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1. Column: Paper craft

Author

Budker, D and Kimball, DJ

Subjects
physics.ed-ph, General Science & Technology
Abstract

Several years ago, one of us, having noticed that inexperienced scientiststend to make largely the same mistakes while writing their first papers, wascompelled to write a one-page note summarizing some dos and don'ts intended tohelp take care of common problems before they occur. Since these days themajority of research papers are written collaboratively by groups ofco-authors, we are compelled to extend these recommendations to collaborativewriting as we observe groups of co-authors falling into the same traps againand again.

Published
2016

2. Paper craft

Author

Budker, Dmitry and Kimball, Derek Jackson

Subjects
physics.ed-ph, General Science & Technology
Abstract

Several years ago, one of us, having noticed that inexperienced scientiststend to make largely the same mistakes while writing their first papers, wascompelled to write a one-page note summarizing some dos and don'ts intended tohelp take care of common problems before they occur. Since these days themajority of research papers are written collaboratively by groups ofco-authors, we are compelled to extend these recommendations to collaborativewriting as we observe groups of co-authors falling into the same traps againand again.

Published
2016

3. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development

Author

Gorkin, David U, Barozzi, Iros, Zhao, Yuan, Zhang, Yanxiao, Huang, Hui, Lee, Ah Young, Li, Bin, Chiou, Joshua, Wildberg, Andre, Ding, Bo, Zhang, Bo, Wang, Mengchi, Strattan, J Seth, Davidson, Jean M, Qiu, Yunjiang, Afzal, Veena, Akiyama, Jennifer A, Plajzer-Frick, Ingrid, Novak, Catherine S, Kato, Momoe, Garvin, Tyler H, Pham, Quan T, Harrington, Anne N, Mannion, Brandon J, Lee, Elizabeth A, Fukuda-Yuzawa, Yoko, He, Yupeng, Preissl, Sebastian, Chee, Sora, Han, Jee Yun, Williams, Brian A, Trout, Diane, Amrhein, Henry, Yang, Hongbo, Cherry, J Michael, Wang, Wei, Gaulton, Kyle, Ecker, Joseph R, Shen, Yin, Dickel, Diane E, Visel, Axel, Pennacchio, Len A, and Ren, Bing

Subjects
Reproductive Medicine, Biomedical and Clinical Sciences, General Science & Technology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

4. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development.

Author

Gorkin, David U, Barozzi, Iros, Zhao, Yuan, Zhang, Yanxiao, Huang, Hui, Lee, Ah Young, Li, Bin, Chiou, Joshua, Wildberg, Andre, Ding, Bo, Zhang, Bo, Wang, Mengchi, Strattan, J Seth, Davidson, Jean M, Qiu, Yunjiang, Afzal, Veena, Akiyama, Jennifer A, Plajzer-Frick, Ingrid, Novak, Catherine S, Kato, Momoe, Garvin, Tyler H, Pham, Quan T, Harrington, Anne N, Mannion, Brandon J, Lee, Elizabeth A, Fukuda-Yuzawa, Yoko, He, Yupeng, Preissl, Sebastian, Chee, Sora, Han, Jee Yun, Williams, Brian A, Trout, Diane, Amrhein, Henry, Yang, Hongbo, Cherry, J Michael, Wang, Wei, Gaulton, Kyle, Ecker, Joseph R, Shen, Yin, Dickel, Diane E, Visel, Axel, Pennacchio, Len A, and Ren, Bing

Subjects
General Science & Technology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

5. Author Correction: Structure of human GABAB receptor in an inactive state

Author

Park, Jinseo, Fu, Ziao, Frangaj, Aurel, Liu, Jonathan, Mosyak, Lidia, Shen, Tong, Slavkovich, Vesna N, Ray, Kimberly M, Taura, Jaume, Cao, Baohua, Geng, Yong, Zuo, Hao, Kou, Yongjun, Grassucci, Robert, Chen, Shaoxia, Liu, Zheng, Lin, Xin, Williams, Justin P, Rice, William J, Eng, Edward T, Huang, Rick K, Soni, Rajesh K, Kloss, Brian, Yu, Zhiheng, Javitch, Jonathan A, Hendrickson, Wayne A, Slesinger, Paul A, Quick, Matthias, Graziano, Joseph, Yu, Hongtao, Fiehn, Oliver, Clarke, Oliver B, Frank, Joachim, and Fan, Qing R

