List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

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2022
K. Olszewski, Barsotti, A., Feng, X. - J., Momcilovic, M., Liu, K. G., Kim, J. - I., Morris, K., Lamarque, C., Gaffney, J., Yu, X., Patel, J. P., Rabinowitz, J. D., Shackelford, D. B., and Poyurovsky, M. V., “Inhibition of glucose transport synergizes with chemical or genetic disruption of mitochondrial metabolism and suppresses TCA cycle-deficient tumors.”, Cell Chem Biol, vol. 29, no. 3, pp. 423-435.e10, 2022.
L. Wang, Xing, X., Zeng, X., S Jackson, R. E., TeSlaa, T., Al-Dalahmah, O., Samarah, L. Z., Goodwin, K., Yang, L., McReynolds, M. R., Li, X., Wolff, J. J., Rabinowitz, J. D., and Davidson, S. M., “Spatially resolved isotope tracing reveals tissue metabolic activity.”, Nat Methods, vol. 19, no. 2, pp. 223-230, 2022.
L. Wang, Xing, X., Zeng, X., S Jackson, R. E., TeSlaa, T., Al-Dalahmah, O., Samarah, L. Z., Goodwin, K., Yang, L., McReynolds, M. R., Li, X., Wolff, J. J., Rabinowitz, J. D., and Davidson, S. M., “Spatially resolved isotope tracing reveals tissue metabolic activity.”, Nat Methods, vol. 19, no. 2, pp. 223-230, 2022.
L. Wang, Xing, X., Zeng, X., S Jackson, R. E., TeSlaa, T., Al-Dalahmah, O., Samarah, L. Z., Goodwin, K., Yang, L., McReynolds, M. R., Li, X., Wolff, J. J., Rabinowitz, J. D., and Davidson, S. M., “Spatially resolved isotope tracing reveals tissue metabolic activity.”, Nat Methods, vol. 19, no. 2, pp. 223-230, 2022.
2019
J. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., “Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
J. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., “Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
J. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., “Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
J. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., “Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
C. Cao, Lemaire, L. A., Wang, W., Yoon, P. H., Choi, Y. A., Parsons, L. R., Matese, J. C., Wang, W., Levine, M., and Chen, K., “Comprehensive single-cell transcriptome lineages of a proto-vertebrate.”, Nature, vol. 571, no. 7765, pp. 349-354, 2019.
C. Cao, Lemaire, L. A., Wang, W., Yoon, P. H., Choi, Y. A., Parsons, L. R., Matese, J. C., Wang, W., Levine, M., and Chen, K., “Comprehensive single-cell transcriptome lineages of a proto-vertebrate.”, Nature, vol. 571, no. 7765, pp. 349-354, 2019.
S. Tucci and Akey, J. M., “The long walk to African genomics.”, Genome Biol, vol. 20, no. 1, p. 130, 2019.
K. K. Benson, Hu, W., Weller, A. H., Bennett, A. H., Chen, E. R., Khetarpal, S. A., Yoshino, S., Bone, W. P., Wang, L., Rabinowitz, J. D., Voight, B. F., and Soccio, R. E., “Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene.”, Proc Natl Acad Sci U S A, vol. 116, no. 46, pp. 23232-23242, 2019.
K. K. Benson, Hu, W., Weller, A. H., Bennett, A. H., Chen, E. R., Khetarpal, S. A., Yoshino, S., Bone, W. P., Wang, L., Rabinowitz, J. D., Voight, B. F., and Soccio, R. E., “Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene.”, Proc Natl Acad Sci U S A, vol. 116, no. 46, pp. 23232-23242, 2019.
K. K. Benson, Hu, W., Weller, A. H., Bennett, A. H., Chen, E. R., Khetarpal, S. A., Yoshino, S., Bone, W. P., Wang, L., Rabinowitz, J. D., Voight, B. F., and Soccio, R. E., “Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene.”, Proc Natl Acad Sci U S A, vol. 116, no. 46, pp. 23232-23242, 2019.
