SS/SC Brown Bag Seminar Series
The seminar should give staff scientists a platform to present and discuss their science. As SS/SC we are highly specialized and have greatly varying scientific interests, and we liked for the seminar to represent this; thus, the choice of topic and format will be speaker driven.
The seminar could be:
regular 45 min talk about your research, chalk talk, summary of cool new stuff you heard about at a conference you recently went to, talk you need feedback for, presentation of a manuscript you liked to get feedback on, talk about a project that just can’t get off the ground and needs troubleshooting, presentation of a new technology/possible equipment purchases, presentations by several SSSC together or several shorter presentations.
We are also well aware that there is no time and location that fits all. We booked 37/2041 for the first Thursday of each month from 12(noon) to 1PM, however, if you wish to present a seminar at another time / location just find a room that suits you better and let us know.
If you would like to schedule your talk or have any questions, please contact:
Christina Stuelten (christu@mail.nih.gov), Yoshimi Greer (greery@mail.nih.gov) or Emily Tai (taic@mail.nih.gov)
2024 Spring Series – "Network and share your work "
Didn’t have a chance to meet other SS / SC and talk science lately? - We invite you to share your work as a poster or a short talk with other SS/SC in a series Brown Bag Lunch Seminars.
Date and Time | Title | Speaker | Affiliation | WebEx Link/Sildes |
3/1 (Fri) noon-1:30 | TGF-beta regulated mRNA splicing | Christina Stuelten | LCMB |
2023 Summer Series – "Network and share your work "
Didn’t have a chance to meet other SS / SC and talk science lately? - We invite you to share your work as a poster or a short talk with other SS/SC in a series Brown Bag Lunch Seminars.
Date and Time | Title | Speaker | Affiliation | WebEx Link/Sildes |
6/8 (Thu) noon-1:00 | Empowering your research with services from the CCR Genomics Core | Madeline Wong | CCR Genomics Core | |
8/17 (Thu) noon-2:00 | Repurposing anti-viral vaccines for in situ cancer immunotherapy | Nicolas Cuburu | LCO | |
Thermal Proteome Profiling for Global Analysis of Drug Effects | Lisa Jenkins | LCB | ||
9/21 (Thu) noon-2:00 | TumorMiner a new tool for precision medicine | Fathi Eloumi | DTB | |
Single Molecule Analysis of CENP-A Chromatin by High-Speed Atomic Force Microscopy | Daniël Melters | LRBGE | ||
'Inside out’, a novel CD47 signaling mediated via extracellular vesicles shed by immune and cancer cells | Sukhbir Kaur | Lab of Pathology | ||
10/19 (Thu) noon-2:00 | Addressing transcriptomic spillover in NGS analysis of PDX models of metastasis | Brian Capaldo | Laboratory of Genitourinary Cancer Pathogenesis | https://cbiit.webex.com/cbiit/j.php?MTID=m12c0742ea9739c4c079bdf5ed59a8506 |
2021 Fall/2022 Winter Series – "SS/SC Alumni - Where are they now?"
We are inviting our alumni who moved on to other positions in NCI, other ICs in NIH, FDA, academia or industry to share their experience with us.
Date and Time | Title | Speaker | Affiliation | WebEx Link/Sildes |
9/13 (Mon) 11:30 -12:30 | Staying at NIH BUT leaving the bench | Zack Howard | Center for Scientific Review, NIH | |
11/1 (Mon) noon-1:00 | Outside of the lab BUT close to the science | Ana Robles | Office of Cancer Clinical Proteomics Research, DCTD, NCI | |
1/26 (Wed) noon-1:00 | Research in a regulatory agency: the advantages of the researcher/assessor model at OPQ/CDER | Carole Sourbier | Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, FDA | |
3/23 (Wed) noon-1:00 | Supporting Cancer Research through Planning and Analysis | Diane Palmieri | Center for Research Strategy, NCI | |
4/22 (Fri) noon-1:00 | Transition from Staff Scientist to Pharma | Even Walseng | AstraZeneca R&D Biologics Engineering |
2021 Spring Series –
Understanding Tumor Heterogeneity and Plasticity through the Lens of Machine Learning and Mathematics
Maxwell Lee will review different approaches to understand tumor heterogeneity and plasticity. The topics includes using mixture models to deconvolute bulk RNA-seq data, clustering and classification of single cell RNA-seq to study tumor subtypes, and mathematic tools to predict cancer cell evolution. His talk abstract, outline, the topic of each week are listed below. Slides will be posted Monday morning before the talk and the video recording will be available afterwards.
