QBC Journal Club | PhD Degree Program in Biological and Medical Informatics (BMI)

When	Tuesdays, 10:45 a.m. to 12:00 noon Pacific time

QBC Journal Club Orientation.pptx (PowerPoint, 6 slides, 6.1 MB)

Academic Year 2026

Date	Details
11/18/25	Sophie-Christine Porak (Biophysics) Identification of medication–microbiome interactions that affect gut infection Kumar, A., et al. Nature 644, 506–515 (16 July 2025). Jongbin Kim (PSPG) Targeting protein-ligand neosurfaces with a generalizable deep learning tool Marchand, A., Buckley, S., Schneuing, A. et al. Nature 639, 522–531 (15 January 2025). Elizabeth Hardy (PSPG) Oligodendrocyte precursor cells facilitate neuronal lysosome release Fang, LP., Lin, CH., Medlej, Y. et al. Nat Commun 16, 1175 (30 January 2025). Julius Pampel (CCB) Mining the CRBN target space redefines rules for molecular glue–induced neosubstrate recognition Petzold, G., Gainza, P., Annunziato, S., et al. Science (New York, N.Y.) vol. 389,6755 (3 July 2025).
11/25/25	Dylan Boselli (CCB) Neuropeptides specify and reprogram division of labor in the leafcutter and Atta cephalotes Gilbert, M.B., Glastad, K.M., Fioriti, M., Cell. Volume 188, Issue 15, Pages 3974-3991 (24 July 2025). Zoe Chen (Bioinformatics) Isabella Glenn (Biophysics) Mitochondrial origins of the pressure to sleep Sarnataro, R., Velasco, C.D., Monaco, N. et al. Nature 645, 722–728 (16 July 2025). Valeria Sanchez Estrada (Bioinformatics) Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities Goldman, D.A., Xue, K.S., Parrott, A.B., et al. Proceedings of the National Academy of Sciences of the United States of America (10 March 2025).
12/2/25	William Johnson (Bioinformatics) Sabine Cismoski (CCB) Caroline Huang (PSPG) A cGAS-mediated mechanism in naked mole-rats potentiates DNA repair and delays aging Chen, Yu., Chen Z., Wang H., et al. Science vol. 390,6769 (9 October 2025). Nikhil Gupta (Biophysics)
12/9/25	Yulia Gutierrez (Biophysics) McKenna Crawford (CCB) Rashad Reid (Bioinformatics) An efficient framework to decipher microRNA regulatory programs applied to T cells Zhu, H., Ganapathi Sankaran, D., Smith, N.L. et al. Genes Immun 26, 486–496 (6 August 2025). Kaylee Lee (PSPG) Physical activity as a modifiable risk factor in preclinical Alzheimer’s disease Yau, WY.W., Kirn, D.R., Rabin, J.S. et al. Nat Med (3 November 2025).
1/6/26	Chris Thompson (Bioinformatics) Annabel Menendez (PSPG) Sydney Figueroa (CCB) Isaiah Hazelwood (Biophysics)
1/13/26	Gyuna Kim (Biophysics) Ally Nicolella (Bioinformatics) Safwaan Khan (PSPG) Sungwon Jung (CCB)
1/20/26	An Nguyen (CCB) Sanjay Rangavajjhala (Bioinformatics) Harshu Musunuri (Biophysics) Amanda Lipford (PSPG) Phase behavior of Cacio e Pepe sauce Bartolucci, G., Busiello, D. M., Ciarchi, et al. Physics of Fluids; (1 April 2025).
1/27/26	Rochel Munitz (Biophysics) Alex Pacheco (CCB) Chad Buteo (CCB) Runa Cheng (Bioinformatics)
2/3/26	Izabella Zamora (Bioinformatics) Eden Chun (PSPG) Jocelyn Chavez Rios (Biophysics) Daniel Torres Pomares (CCB)
2/10/26	Andrew Condon (CCB) Carlos Gomez (Bioinformatics) Vianna Quach (PSPG) Taylor Womack (Biophysics)
2/17/26	Jessica Flowers (Biophysics) Rayo Suseno (Bioinformatics) Alice Dang (PSPG) Abigail Spray (CCB)
2/24/26	Melissa Plata (PSPG) Chloe Fields (CCB) Malavika Vinod (Biophysics) Alexander Ho (Bioinformatics)
3/3/26	Ethan Shurberg (Bioinformatics) Talia Delambre (PSPG) Haley Gauer (CCB) Delia Gagnon (Biophysics)
3/10/26	Robert Gottschalk (CCB) Sara Lichtarge (Bioinformatics) Devin Hemmans (Biophysics) Maya Druch (PSPG)
3/17/26	Beau Lonnquist (Biophysics) Akshita Saxena (Bioinformatics) Emily Ho (CCB) Poorvi Dua (PSPG)
3/24/26	Jonah Frazier (PSPG) Beatrice Mihalache (Biophysics) Sirawit Lertwiriyapiti (CCB) Enock Niyonkuru (Bioinformatics)
3/31/26	Faye Orcales (Bioinformatics) Evan Marshman (PSPG) Ysabella Mello (CCB)
4/7/26	Katie Scukas (CCB) Oliver Sampson-Tonge (CCB) Keerthi Renduchintala (Biophysics) Ben Sokol (CCB)
4/14/26	Zuriah Meacham (PSPG) Anastasiia Grynyova (CCB)