K. M. Chen, Cofer, E. M., Zhou, J., and Troyanskaya, O. G., “Selene: a PyTorch-based deep learning library for sequence data.”, Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
K. M. Chen, Cofer, E. M., Zhou, J., and Troyanskaya, O. G., “Selene: a PyTorch-based deep learning library for sequence data.”, Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
S. Nadimpalli Kobren and Singh, M., “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
2018
S. R. Browning, Browning, B. L., Zhou, Y., Tucci, S., and Akey, J. M., “Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture.”, Cell, vol. 173, no. 1, pp. 53-61.e9, 2018.
N. N. Pavlova, Hui, S., Ghergurovich, J. M., Fan, J., Intlekofer, A. M., White, R. M., Rabinowitz, J. D., Thompson, C. B., and Zhang, J., “As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid.”, Cell Metab, vol. 27, no. 2, pp. 428-438.e5, 2018.
P. A. Gibney, Schieler, A., Chen, J. C., Bacha-Hummel, J. M., Botstein, M., Volpe, M., Silverman, S. J., Xu, Y., Bennett, B. D., Rabinowitz, J. D., and Botstein, D., “Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast.”, Mol Biol Cell, vol. 29, no. 8, pp. 897-910, 2018.
P. A. Gibney, Schieler, A., Chen, J. C., Bacha-Hummel, J. M., Botstein, M., Volpe, M., Silverman, S. J., Xu, Y., Bennett, B. D., Rabinowitz, J. D., and Botstein, D., “Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast.”, Mol Biol Cell, vol. 29, no. 8, pp. 897-910, 2018.
P. A. Gibney, Schieler, A., Chen, J. C., Bacha-Hummel, J. M., Botstein, M., Volpe, M., Silverman, S. J., Xu, Y., Bennett, B. D., Rabinowitz, J. D., and Botstein, D., “Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast.”, Mol Biol Cell, vol. 29, no. 8, pp. 897-910, 2018.
P. A. Gibney, Schieler, A., Chen, J. C., Bacha-Hummel, J. M., Botstein, M., Volpe, M., Silverman, S. J., Xu, Y., Bennett, B. D., Rabinowitz, J. D., and Botstein, D., “Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast.”, Mol Biol Cell, vol. 29, no. 8, pp. 897-910, 2018.
J. Zhou, Theesfeld, C. L., Yao, K., Chen, K. M., Wong, A. K., and Troyanskaya, O. G., “Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.”, Nat Genet, vol. 50, no. 8, pp. 1171-1179, 2018.
J. Zhou, Theesfeld, C. L., Yao, K., Chen, K. M., Wong, A. K., and Troyanskaya, O. G., “Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.”, Nat Genet, vol. 50, no. 8, pp. 1171-1179, 2018.
J. Zhou, Theesfeld, C. L., Yao, K., Chen, K. M., Wong, A. K., and Troyanskaya, O. G., “Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.”, Nat Genet, vol. 50, no. 8, pp. 1171-1179, 2018.
D. Guan, Xiong, Y., Borck, P. C., Jang, C., Doulias, P. - T., Papazyan, R., Fang, B., Jiang, C., Zhang, Y., Briggs, E. R., Hu, W., Steger, D., Ischiropoulos, H., Rabinowitz, J. D., and Lazar, M. A., “Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes.”, Cell, vol. 174, no. 4, pp. 831-842.e12, 2018.
Y. - F. Xu, Lu, W., Chen, J. C., Johnson, S. A., Gibney, P. A., Thomas, D. G., Brown, G., May, A. L., Campagna, S. R., Yakunin, A. F., Botstein, D., and Rabinowitz, J. D., “Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase.”, ACS Chem Biol, vol. 13, no. 10, pp. 3011-3020, 2018.
