The Computational Integrative Biomedical Research Center offers a seminar series as a platform for center faculty members to present their ongoing research to the Baylor College of Medicine and Texas Medical Center community. Alternating with Journal Club sessions, the Short Talks form an integral component of the Quantitative and Computational Biosciences course Current Topics in Computational Biomedicine. Presenters are faculty from throughout the Baylor and TMC community. Presentations happen at noon every other Wednesday, and all are welcome to attend.
The schedule of speakers and Journal Club sessions are listed below, and previous QCB Journal Club Papers are listed at the bottom of the page.
Date |
Time |
Event Presenters |
Room Number |
Topics |
---|---|---|---|---|
Jan. 13, 2021 | Noon-1 p.m. | Traver Hart | ||
Jan. 13, 2021 | Noon-1 p.m. | Xaq Pitkow | ||
Jan. 27, 2021 | Noon-1 p.m. | Bing Zhang | ||
Jan. 27, 2021 | Noon-1 p.m. | Andreas Tolias | ||
Feb. 10, 2021 | Noon-1 p.m. | Nidhi Sahni | ||
Feb. 10, 2021 | Noon-1 p.m. | Chris Jermaine | ||
Feb. 24, 2021 | Noon-1 p.m. | Laura Segatori | ||
Feb. 24, 2021 | Noon-1 p.m. | Nick Young | ||
March 17, 2021 | Noon-1 p.m. | |||
March 17, 2021 | Noon-1 p.m. | |||
March 31, 2021 | Noon-1 p.m. | |||
March 31, 2021 | Noon-1 p.m. | |||
April 14, 2021 | Noon - 1 p.m. | |||
April 14, 2021 | Noon-1 p.m. | |||
April 21, 2021 | Noon-1 p.m. | |||
April 21, 2021 | Noon-1 p.m. | |||
April 28, 2021 | Noon-1 p.m. | |||
April 28, 2021 | Noon-1 p.m. |
Date | Time | Faculty | Room |
---|---|---|---|
Jan. 20, 2021 | Noon-1 p.m. | ||
Feb. 3, 2021 | Noon-1 p.m. | ||
Feb. 17, 2021 | Noon-1 p.m. | Pavel Sumazin | |
March 3, 2021 | Noon-1 p.m. | Ming Zhou | |
March 24, 2021 | |||
April 7, 2021 | Noon-1 p.m. | ||
April 21, 2021 | Noon-1 p.m. | Fabrizio Gabbiani | |
May 5, 2021 | Noon-1 p.m. | Chad Shaw |
Faculty |
Date |
Paper Name |
Author |
Journal |
---|---|---|---|---|
Elena Grigorenko |
11/14/18 |
Strategies for integrated analysis in imaging genetics studies |
Natalia Vilor-Tejedora, Silvia Alemany, Alejandro Caceresa, Mariona Bustamante Jesus Pujolf, Jordi Sunyera, Juan R. Gonzalez |
Neuroscience and Biobehavioral Reviews 93 (2018) 57–70 |
Elena Grigorenko |
11/14/18 |
Genome-wide association studies of brain |
Lloyd T. Elliott, Kevin Sharp, Fidel Alfaro-Almagro, Sinan Shi, Karla l. Miller, Gwenaelle Douaud, Jonathan Marchini and Stephen M. Smit |
Nature | Vol 562 | 11 October 2018 |
Kim Worley |
10/31/18 |
Basic Local Alignment Search Tool |
Stephen F. Altschul, Warren Gish, Webb Miller, Eugene W. Myers and David J. Lipman |
J . Mol.Biol.(1990)215, 403-410 |
Kim Worley |
10/31/18 |
MUMmer4: A fast and versatile genome |
Guillaume Marcais, Arthur L. Delcher, Adam M. Phillippy, Rachel Coston, Steven L. Salzberg and Aleksey Zimin |
PLOS Computational Biology January 26, 2018 |
Kim Worley |
10/31/18 |
BLAT—The BLAST-Like Alignment Tool |
W. James Kent |
Genome Research 12:656–664 |
Chad Creighton |
10/17/18 |
Recurrent Fusion of TMPRSS2 and |
Scott A. Tomlins,Daniel R. Rhodes, Sven Perner, Saravana M. Dhanasekaran, Rohit Mehra, Xiao-Wei Sun, Sooryanarayana Varambally, Xuhong Cao, Joelle Tchinda, Rainer Kuefer, Charles Lee, James E. Montie, Rajal B. Shah, Kenneth J. Pienta, Mark A. Rubin, Arul M. Chinnaiyan |
Science 28 October 2005 Vol 310 |
Chad Creighton |
10/17/18 |
TumorFusions: an integrative resource for |
