.

Research output: Contribution to journalArticle

5 Scopus citations

Stability selection for regression-based models of transcription factor-DNA binding specificity

Mordelet, F., Horton, J., Hartemink, A. J., Engelhardt Martin, B. & Gordân, R., Jul 1 2013, In : Bioinformatics. 29, 13, p. i117-i125

Research output: Contribution to journalArticle

28 Scopus citations
2012

Genome-Wide Association Study of d-Amphetamine Response in Healthy Volunteers Identifies Putative Associations, Including Cadherin 13 (CDH13)

Hart, A. B., Engelhardt Martin, B., Wardle, M. C., Sokoloff, G., Stephens, M., de Wit, H. & Palmer, A. A., Aug 28 2012, In : PloS one. 7, 8, e42646.

Research output: Contribution to journalArticle

53 Scopus citations
2011

Genome-scale phylogenetic function annotation of large and diverse protein families

Engelhardt Martin, B., Jordan, M. I., Srouji, J. R. & Brenner, S. E., Nov 1 2011, In : Genome Research. 21, 11, p. 1969-1980 12 p.

Research output: Contribution to journalArticle

39 Scopus citations
2010

Analysis of population structure: A unifying framework and novel methods based on sparse factor analysis

Engelhardt Martin, B. & Stephens, M., Sep 1 2010, In : PLoS genetics. 6, 9, e1001117.

Research output: Contribution to journalArticle

78 Scopus citations

Understanding mechanisms underlying human gene expression variation with RNA sequencing

Pickrell, J. K., Marioni, J. C., Pai, A. A., Degner, J. F., Engelhardt, B. E., Nkadori, E., Veyrieras, J. B., Stephens, M., Gilad, Y. & Pritchard, J. K., Apr 1 2010, In : Nature. 464, 7289, p. 768-772 5 p.

Research output: Contribution to journalArticle

827 Scopus citations
2005

Protein Molecular Function Prediction by Bayesian Phylogenomics

Engelhardt Martin, B., Jordan, M. I., Muratore, K. E. & Brersfser, S. E., Dec 1 2005, In : PLoS computational biology. 1, 5, p. 432-445 14 p.

Research output: Contribution to journalArticle

128 Scopus citations
2003

Factored planning

Amir, E. & Engelhardt Martin, B., Dec 1 2003, In : IJCAI International Joint Conference on Artificial Intelligence. p. 929-935 7 p.

Research output: Contribution to journalArticle

64 Scopus citations