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See Google Scholar for a more up-to-date list.
- Amit, I., Regev, A., and Hacohen, N. (2011). Strategies to discover regulatory circuits of the mammalian immune system. Nature Reviews Immunology 11, 873--880.
- Benson, C.C., Zhou, Q., Long, X., and Miano, J.M. (2011). Identifying functional single nucleotide polymorphisms in the human CArGome. Physiological Genomics 43, 1038--1048.
- Buske, O.J., Hoffman, M.M., Ponts, N., Le Roch, K.G., and Noble, W.S. (2011). Exploratory analysis of genomic segmentations with Segtools. BMC Bioinformatics 12,.
- Capellini, T.D., Handschuh, K., Quintana, L., Ferretti, E., Di Giacomo, G., Fantini, S., Vaccari, G., Clarke, S.L., Wenger, A.M., Bejerano, G., et al. (2011a). Control of Pelvic Girdle Development by Genes of the Pbx Family and Emx2. Developmental Dynamics 240, 1173--1189.
- Capellini, T.D., Zappavigna, V., and Selleri, L. (2011b). Pbx Homeodomain Proteins: TALEnted Regulators of Limb Patterning and Outgrowth. Developmental Dynamics 240, 1063--1086.
- Chu, C., Qu, K., Zhong, F.L., Artandi, S.E., and Chang, H.Y. (2011). Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions. Molecular Cell 44, 667--678.
- Cullum, R., Alder, O., and Hoodless, P.A. (2011). The next generation: Using new sequencing technologies to analyse gene regulation. Respirology 16, 210--222.
- Diep, D., Plongthongkum, N., Gore, A., Fung, H.L., Shoemaker, R., and Zhang, K. (2012). Library-free methylation sequencing with bisulfite padlock probes. Nature Methods 9, 270-U69.
- Donaldson, I.J., Amin, S., Hensman, J.J., Kutejova, E., Rattray, M., Lawrence, N., Hayes, A., Ward, C.M., and Bobola, N. (2012). Genome-wide occupancy links Hoxa2 to Wnt--?-catenin signaling in mouse embryonic development. Nucleic Acids Research.
- Dozmorov, M.G., Cara, L.R., Giles, C.B., and Wren, J.D. (2012). GenomeRunner: automating genome exploration. Bioinformatics 28, 419--420.
- Fernández, M., and Miranda-Saavedra, D. (2012). Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines. Nucleic Acids Research.
- Fujita, P.A., Rhead, B., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Cline, M.S., Goldman, M., Barber, G.P., Clawson, H., Coelho, A., et al. (2011). The UCSC Genome Browser database: update 2011. Nucleic Acids Research 39, D876--D882.
- Gao, Z., Zhang, J., Bonasio, R., Strino, F., Sawai, A., Parisi, F., Kluger, Y., and Reinberg, D. (2012). PCGF Homologs, CBX Proteins, and RYBP Define Functionally Distinct PRC1 Family Complexes. Molecular Cell 45, 344--356.
- Giannopoulou, E.G., and Elemento, O. (2011). An integrated ChIP-seq analysis platform with customizable workflows. BMC Bioinformatics 12.
- Goeke, J., Jung, M., Behrens, S., Chavez, L., O'Keeffe, S., Timmermann, B., Lehrach, H., Adjaye, J., and Vingron, M. (2011). Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development. PLoS Computational Biology 7.
- Hutchins, A.P., Poulain, S., and Miranda-Saavedra, D. (2012). Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages. Blood.
- Karczewski, K.J., Tatonetti, N.P., Landt, S.G., Yang, X., Slifer, T., Altman, R.B., and Snyder, M. (2011). Cooperative transcription factor associations discovered using regulatory variation. Proceedings of the National Academy of Sciences of the United States of America 108, 13353--13358.
- Kong, L., Wang, J., Zhao, S., Gu, X., Luo, J., and Gao, G. (2012). ABrowse-a customizable next-generation genome browser framework. BMC Bioinformatics 13, 2.
- Lee, B.K., Bhinge, A.A., Battenhouse, A., McDaniell, R.M., Liu, Z., Song, L., Ni, Y., Birney, E., Lieb, J.D., Furey, T.S., et al. (2012). Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Research 22, 9-24.
- Liu, Z., Scannell, D.R., Eisen, M.B., and Tjian, R. (2011). Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell 146, 720.
- Lowe, C.B., Kellis, M., Siepel, A., Raney, B.J., Clamp, M., Salama, S.R., Kingsley, D.M., Lindblad-Toh, K., and Haussler, D. (2011). Three Periods of Regulatory Innovation During Vertebrate Evolution. Science 333, 1019--1024.
- Luo, G. (2012). Gabriel Etienne Zentner Doctor of Philosophy. Case Western Reserve University.
- Ma, Z., Swigut, T., Valouev, A., Rada-Iglesias, A., and Wysocka, J. (2011). Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates. Nature Structural & Molecular Biology 18, 120--U175.