Subjects
Historical Studies, Biomedical and Clinical Sciences, History, Heritage and Archaeology, General Science & Technology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

7. Author Correction: Complete biosynthesis of cannabinoids and their unnatural analogues in yeast

Author

Luo, Xiaozhou, Reiter, Michael A, d’Espaux, Leo, Wong, Jeff, Denby, Charles M, Lechner, Anna, Zhang, Yunfeng, Grzybowski, Adrian T, Harth, Simon, Lin, Weiyin, Lee, Hyunsu, Yu, Changhua, Shin, John, Deng, Kai, Benites, Veronica T, Wang, George, Baidoo, Edward EK, Chen, Yan, Dev, Ishaan, Petzold, Christopher J, and Keasling, Jay D

Subjects
Economics, Pure Mathematics, Mathematical Sciences, General Science & Technology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

8. Author Correction: Complete biosynthesis of cannabinoids and their unnatural analogues in yeast.

Author

Luo, Xiaozhou, Reiter, Michael A, d'Espaux, Leo, Wong, Jeff, Denby, Charles M, Lechner, Anna, Zhang, Yunfeng, Grzybowski, Adrian T, Harth, Simon, Lin, Weiyin, Lee, Hyunsu, Yu, Changhua, Shin, John, Deng, Kai, Benites, Veronica T, Wang, George, Baidoo, Edward EK, Chen, Yan, Dev, Ishaan, Petzold, Christopher J, and Keasling, Jay D

Subjects
General Science & Technology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

10. Author Correction: Investigation of the fine structure of antihydrogen

Author

ALPHA Collaboration

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, ALPHA Collaboration, General Science & Technology
Abstract

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03367-9.

Published
2021

12. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development

Author

Gorkin, David U, Barozzi, Iros, Zhao, Yuan, Zhang, Yanxiao, Huang, Hui, Lee, Ah Young, Li, Bin, Chiou, Joshua, Wildberg, Andre, Ding, Bo, Zhang, Bo, Wang, Mengchi, Strattan, J Seth, Davidson, Jean M, Qiu, Yunjiang, Afzal, Veena, Akiyama, Jennifer A, Plajzer-Frick, Ingrid, Novak, Catherine S, Kato, Momoe, Garvin, Tyler H, Pham, Quan T, Harrington, Anne N, Mannion, Brandon J, Lee, Elizabeth A, Fukuda-Yuzawa, Yoko, He, Yupeng, Preissl, Sebastian, Chee, Sora, Han, Jee Yun, Williams, Brian A, Trout, Diane, Amrhein, Henry, Yang, Hongbo, Cherry, J Michael, Wang, Wei, Gaulton, Kyle, Ecker, Joseph R, Shen, Yin, Dickel, Diane E, Visel, Axel, Pennacchio, Len A, and Ren, Bing

Subjects
Reproductive Medicine, Biomedical and Clinical Sciences, Pediatric, General Science & Technology
Abstract

A Correction to this paper has been published: https://doi.org/10.1038/s41586-020-03089-4.

Published
2021

13. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development.

Author

Gorkin, David U, Barozzi, Iros, Zhao, Yuan, Zhang, Yanxiao, Huang, Hui, Lee, Ah Young, Li, Bin, Chiou, Joshua, Wildberg, Andre, Ding, Bo, Zhang, Bo, Wang, Mengchi, Strattan, J Seth, Davidson, Jean M, Qiu, Yunjiang, Afzal, Veena, Akiyama, Jennifer A, Plajzer-Frick, Ingrid, Novak, Catherine S, Kato, Momoe, Garvin, Tyler H, Pham, Quan T, Harrington, Anne N, Mannion, Brandon J, Lee, Elizabeth A, Fukuda-Yuzawa, Yoko, He, Yupeng, Preissl, Sebastian, Chee, Sora, Han, Jee Yun, Williams, Brian A, Trout, Diane, Amrhein, Henry, Yang, Hongbo, Cherry, J Michael, Wang, Wei, Gaulton, Kyle, Ecker, Joseph R, Shen, Yin, Dickel, Diane E, Visel, Axel, Pennacchio, Len A, and Ren, Bing

Subjects
General Science & Technology
Abstract

A Correction to this paper has been published: https://doi.org/10.1038/s41586-020-03089-4.

