Focus on:
All days
Jan 19, 2021
Jan 20, 2021
Jan 21, 2021
Jan 22, 2021
All sessions
CCB Happy Hour/Wine Tasting
Hide Contributions
Indico style
Indico style - inline minutes
Indico style - numbered
Indico style - numbered + minutes
Indico Weeks View
Choose Timezone
Use the event/category timezone
Specify a timezone
Africa/Abidjan
Africa/Accra
Africa/Addis_Ababa
Africa/Algiers
Africa/Asmara
Africa/Bamako
Africa/Bangui
Africa/Banjul
Africa/Bissau
Africa/Blantyre
Africa/Brazzaville
Africa/Bujumbura
Africa/Cairo
Africa/Casablanca
Africa/Ceuta
Africa/Conakry
Africa/Dakar
Africa/Dar_es_Salaam
Africa/Djibouti
Africa/Douala
Africa/El_Aaiun
Africa/Freetown
Africa/Gaborone
Africa/Harare
Africa/Johannesburg
Africa/Juba
Africa/Kampala
Africa/Khartoum
Africa/Kigali
Africa/Kinshasa
Africa/Lagos
Africa/Libreville
Africa/Lome
Africa/Luanda
Africa/Lubumbashi
Africa/Lusaka
Africa/Malabo
Africa/Maputo
Africa/Maseru
Africa/Mbabane
Africa/Mogadishu
Africa/Monrovia
Africa/Nairobi
Africa/Ndjamena
Africa/Niamey
Africa/Nouakchott
Africa/Ouagadougou
Africa/Porto-Novo
Africa/Sao_Tome
Africa/Tripoli
Africa/Tunis
Africa/Windhoek
America/Adak
America/Anchorage
America/Anguilla
America/Antigua
America/Araguaina
America/Argentina/Buenos_Aires
America/Argentina/Catamarca
America/Argentina/Cordoba
America/Argentina/Jujuy
America/Argentina/La_Rioja
America/Argentina/Mendoza
America/Argentina/Rio_Gallegos
America/Argentina/Salta
America/Argentina/San_Juan
America/Argentina/San_Luis
America/Argentina/Tucuman
America/Argentina/Ushuaia
America/Aruba
America/Asuncion
America/Atikokan
America/Bahia
America/Bahia_Banderas
America/Barbados
America/Belem
America/Belize
America/Blanc-Sablon
America/Boa_Vista
America/Bogota
America/Boise
America/Cambridge_Bay
America/Campo_Grande
America/Cancun
America/Caracas
America/Cayenne
America/Cayman
America/Chicago
America/Chihuahua
America/Costa_Rica
America/Creston
America/Cuiaba
America/Curacao
America/Danmarkshavn
America/Dawson
America/Dawson_Creek
America/Denver
America/Detroit
America/Dominica
America/Edmonton
America/Eirunepe
America/El_Salvador
America/Fort_Nelson
America/Fortaleza
America/Glace_Bay
America/Goose_Bay
America/Grand_Turk
America/Grenada
America/Guadeloupe
America/Guatemala
America/Guayaquil
America/Guyana
America/Halifax
America/Havana
America/Hermosillo
America/Indiana/Indianapolis
America/Indiana/Knox
America/Indiana/Marengo
America/Indiana/Petersburg
America/Indiana/Tell_City
America/Indiana/Vevay
America/Indiana/Vincennes
America/Indiana/Winamac
America/Inuvik
America/Iqaluit
America/Jamaica
America/Juneau
America/Kentucky/Louisville
America/Kentucky/Monticello
America/Kralendijk
America/La_Paz
America/Lima
America/Los_Angeles
America/Lower_Princes
America/Maceio
America/Managua
America/Manaus
America/Marigot
America/Martinique
America/Matamoros
America/Mazatlan
America/Menominee
America/Merida
America/Metlakatla
America/Mexico_City
America/Miquelon
America/Moncton
America/Monterrey
America/Montevideo
America/Montserrat
America/Nassau
America/New_York
America/Nome
America/Noronha
America/North_Dakota/Beulah
America/North_Dakota/Center
America/North_Dakota/New_Salem