Xin Hu, Qianghu Wang, Ming Tang, Floris Barthel, Samirkumar Amin, Kosuke Yoshihara, Frederick M. Lang, Emmanuel Martinez-Ledesma, Soo Hyun Lee, Siyuan Zheng and Roel G.W. Verhaak |
Nucleic Acids Research, 2018, Vol. 46 |
Matthew Baker |
9/19/18 |
Improved metrics for comparing structures of macromolecular |
Agnel Praveen Joseph, Ingvar Lagerstedt, Ardan Patwardhan, Maya Topf and Martyn Winn |
Journal of Structural Biology 199 (2017) 12–26 |
Matthew Baker |
9/19/18 |
A structure of cytoplasmic polyhedrosis virus by cryoelectron |
Xuekui Yu, Lei Jin and Z. Hong Zhou |
Nature. 2008 May 15; 453(7193): 415–419 |
Rainer Lanz |
9/5/18 |
Mutations of bacteria from virus sensitivity to virus resistance |
S. E. Lurias and M. Delbrock |
Genetics 28: 491 November 1943 |
Rainer Lanz |
9/5/18 |
Evolution of resistance during clonal expansion |
Yoh Iwasa, Martin A. Nowak and Franziska Michor |
Genetics 172: 2557–2566 (April 2006) |
Rainer Lanz |
9/5/18 |
Immune Landscape of Cancer |
Vesteinn Thorsson, David L. Gibbs, Scott D. Brown, ..., Mary L. Disis, Benjamin G. Vincent, llya Shmulevich |
Immunity 2018, 48, 1–19 |
Marek Kimmel |
8/22/18 |
Canceled |
|
|
Zhandong Liu |
8/8/18 |
Deep learning |
Yann LeCun, Yoshua Bengio and Geoffrey Hinton |
Nature |Vol 521|28 May 2015 |
Zhandong Liu |
8/8/18 |
Reducing the Dimensionality of |
G. E. Hinton and R. R. Salakhutdinov |
Science 28 JULY 2006 VOL 313 |
Elena Grigorenko |
5/2/18 |
Do Candidate Genes Affect the Brain's White Matter Microstructure? |
Neda Jahanshad, Habib Ganjgahi, Janita Bralten, Anouk den Braber, Joshua Faskowitz, Annchen R Knod, et. al |
bioRxiv preprint first posted online Feb. 20, 2017 |
Elena Grigorenko |
5/2/18 |
Imaging structural and functional |
John H. Gilmore, Rebecca C. Knickmeyer and Wei Gao |
Neuroscience Volume 19 | March 2018 | 123 |
Bing Zhang |
4/18/18 |
Performance-optimized hierarchical models predict |
Yunan Luo, Jianzhu Ma, Yang Liu , Qing Ye, Trey Ideker, Jian Peng |
bioRxiv preprint first posted online Mar. 25, 2018 |
Ankit Patel |
4/4/18 |
How Does the Brain Solve |
James J. DiCarlo, Davide Zoccolan and Nicole C. Rust |
Neuron 73, February 9, 2012 |
Ankit Patel |
4/4/18 |
Performance-optimized hierarchical models predict |
Daniel L. K. Yaminsa, Ha Honga, Charles F. Cadieua, Ethan A. Solomona, Darren Seiberta, and James J. DiCarlo |
PNAS | June 10, 2014 | vol. 111 | no. 23 | 8619–8624 |
Nidhi Sahni |
3/21/18 |
Alternative splicing of intrinsically disordered regions and |
Marija Buljan, Guilhem Chalancon, A Keith Dunker, Alex Bateman, S Balaji, Monika Fuxreiter and M Madan Babu |
Current Opinion in Structural Biology 2013, 23:443–450 |
Nidhi Sahni |
3/21/18 |
Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks |
Marija Buljan, Guilhem Chalancon, Sebastian Eustermann, Gunter P. Wagner, Monika Fuxreiter, Alex Bateman and M. Madan Babu |
Mol Cell. 2012 Jun 29; 46(6): 871–883 |
Nidhi Sahni |
3/21/18 |
Widespread expansion of protein interaction capabilities by alternative splicing |
Xinping Yang, Jasmin Coulombe-Huntington, Shuli Kang, Gloria M. Sheynkman et. al |
Cell. 2016 February 11; 164(4): 805–817 |
Courtney Hodges |
2/21/18 |
Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping |
Viviana I. Risca, Sarah K. Denny, Aaron F. Straight and William J. Greenleaf |
Nature. 2017 January 12; 541(7636): 237–241 |
Courtney Hodges |
2/21/18 |
High-Resolution Profiling of Histone Methylations in the Human Genome |
Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Dustin E. Schones, Zhibin Wang, Gang Wei, Iouri Chepelev and Keji Zhao |