- Maienschein-Cline, M., Zhou, J., White, K.P., Sciammas, R., and Dinner, A.R. (2012). Discovering transcription factor regulatory targets using gene expression and binding data. Bioinformatics 28, 206--213.
- Marban, C., Su, T., Ferrari, R., Li, B., Vatakis, D., Pellegrini, M., Zack, J.A., Rohr, O., and Kurdistani, S.K. (2011). Genome-Wide Binding Map of the HIV-1 Tat Protein to the Human Genome. PLoS One 6.
- Martin, D.I.K., Singer, M., Dhahbi, J., Mao, G., Zhang, L., Schroth, G.P., Pachter, L., and Boffelli, D. (2011). Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. Genome Research 21, 2049--2057.
- May, D., Blow, M.J., Kaplan, T., McCulley, D.J., Jensen, B.C., Akiyama, J.A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., et al. (2012). Large-scale discovery of enhancers from human heart tissue. Nature Genetics 44, 89--U125.
- McLean, C.Y., Reno, P.L., Pollen, A.A., Bassan, A.I., Capellini, T.D., Guenther, C., Indjeian, V.B., Lim, X., Menke, D.B., Schaar, B.T., et al. (2011). Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471, 216--219.
- McLean, C.Y.. (2011). Computational analysis of the mammalian cis-regulatory landscape (Stanford University).
- Nanda, V., and Miano, J.M. (2012). Leiomodin 1, a New Serum Response Factor-dependent Target Gene Expressed Preferentially in Differentiated Smooth Muscle Cells. Journal of Biological Chemistry 287, 2459--2467.
- Novershtern, N., Subramanian, A., Lawton, L.N., Mak, R.H., Haining, W.N., McConkey, M.E., Habib, N., Yosef, N., Chang, C.Y., Shay, T., et al. (2011). Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis. Cell 144, 296--309.
- Patel, M., Simon, J.M., Iglesia, M.D., Wu, S.B., McFadden, A.W., Lieb, J.D., and Davis, I.J. (2012). Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription. Genome Research 22, 259--270.
- Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S.A., Flynn, R.A., and Wysocka, J. (2011). A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279--+.
- Rödelsperger, C., Vingron, M., and Robinson, P.D.D.P.. (2011). Computational Characterization of Genome-wide DNA-binding Profiles.
- Ryu, S.H., Yoo, T., Kang, K., Park, S.Y., Joe, C.O., and Chung, J.H. (2011). Transcriptional changes of secreted Wnt antagonists in hindlimb skeletal muscle during the lifetime of the C57BL/6J mouse. Mechanisms of Ageing and Development 132, 511-514.
- Sakabe, N.J., Aneas, I., Shen, T., Shokri, L., Park, S.Y., Bulyk, M.L., Evans, S.M., and Nobrega, M.A. (2012). Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. Human Molecular Genetics.
- Sandve, G.K., Gundersen, S., Rydbeck, H., Glad, I.K., Holden, L., Holden, M., Liestol, K., Clancy, T., Drablos, F., Ferkingstad, E., et al. (2011). The differential disease regulome. BMC Genomics 12.
- Soccio, R.E., Tuteja, G., Everett, L.J., Li, Z., Lazar, M.A., and Kaestner, K.H. (2011). Species-Specific Strategies Underlying Conserved Functions of Metabolic Transcription Factors. Molecular Endocrinology 25, 694--706.
- Stroud, H., Feng, S., Kinney, S.M., Pradhan, S., and Jacobsen, S.E. (2011). 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biology 12.
- Sullivan, A.L., Benner, C., Heinz, S., Huang, W., Xie, L., Miano, J.M., and Glass, C.K. (2011). Serum Response Factor Utilizes Distinct Promoter- and Enhancer-Based Mechanisms To Regulate Cytoskeletal Gene Expression in Macrophages. Molecular and Cellular Biology 31, 861--875.
- Tijssen, M.R., Cvejic, A., Joshi, A., Hannah, R.L., Ferreira, R., Forrai, A., Bellissimo, D.C., Oram, S.H., Smethurst, P.A., Wilson, N.K., et al. (2011). Genome-wide Analysis of Simultaneous GATA1/2, RUNX1, FLI1, and SCL Binding in Megakaryocytes Identifies Hematopoietic Regulators. Developmental Cell 20, 597--609.
- Trompouki, E., Bowman, T.V., Lawton, L.N., Fan, Z.P., Wu, D.C., DiBiase, A., Martin, C.S., Cech, J.N., Sessa, A.K., Leblanc, J.L., et al. (2011). Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. Cell 147, 577--589.
- Tuteja, G. (2012). DNA-Protein Interaction Analysis (ChIP-Seq). Bioinformatics for High Throughput Sequencing 127-149.
- Yoon, S.J., Wills, A.E., Chuong, E., Gupta, R., and Baker, J.C. (2011). HEB and E2A function as SMAD/FOXH1 cofactors. Genes & Development 25, 1654-1661.
- Zentner, G.E., Tesar, P.J., and Scacheri, P.C. (2011). Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Research 21, 1273--1283.
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