Published
2021

14. Pan-cancer analysis of whole genomes

Author

Campbell, Peter J, Getz, Gad, Korbel, Jan O, Stuart, Joshua M, Jennings, Jennifer L, Stein, Lincoln D, Perry, Marc D, Nahal-Bose, Hardeep K, Ouellette, BF Francis, Li, Constance H, Rheinbay, Esther, Nielsen, G Petur, Sgroi, Dennis C, Wu, Chin-Lee, Faquin, William C, Deshpande, Vikram, Boutros, Paul C, Lazar, Alexander J, Hoadley, Katherine A, Louis, David N, Dursi, L Jonathan, Yung, Christina K, Bailey, Matthew H, Saksena, Gordon, Raine, Keiran M, Buchhalter, Ivo, Kleinheinz, Kortine, Schlesner, Matthias, Zhang, Junjun, Wang, Wenyi, Wheeler, David A, Ding, Li, Simpson, Jared T, O'Connor, Brian D, Yakneen, Sergei, Ellrott, Kyle, Miyoshi, Naoki, Butler, Adam P, Royo, Romina, Shorser, Solomon I, Vazquez, Miguel, Rausch, Tobias, Tiao, Grace, Waszak, Sebastian M, Rodriguez-Martin, Bernardo, Shringarpure, Suyash, Wu, Dai-Ying, Demidov, German M, Delaneau, Olivier, Hayashi, Shuto, Imoto, Seiya, Habermann, Nina, Segre, Ayellet V, Garrison, Erik, Cafferkey, Andy, Alvarez, Eva G, Maria Heredia-Genestar, Jose, Muyas, Francesc, Drechsel, Oliver, Bruzos, Alicia L, Temes, Javier, Zamora, Jorge, Baez-Ortega, Adrian, Kim, Hyung-Lae, Mashl, R Jay, Ye, Kai, DiBiase, Anthony, Huang, Kuan-lin, Letunic, Ivica, McLellan, Michael D, Newhouse, Steven J, Shmaya, Tal, Kumar, Sushant, Wedge, David C, Wright, Mark H, Yellapantula, Venkata D, Gerstein, Mark, Khurana, Ekta, Marques-Bonet, Tomas, Navarro, Arcadi, Bustamante, Carlos D, Siebert, Reiner, Nakagawa, Hidewaki, Easton, Douglas F, Ossowski, Stephan, Tubio, Jose MC, De La Vega, Francisco M, Estivill, Xavier, Yuen, Denis, Mihaiescu, George L, Omberg, Larsson, Ferretti, Vincent, Sabarinathan, Radhakrishnan, Pich, Oriol, Gonzalez-Perez, Abel, Weiner, Amaro Taylor, Fittall, Matthew W, Demeulemeester, Jonas, Tarabichi, Maxime, and Roberts, Nicola D

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Bioinformatics and Computational Biology, Genetics, Oncology and Carcinogenesis, Cancer Genomics, Biotechnology, Human Genome, Cancer, Prevention, 2.1 Biological and endogenous factors, Cell Proliferation, Cellular Senescence, Chromothripsis, Cloud Computing, DNA Mutational Analysis, Evolution, Molecular, Female, Genome, Human, Genomics, Germ-Line Mutation, High-Throughput Nucleotide Sequencing, Humans, Information Dissemination, Male, Mutagenesis, Mutation, Neoplasms, Oncogenes, Promoter Regions, Genetic, RNA Splicing, Reproducibility of Results, Telomerase, Telomere, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, General Science & Technology
Abstract

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Published
2020

15. Pan-cancer analysis of whole genomes.

Author

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium

Subjects
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Telomere, Humans, Neoplasms, Telomerase, Reproducibility of Results, DNA Mutational Analysis, Information Dissemination, Genomics, Evolution, Molecular, Cell Proliferation, RNA Splicing, Mutagenesis, Mutation, Germ-Line Mutation, Oncogenes, Genome, Human, Female, Male, Promoter Regions, Genetic, High-Throughput Nucleotide Sequencing, Cloud Computing, Chromothripsis, Cellular Senescence, Cancer, Genetics, Biotechnology, Prevention, Human Genome, 2.1 Biological and endogenous factors, General Science & Technology
Abstract

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Published
2020