Y. - F. Xu, Lu, W., Chen, J. C., Johnson, S. A., Gibney, P. A., Thomas, D. G., Brown, G., May, A. L., Campagna, S. R., Yakunin, A. F., Botstein, D., and Rabinowitz, J. D., “Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase.”, ACS Chem Biol, vol. 13, no. 10, pp. 3011-3020, 2018.
Y. -suk Lee, Wong, A. K., Tadych, A., Hartmann, B. M., Park, C. Y., DeJesus, V. A., Ramos, I., Zaslavsky, E., Sealfon, S. C., and Troyanskaya, O. G., “Interpretation of an individual functional genomics experiment guided by massive public data.”, Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
Y. -suk Lee, Wong, A. K., Tadych, A., Hartmann, B. M., Park, C. Y., DeJesus, V. A., Ramos, I., Zaslavsky, E., Sealfon, S. C., and Troyanskaya, O. G., “Interpretation of an individual functional genomics experiment guided by massive public data.”, Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
A. V. Rangan, McGrouther, C. C., Kelsoe, J., Schork, N., Stahl, E., Zhu, Q., Krishnan, A., Yao, V., Troyanskaya, O., Bilaloglu, S., Raghavan, P., Bergen, S., Jureus, A., and Landen, M., “A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data.”, PLoS Comput Biol, vol. 14, no. 5, p. e1006105, 2018.
A. V. Rangan, McGrouther, C. C., Kelsoe, J., Schork, N., Stahl, E., Zhu, Q., Krishnan, A., Yao, V., Troyanskaya, O., Bilaloglu, S., Raghavan, P., Bergen, S., Jureus, A., and Landen, M., “A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data.”, PLoS Comput Biol, vol. 14, no. 5, p. e1006105, 2018.
M. O. Press, McCoy, R. C., Hall, A. N., Akey, J. M., and Queitsch, C., “Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana.”, Genome Res, vol. 28, no. 8, pp. 1169-1178, 2018.
C. Jang, Chen, L., and Rabinowitz, J. D., “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 2018.
R. J. Morscher, Ducker, G. S., Li, S. Hsin- Jung, Mayer, J. A., Gitai, Z., Sperl, W., and Rabinowitz, J. D., “Mitochondrial translation requires folate-dependent tRNA methylation.”, Nature, vol. 554, no. 7690, pp. 128-132, 2018.
R. J. Morscher, Ducker, G. S., Li, S. Hsin- Jung, Mayer, J. A., Gitai, Z., Sperl, W., and Rabinowitz, J. D., “Mitochondrial translation requires folate-dependent tRNA methylation.”, Nature, vol. 554, no. 7690, pp. 128-132, 2018.
R. J. Morscher, Ducker, G. S., Li, S. Hsin- Jung, Mayer, J. A., Gitai, Z., Sperl, W., and Rabinowitz, J. D., “Mitochondrial translation requires folate-dependent tRNA methylation.”, Nature, vol. 554, no. 7690, pp. 128-132, 2018.
A. B. Wolf and Akey, J. M., “Outstanding questions in the study of archaic hominin admixture.”, PLoS Genet, vol. 14, no. 5, p. e1007349, 2018.
A. B. Wolf and Akey, J. M., “Outstanding questions in the study of archaic hominin admixture.”, PLoS Genet, vol. 14, no. 5, p. e1007349, 2018.
A. B. Wolf and Akey, J. M., “Outstanding questions in the study of archaic hominin admixture.”, PLoS Genet, vol. 14, no. 5, p. e1007349, 2018.
S. E. McKee, Zhang, S., Chen, L., Rabinowitz, J. D., and Reyes, T. M., “Perinatal high fat diet and early life methyl donor supplementation alter one carbon metabolism and DNA methylation in the brain.”, J Neurochem, vol. 145, no. 5, pp. 362-373, 2018.
R. Menon, Otto, E. A., Kokoruda, A., Zhou, J., Zhang, Z., Yoon, E., Chen, Y. - C., Troyanskaya, O., Spence, J. R., Kretzler, M., and Cebrián, C., “Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.”, Development, vol. 145, no. 16, 2018.
