Broad Institute of MIT & Harvard

1. Interplay of Mendelian and polygenic risk factors in Arab breast cancer patients

   Authors: Mohammed Al-Jumaan, Hoyin Chu, Abdullah Alsulaiman, Sabrina Y. Camp, Seunghun Han, Riaz Gillani, Yousef Al Marzooq, Fatmah Almulhim, Chittibabu Vatte, Areej Al Nemer, Afnan Almuhanna, Eliezer M. Van Allen, Amein Al-Ali and Saud H. AlDubayan

   Citation: Genome Medicine 2023 15:65

   Content type: Research Published on: 1 September 2023

2. Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal

   Authors: J. Michael Krill-Burger, Joshua M. Dempster, Ashir A. Borah, Brenton R. Paolella, David E. Root, Todd R. Golub, Jesse S. Boehm, William C. Hahn, James M. McFarland, Francisca Vazquez and Aviad Tsherniak

   Citation: Genome Biology 2023 24:192

   Content type: Research Published on: 23 August 2023

3. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

   Authors: Jennifer R. S. Meadows, Jeffrey M. Kidd, Guo-Dong Wang, Heidi G. Parker, Peter Z. Schall, Matteo Bianchi, Matthew J. Christmas, Katia Bougiouri, Reuben M. Buckley, Christophe Hitte, Anthony K. Nguyen, Chao Wang, Vidhya Jagannathan, Julia E. Niskanen, Laurent A. F. Frantz, Meharji Arumilli…

   Citation: Genome Biology 2023 24:187

   Content type: Research Published on: 15 August 2023

4. Morphological and transcriptomic analyses of stem cell-derived cortical neurons reveal mechanisms underlying synaptic dysfunction in schizophrenia

   Authors: Annie Kathuria, Kara Lopez-Lengowski, Bradley Watmuff and Rakesh Karmacharya

   Citation: Genome Medicine 2023 15:58

   Content type: Research Published on: 28 July 2023

5. An Atlas of Variant Effects to understand the genome at nucleotide resolution

   Authors: Douglas M. Fowler, David J. Adams, Anna L. Gloyn, William C. Hahn, Debora S. Marks, Lara A. Muffley, James T. Neal, Frederick P. Roth, Alan F. Rubin, Lea M. Starita and Matthew E. Hurles

   Citation: Genome Biology 2023 24:147

   Content type: Correspondence Published on: 3 July 2023

6. The effect of background noise and its removal on the analysis of single-cell expression data

   Authors: Philipp Janssen, Zane Kliesmete, Beate Vieth, Xian Adiconis, Sean Simmons, Jamie Marshall, Cristin McCabe, Holger Heyn, Joshua Z. Levin, Wolfgang Enard and Ines Hellmann

   Citation: Genome Biology 2023 24:140

   Content type: Research Published on: 19 June 2023

7. RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities

   Authors: Ya Wang, Kelsey N. Thompson, Yan Yan, Meghan I. Short, Yancong Zhang, Eric A. Franzosa, Jiaxian Shen, Erica M. Hartmann and Curtis Huttenhower

   Citation: Microbiome 2023 11:131

   Content type: Research Published on: 13 June 2023

8. Rescuing biologically relevant consensus regions across replicated samples

   Authors: Vahid Jalili, Marzia A. Cremona and Fernando Palluzzi

   Citation: BMC Bioinformatics 2023 24:240

   Content type: Research Published on: 7 June 2023

9. Prediction of treatment response to antipsychotic drugs for precision medicine approach to schizophrenia: randomized trials and multiomics analysis

   Authors: Liang-Kun Guo, Yi Su, Yu-Ya-Nan Zhang, Hao Yu, Zhe Lu, Wen-Qiang Li, Yong-Feng Yang, Xiao Xiao, Hao Yan, Tian-Lan Lu, Jun Li, Yun-Dan Liao, Zhe-Wei Kang, Li-Fang Wang, Yue Li, Ming Li…