America/Nuuk
America/Ojinaga
America/Panama
America/Pangnirtung
America/Paramaribo
America/Phoenix
America/Port-au-Prince
America/Port_of_Spain
America/Porto_Velho
America/Puerto_Rico
America/Punta_Arenas
America/Rankin_Inlet
America/Recife
America/Regina
America/Resolute
America/Rio_Branco
America/Santarem
America/Santiago
America/Santo_Domingo
America/Sao_Paulo
America/Scoresbysund
America/Sitka
America/St_Barthelemy
America/St_Johns
America/St_Kitts
America/St_Lucia
America/St_Thomas
America/St_Vincent
America/Swift_Current
America/Tegucigalpa
America/Thule
America/Tijuana
America/Toronto
America/Tortola
America/Vancouver
America/Whitehorse
America/Winnipeg
America/Yakutat
America/Yellowknife
Antarctica/Casey
Antarctica/Davis
Antarctica/DumontDUrville
Antarctica/Macquarie
Antarctica/Mawson
Antarctica/McMurdo
Antarctica/Palmer
Antarctica/Rothera
Antarctica/Syowa
Antarctica/Troll
Antarctica/Vostok
Arctic/Longyearbyen
Asia/Aden
Asia/Almaty
Asia/Amman
Asia/Anadyr
Asia/Aqtau
Asia/Aqtobe
Asia/Ashgabat
Asia/Atyrau
Asia/Baghdad
Asia/Bahrain
Asia/Baku
Asia/Bangkok
Asia/Barnaul
Asia/Beirut
Asia/Bishkek
Asia/Brunei
Asia/Chita
Asia/Choibalsan
Asia/Colombo
Asia/Damascus
Asia/Dhaka
Asia/Dili
Asia/Dubai
Asia/Dushanbe
Asia/Famagusta
Asia/Gaza
Asia/Hebron
Asia/Ho_Chi_Minh
Asia/Hong_Kong
Asia/Hovd
Asia/Irkutsk
Asia/Jakarta
Asia/Jayapura
Asia/Jerusalem
Asia/Kabul
Asia/Kamchatka
Asia/Karachi
Asia/Kathmandu
Asia/Khandyga
Asia/Kolkata
Asia/Krasnoyarsk
Asia/Kuala_Lumpur
Asia/Kuching
Asia/Kuwait
Asia/Macau
Asia/Magadan
Asia/Makassar
Asia/Manila
Asia/Muscat
Asia/Nicosia
Asia/Novokuznetsk
Asia/Novosibirsk
Asia/Omsk
Asia/Oral
Asia/Phnom_Penh
Asia/Pontianak
Asia/Pyongyang
Asia/Qatar
Asia/Qostanay
Asia/Qyzylorda
Asia/Riyadh
Asia/Sakhalin
Asia/Samarkand
Asia/Seoul
Asia/Shanghai
Asia/Singapore
Asia/Srednekolymsk
Asia/Taipei
Asia/Tashkent
Asia/Tbilisi
Asia/Tehran
Asia/Thimphu
Asia/Tokyo
Asia/Tomsk
Asia/Ulaanbaatar
Asia/Urumqi
Asia/Ust-Nera
Asia/Vientiane
Asia/Vladivostok
Asia/Yakutsk
Asia/Yangon
Asia/Yekaterinburg
Asia/Yerevan
Atlantic/Azores
Atlantic/Bermuda
Atlantic/Canary
Atlantic/Cape_Verde
Atlantic/Faroe
Atlantic/Madeira
Atlantic/Reykjavik
Atlantic/South_Georgia
Atlantic/St_Helena
Atlantic/Stanley
Australia/Adelaide
Australia/Brisbane
Australia/Broken_Hill
Australia/Darwin
Australia/Eucla
Australia/Hobart
Australia/Lindeman
Australia/Lord_Howe
Australia/Melbourne
Australia/Perth
Australia/Sydney
Canada/Atlantic
Canada/Central
Canada/Eastern
Canada/Mountain
Canada/Newfoundland
Canada/Pacific
Europe/Amsterdam
Europe/Andorra
Europe/Astrakhan
Europe/Athens
Europe/Belgrade
Europe/Berlin
Europe/Bratislava
Europe/Brussels
Europe/Bucharest
Europe/Budapest
Europe/Busingen
Europe/Chisinau
Europe/Copenhagen
Europe/Dublin
Europe/Gibraltar
Europe/Guernsey
Europe/Helsinki
Europe/Isle_of_Man
Europe/Istanbul
Europe/Jersey
Europe/Kaliningrad
Europe/Kirov
Europe/Kyiv
Europe/Lisbon
Europe/Ljubljana
Europe/London
Europe/Luxembourg
Europe/Madrid
Europe/Malta
Europe/Mariehamn
Europe/Minsk
Europe/Monaco
Europe/Moscow
Europe/Oslo
Europe/Paris
Europe/Podgorica
Europe/Prague
Europe/Riga
Europe/Rome
Europe/Samara
Europe/San_Marino
Europe/Sarajevo
