Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP

by Gogakos, Tasos, Brown, Miguel, Garzia, Aitor, Meyer, Cindy, Hafner, Markus, Tuschl, Thomas
Published in Cell reports (Cambridge)

Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations

by Williams, Zev, Ben-Dov, Iddo Z., Elias, Rony, Mihailovic, Aleksandra, Brown, Miguel, Rosenwaks, Zev, Tuschl, Thomas
Published in Proceedings of the National Academy of Sciences - PNAS

Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers

by Akat, Kemal Marc, Moore-McGriff, D'Vesharronne, Morozov, Pavel, Brown, Miguel, Gogakos, Tasos, Da Rosa, Joel Correa, Mihailovic, Aleksandra, Sauer, Markus, Ji, Ruiping, Ramarathnam, Aarthi, Totary-Jain, Hana, Williams, Zev, Tuschl, Thomas, Schulze, P. Christian
Published in Proceedings of the National Academy of Sciences - PNAS

Integrated molecular subtyping defines a curable oligometastatic state in colorectal liver metastasis

by Pitroda, Sean P, Khodarev, Nikolai N, Huang, Lei, Uppal, Abhineet, Wightman, Sean C, Ganai, Sabha, Joseph, Nora, Pitt, Jason, Brown, Miguel, Forde, Martin, Mangold, Kathy, Xue, Lai, Weber, Christopher, Segal, Jeremy P, Kadri, Sabah, Stack, Melinda E, Khan, Sajid, Paty, Philip, Kaul, Karen, Andrade, Jorge, White, Kevin P, Talamonti, Mark, Posner, Mitchell C, Hellman, Samuel, Weichselbaum, Ralph R
Published in Nature communications

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

by Hafner, Markus, Renwick, Neil, Brown, Miguel, Mihailović, Aleksandra, Holoch, Daniel, Lin, Carolina, Pena, John T G, Nusbaum, Jeffrey D, Morozov, Pavel, Ludwig, Janos, Ojo, Tolulope, Luo, Shujun, Schroth, Gary, Tuschl, Thomas
Published in RNA (Cambridge)

Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition

by Hafner, Markus, Max, Klaas E A, Bandaru, Pradeep, Morozov, Pavel, Gerstberger, Stefanie, Brown, Miguel, Molina, Henrik, Tuschl, Thomas
Published in RNA (Cambridge)

AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification

by Kim, Jung, Naqvi, Ammar S, Corbett, Ryan J, Kaufman, Rebecca S, Vaksman, Zalman, Brown, Miguel A, Miller, Daniel P, Phul, Saksham, Geng, Zhuangzhuang, Storm, Phillip B, Resnick, Adam C, Stewart, Douglas R, Rokita, Jo Lynne, Diskin, Sharon J
Published in Bioinformatics (Oxford, England)

MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

by FARAZI, Thalia A, HORLINGS, Hugo M, KREIKE, Bas, SIE, Daoud, HOVESTADT, Volker, WESSELS, Lodewyk F. A, VAN DE VIJVER, Marc J, TUSCHL, Thomas, TEN HOEVE, Jelle J, MIHAILOVIC, Aleksandra, HALFWERK, Hans, MOROZOV, Pavel, BROWN, Miguel, HAFNER, Markus, REYAL, Fabien, VAN KOUWENHOVE, Marieke
Published in Cancer research (Chicago, Ill.)

Human CLP1 Mutations Alter tRNA Biogenesis, Affecting Both Peripheral and Central Nervous System Function

by Karaca, Ender, Weitzer, Stefan, Pehlivan, Davut, Shiraishi, Hiroshi, Gogakos, Tasos, Hanada, Toshikatsu, Jhangiani, Shalini N., Wiszniewski, Wojciech, Withers, Marjorie, Campbell, Ian M., Erdin, Serkan, Isikay, Sedat, Franco, Luis M., Gonzaga-Jauregui, Claudia, Gambin, Tomasz, Gelowani, Violet, Hunter, Jill V., Yesil, Gozde, Koparir, Erkan, Yilmaz, Sarenur, Brown, Miguel, Briskin, Daniel, Hafner, Markus, Morozov, Pavel, Farazi, Thalia A., Bernreuther, Christian, Glatzel, Markus, Trattnig, Siegfried, Friske, Joachim, Kronnerwetter, Claudia, Bainbridge, Matthew N., Gezdirici, Alper, Seven, Mehmet, Muzny, Donna M., Boerwinkle, Eric, Ozen, Mustafa, Clausen, Tim, Tuschl, Thomas, Yuksel, Adnan, Hess, Andreas, Gibbs, Richard A., Martinez, Javier, Penninger, Josef M., Lupski, James R.
Published in Cell