R. Menon, Otto, E. A., Kokoruda, A., Zhou, J., Zhang, Z., Yoon, E., Chen, Y. - C., Troyanskaya, O., Spence, J. R., Kretzler, M., and Cebrián, C., “Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.”, Development, vol. 145, no. 16, 2018.
C. Jang, Hui, S., Lu, W., Cowan, A. J., Morscher, R. J., Lee, G., Liu, W., Tesz, G. J., Birnbaum, M. J., and Rabinowitz, J. D., “The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids.”, Cell Metab, vol. 27, no. 2, pp. 351-361.e3, 2018.
R. A. Miller, Shi, Y., Lu, W., Pirman, D. A., Jatkar, A., Blatnik, M., Wu, H., Cárdenas, C., Wan, M., J Foskett, K., Park, J. O., Zhang, Y., Holland, W. L., Rabinowitz, J. D., and Birnbaum, M. J., “Targeting hepatic glutaminase activity to ameliorate hyperglycemia.”, Nat Med, vol. 24, no. 4, pp. 518-524, 2018.
R. A. Miller, Shi, Y., Lu, W., Pirman, D. A., Jatkar, A., Blatnik, M., Wu, H., Cárdenas, C., Wan, M., J Foskett, K., Park, J. O., Zhang, Y., Holland, W. L., Rabinowitz, J. D., and Birnbaum, M. J., “Targeting hepatic glutaminase activity to ameliorate hyperglycemia.”, Nat Med, vol. 24, no. 4, pp. 518-524, 2018.
R. A. Miller, Shi, Y., Lu, W., Pirman, D. A., Jatkar, A., Blatnik, M., Wu, H., Cárdenas, C., Wan, M., J Foskett, K., Park, J. O., Zhang, Y., Holland, W. L., Rabinowitz, J. D., and Birnbaum, M. J., “Targeting hepatic glutaminase activity to ameliorate hyperglycemia.”, Nat Med, vol. 24, no. 4, pp. 518-524, 2018.
2017
R. C. Oslund, Su, X., Haugbro, M., Kee, J. - M., Esposito, M., David, Y., Wang, B., Ge, E., Perlman, D. H., Kang, Y., Muir, T. W., and Rabinowitz, J. D., “Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate.”, Nat Chem Biol, vol. 13, no. 10, pp. 1081-1087, 2017.
P. F. Przytycki and Singh, M., “Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.”, Genome Med, vol. 9, no. 1, p. 79, 2017.
P. F. Przytycki and Singh, M., “Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.”, Genome Med, vol. 9, no. 1, p. 79, 2017.
P. F. Przytycki and Singh, M., “Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.”, Genome Med, vol. 9, no. 1, p. 79, 2017.
P. F. Przytycki and Singh, M., “Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.”, Genome Med, vol. 9, no. 1, p. 79, 2017.
S. Hong, Zhou, W., Fang, B., Lu, W., Loro, E., Damle, M., Ding, G., Jager, J., Zhang, S., Zhang, Y., Feng, D., Chu, Q., Dill, B. D., Molina, H., Khurana, T. S., Rabinowitz, J. D., Lazar, M. A., and Sun, Z., “Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion.”, Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
S. Hong, Zhou, W., Fang, B., Lu, W., Loro, E., Damle, M., Ding, G., Jager, J., Zhang, S., Zhang, Y., Feng, D., Chu, Q., Dill, B. D., Molina, H., Khurana, T. S., Rabinowitz, J. D., Lazar, M. A., and Sun, Z., “Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion.”, Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
Y. Zhang, Kurupati, R., Liu, L., Zhou, X. Yang, Zhang, G., Hudaihed, A., Filisio, F., Giles-Davis, W., Xu, X., Karakousis, G. C., Schuchter, L. M., Xu, W., Amaravadi, R., Xiao, M., Sadek, N., Krepler, C., Herlyn, M., Freeman, G. J., Rabinowitz, J. D., and Ertl, H. C. J., “Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy.”, Cancer Cell, vol. 32, no. 3, pp. 377-391.e9, 2017.