Europe/Saratov
Europe/Simferopol
Europe/Skopje
Europe/Sofia
Europe/Stockholm
Europe/Tallinn
Europe/Tirane
Europe/Ulyanovsk
Europe/Vaduz
Europe/Vatican
Europe/Vienna
Europe/Vilnius
Europe/Volgograd
Europe/Warsaw
Europe/Zagreb
Europe/Zurich
GMT
Indian/Antananarivo
Indian/Chagos
Indian/Christmas
Indian/Cocos
Indian/Comoro
Indian/Kerguelen
Indian/Mahe
Indian/Maldives
Indian/Mauritius
Indian/Mayotte
Indian/Reunion
Pacific/Apia
Pacific/Auckland
Pacific/Bougainville
Pacific/Chatham
Pacific/Chuuk
Pacific/Easter
Pacific/Efate
Pacific/Fakaofo
Pacific/Fiji
Pacific/Funafuti
Pacific/Galapagos
Pacific/Gambier
Pacific/Guadalcanal
Pacific/Guam
Pacific/Honolulu
Pacific/Kanton
Pacific/Kiritimati
Pacific/Kosrae
Pacific/Kwajalein
Pacific/Majuro
Pacific/Marquesas
Pacific/Midway
Pacific/Nauru
Pacific/Niue
Pacific/Norfolk
Pacific/Noumea
Pacific/Pago_Pago
Pacific/Palau
Pacific/Pitcairn
Pacific/Pohnpei
Pacific/Port_Moresby
Pacific/Rarotonga
Pacific/Saipan
Pacific/Tahiti
Pacific/Tarawa
Pacific/Tongatapu
Pacific/Wake
Pacific/Wallis
US/Alaska
US/Arizona
US/Central
US/Eastern
US/Hawaii
US/Mountain
US/Pacific
UTC
Save
America/New_York
English (United States)
Deutsch (Deutschland)
English (United Kingdom)
English (United States)
Español (España)
Français (France)
Polski (Polska)
Português (Brasil)
Türkçe (Türkiye)
Монгол (Монгол)
Українська (Україна)
中文 (中国)
Login
CCB Virtual Retreat 2021
from
Tuesday, January 19, 2021 (5:00 PM)
to
Friday, January 22, 2021 (5:00 PM)
Monday, January 18, 2021
Tuesday, January 19, 2021
5:00 PM
Happy Hour/Wine Tasting
Happy Hour/Wine Tasting
5:00 PM - 7:00 PM
Wednesday, January 20, 2021
10:00 AM
Welcome & Opening
-
Michael J. Shelley
Welcome & Opening
Michael J. Shelley
10:00 AM - 10:10 AM
10:10 AM
Systems Biology in 2021
-
Rich Bonneau
Systems Biology in 2021
Rich Bonneau
10:10 AM - 10:30 AM
10:30 AM
Genomics in 2021
-
Olga Troyanskaya
Genomics in 2021
Olga Troyanskaya
10:30 AM - 10:50 AM
10:50 AM
Biophysical Modeling in 2021
-
Michael Shelley
Biophysical Modeling in 2021
Michael Shelley
10:50 AM - 11:10 AM
11:10 AM
Developmental Dynamics in 2021
-
Stas Shvartsman
Developmental Dynamics in 2021
Stas Shvartsman
11:10 AM - 11:30 AM
11:30 AM
Break/Overflow Time
Break/Overflow Time
11:30 AM - 11:40 AM
11:40 AM
Excited about Structural and Molecular Biophysics (Sonya Hanson, Structural and Molecular Biophysics)
-
Sonya Hanson
Excited about Structural and Molecular Biophysics (Sonya Hanson, Structural and Molecular Biophysics)
Sonya Hanson
11:40 AM - 11:50 AM
As Richard Feynman said in The Feynman Lectures on Physics “if we were to name the most powerful assumption of all, which leads one on and on in an attempt to understand life, it is that all things are made of atoms, and that everything that living things do can be understood in terms of the jigglings and wigglings of atoms.” Understanding how these 'jigglings and wigglings of atoms' translate into the mechanisms of key biological processes is an exciting topic of modern science. I will be talking about upcoming projects in our new little team, most but not all of which relate to elucidating mechanisms of biological temperature sensing.
