Integrative analysis of the melanoma transcriptome by Berger, Michael F., Levin, Joshua Z., Vijayendran, Krishna, Sivachenko, Andrey, Adiconis, Xian, Maguire, Jared, Johnson, Laura A., Robinson, James, Verhaak, Roel G., Sougnez, Carrie, Onofrio, Robert, Ziaugra, Liuda, Cibulskis, Kristian, Laine, Elisabeth, Barretina, Jordi, Winckler, Wendy, Fisher, David E., Getz, Gad, Meyerson, Matthew L., Jaffe, David B., Gabriel, Stacey B., Dummer, Reinhard, Gnirke, Andreas, Nusbaum, Chad, Garraway, Levi A., Lander, Eric Steven

“…We developed a systematic approach to characterize the spectrum of cancer-associated mRNA alterations through integration of transcriptomic and structural genomic data, and we applied this approach to generate new insights into melanoma biology. …”
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Integrated genomic analyses of ovarian carcinoma by Meyerson, Matthew L., Lander, Eric Steven

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Integrated genomic characterization of endometrial carcinoma by Park, Peter J., Lander, Eric Steven

“…We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array- and sequencing-based technologies. …”
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Electrical and synaptic integration of glioma into neural circuits by Venkatesh, Humsa S., Morishita, Wade, Geraghty, Anna C., Silverbush, Dana, Gillespie, Shawn M., Arzt, Marlene, Tam, Lydia T., Espenel, Cedric, Ponnuswami, Anitha, Ni, Lijun, Woo, Pamelyn J., Taylor, Kathryn R., Agarwal, Amit, Regev, Aviv, Brang, David, Vogel, Hannes, Hervey-Jumper, Shawn, Bergles, Dwight E., Suvà, Mario L., Malenka, Robert C., Monje, Michelle

“…Together, these findings indicate that synaptic and electrical integration into neural circuits promotes glioma progression.…”
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Integration of contractile forces during tissue invagination by Martin, Adam C., Gelbart, Michael A., Fernandez-Gonzalez, Rodrigo, Kaschube, Matthias, Wieschaus, Eric F.

“…Here, we investigate how contractile forces are integrated across the tissue. Reducing adherens junction (AJ) levels or ablating actomyosin meshworks causes tissue-wide epithelial tears, which release tension that is predominantly oriented along the anterior–posterior (a-p) embryonic axis. …”
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Integrative Gene Set Analysis: Application to Platinum Pharmacogenomics by Fridley, Brooke L., Tan, Xiang-Lin, Jenkins, Gregory D., Batzler, Anthony, Moyer, Ann M., Biernacka, Joanna M., Wang, Liewei, Abo, Ryan

“…Application of the integrative GS analysis implicated the role of the RNA binding and cytoskeletal part GSs. …”
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Actomyosin Pulsing in Tissue Integrity Maintenance during Morphogenesis by Coravos, Jonathan Stuck, Mason, Frank M, Martin, Adam C

“…In epithelia, evidence suggests that actomyosin pulsing, and more generally, actomyosin turnover, is required to maintain tissue integrity during contractile processes. This review explores possible functions for pulsing in the many instances during which pulsing has been observed, and also highlights proposed molecular mechanisms that drive pulsing.…”
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An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma by Regev, Aviv

“…Our work provides a blueprint for glioblastoma, integrating the malignant cell programs, their plasticity, and their modulation by genetic drivers. …”
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Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace by Qu, Kun, Garamszegi, Sara, Wu, Felix, Thorvaldsdottir, Helga, Liefeld, Ted, Ocana, Marco, Pochet, Nathalie, Robinson, James T, Demchak, Barry, Hull, Tim, Ben-Artzi, Gil, Blankenberg, Daniel, Barber, Galt P, Lee, Brian T, Kuhn, Robert M, Nekrutenko, Anton, Segal, Eran, Ideker, Trey, Reich, Michael, Chang, Howard Y, Mesirov, Jill P, Borges-Rivera, Diego Ramon, Regev, Aviv