Y. Zhang, Kurupati, R., Liu, L., Zhou, X. Yang, Zhang, G., Hudaihed, A., Filisio, F., Giles-Davis, W., Xu, X., Karakousis, G. C., Schuchter, L. M., Xu, W., Amaravadi, R., Xiao, M., Sadek, N., Krepler, C., Herlyn, M., Freeman, G. J., Rabinowitz, J. D., and Ertl, H. C. J., “Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy.”, Cancer Cell, vol. 32, no. 3, pp. 377-391.e9, 2017.
H. In Kim, Raffler, J., Lu, W., Lee, J. - J., Abbey, D., Saleheen, D., Rabinowitz, J. D., Bennett, M. J., Hand, N. J., Brown, C., and Rader, D. J., “Fine Mapping and Functional Analysis Reveal a Role of SLC22A1 in Acylcarnitine Transport.”, Am J Hum Genet, vol. 101, no. 4, pp. 489-502, 2017.
H. In Kim, Raffler, J., Lu, W., Lee, J. - J., Abbey, D., Saleheen, D., Rabinowitz, J. D., Bennett, M. J., Hand, N. J., Brown, C., and Rader, D. J., “Fine Mapping and Functional Analysis Reveal a Role of SLC22A1 in Acylcarnitine Transport.”, Am J Hum Genet, vol. 101, no. 4, pp. 489-502, 2017.
Y. Pritykin, Brito, T., Schüpbach, T., Singh, M., and Pane, A., “Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation.”, RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
Y. Pritykin, Brito, T., Schüpbach, T., Singh, M., and Pane, A., “Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation.”, RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
W. Lu, Su, X., Klein, M. S., Lewis, I. A., Fiehn, O., and Rabinowitz, J. D., “Metabolite Measurement: Pitfalls to Avoid and Practices to Follow.”, Annu Rev Biochem, vol. 86, pp. 277-304, 2017.
W. Lu, Su, X., Klein, M. S., Lewis, I. A., Fiehn, O., and Rabinowitz, J. D., “Metabolite Measurement: Pitfalls to Avoid and Practices to Follow.”, Annu Rev Biochem, vol. 86, pp. 277-304, 2017.
W. Lu, Su, X., Klein, M. S., Lewis, I. A., Fiehn, O., and Rabinowitz, J. D., “Metabolite Measurement: Pitfalls to Avoid and Practices to Follow.”, Annu Rev Biochem, vol. 86, pp. 277-304, 2017.
J. Choi, Rajagopal, A., Xu, Y. - F., Rabinowitz, J. D., and O'Shea, E. K., “A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae.”, PLoS One, vol. 12, no. 5, p. e0176085, 2017.
J. Choi, Rajagopal, A., Xu, Y. - F., Rabinowitz, J. D., and O'Shea, E. K., “A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae.”, PLoS One, vol. 12, no. 5, p. e0176085, 2017.
W. A. Rogers, Goyal, Y., Yamaya, K., Shvartsman, S. Y., and Levine, M. S., “Uncoupling neurogenic gene networks in the Drosophila embryo.”, Genes Dev, vol. 31, no. 7, pp. 634-638, 2017.
W. A. Rogers, Goyal, Y., Yamaya, K., Shvartsman, S. Y., and Levine, M. S., “Uncoupling neurogenic gene networks in the Drosophila embryo.”, Genes Dev, vol. 31, no. 7, pp. 634-638, 2017.