Cell 129, 823–837, May 18, 2007 |
Marek Kimmel |
2/7/18 |
Embryonic development of the human hematopoietic system |
Manuela Tavian and Bruno Peault |
Int. J. Dev. Biol. 49: 243-250 (2005) |
Marek Kimmel |
2/7/18 |
Lifelong haematopoiesis is established by hundreds of precursors throughout mammalian ontogeny |
Miguel Ganuza, Trent Hall, David Finkelstein, Ashley Chabot, Guolian Kang and Shannon McKinney-Freeman |
Nature Cell Biology Volume 19 | Number 10 | October 2017 |
Xaq Pitkow |
1/24/18 |
Neural networks and physical systems with emergent collective computational abilities |
J.J.Hopfield |
Proc.NatLAcad.Sci.USA79(1982) |
Xaq Pitkow |
1/24/18 |
Structure in neural population recordings: an expected |
Gamaleldin F Elsayed and John P Cunningham |
Nature Neuroscience Volume 20 | Number 9 | September 2017 |
Fuli Yu |
1/10/18 |
The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease |
Peter N. Robinson, Sebastian Kohler, Sebastian Bauer, Dominik Seelow, Denise Horn and Stefan Mundlos |
The American Journal of Human Genetics 83, 610–615, November 7, 2008 615 |
Fuli Yu |
1/10/18 |
Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics |
Ekta Khurana et al. |
Science 342, (2013) |
Zhangdong Liu |
10/11/17 |
Robust enumeration of cell subsets from tissue expression profiles |
Aaron M. Newman, Chih Long Liu, Michael R. Green, Andrew J. Gentles, Weiguo Feng, Yue Xu, Chuong D. Hoang, Maximilian Diehn and Ash A. Alizadeh |
Nat Methods. 2015 May ; 12(5): 453–457. doi:10.1038/nmeth.3337. |
Zhangdong Liu |
10/11/17 |
Cell type–specific gene expression differences in complex tissues |
Shai S Shen-Orr, Robert Tibshirani, Purvesh Khatri, Dale L Bodian, Frank Staedtler, Nicholas M Perry, Trevor Hastie, Minnie M Sarwal, Mark M Davis and Atul J Butte |
Nat Methods. 2010 April ; 7(4): 287–289. doi:10.1038/nmeth.1439. |
Matt Baker |
9/20/17 |
A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition |
Soojay Banerjee, Alberto Bartesaghi, Alan Merk, Prashant Rao, Stacie L. Bulfer, Yongzhao Yan, Neal Green, Barbara Mroczkowski, R. Jeffrey Neitz, Peter Wipf, Veronica Falconieri, Raymond J. Deshaies, Jacqueline L. S. Milne, Donna Huryn, Michelle Arkin, Sriram Subramaniam |
Cite as: S. Banerjee et al., Science 10.1126/science.aad7974 (2016). |
Matt Baker |
9/20/17 |
Magnetosomes Are Cell Membrane Invaginations Organized by the Actin-Like Protein MamK |
Arash Komeili, Zhuo Li, Dianne K. Newman, Grant J. Jensen |
13 January 2006 Vol 311 Science |
Charles Lin |
8/23/17 |
Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution |
Hannah K. Long, Sara L. Prescott and Joanna Wysocka |
Cell 167, November 17, 2016, pp1170-1187 |
Charles Lin |
8/23/17 |
An Atomic Model of the Interferon-b Enhanceosome |
Daniel Panne, Tom Maniatis, and Stephen C. Harrison |
Cell 129, 1111–1123, June 15, 2007 |
Charles Lin |
8/23/17 |
Suboptimization of developmental enhancers |
Emma K. Farley, Katrina M. Olson, Wei Zhang, Alexander J. Brandt, Daniel S. Rokhsar, Michael S. Levine |
Science, 16 October 2015 • Vol 350 Issue 6258 |
Susan Marriott |
8/9/17 |
It's not just you: science papers are getting harder to read |
Richard Haughton |
Nature doi:10.1038/nature.2017.21751, March 30, 2017 |
Susan Marriott |
8/9/17 |
Ten Simple (Empirical) Rules for Writing Science |
Cody J. Weinberger, James A. Evans, Stefano Allesina |
PLoS Comput Biol 11(4): e1004205. doi:10.1371/journal.pcbi.1004205 |