4/21/26	John Gonzales (PSPG) Vishvak Subramanyam (Bioinformatics) Hannah Radhika Allegakoen (CCB) Yagmur Doruk Polcyn (Biophysics)
10/28/25	Justin Sim (Biophysics) Megabase-scale human genome rearrangement with programmable bridge recombinases Perry, N. T., Bartie, L. J., Katrekar, D., et al. Science (25 September 2025). Isobel Beasley (Bioinformatics) Pan-UK Biobank genome-wide association analyses enhance discovery and resolution of ancestry-enriched effects Karczewski, K.J., Gupta, R., Kanai, M. et al. Nat Genet 57, 2408–2417 (18 September 2025). Leah Ragosta (CCB) Sub-micron sampling of living cells by macrophages Fan, A., Thota, R., Serwas, N., et al. bioRxiv (10 April 2025). Marisol Contreras (PSPG) Tailored structured peptide design with a key-cutting machine approach Leyva, Y.C., Torres, M.D.T., Oliva, C.A. et al. Nat Mach Intell (21 October 2025).
10/21/25	Christine Wan (PSPG) Genome-to-genome analysis reveals associations between human and mycobacterial genetic variation in tuberculosis patients from Tanzania Xu, Z.M., Zwyer, M., Hiza, H. et al. BMC Med Genomics 18, 99 (02 June 2025). Keana Davis (Biophysics) Choroid Plexus Hosts the Earliest Detectable Circadian Clock in the Brain Sládek ,M., Houdek, P., Myung, J., et al. Fluids Barriers CNS vol. 21,1 46. 27 (27 May 2024). John Matthew Suntay (Bioinformatics) Bilingualism Is Associated with Significant Structural and Connectivity Alterations in the Thalamus in Adulthood Ayyildiz B, Sayman D, Ayyildiz S, et al. J Cogn Neurosci. vol. 37,7: 1238-1256 (1 July 2025). Jennifer Alvarenga Vasquez (CCB) Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies Glanville, J., Bellin, M., Pletnev S., et al. Cell vol. 188,12 (12 June 2025).
10/14/25	Maria Tarazona Guzman (CCB) Targeting the SHOC2–RAS interaction in RAS-mutant cancers Hauseman, Z.J., Stauffer, F., Beyer, K.S. et al. Nature 642, 232–241 (7 May 2025). Katherine Bang (PSPG) A defined microbial community reproduces attributes of fine flavour chocolate fermentation Gopaulchan, D., Moore, C., Ali, N. et al. Nat Microbiol (18 August 2025). Craig Soares (Biophysics) Macrophages recycle phagocytosed bacteria to fuel immunometabolic responses Lesbats, J., Brillac, A., Reisz, J.A. et al. Nature 640, 524–533 (26 February 2025). Noah Baker (Bioinformatics) Evaluating generalizability of oncology trial results to real-world patients using machine learning-based trial emulations Orcutt, X., Chen, K., Mamtani, R. et al. Nat Med 31, 457–465 (3 January 2025).
10/7/25	Ipsa Mittra (Bioinformatics) Snord67 promotes breast cancer metastasis by guiding U6 modification and modulating the splicing landscape Chao, Y.L., Zhou, K.I., Forbes, K.K. et al. Nat Commun 16, 4118 (2 May 2025). Benjamin Ahn (CCB) In vivo antibody-selective conjugation technology for long-acting drugs Kitahara K., Rondon A., Miller E., et al, Chem, (19 Aug 2025), Aurora de Tagyos (PSPG) Quantitative chemoproteomics reveals dopamine’s protective modification of Tau Wang, Q., Liu, Z., Wang, Y. et al. Nat Chem Biol 21, 1341–1350 (20 February 2025). Garrison Asper (Biophysics) Quorum sensing mediates morphology and motility transitions in the model archaeon Haloferax volcanii Chatterjee P, Consoli CE, Schiller H, et al. Preprint. bioRxiv. (14 Jan 2025).
9/30/25	Harshu Musunuri (Biophysics) Potentiation of mitochondrial function by mitoDREADD-Gs reverses pharmacological and neurodegenerative cognitive impairment in mice Pagano Zottola, A.C., Martín-Jiménez, R., Lavanco, G. et al. Nat Neurosci 28, 1844–1857 (11 August 2025). Sarah Ancheta (Bioinformatics) Predicting cellular responses to perturbation across diverse contexts with STATE Adduri, A. K., Gautam, D., Bevilacqua, B., et al. bioRxiv (10 July 2025). Oleksandr Zginnyk (CCB) Neutrophils drive vascular occlusion, tumour necrosis and metastasis Adrover, J.M., Han, X., Sun, L. et al. Nature 645, 484–495 (16 July 2025). Abe Arab (PSPG) Learning Universal Representations of Intermolecular Interactions with ATOMICA Fang, A., Zhang, Z., Zhou, A. et al. bioRxiv (15 July 2025).