2016
X. Nuttle, Giannuzzi, G., Duyzend, M. H., Schraiber, J. G., Narvaiza, I., Sudmant, P. H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H. A. F., Marchetto, M. C. N., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., W Tang, J., Ventura, M., Banci, L., Antonacci, F., Akey, J. M., Amemiya, C. T., Gage, F. H., Reymond, A., and Eichler, E. E., “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
X. Nuttle, Giannuzzi, G., Duyzend, M. H., Schraiber, J. G., Narvaiza, I., Sudmant, P. H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H. A. F., Marchetto, M. C. N., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., W Tang, J., Ventura, M., Banci, L., Antonacci, F., Akey, J. M., Amemiya, C. T., Gage, F. H., Reymond, A., and Eichler, E. E., “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
C. Shi and Murphy, C. T., “Feeding the germline.”, Genes Dev, vol. 30, no. 3, pp. 249-50, 2016.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.”, Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.”, Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.”, Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., “A global genetic interaction network maps a wiring diagram of cellular function.”, Science, vol. 353, no. 6306, 2016.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., “A global genetic interaction network maps a wiring diagram of cellular function.”, Science, vol. 353, no. 6306, 2016.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., “A global genetic interaction network maps a wiring diagram of cellular function.”, Science, vol. 353, no. 6306, 2016.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., “A global genetic interaction network maps a wiring diagram of cellular function.”, Science, vol. 353, no. 6306, 2016.
N. Ouzounov, Nguyen, J. P., Bratton, B. P., Jacobowitz, D., Gitai, Z., and Shaevitz, J. W., “MreB Orientation Correlates with Cell Diameter in Escherichia coli.”, Biophys J, vol. 111, no. 5, pp. 1035-43, 2016.
I. A. Navarrete and Levine, M., “Nodal and FGF coordinate ascidian neural tube morphogenesis.”, Development, vol. 143, no. 24, pp. 4665-4675, 2016.
I. A. Navarrete and Levine, M., “Nodal and FGF coordinate ascidian neural tube morphogenesis.”, Development, vol. 143, no. 24, pp. 4665-4675, 2016.
R. Papazyan, Sun, Z., Kim, Y. Hoon, Titchenell, P. M., Hill, D. A., Lu, W., Damle, M., Wan, M., Zhang, Y., Briggs, E. R., Rabinowitz, J. D., and Lazar, M. A., “Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP.”, Cell Metab, vol. 24, no. 6, pp. 863-874, 2016.
Q. Wang, J Taliaferro, M., Klibaite, U., Hilgers, V., Shaevitz, J. W., and Rio, D. C., “The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila.”, Proc Natl Acad Sci U S A, vol. 113, no. 19, pp. 5269-74, 2016.
2015
R. DiLoreto and Murphy, C. T., “The cell biology of aging.”, Mol Biol Cell, vol. 26, no. 25, pp. 4524-31, 2015.
J. Wang, Kaletsky, R., Silva, M., Williams, A., Haas, L. A., Androwski, R. J., Landis, J. N., Patrick, C., Rashid, A., Santiago-Martinez, D., Gravato-Nobre, M., Hodgkin, J., Hall, D. H., Murphy, C. T., and Barr, M. M., “Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis.”, Curr Biol, vol. 25, no. 24, pp. 3232-8, 2015.
J. P. Bothma, Garcia, H. G., Ng, S., Perry, M. W., Gregor, T., and Levine, M., “Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo.”, Elife, vol. 4, 2015.
L. Zwarts, Broeck, L. Vanden, Cappuyns, E., Ayroles, J. F., Magwire, M. M., Vulsteke, V., Clements, J., Mackay, T. F. C., and Callaerts, P., “The genetic basis of natural variation in mushroom body size in Drosophila melanogaster.”, Nat Commun, vol. 6, p. 10115, 2015.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T., “Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs.”, Neuron, vol. 85, no. 2, pp. 330-45, 2015.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T., “Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs.”, Neuron, vol. 85, no. 2, pp. 330-45, 2015.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T., “Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs.”, Neuron, vol. 85, no. 2, pp. 330-45, 2015.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T., “Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs.”, Neuron, vol. 85, no. 2, pp. 330-45, 2015.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T., “Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs.”, Neuron, vol. 85, no. 2, pp. 330-45, 2015.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T., “Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs.”, Neuron, vol. 85, no. 2, pp. 330-45, 2015.