   Citation: Military Medical Research 2023 10:24

   Content type: Research Published on: 2 June 2023

10. Transcriptional diversity in specific synaptic gene sets discriminates cortical neuronal identity

    Authors: Amparo Roig Adam, José A. Martínez-López, Sophie J. F. van der Spek, Patrick F. Sullivan, August B. Smit, Matthijs Verhage and Jens Hjerling-Leffler

    Citation: Biology Direct 2023 18:22

    Content type: Research Published on: 9 May 2023

11. Study protocol of the Berlin Research Initiative for Diagnostics, Genetics and Environmental Factors in Schizophrenia (BRIDGE-S)

    Authors: Alice Braun, Julia Kraft and Stephan Ripke

    Citation: BMC Psychiatry 2023 23:31

    Content type: Study Protocol Published on: 12 January 2023

12. Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing

    Authors: Haris Smajlović, Ariya Shajii, Bonnie Berger, Hyunghoon Cho and Ibrahim Numanagić

    Citation: Genome Biology 2023 24:5

    Content type: Software Published on: 11 January 2023

13. Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics

    Authors: Ayshwarya Subramanian, Mikhail Alperovich, Yiming Yang and Bo Li

    Citation: Genome Biology 2022 23:267

    Content type: Research Published on: 27 December 2022

14. Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

    Authors: Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier and Curtis Huttenhower

    Citation: Genome Biology 2022 23:208

    Content type: Method Published on: 3 October 2022

15. Whole genome sequencing reveals the independent clonal origin of multifocal ileal neuroendocrine tumors

    Authors: Netta Mäkinen, Meng Zhou, Zhouwei Zhang, Yosuke Kasai, Elizabeth Perez, Grace E. Kim, Chrissie Thirlwell, Eric Nakakura and Matthew Meyerson

    Citation: Genome Medicine 2022 14:82

    Content type: Research Published on: 3 August 2022

16. Using zebrafish to understand reciprocal interactions between the nervous and immune systems and the microbial world

    Authors: Jean-Pierre Levraud, John F. Rawls and Anne E. Clatworthy

    Citation: Journal of Neuroinflammation 2022 19:170

    Content type: Review Published on: 28 June 2022

17. Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

    Authors: Rauf Salamzade, Abigail L. Manson, Bruce J. Walker, Thea Brennan-Krohn, Colin J. Worby, Peijun Ma, Lorrie L. He, Terrance P. Shea, James Qu, Sinéad B. Chapman, Whitney Howe, Sarah K. Young, Jenna I. Wurster, Mary L. Delaney, Sanjat Kanjilal, Andrew B. Onderdonk…

    Citation: Genome Medicine 2022 14:37

    Content type: Research Published on: 5 April 2022

18. StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities

    Authors: Lucas R. van Dijk, Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber IV, Christine Anyansi, Amy J. Pickering, Scott J. Hultgren, Abigail L. Manson, Thomas Abeel and Ashlee M. Earl

    Citation: Genome Biology 2022 23:74

    Content type: Method Published on: 7 March 2022

19. Melanocortin 1 receptor activation protects against alpha-synuclein pathologies in models of Parkinson’s disease

    Authors: Waijiao Cai, Pranay Srivastava, Danielle Feng, Yue Lin, Charles R. Vanderburg, Yuehang Xu, Pamela Mclean, Matthew P. Frosch, David E. Fisher, Michael A. Schwarzschild and Xiqun Chen

    Citation: Molecular Neurodegeneration 2022 17:16

    Content type: Research article Published on: 23 February 2022

20. Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects

    Authors: Joshua M. Dempster, Isabella Boyle, Francisca Vazquez, David E. Root, Jesse S. Boehm, William C. Hahn, Aviad Tsherniak and James M. McFarland

    Citation: Genome Biology 2021 22:343

    Content type: Method Published on: 20 December 2021