Monday 10:00AM-11:00AM
WebEx Link: https://cbiit.webex.com/cbiit/j.php?MTID=mc31fec457279698a34e0aa990172743e
Meeting number: 157 260 1880 Meeting Password: UEuBV2P2Z$3
Abstract and Outline:
Date | Title | Speaker | Affiliation | Slides | Video Recording Link |
4/12 | Cancer stem cell model and evolutionary dynamics | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | ||
4/26 | Cell fate decision determined by Gene Regulatory Network (GRN) | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | ||
5/10 | Waddington’s epigenetic landscape quantified with quasi-potential | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | ||
5/24 | Network motifs and dynamics of cellular states | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | ||
6/7 | Network motifs for desensitization and history of the treatment exposure | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | ||
6/21 | Drug-tolerant persister (DTP) and cancer dynamics | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR |
2020 Fall/Winter Series – Clustering Methods: from k-means to Gaussian mixture model and Louvain algorithm
Maxwell Lee will review some basic concepts of clustering analyses that are commonly used in cancer research, including 1) traditional methods of hierarchical clustering and k-means; 2) Gaussian mixture model (GMM) and latent Dirichlet allocation (LDA); 3) graph-based approaches, which are the state-of-the-art technologies used in the single cell data analysis. Max will provide practical examples to illustrate how each method works, how to interpret the results of clustering analysis and explain the pros and cons of each method. His talk abstract, outline, the topic of each week are listed below for your reference. Slides will be posted the weekend before the talk and the video recording will be available afterwards.
Monday 10:00AM-11:00AM
WebEx Link: https://cbiit.webex.com/cbiit/j.php?MTID=m593aca29c65d0e9f7be43bfc2ad1b092
Meeting number: 172 414 1612 Meeting Password: AmWdZgu*775
Abstract and Outline:
Date | Title | Speaker | Affiliation | Slides | Video Recording Link |
9/21 | Introduction and k-means clustering | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | ||
10/5 | Gaussian mixture model (GMM) and Latent Dirichlet Allocation (LDA) | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | ||
10/19 | Non-negative matrix factorization (NMF) and its connection to k-means clustering | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | ||
11/2 | Hierarchical clustering | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | ||
11/16 | Spectral clustering and its connection to Laplacian Eigenmaps | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | ||
12/21 | Louvain clustering and its application to single cell RNAseq data analysis | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | ||
1/25 | Latent Dirichlet Allocation (LDA) and its application to sequence motif analysis | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | LDA video link click here |
2020 Spring/Summer Series
12:00 PM - 01:00 PM, Building 37, Room 2041 (second floor conference room) - please note the location and time may be different in some cases
Date | Title | Speaker(s) | Affiliation | Slides | WebEx Link, Video Recording Link and Abstract |
04/16 | Dimension Reduction Methods: from PCA to TSNE and UMAP - Part I
| Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | Principal Component Analysis (PCA) provides a foundation to understanding various dimension reduction methods. Principal components are the linear combinations of the original variables with the 1st principal component captures the largest variance, followed by a descending order for the rest of the principal components and subject to the principal components being orthonormal. A geometric perspective of PCA is the rotation of coordinate system. | |
04/23 | Dimension Reduction Methods: from PCA to TSNE and UMAP - Part II | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | Multidimensional Scaling (MDS) provides an alternative strategy for dimension reduction. The data matrix is pairwise distance matrix. The distance matrix is converted to Gram matrix (similarity matrix). Eigen decomposition of Gram matrix generates eigen vectors and eigen values. The product of eigen vector matrix and square root of eigen value matrix is identical to principal component matrix. | |
| 04/30 | Dimension Reduction Methods: from PCA to TSNE and UMAP - Part III | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | Non-linear dimension reduction is essential for the analysis of data that lie in non-Euclidian space. Geodesic distance is better measurement for points on a curve or curved surface. Isomap is similar to MDS except that pairwise distance matrix uses geodesic distance instead of Euclidian distance.
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| 05/07 | Dimension Reduction Methods: from PCA to TSNE and UMAP - Part IV | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | TSNE models data in high-dimension with Gaussian distribution and data in low-dimension with t-distribution. Covariance matrix adjusted distance matrix is converted to similarity matrix through Gaussian distribution. The cost function is KL divergence to minimize the two probability distributions. Seurat package was used to analyze RNAseq data. Effect of mitochondria gene percentage cutoff was analyzed | |
| 05/14 | Dimension Reduction Methods: from PCA to TSNE and UMAP - Part V | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | TSNE and UMAP were compared. UMAP uses k-nearest neighbor (KNN) and calculates weight matrix. The cost function is binary cross-entropy. It is much fast than TSNE and also achieves better separation between clusters.
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| 05/28 | Dimension Reduction Methods: from PCA to TSNE and UMAP - Part VI | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | More detailed analyses of scRNAseq data with UMAP were performed. The effect of filtering out cells with high mitochondrial genes was discussed. Algorithm of UMAP was explained.