D. Gorenshteyn, Zaslavsky, E., Fribourg, M., Park, C. Y., Wong, A. K., Tadych, A., Hartmann, B. M., Albrecht, R. A., García-Sastre, A., Kleinstein, S. H., Troyanskaya, O. G., and Sealfon, S. C., “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”, Immunity, vol. 43, no. 3, pp. 605-14, 2015.
P. Barron Abitua, T Gainous, B., Kaczmarczyk, A. N., Winchell, C. J., Hudson, C., Kamata, K., Nakagawa, M., Tsuda, M., Kusakabe, T. G., and Levine, M., “The pre-vertebrate origins of neurogenic placodes.”, Nature, vol. 524, no. 7566, pp. 462-5, 2015.
S. D. Kocher, Tsuruda, J. M., Gibson, J. D., Emore, C. M., Arechavaleta-Velasco, M. E., Queller, D. C., Strassmann, J. E., Grozinger, C. M., Gribskov, M. R., San Miguel, P., Westerman, R., and Hunt, G. J., “A Search for Parent-of-Origin Effects on Honey Bee Gene Expression.”, G3 (Bethesda), vol. 5, no. 8, pp. 1657-62, 2015.
S. D. Kocher, Tsuruda, J. M., Gibson, J. D., Emore, C. M., Arechavaleta-Velasco, M. E., Queller, D. C., Strassmann, J. E., Grozinger, C. M., Gribskov, M. R., San Miguel, P., Westerman, R., and Hunt, G. J., “A Search for Parent-of-Origin Effects on Honey Bee Gene Expression.”, G3 (Bethesda), vol. 5, no. 8, pp. 1657-62, 2015.
S. D. Kocher, Tsuruda, J. M., Gibson, J. D., Emore, C. M., Arechavaleta-Velasco, M. E., Queller, D. C., Strassmann, J. E., Grozinger, C. M., Gribskov, M. R., San Miguel, P., Westerman, R., and Hunt, G. J., “A Search for Parent-of-Origin Effects on Honey Bee Gene Expression.”, G3 (Bethesda), vol. 5, no. 8, pp. 1657-62, 2015.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
E. K. Farley, Olson, K. M., Zhang, W., Brandt, A. J., Rokhsar, D. S., and Levine, M. S., “Suboptimization of developmental enhancers.”, Science, vol. 350, no. 6258, pp. 325-8, 2015.
E. K. Farley, Olson, K. M., Zhang, W., Brandt, A. J., Rokhsar, D. S., and Levine, M. S., “Suboptimization of developmental enhancers.”, Science, vol. 350, no. 6258, pp. 325-8, 2015.
2014
B. He, Doubrovinski, K., Polyakov, O., and Wieschaus, E., “Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation.”, Nature, vol. 508, no. 7496, pp. 392-6, 2014.
P. Jiang and Singh, M., “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
P. Jiang and Singh, M., “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
P. Jiang and Singh, M., “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
C. P. Broedersz, Wang, X., Meir, Y., Loparo, J. J., Rudner, D. Z., and Wingreen, N. S., “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
C. P. Broedersz, Wang, X., Meir, Y., Loparo, J. J., Rudner, D. Z., and Wingreen, N. S., “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
C. P. Broedersz, Wang, X., Meir, Y., Loparo, J. J., Rudner, D. Z., and Wingreen, N. S., “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
R. G. Tepper, Murphy, C. T., and Bussemaker, H. J., “DAF-16 and PQM-1: partners in longevity.”, Aging (Albany NY), vol. 6, no. 1, pp. 5-6, 2014.
A. V. Persikov, Rowland, E. F., Oakes, B. L., Singh, M., and Noyes, M. B., “Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.”, Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 2014.