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

by Gaonkar, Krutika S, Marini, Federico, Rathi, Komal S, Jain, Payal, Zhu, Yuankun, Chimicles, Nicholas A, Brown, Miguel A, Naqvi, Ammar S, Zhang, Bo, Storm, Phillip B, Maris, John M, Raman, Pichai, Resnick, Adam C, Strauch, Konstantin, Taroni, Jaclyn N, Rokita, Jo Lynne
Published in BMC bioinformatics

Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets

by Farazi, Thalia A, Ten Hoeve, Jelle J, Brown, Miguel, Mihailovic, Aleksandra, Horlings, Hugo M, van de Vijver, Marc J, Tuschl, Thomas, Wessels, Lodewyk F A
Published in Genome biology

A genome-wide view of the expression and processing patterns of Thermus thermophilus HB8 CRISPR RNAs

by Juranek, Stefan, Eban, Tali, Altuvia, Yael, Brown, Miguel, Morozov, Pavel, Tuschl, Thomas, Margalit, Hanah
Published in RNA (Cambridge)

P832: Discovering phenotype-gene correlations using Variant WorkBench

by Guo, Yiran, Li, Qi, Rozowsky, Jared, Costanza, Jeremy, Mattioni, Michele, Thibert, Jean-Philippe, Brown, Miguel, Higgins, David, Zhu, Yuankun, Heath, Allison, Resnick, Adam, Ferretti, Vincent
Published in Genetics in Medicine Open

CpG DNA activation and plasma-cell differentiation of CD27− naive human B cells

by Huggins, Jennifer, Pellegrin, Tina, Felgar, Raymond E., Wei, Chungwen, Brown, Miguel, Zheng, Bo, Milner, Eric C.B., Bernstein, Steven H., Sanz, Ignacio, Zand, Martin S.
Published in Blood

Modulation of Single-Cell IgG Secretion Frequency and Rates in Human Memory B Cells by CpG DNA, CD40L, IL-21, and Cell Division

by Henn, Alicia D, Rebhahn, Jonathan, Brown, Miguel A, Murphy, Alison J, Coca, Mircea N, Hyrien, Ollivier, Pellegrin, Tina, Mosmann, Tim, Zand, Martin S
Published in The Journal of immunology (1950)

Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression

by Luo, Guan-Zheng, Hafner, Markus, Shi, Zhimin, Brown, Miguel, Feng, Gui-Hai, Tuschl, Thomas, Wang, Xiu-Jie, Li, XiaoChing
Published in BMC genomics

Author Correction: Integrated molecular subtyping defines a curable oligometastatic state in colorectal liver metastasis

by Pitroda, Sean P, Khodarev, Nikolai N, Huang, Lei, Uppal, Abhineet, Wightman, Sean C, Ganai, Sabha, Joseph, Nora, Pitt, Jason, Brown, Miguel, Forde, Martin, Mangold, Kathy, Xue, Lai, Weber, Christopher, Segal, Jeremy P, Kadri, Sabah, Stack, Melinda E, Khan, Sajid, Paty, Philip, Kaul, Karen, Andrade, Jorge, White, Kevin P, Talamonti, Mark, Posner, Mitchell C, Hellman, Samuel, Weichselbaum, Ralph R
Published in Nature communications

