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Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
Sanborn, Adrian L., Rao, Suhas S. P., Huang, Su-Chen, Durand, Neva C., Huntley, Miriam H., Jewett, Andrew I., Bochkov, Ivan D., Chinnappan, Dharmaraj, Cutkosky, Ashok, Li, Jian, Geeting, Kristopher P., Gnirke, Andreas, Melnikov, Alexandre, McKenna, Doug, Stamenova, Elena K., Lander, Eric S., Aiden, Erez Lieberman
Published in Proceedings of the National Academy of Sciences - PNAS (24.11.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (24.11.2015)
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Journal Article
Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits
Ulirsch, Jacob C., Nandakumar, Satish K., Wang, Li, Giani, Felix C., Zhang, Xiaolan, Rogov, Peter, Melnikov, Alexandre, McDonel, Patrick, Do, Ron, Mikkelsen, Tarjei S., Sankaran, Vijay G.
Published in Cell (02.06.2016)
Published in Cell (02.06.2016)
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Journal Article
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
Melnikov, Alexandre, Murugan, Anand, Zhang, Xiaolan, Tesileanu, Tiberiu, Wang, Li, Rogov, Peter, Feizi, Soheil, Gnirke, Andreas, Callan, Curtis G, Kinney, Justin B, Kellis, Manolis, Lander, Eric S, Mikkelsen, Tarjei S
Published in Nature biotechnology (01.03.2012)
Published in Nature biotechnology (01.03.2012)
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Journal Article
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
Kheradpour, Pouya, Ernst, Jason, Melnikov, Alexandre, Rogov, Peter, Wang, Li, Zhang, Xiaolan, Alston, Jessica, Mikkelsen, Tarjei S., Kellis, Manolis
Published in Genome research (01.05.2013)
Published in Genome research (01.05.2013)
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Journal Article
Systematic dissection of genomic features determining transcription factor binding and enhancer function
Grossman, Sharon R., Zhang, Xiaolan, Wang, Li, Engreitz, Jesse, Melnikov, Alexandre, Rogov, Peter, Tewhey, Ryan, Isakova, Alina, Deplancke, Bart, Bernstein, Bradley E., Mikkelsen, Tarjei S., Lander, Eric S.
Published in Proceedings of the National Academy of Sciences - PNAS (14.02.2017)
Published in Proceedings of the National Academy of Sciences - PNAS (14.02.2017)
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Journal Article
Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance
Cerqueira, Gustavo C., Cheeseman, Ian H., Schaffner, Steve F., Nair, Shalini, McDew-White, Marina, Phyo, Aung Pyae, Ashley, Elizabeth A., Melnikov, Alexandre, Rogov, Peter, Birren, Bruce W., Nosten, François, Anderson, Timothy J. C., Neafsey, Daniel E.
Published in Genome Biology (28.04.2017)
Published in Genome Biology (28.04.2017)
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Journal Article
Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts
Ma, Liang, Chen, Zehua, Huang, Da Wei, Kutty, Geetha, Ishihara, Mayumi, Wang, Honghui, Abouelleil, Amr, Bishop, Lisa, Davey, Emma, Deng, Rebecca, Deng, Xilong, Fan, Lin, Fantoni, Giovanna, Fitzgerald, Michael, Gogineni, Emile, Goldberg, Jonathan M., Handley, Grace, Hu, Xiaojun, Huber, Charles, Jiao, Xiaoli, Jones, Kristine, Levin, Joshua Z., Liu, Yueqin, Macdonald, Pendexter, Melnikov, Alexandre, Raley, Castle, Sassi, Monica, Sherman, Brad T., Song, Xiaohong, Sykes, Sean, Tran, Bao, Walsh, Laura, Xia, Yun, Yang, Jun, Young, Sarah, Zeng, Qiandong, Zheng, Xin, Stephens, Robert, Nusbaum, Chad, Birren, Bruce W., Azadi, Parastoo, Lempicki, Richard A., Cuomo, Christina A., Kovacs, Joseph A.
Published in Nature communications (22.02.2016)
Published in Nature communications (22.02.2016)
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Journal Article
Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice
Donaldson, Gregory P., Chou, Wen-Chi, Manson, Abigail L., Rogov, Peter, Abeel, Thomas, Bochicchio, James, Ciulla, Dawn, Melnikov, Alexandre, Ernst, Peter B., Chu, Hiutung, Giannoukos, Georgia, Earl, Ashlee M., Mazmanian, Sarkis K.
Published in Nature microbiology (01.05.2020)
Published in Nature microbiology (01.05.2020)
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Journal Article
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts
Levin, Joshua Z, Berger, Michael F, Adiconis, Xian, Rogov, Peter, Melnikov, Alexandre, Fennell, Timothy, Nusbaum, Chad, Garraway, Levi A, Gnirke, Andreas
Published in Genome biology (16.10.2009)
Published in Genome biology (16.10.2009)
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Journal Article
Development of a Single Nucleotide Polymorphism Barcode to Genotype Plasmodium vivax Infections
Baniecki, Mary Lynn, Faust, Aubrey L., Schaffner, Stephen F., Park, Daniel J., Galinsky, Kevin, Daniels, Rachel F., Hamilton, Elizabeth, Ferreira, Marcelo U., Karunaweera, Nadira D., Serre, David, Zimmerman, Peter A., Sá, Juliana M., Wellems, Thomas E., Musset, Lise, Legrand, Eric, Melnikov, Alexandre, Neafsey, Daniel E., Volkman, Sarah K., Wirth, Dyann F., Sabeti, Pardis C.
