HudsonAlpha Journal Club
The HudsonAlpha Journal Club gives trainees an opportunity to present and discuss publications relevant to their research areas. The meetings provide the trainees in HudsonAlpha labs valuable experience with science communication and presentations. Journal Club is hosted by HudsonAlpha faculty investigator Sara Cooper, PhD.
Upcoming Journal Club Meetings
Kimberly Hobbs, April 25, 2018
Böni-Schnetzler, Marianne, Stéphanie P. Häuselmann, Elise Dalmas, Daniel T. Meier, Constanze Thienel, Shuyang Traub, Friederike Schulze et al. “β Cell-Specific Deletion of the IL-1 Receptor Antagonist Impairs β Cell Proliferation and Insulin Secretion.” Cell reports 22, no. 7 (2018): 1774-1786.
Surya Chhetri, April 4, 2018
Charlton, Jocelyn, Timothy L. Downing, Zachary D. Smith, Hongcang Gu, Kendell Clement, Ramona Pop, Veronika Akopian et al. “Global delay in nascent strand DNA methylation.” Nature structural & molecular biology (2018): 1.
James Lawlor, March 21, 2018
Imamovic, Lejla, Mostafa Mostafa Hashim Ellabaan, Ana Manuel Dantas Machado, Linda Citterio, Tune Wulff, Soren Molin, Helle Krogh Johansen, and Morten Otto Alexander Sommer. “Drug-Driven Phenotypic Convergence Supports Rational Treatment Strategies of Chronic Infections.” Cell (2018).
Bryan Moyers, March 3, 2018
Donaghey, Julie, Sudhir Thakurela, Jocelyn Charlton, Jennifer S. Chen, Zachary D. Smith, Hongcang Gu, Ramona Pop et al. “Genetic determinants and epigenetic effects of pioneer-factor occupancy.” Nature Genetics (2018): 1.
Matthew Neu, February 21, 2018
Rishishwar, Lavanya, Leonardo Mariño-Ramírez, and I. King Jordan. “Benchmarking computational tools for polymorphic transposable element detection.” Briefings in bioinformatics 18, no. 6 (2016): 908-918.
Megan Breitbach, February 7, 2018
Cohen, Joshua D., Lu Li, Yuxuan Wang, Christopher Thoburn, Bahman Afsari, Ludmila Danilova, Christopher Douville et al. “Detection and localization of surgically resectable cancers with a multi-analyte blood test.” Science (2018): eaar3247.
Jaimie Richards, January 24, 2018
Gray, Stacy W., Katherine Hicks-Courant, Christopher S. Lathan, Levi Garraway, Elyse R. Park, and Jane C. Weeks. “Attitudes of patients with cancer about personalized medicine and somatic genetic testing.” Journal of oncology practice 8, no. 6 (2012): 329-335.
Michelle Amaral, January 3, 2018
Dasgupta, Sanjoy, Charles F. Stevens, and Saket Navlakha. “A neural algorithm for a fundamental computing problem.” Science 358, no. 6364 (2017): 793-796.
Megan Breitbach, December 6, 2017
Chang, Diana, Mike A. Nalls, Ingileif B. Hallgrímsdóttir, Julie Hunkapiller, Marcel van der Brug, Fang Cai, Geoffrey A. Kerchner et al. “A meta-analysis of genome-wide association studies identifies 17 new Parkinson’s disease risk loci.” Nature genetics 49 (2017): 1511.
Emily Gordon, November 15, 2017
Roe, Jae-Seok, Chang-Il Hwang, Tim DD Somerville, Joseph P. Milazzo, Eun Jung Lee, Brandon Da Silva, Laura Maiorino et al. “Enhancer reprogramming promotes pancreatic cancer metastasis.” Cell 170, no. 5 (2017): 875-888.
Nick Cochran, October 25, 2017
Shinmyo, Yohei, Yukari Terashita, Tung Anh Dinh Duong, Toshihide Horiike, Muneo Kawasumi, Kazuyoshi Hosomichi, Atsushi Tajima, and Hiroshi Kawasaki. “Folding of the Cerebral Cortex Requires Cdk5 in Upper-Layer Neurons in Gyrencephalic Mammals.” Cell Reports 20, no. 9 (2017): 2131-2143.
Drew Hardigan, September 20, 2017
Patel, Shashank J., Neville E. Sanjana, Rigel J. Kishton, Arash Eidizadeh, Suman K. Vodnala, Maggie Cam, Jared J. Gartner et al. “Identification of essential genes for cancer immunotherapy.” Nature 548, no. 7669 (2017): 537-542.
Jana Whittle, September 13, 2017
Ezkurdia, Iakes, Jose Manuel Rodriguez, Enrique Carrillo-de Santa Pau, Jesús Vázquez, Alfonso Valencia, and Michael L. Tress. “Most highly expressed protein-coding genes have a single dominant isoform.” Journal of proteome research 14, no. 4 (2015): 1880-1887.
Ryne Ramaker, August 16, 2017
Dixit, Atray, Oren Parnas, Biyu Li, Jenny Chen, Charles P. Fulco, Livnat Jerby-Arnon, Nemanja D. Marjanovic et al. “Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens.” Cell 167, no. 7 (2016): 1853-1866.
Emily Ross, August 2, 2017
Musah, Samira, Akiko Mammoto, Thomas C. Ferrante, Sauveur SF Jeanty, Mariko Hirano-Kobayashi, Tadanori Mammoto, Kristen Roberts et al. “Mature induced-pluripotent-stem-cell-derived human podocytes reconstitute kidney glomerular-capillary-wall function on a chip.” Nature biomedical engineering 1 (2017).