Mapping genomic loci implicates genes and synaptic biology in schizophrenia

by Panagiotaropoulou, Georgia, Bigdeli, Tim B, Bryois, Julien, Dennison, Charlotte A, Lam, Max, Watanabe, Kyoko, Frei, Oleksandr, Magnusson, Sigurdur, Agartz, Ingrid, Alexander, Madeline, Alizadeh, Behrooz Z, Bass, Nicholas J, Bene, Judit, Calkins, Monica E, Castle, David, Chong, Siow Ann, Cohen, David, Curtis, Charles, Davidson, Michael, de Haan, Lieuwe, Djurovic, Srdjan, Ducci, Giuseppe, Fañanás, Lourdes, Gershon, Elliot S, González-Pinto, Ana, Gratten, Jacob, Gülöksüz, Sinan, Harvey, Carol, Ikeda, Masashi, Joa, Inge, Julià, Antonio, Kebir, Oussama, Kondratiev, Nikolay, Kusumawardhani, Agung, Lazzeroni, Laura C, Legge, Sophie E, Limborska, Svetlana, Liu, Chih-Min, Macek, Jr, Milan, Malaspina, Dolores, Martorell, Lourdes, Mattheisen, Manuel, McDonald, Colm, Medeiros, Helena, Milani, Lili, Mitjans, Marina, Molden, Espen, Muntané, Gerard, Nestadt, Gerald, Nikitina-Zake, Liene, Oh, Sang-Yun, Ota, Vanessa Kiyomi, Pellegrino, Renata, Pfuhlmann, Bruno, Rapaport, Mark H, Rutten, Bart P F, Saker-Delye, Safaa, Seidman, Larry J, Sim, Kang, Skarabis, Nora, Söderman, Erik, Stain, Helen J, Suvisaari, Jaana, Szatkiewicz, Jin P, Takahashi, Atsushi, Terao, Chikashi, Thibaut, Florence, Torretta, Silvia, Vaaler, Arne, van Amelsvoort, Therese, Waterreus, Anna, Wu, Jing Qin, Zai, Clement C, Zimprich, Fritz, Cloninger, C Robert, Petryshen, Tracey L, Pulver, Ann E, Schulze, Thomas G, Wang, Shi-Heng, Xu, Shuhua, Arango, Celso, Corvin, Aiden, Gawlik, Micha, Gejman, Pablo V, Khusnutdinova, Elza, Li, Qingqin S, Liu, Jianjun, Malhotra, Anil K, McQuillin, Andrew, Riley, Brien P, Stefansson, Kari, van Os, Jim, Weinberger, Daniel R, Wildenauer, Dieter B, Yue, Weihua, Holmans, Peter A, Yang, Jian, Wray, Naomi R, Neale, Benjamin M, Ripke, Stephan
Published in Nature (London)

Comprehensive functional genomic resource and integrative model for the human brain

by Wang, Daifeng, Liu, Shuang, Warrell, Jonathan, Won, Hyejung, Shi, Xu, Navarro, Fabio C P, Clarke, Declan, Gu, Mengting, Emani, Prashant, Yang, Yucheng T, Xu, Min, Gandal, Michael J, Lou, Shaoke, Zhang, Jing, Park, Jonathan J, Yan, Chengfei, Rhie, Suhn Kyong, Manakongtreecheep, Kasidet, Zhou, Holly, Nathan, Aparna, Peters, Mette, Mattei, Eugenio, Fitzgerald, Dominic, Brunetti, Tonya, Moore, Jill, Jiang, Yan, Girdhar, Kiran, Hoffman, Gabriel E, Kalayci, Selim, Gümüş, Zeynep H, Crawford, Gregory E, Roussos, Panos, Akbarian, Schahram, Jaffe, Andrew E, White, Kevin P, Weng, Zhiping, Sestan, Nenad, Geschwind, Daniel H, Knowles, James A, Gerstein, Mark B
Published in Science (American Association for the Advancement of Science)

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

by Li, Mingfeng, Santpere, Gabriel, Imamura Kawasawa, Yuka, Evgrafov, Oleg V, Gulden, Forrest O, Pochareddy, Sirisha, Sunkin, Susan M, Li, Zhen, Shin, Yurae, Zhu, Ying, Sousa, André M M, Werling, Donna M, Kitchen, Robert R, Kang, Hyo Jung, Pletikos, Mihovil, Choi, Jinmyung, Muchnik, Sydney, Xu, Xuming, Wang, Daifeng, Lorente-Galdos, Belen, Liu, Shuang, Giusti-Rodríguez, Paola, Won, Hyejung, de Leeuw, Christiaan A, Pardiñas, Antonio F, Hu, Ming, Jin, Fulai, Li, Yun, Owen, Michael J, O'Donovan, Michael C, Walters, James T R, Posthuma, Danielle, Reimers, Mark A, Levitt, Pat, Weinberger, Daniel R, Hyde, Thomas M, Kleinman, Joel E, Geschwind, Daniel H, Hawrylycz, Michael J, State, Matthew W, Sanders, Stephan J, Sullivan, Patrick F, Gerstein, Mark B, Lein, Ed S, Knowles, James A, Sestan, Nenad
Published in Science (American Association for the Advancement of Science)