D. G. Robinson, Chen, W., Storey, J. D., and Gresham, D., “Design and analysis of Bar-seq experiments.”, G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
D. G. Robinson, Chen, W., Storey, J. D., and Gresham, D., “Design and analysis of Bar-seq experiments.”, G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
J. P. Bothma, Garcia, H. G., Esposito, E., Schlissel, G., Gregor, T., and Levine, M., “Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos.”, Proc Natl Acad Sci U S A, vol. 111, no. 29, pp. 10598-603, 2014.
J. S. Breunig, Hackett, S. R., Rabinowitz, J. D., and Kruglyak, L., “Genetic basis of metabolome variation in yeast.”, PLoS Genet, vol. 10, no. 3, p. e1004142, 2014.
A. M. Berezhkovskii and Shvartsman, S. Y., “On the GFP-based analysis of dynamic concentration profiles.”, Biophys J, vol. 106, no. 3, pp. L13-5, 2014.
J. Zhou and Troyanskaya, O. G., “Global quantitative modeling of chromatin factor interactions.”, PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
T. T. Marstrand and Storey, J. D., “Identifying and mapping cell-type-specific chromatin programming of gene expression.”, Proc Natl Acad Sci U S A, vol. 111, no. 6, pp. E645-54, 2014.
D. Ghersi and Singh, M., “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
D. Botstein, “Lasker∼Koshland to genetics pioneer.”, Cell, vol. 158, no. 6, pp. 1230-2, 2014.
M. Levine, Cattoglio, C., and Tjian, R., “Looping back to leap forward: transcription enters a new era.”, Cell, vol. 157, no. 1, pp. 13-25, 2014.
D. Krotov, Dubuis, J. O., Gregor, T., and Bialek, W., “Morphogenesis at criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
D. Krotov, Dubuis, J. O., Gregor, T., and Bialek, W., “Morphogenesis at criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
Z. Khan, Wang, Y. - C., Wieschaus, E. F., and Kaschube, M., “Quantitative 4D analyses of epithelial folding during Drosophila gastrulation.”, Development, vol. 141, no. 14, pp. 2895-900, 2014.
J. Fan, Ye, J., Kamphorst, J. J., Shlomi, T., Thompson, C. B., and Rabinowitz, J. D., “Quantitative flux analysis reveals folate-dependent NADPH production.”, Nature, vol. 510, no. 7504, pp. 298-302, 2014.
J. Fan, Ye, J., Kamphorst, J. J., Shlomi, T., Thompson, C. B., and Rabinowitz, J. D., “Quantitative flux analysis reveals folate-dependent NADPH production.”, Nature, vol. 510, no. 7504, pp. 298-302, 2014.
K. Drescher, Nadell, C. D., Stone, H. A., Wingreen, N. S., and Bassler, B. L., “Solutions to the public goods dilemma in bacterial biofilms.”, Curr Biol, vol. 24, no. 1, pp. 50-5, 2014.
S. R McIsaac, Gibney, P. A., Chandran, S. S., Benjamin, K. R., and Botstein, D., “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.”, Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
S. R McIsaac, Gibney, P. A., Chandran, S. S., Benjamin, K. R., and Botstein, D., “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.”, Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
S. R McIsaac, Gibney, P. A., Chandran, S. S., Benjamin, K. R., and Botstein, D., “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.”, Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
2013
J. O. Dubuis, Samanta, R., and Gregor, T., “Accurate measurements of dynamics and reproducibility in small genetic networks.”, Mol Syst Biol, vol. 9, p. 639, 2013.
J. O. Dubuis, Samanta, R., and Gregor, T., “Accurate measurements of dynamics and reproducibility in small genetic networks.”, Mol Syst Biol, vol. 9, p. 639, 2013.
J. O. Dubuis, Samanta, R., and Gregor, T., “Accurate measurements of dynamics and reproducibility in small genetic networks.”, Mol Syst Biol, vol. 9, p. 639, 2013.
S. L. Grady, Purdy, J. G., Rabinowitz, J. D., and Shenk, T., “Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection.”, Proc Natl Acad Sci U S A, vol. 110, no. 51, pp. E5006-15, 2013.
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