Timley Watkins, July 19, 2017
Halpern, Keren Bahar, Rom Shenhav, Orit Matcovitch-Natan, Beáta Tóth, Doron Lemze, Matan Golan, Efi E. Massasa et al. “Single-cell spatial reconstruction reveals global division of labour in the mammalian liver.” Nature 542, no. 7641 (2017): 352-356.
Matthew Neu, July 5, 2017
Stessman, H.A., Xiong, B., Coe, B.P., Wang, T., Hoekzema, K., Fenckova, M., Kvarnung, M., Gerdts, J., Trinh, S., Cosemans, N. and Vives, L., 2017. Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases. Nature genetics, 49(4), pp.515-526.
Brian Moyers, June 21, 2017
Li, S., Alvarez, R.V., Sharan, R., Landsman, D. and Ovcharenko, I., 2016. Quantifying deleterious effects of regulatory variants. Nucleic acids research, 45(5), pp.2307-2317.
James Lawlor, June 7, 2017
Zhang, Yu, Lin An, Feng Yue, and Ross C. Hardison. “Jointly characterizing epigenetic dynamics across multiple human cell types.” Nucleic acids research 44, no. 14 (2016): 6721-6731.
Kimberly Hobbs, May 24, 2017
Klann, Tyler S., Joshua B. Black, Malathi Chellappan, Alexias Safi, Lingyun Song, Isaac B. Hilton, Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.” Nature biotechnology (2017).
Kevin Bowling, May 3, 2017
Saleheen, Danish, Pradeep Natarajan, Irina M. Armean, Wei Zhao, Asif Rasheed, Sumeet A. Khetarpal, Hong-Hee Won et al. “Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity.” Nature 544, no. 7649 (2017): 235-239.
Jaimie Richards, April 19, 2017
Yusuf, Rafeek A., Deevakar Rogith, Shelly RA Hovick, Susan K. Peterson, Allison M. Burton‐Chase, Bryan M. Fellman, Yisheng Li, Carolyn McKinney, Elmer V. Bernstam, and Funda Meric‐Bernstam. “Attitudes toward molecular testing for personalized cancer therapy.” Cancer 121, no. 2 (2015): 243-250.
Megan Breitbach, April 5, 2017
Erikson, Galina A., Dale L. Bodian, Manuel Rueda, Bhuvan Molparia, Erick R. Scott, Ashley A. Scott-Van Zeeland, Sarah E. Topol et al. “Whole-genome sequencing of a healthy aging cohort.” Cell 165, no. 4 (2016): 1002-1011.
Michelle Amaral, March 15, 2017
Sambandan, S., Akbalik, G., Kochen, L., Rinne, J., Kahlstatt, J., Glock, C., … & Schuman, E. M. (2017). Activity-dependent spatially localized miRNA maturation in neuronal dendrites. Science, 355(6325), 634-637.
Emily Gordon, March 1, 2017
Verissimo, C. S., Overmeer, R. M., Ponsioen, B., Drost, J., Mertens, S., Verlaan-Klink, I., … & Bernards, R. (2016). Targeting mutant RAS in patient-derived colorectal cancer organoids by combinatorial drug screening. eLife, 5, e18489.
Krysta Engel, February 15, 2017
Jagannathan, S., & Bradley, R. K. (2016). Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population. Genome Research, 26(12), 1639-1650.
Nick Cochran, January 25, 2017
Chailangkarn, T., Trujillo, C. A., Freitas, B. C., Hrvoj-Mihic, B., Herai, R. H., Diana, X. Y., … & Stefanacci, L. (2016). A human neurodevelopmental model for Williams syndrome. Nature, 536(7616), 338-343.
Drew Hardigan, December 7, 2016
Javierre, Biola M., Oliver S. Burren, Steven P. Wilder, Roman Kreuzhuber, Steven M. Hill, Sven Sewitz, Jonathan Cairns et al. “Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.” Cell 167, no. 5 (2016): 1369-1384.
Brittany Lasseigne, November 16, 2016
Hause, R. J., Pritchard, C. C., Shendure, J., & Salipante, S. J. (2016). Classification and characterization of microsatellite instability across 18 cancer types. Nature Medicine.
Ryan Ramaker, November 2, 2016
Katainen, R., Dave, K., Pitkänen, E., Palin, K., Kivioja, T., Välimäki, N., … & Kondelin, J. (2015). CTCF/cohesin-binding sites are frequently mutated in cancer. Nature genetics, 47(7), 818-821.
Jaimie Richards, October 19, 2016
Ewing, A., Thompson, N., & Ricks-Santi, L. (2015). Strategies for enrollment of African Americans into cancer genetic studies. Journal of Cancer Education, 30(1), 108-115.
Keenan, T., Moy, B., Mroz, E. A., Ross, K., Niemierko, A., Rocco, J. W., … & Bardia, A. (2015). Comparison of the genomic landscape between primary breast cancer in African American versus white women and the association of racial differences with tumor recurrence. Journal of Clinical Oncology, JCO-2015.
Timley Watkins, October 5, 2016
Chew, W. L., Tabebordbar, M., Cheng, J. K., Mali, P., Wu, E. Y., Ng, A. H., … & Church, G. M. (2016). A multifunctional AAV-CRISPR-Cas9 and its host response. Nature Methods, 13(10), 868-874.
Matthew Neu, September 15, 2016
Krishnan, A., Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., … & Troyanskaya, O. G. (2016). Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. Nature Neuroscience.