11:50 AM
A Bayesian Approach for Extracting Free Energy Profiles from Cryo-electron Microscopy Experiments Using a Path Collective Variable (Pilar Cossio, Structural and Molecular Biophysics)
-
Pilar Cossio
A Bayesian Approach for Extracting Free Energy Profiles from Cryo-electron Microscopy Experiments Using a Path Collective Variable (Pilar Cossio, Structural and Molecular Biophysics)
Pilar Cossio
11:50 AM - 12:00 PM
Cryo-electron microscopy (cryo-EM) extracts single-particle density projections of individual biolmolecules. Although cryo-EM is widely used for 3D reconstruction, due to its single-particle nature, it has the potential to provide information about a biomolecule's conformational variability and underlying free energy landscape. However, treating cryo-EM as a single-molecule technique is challenging because of the low signal-to-noise ratio in the individual particles. In this work, we developed a Bayesian framework that uses a path collective variable to extract free energy profiles and their uncertainties from cryo-EM images. We tested the framework over several systems, finding that for realistic cryo-EM environments, and relevant biomolecular systems, it is possible to recover the underlying free energy.
12:00 PM
Cell Division, Energy and Embryos (Daniel Needleman, Biophysical Modeling)
-
Daniel Needleman
Cell Division, Energy and Embryos (Daniel Needleman, Biophysical Modeling)
Daniel Needleman
12:00 PM - 12:10 PM
12:10 PM
3D Instance Segmentation of Nuclei in Mouse Embryogenesis (Lisa Brown, Developmental Dynamics)
-
Lisa Brown
3D Instance Segmentation of Nuclei in Mouse Embryogenesis (Lisa Brown, Developmental Dynamics)
Lisa Brown
12:10 PM - 12:20 PM
We are developing 3D models for instance segmentation of nuclei during mouse embryogenesis. To that end, we are creating the first 3D dataset of nuclei acquired with light-sheet microscopy with 3D instances fully annotated. We are designing an end-to-end 3D instance segmentation model, using extensive data augmentation based on the noise properties of our light-sheet microscope and a statistical model of nuclei shape properties.
12:20 PM
Further Applications of Quantum Computing for Biology and Biochemistry (Vikram Mulligan, Systems Biology)
-
Vikram Mulligan
Further Applications of Quantum Computing for Biology and Biochemistry (Vikram Mulligan, Systems Biology)
Vikram Mulligan
12:20 PM - 12:30 PM
Protein design involves hard combinatorial problems, and we have shown that these can be mapped to current-generation quantum computers. This talk will briefly summarize our past work in applying quantum computing to design molecules (including candidate COVID-19 therapeutics), and will introduce new directions in which we hope to expand this nascent field in the coming year.
12:30 PM
Lunch/Break
Lunch/Break
12:30 PM - 2:00 PM
1:00 PM
Yoga (Lucianna Silvestri)
Yoga (Lucianna Silvestri)
1:00 PM - 2:00 PM
2:00 PM
Building a Three-Dimensional Model of Human Nephrogenesis (Rachel Sealfon, Genomics)
-
Rachel Sealfon
Building a Three-Dimensional Model of Human Nephrogenesis (Rachel Sealfon, Genomics)
Rachel Sealfon
2:00 PM - 2:10 PM
The function of organs is underpinned by their three-dimensional structures, but it is challenging to precisely characterize the molecular features of these structures. Here we address this challenge specifically as it relates to the complex process of nephrogenesis, which is critical to understand for improving treatment for congenital abnormalities of the kidney and building kidney organoids. We develop a three-dimensional model of the developing human kidney by integrating single-cell expression data with three-dimensional protein confocal microscopy images using a data-driven framework.
2:10 PM
Simulating Active Fluids (David Stein, Biophysical Modeling)
-
David Stein
Simulating Active Fluids (David Stein, Biophysical Modeling)
David Stein
2:10 PM - 2:20 PM
Complex and active fluids can serve as simplified models for many biophysical systems. I'll discuss some methods we've developed to enable fast, scalable simulations of these fluids confined within evolving geometries, such as deforming droplets or vesicles.
2:20 PM
AMSOS: Biology, Optimization, and HPC (Wen Yan, Biophysical Modeling)
-
Wen Yan
AMSOS: Biology, Optimization, and HPC (Wen Yan, Biophysical Modeling)
Wen Yan
2:20 PM - 2:30 PM
Some large scale bio-assembly simulations and how we implemented them.
