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Research

Short Talk Seminar Series

Master
Content

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.

Content
Fall 2020 Seminar Series

Date

Time

Event Presenters

Room Number

Topics

Aug. 5

Noon-1 p.m.

Fritz Sedlazeck

 

 

 

Aug. 5

Noon-1 p.m.

Chris Amos

 

 

Aug. 19

Noon-1 p.m.

Todd Treangen

 

 

 

Aug. 19

Noon-1 p.m.

Abiodun Oluyomi

 

 

Sept. 2

Noon-1 p.m.

Stephen Wong

 

 

Sept. 2

Noon-1 p.m.

Maria Oden

 

 

Sept. 16

Noon-1 p.m.

 

Prahlad Ram

 

 

Sept. 16

Noon-1 p.m.

Kjersti Aagard

 

 

 

Oct. 14

Noon-1 p.m.

Harel Shouval

 

 

Oct. 28

Noon-1 p.m.

Jeff Rogers

 

 

Nov. 11

Noon-1 p.m.

Tao Wu

 

 

 

Nov. 11

Noon-1 p.m.

Chenghang Zong

 

 

 

Dec. 2

Noon - 1 p.m.

Assaf Gottlieb

 

 

Dec. 2

Noon-1 p.m.

Uma Ramamurthy

 

 

Content
Fall 2020 CIBR/QCB Journal Club

Date

Time

Faculty

Room

Aug. 12

Noon-1 p.m.

Matt Baker

 

Aug. 26

Noon-1 p.m.

Zhao Wang

 

Sept. 9

Noon-1 p.m.

Wenyi Wang

 

Sept. 23 Noon-1 p.m. Chad Creighton  

Oct. 21

Noon-1 p.m.

Matt McGinley

 

Nov. 4

Noon-1 p.m.

 

 

Nov. 18

Noon-1 p.m.

Fuli Yu

 

Content
Previous QCB Journal Club Papers

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
imaging phenotypes in UK Biobank

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
alignment system

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
ETS Transcription Factor Genes in
Prostate Cancer

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
cancer-associated transcript fusions

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
assemblies determined by 3D electron-microscopy

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
microscopy

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
Data with Neural Networks

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?
Large-Scale Evaluation of 6,165 Diffusion MRI Scans

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
brain development in early childhood

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
neural responses in higher visual cortex

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
Visual Object Recognition?

James J. DiCarlo, Davide Zoccolan and Nicole C. Rust

Neuron 73, February 9, 2012

Ankit Patel

4/4/18

Performance-optimized hierarchical models predict
neural responses in higher visual cortex

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
rewiring of protein interactions

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
byproduct of simpler phenomena?

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