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| 06/04 | Dimension Reduction Methods: from PCA to TSNE and UMAP - Part VII | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | Trajectory analysis was performed using Monocle 2 and 3 packages. Two datasets were analyzed, Human Skeletal Muscle Myoblasts (HSMM) and neural crest cells from Mouse Organogenesis Cell Atlas (MOCA). Monocle 2 uses minimal spanning tree model where Monocle 3 uses general graph and produces trajectory analysis for multiple subgraphs. | |
| 06/18 | Dimension Reduction Methods: from PCA to TSNE and UMAP - Part VIII and Q&A | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | Webex https://cbiit.webex.com/cbiit/j.php?MTID=md38682248ab766611823beee46acab18 Meeting number (access code): 476 578 641
Summary of comparison between Monocle 2 and 3 analysis. Monocle 2 generates plot with coordinates resulted from the reversed graph embedding. Monocle 3 plot uses UMAP data and shows trajectory for multiple subgraphs. The objective function Monocle 2 has 3 parts: Pearson residuals in high-dimension, cost function for the minimal spanning tree, and k-means like clustering. | |
| 07/15 | What Should Staff Scientists & Staff Clinicians (SSSCs) Know About Technology Transfer? | CCR SSSC Professional Development Committee Aida Cremesti Laura Prestia | Special Seminar from the CCR SSSC Professional Development Committee and NCI’s Technology Transfer Center (TTC) | WebexWed, July 15, 12noon - 1pm https://cbiit.webex.com/cbiit/j.php?MTID=m610dac8f56d3c290997f2bf6c97 The following topics will be covered in an interactive Webex:
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2019 Series
12:00 PM - 01:00 PM, Building 37, Room 2041 (second floor conference room) - please note the location and time may be different in some cases
Date | Title | Speaker(s) | Affiliation | Slides | Location |
01/04 | Five reasons to pay attention to SAXS-assisted protein structure prediction | Susan Tsutakawa | Lawrence Berkeley National Laboratory, | 3-4pm | |
01/25 | Principles of cancer modeling in mice | Chi-Ping Day | Laboratory of Cancer Biology and Genetics, NCI/CCR | 12-1pm 37/2041 | |
| 03/01 | The Advanced Imaging & Microscopy Resource: | Harsh Vishwasrao | Director, Advanced Imaging and Microscopy Resource, NIH | 1-2 pm 37/6041 | |
| 03/28 | The Genome Modification Core at the Frederick National Lab for Cancer Research – a collaborative resource for the NCI CCR | Raj Chari | Director, Genome Modification Core, NCI/FNLCR | 12-1pm 37/2041 |
2018 Series
12:00 PM - 01:00 PM, Building 37, Room 2041 (second floor conference room)
Date | Title | Speaker(s) | Affiliation | Slides |
02/15 | Single Cell Genomics - CCR new initiative and practical tips | Liz Conner | CCR Genomics Core | |
03/01 | Mass Spectrometry – How it works, what it does, and how it can help you | Lisa Jenkins | Mass Spectrometry Program, | |
04/27 | Statistical analysis: concept, practice, and interpretation. Part I | Maxwell Lee | Laboratory of Cancer Biology and Genetics, NCI/CCR | |
05/03 | Statistical analysis: application to NGS data with DESeq2 and GSEA. Part II | Howard Yang | Laboratory of Cancer Biology and Genetics, NCI/CCR | |
| 05/31 | High-Throughput Imaging for System Cell Biology | Gianluca Pegararo | Laboratory of Receptor Biology and Gene Expression, NCI/CCR | |
| 09/27 | Cutting edge protein analysis technologies - advancing quantitative proteomic research, | Jinqiu (Jessie) Chen | Collaborative Protein Technology Resource, |
2017 Series
12:00 PM - 01:00 PM, Building 37, Room 2041 (second floor conference room)
Date | Title | Speaker(s) | Affiliation |
04/06 | Innovative Sequencing Resources in the CCR Sequencing Facility | Bao Tran | CCR, Sequencing Facility |
05/18 | ONC201 Kills Breast Cancer Cells by Inhibiting Mitochondrial Respiration | Yoshimi Endo Greer | Women's Malignancies Branch |
06/01 | Kicking Lymphoma When It’s Down - How we can exploit the apoptotic threshold therapeutically in Diffuse Large B Cell Lymphoma | Art Schaffer | Lymphoid Malignancies Branch |
| 07/06 | Leukocyte adhesion deficiency in a cat due to a deletion in the CD18 gene | Thomas Bauer | Experimental Transplantation and Immunology Branch |
12/01 | Predicting targets of T cell responses in cancer: Evaluating algorithms and lessons learned from the Immune Epitope Database | Bjorn Peters | La Jolla Institute for Allergy and Immunology |
| 12/07 | CCR Collaborative Bioinformatics Resource: Our NGS Pipeline Tools (Introduction by Maggie Cam) | Justin Lack | CCR Collaborative Bioinformatics Resource (CCBR) |
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