Published in PLoS neglected tropical diseases (01.03.2015)
Published in PLoS neglected tropical diseases (01.03.2015)
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Journal Article
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
Gnirke, Andreas, Melnikov, Alexandre, Maguire, Jared, Rogov, Peter, LeProust, Emily M, Brockman, William, Fennell, Timothy, Giannoukos, Georgia, Fisher, Sheila, Russ, Carsten, Gabriel, Stacey, Jaffe, David B, Lander, Eric S, Nusbaum, Chad
Published in Nature biotechnology (01.02.2009)
Published in Nature biotechnology (01.02.2009)
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Journal Article
Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax
Hupalo, Daniel N, Luo, Zunping, Melnikov, Alexandre, Sutton, Patrick L, Rogov, Peter, Escalante, Ananias, Vallejo, Andrés F, Herrera, Sócrates, Arévalo-Herrera, Myriam, Fan, Qi, Wang, Ying, Cui, Liwang, Lucas, Carmen M, Durand, Salomon, Sanchez, Juan F, Baldeviano, G Christian, Lescano, Andres G, Laman, Moses, Barnadas, Celine, Barry, Alyssa, Mueller, Ivo, Kazura, James W, Eapen, Alex, Kanagaraj, Deena, Valecha, Neena, Ferreira, Marcelo U, Roobsoong, Wanlapa, Nguitragool, Wang, Sattabonkot, Jetsumon, Gamboa, Dionicia, Kosek, Margaret, Vinetz, Joseph M, González-Cerón, Lilia, Birren, Bruce W, Neafsey, Daniel E, Carlton, Jane M
Published in Nature genetics (01.08.2016)
Published in Nature genetics (01.08.2016)
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Journal Article
Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection
Weiss, Eric R., Lamers, Susanna L., Henderson, Jennifer L., Melnikov, Alexandre, Somasundaran, Mohan, Garber, Manuel, Selin, Liisa, Nusbaum, Chad, Luzuriaga, Katherine
Published in Journal of virology (15.01.2018)
Published in Journal of virology (15.01.2018)
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Journal Article
Massively Parallel Reporter Assays in Cultured Mammalian Cells
Melnikov, Alexandre, Zhang, Xiaolan, Rogov, Peter, Wang, Li, Mikkelsen, Tarjei S.
Published in Journal of visualized experiments (17.08.2014)
Published in Journal of visualized experiments (17.08.2014)
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Journal Article
Hybrid selection for sequencing pathogen genomes from clinical samples
Melnikov, Alexandre, Galinsky, Kevin, Rogov, Peter, Fennell, Timothy, Van Tyne, Daria, Russ, Carsten, Daniels, Rachel, Barnes, Kayla G, Bochicchio, James, Ndiaye, Daouda, Sene, Papa D, Wirth, Dyann F, Nusbaum, Chad, Volkman, Sarah K, Birren, Bruce W, Gnirke, Andreas, Neafsey, Daniel E
Published in Genome biology (11.08.2011)
Published in Genome biology (11.08.2011)
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Journal Article
Abstract 242: Functional Characterization of a Cis-eQTL Locus for Plasma Cholesterol Using CRISPR/Cas Genome Editing in Human Pluripotent Stem Cells
Raghavan, Avanthi, Peters, Derek, Kuperwasser, Nicolas, Melnikov, Alexandre, Rogov, Peter, Wang, Li, Zhang, Xiaolan, Mikkelsen, Tarjei, Musunuru, Kiran
Published in Arteriosclerosis, thrombosis, and vascular biology (01.05.2014)
Published in Arteriosclerosis, thrombosis, and vascular biology (01.05.2014)
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Journal Article
Massively Parallel Reporter Assays in Cultured Mammalian Cells
Melnikov, Alexandre, Zhang, Xiaolan, Rogov, Peter, Wang, Li, Mikkelsen, Tarjei S.
Published in Journal of visualized experiments (17.08.2014)
Published in Journal of visualized experiments (17.08.2014)
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Journal Article
Development of a Single Nucleotide Polymorphism Barcode to Genotype Plasmodium vivax Infections: e0003539
Baniecki, Mary Lynn, Faust, Aubrey L, Schaffner, Stephen F, Park, Daniel J, Galinsky, Kevin, Daniels, Rachel F, Hamilton, Elizabeth, Ferreira, Marcelo U, Karunaweera, Nadira D, Serre, David, Zimmerman, Peter A, Sá, Juliana M, Wellems, Thomas E, Musset, Lise, Legrand, Eric, Melnikov, Alexandre, Neafsey, Daniel E, Volkman, Sarah K, Wirth, Dyann F, Sabeti, Pardis C
Published in PLoS neglected tropical diseases (01.03.2015)
Published in PLoS neglected tropical diseases (01.03.2015)
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Journal Article