publications

Hope this list never ends😊

* COmics members

2024

  1. Nature genetics
    Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells
    Karen Grimes, Hyobin Jeong, Amanda Amoah, Nuo Xu, Julian Niemann, Benjamin Raeder, Patrick Hasenfeld, Catherine Stober, Tobias Rausch, Eva Benito, Johann-Christoph Jann, Daniel Nowak, Ramiz Emini, Markus Hoenicka, Andreas Liebold, Anthony Ho, Shimin Shuai, Hartmut Geiger, Ashley D Sanders, and Jan O Korbel
    Nature genetics (2024)

2023

  1. Pan-cancer analysis reveals tumor microbiome associations with host molecular aberrations
    Chenchen Ma, Changxing Su, Jiaxuan Li, Jiuxin Qu, and Shimin Shuai
    bioRxiv (2023)

2022

  1. PanCancer analysis of somatic mutations in repetitive regions reveals recurrent mutations in snRNA U2
    Pablo Bousquets-Muñoz, Ander Dı́az-Navarro, Ferran Nadeu, Ana Sánchez-Pitiot, Sara López-Tamargo, Shimin Shuai, Milagros Balbı́n, Jose M C Tubio, Sı́lvia Beà, Jose I Martin-Subero, Ana Gutiérrez-Fernández, Lincoln D Stein, Elı́as Campo, and Xose S Puente
    NPJ genomic medicine (2022)
  2. Cdx1b protects intestinal cell fate by repressing signaling networks for liver specification
    Qingxia Jin, Yuqi Gao, Shimin Shuai, Yayue Chen, Kaiyuan Wang, Jun Chen, Jinrong Peng, and Ce Gao
    Journal of genetics and genomics (2022)
  3. Interruption of Klf5 acetylation in basal progenitor cells promotes luminal commitment by activating Notch signaling
    Baotong Zhang, Siyuan Xia, Mingcheng Liu, Xiawei Li, Shimin Shuai, Wei Tao, Yixiang Li, Jianping Jenny Ni, Wei Zhou, Lan Liao, Jianming Xu, and Jin-Tang Dong
    Journal of genetics and genomics (2022)

2020

  1. Combined burden and functional impact tests for cancer driver discovery using DriverPower
    Shimin Shuai, PCAWG Drivers and Functional Interpretation Working Group, Steven Gallinger, Lincoln Stein, and PCAWG Consortium
    Nature communications (2020)
  2. Nature
    Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
    Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E Maruvka, Ciyue Shen, Samirkumar B Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P Hamilton, Nicholas J Haradhvala, Chen Hong, Keren Isaev, Todd A Johnson, Malene Juul, Andre Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D Roberts, Gordon Saksena, Steven E Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M C Tubio, Husen M Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S Lawrence, Christian Mering, Hidewaki Nakagawa, Benjamin J Raphael, Mark A Rubin, Chris Sander, Lincoln D Stein, Joshua M Stuart, Tatsuhiko Tsunoda, David A Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J Campbell, Núria López-Bigas, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, Joachim Weischenfeldt, Rameen Beroukhim, Iñigo Martincorena, Jakob Skou Pedersen, Gad Getz, and PCAWG Consortium
    Nature (2020)
  3. Nature
    Pan-cancer analysis of whole genomes
    ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
    Nature (2020)
  4. Molecular cell
    Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks
    Helen Zhu, Liis Uusküla-Reimand, Keren Isaev, Lina Wadi, Azad Alizada, Shimin Shuai, Vincent Huang, Dike Aduluso-Nwaobasi, Marta Paczkowska, Diala Abd-Rabbo, Oliver Ocsenas, Minggao Liang, J Drew Thompson, Yao Li, Luyao Ruan, Michal Krassowski, Irakli Dzneladze, Jared T Simpson, Mathieu Lupien, Lincoln D Stein, Paul C Boutros, Michael D Wilson, and Jüri Reimand
    Molecular cell (2020)
  5. Integrative pathway enrichment analysis of multivariate omics data
    Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S Fox, Helen Zhu, Diala Abd-Rabbo, Miles W Mee, Paul C Boutros, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, and PCAWG Consortium
    Nature communications (2020)
  6. Pathway and network analysis of more than 2500 whole cancer genomes
    Matthew A Reyna, David Haan, Marta Paczkowska, Lieven P C Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S Lawrence, Jakob Skou Pedersen, Mark A Rubin, David A Wheeler, Søren Brunak, Jose M G Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian Mering, S Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, Joshua M Stuart, Benjamin J Raphael, and PCAWG Consortium
    Nature communications (2020)
  7. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
    Joana Carlevaro-Fita, Andrés Lanzós, Lars Feuerbach, Chen Hong, David Mas-Ponte, Jakob Skou Pedersen, PCAWG Drivers and Functional Interpretation Group, Rory Johnson, and PCAWG Consortium
    Communications biology (2020)

2019

  1. Nature
    The U1 spliceosomal RNA is recurrently mutated in multiple cancers
    Shimin Shuai, Hiromichi Suzuki, Ander Diaz-Navarro, Ferran Nadeu, Sachin A Kumar, Ana Gutierrez-Fernandez, Julio Delgado, Magda Pinyol, Carlos López-Otı́n, Xose S Puente, Michael D Taylor, Elı́as Campo, and Lincoln D Stein
    Nature (2019)
  2. Nature
    Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma
    Hiromichi Suzuki, Sachin A Kumar, Shimin Shuai, Ander Diaz-Navarro, Ana Gutierrez-Fernandez, Pasqualino De Antonellis, Florence M G Cavalli, Kyle Juraschka, Hamza Farooq, Ichiyo Shibahara, Maria C Vladoiu, Jiao Zhang, Namal Abeysundara, David Przelicki, Patryk Skowron, Nicole Gauer, Betty Luu, Craig Daniels, Xiaochong Wu, Antoine Forget, Ali Momin, Jun Wang, Weifan Dong, Seung-Ki Kim, Wieslawa A Grajkowska, Anne Jouvet, Michelle Fèvre-Montange, Maria Luisa Garrè, Amulya A Nageswara Rao, Caterina Giannini, Johan M Kros, Pim J French, Nada Jabado, Ho-Keung Ng, Wai Sang Poon, Charles G Eberhart, Ian F Pollack, James M Olson, William A Weiss, Toshihiro Kumabe, Enrique López-Aguilar, Boleslaw Lach, Maura Massimino, Erwin G Van Meir, Joshua B Rubin, Rajeev Vibhakar, Lola B Chambless, Noriyuki Kijima, Almos Klekner, László Bognár, Jennifer A Chan, Claudia C Faria, Jiannis Ragoussis, Stefan M Pfister, Anna Goldenberg, Robert J Wechsler-Reya, Swneke D Bailey, Livia Garzia, A Sorana Morrissy, Marco A Marra, Xi Huang, David Malkin, Olivier Ayrault, Vijay Ramaswamy, Xose S Puente, John A Calarco, Lincoln Stein, and Michael D Taylor
    Nature (2019)

2017

  1. Nature genetics
    Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma
    Michael E Feigin, Tyler Garvin, Peter Bailey, Nicola Waddell, David K Chang, David R Kelley, Shimin Shuai, Steven Gallinger, John D McPherson, Sean M Grimmond, Ekta Khurana, Lincoln D Stein, Andrew V Biankin, Michael C Schatz, and David A Tuveson
    Nature genetics (2017)