“…We introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate integrative analysis by non-programmers, it offers a growing set of 'recipes', short workflows to guide investigators through high-utility analysis tasks.…”
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Integrative and Conjugative Elements (ICEs): What They Do and How They Work by Johnson, Christopher M., Grossman, Alan D., Johnson, Christopher M, Grossman, Alan Davis

“…Horizontal gene transfer plays a major role in microbial evolution, allowing microbes to acquire new genes and phenotypes. Integrative and conjugative elements (ICEs, a.k.a. conjugative transposons) are modular mobile genetic elements integrated into a host genome and are passively propagated during chromosomal replication and cell division. …”
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Integrative and Conjugative Elements (ICEs): What They Do and How They Work by Grossman, Alan Davis, Johnson, Christopher M

“…Horizontal gene transfer plays a major role in microbial evolution, allowing microbes to acquire new genes and phenotypes. Integrative and conjugative elements (ICEs, a.k.a. conjugative transposons) are modular mobile genetic elements integrated into a host genome and are passively propagated during chromosomal replication and cell division. …”
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Integrated regulatory models for inference of subtype‐specific susceptibilities in glioblastoma by Liu, Yunpeng, Shi, Ning, Regev, Aviv, He, Shan, Hemann, Michael

“…We developed a modular computational pipeline, Integrative Modeling of Transcription Regulatory Interactions for Systematic Inference of Susceptibility in Cancer (inTRINSiC), to dissect subtype-specific regulatory programs and predict genetic dependencies in individual patient tumors. …”
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AVID: An integrative framework for discovering functional relationships among proteins by Jiang, Taijiao, Keating, Amy E.

“…Results: We present AVID, a computational method that uses a multi-stage learning framework to integrate experimental results with sequence information, generating networks reflecting functional similarities among proteins. …”
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Physical Module Networks: an integrative approach for reconstructing transcription regulation by Regev, Aviv, Novershtern, Noa, Friedman, Nir

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Designing a broad-spectrum integrative approach for cancer prevention and treatment by Vander Heiden, Matthew G.

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Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency by Cacchiarelli, Davide, Trapnell, Cole, Ziller, Michael J., Soumillon, Magali, Cesana, Marcella, Karnik, Rahul, Donaghey, Julie, Smith, Zachary D., Ratanasirintrawoot, Sutheera, Zhang, Xiaolan, Ho Sui, Shannan J., Wu, Zhaoting, Akopian, Veronika, Gifford, Casey A., Doench, John, Rinn, John L., Daley, George Q., Meissner, Alexander, Mikkelsen, Tarjei S., Lander, Eric Steven

“…This system enabled integrative transcriptional and epigenomic analysis across the human reprogramming timeline at high resolution. …”
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Integrated genomic analyses of de novo pathways underlying atypical meningiomas by Youngblood, Mark W., Clark, Victoria E., Henegariu, Octavian, Duran, Daniel, Erson-Omay, E. Zeynep, Kaulen, Leon D., Simon, Matthias, Krischek, Boris, Timmer, Marco, Goldbrunner, Roland, Baranoski, Jacob, Bai, Hanwen, Mishra-Gorur, Ketu, Schramm, Johannes, Moliterno, Jennifer, Vortmeyer, Alexander O., Bilg?var, Kaya, Yasuno, Katsuhito, G?nel, Murat, Harmanci, Akdes Serin, Suleyman, Coskun, Omay, S. Bulent, Baran, Burcin, Carrion-Grant, Geneive, Bilguvar, Kaya, Lee, Tong Ihn, Abraham, Brian Joseph, Young, Richard A.

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mTOR: from growth signal integration to cancer, diabetes and ageing by Zoncu, Roberto, Efeyan, Alejo, Sabatini, David

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Selective Pressures to Maintain Attachment Site Specificity of Integrative and Conjugative Elements by Menard, Kayla Lynne, Grossman, Alan Davis

“…Integrative and conjugative elements (ICEs) are widespread mobile genetic elements that are usually found integrated in bacterial chromosomes. …”
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An integrated map of genetic variation from 1,092 human genomes by Altshuler, David, Lander, Eric Steven

“…By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. …”
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