2:30 PM
The Impact of RNA-Binding Protein Dysregulation on Disease Risk (Christopher Park, Genomics)
-
Christopher Park
The Impact of RNA-Binding Protein Dysregulation on Disease Risk (Christopher Park, Genomics)
Christopher Park
2:30 PM - 2:40 PM
Despite the strong genetic basis of developmental disorders, the underlying molecular mechanisms are largely unmapped. RNA-binding proteins (RBPs) are responsible for most posttranscriptional regulation, thus act as key gatekeepers of cellular homeostasis. Here, we quantify the RBP target site dysregulation effects of inherited and de novo mutations and investigate its contribution to disease risk.
2:40 PM
Break/Overflow Time
Break/Overflow Time
2:40 PM - 2:50 PM
2:50 PM
Mapping the Microbiome by Large-Scale Structure and Function prediction (Julia Koehler, Doug Renfrew, and Vladimir Gligorijevic, Systems Biology)
-
Julia Koehler
Vladimir Gligorijevich
Doug Renfrew
Mapping the Microbiome by Large-Scale Structure and Function prediction (Julia Koehler, Doug Renfrew, and Vladimir Gligorijevic, Systems Biology)
Julia Koehler
Vladimir Gligorijevich
Doug Renfrew
2:50 PM - 3:20 PM
The microbiome consists of the about 60% microbial cells in and around our body that give rise to 99% of the genes in our body. We are just beginning to understand the role of the human gut microbiome in numerous diseases such as type 1 diabetes, immune system disorders and digestive disorders such as ulcerative colitis and Crohn’s disease. Here we take a structure-function perspective by running large-scale computational prediction of structures, functions and interactions of the proteins in these microbes to gain insights into disease mechanisms.
3:20 PM
SARS-CoV-2 receptor networks in diabetic and COVID-19–associated kidney disease (Aaron Wong, Genomics)
-
Aaron Wong
SARS-CoV-2 receptor networks in diabetic and COVID-19–associated kidney disease (Aaron Wong, Genomics)
Aaron Wong
3:20 PM - 3:30 PM
COVID-19 morbidity and mortality are increased via unknown mechanisms in patients with diabetes and kidney disease. I will discuss our work developing HumanBase and how the system was used to find molecular network modules induced in kidney cells susceptible to SARS-CoV-2 infection in diabetic kidney disease and linked to viral processes, such as viral entry, immune activation, endomembrane reorganization, and RNA processing.
3:30 PM
Biophysical modeling of early embryogenesis in nematodes (Reza Farhadifar, Biophysical Modeling)
-
Reza Farhadifar
Biophysical modeling of early embryogenesis in nematodes (Reza Farhadifar, Biophysical Modeling)
Reza Farhadifar
3:30 PM - 3:40 PM
Mitotic spindle is the central apparatus driving cell division in all Eukaryotic cells. I will present a simple mathematical model of spindle dynamics and positioning, which quantitatively explains the spindle's universal behavior across nematode species.
3:40 PM
Single Cell Epigenetics and Transcriptomics Data Analysis for Viral and Bacterial Infection (Xi Chen, Genomics)
-
Xi Chen
Single Cell Epigenetics and Transcriptomics Data Analysis for Viral and Bacterial Infection (Xi Chen, Genomics)
Xi Chen
3:40 PM - 3:50 PM
COVID-19 pandemic has already caused over 2 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome. To better interpret immune and cellular responses associated with viral/bacterial infection, we collaborate with Mount Sinai and generate comprehensive cellular maps capturing more than ten different types of infections including SARS-CoV-2 through single-cell sequencing of human blood samples.
4:00 PM
From Molecular Scale Interactions to Phenotypes: Design Principles for Living Materials (Sebastian Fürthauer, Biophysical Modeling)
-
Sebastian Fürthauer
From Molecular Scale Interactions to Phenotypes: Design Principles for Living Materials (Sebastian Fürthauer, Biophysical Modeling)
Sebastian Fürthauer
4:00 PM - 4:10 PM
Our main concern is this: How can large functional structures emerge from smaller scale agents and how are these processes of self-organization controlled? I will give a brief overview of the current challenges and our recent progress in attacking these questions, focussing on the physics of the cytoskeleton.
4:20 PM
BREAKOUT SESSION PLANNING
BREAKOUT SESSION PLANNING
4:20 PM - 4:35 PM
Thursday, January 21, 2021
10:00 AM
Algorithms for Describing and Predicting Chromatin Remodeling during Cortical Interneuron Development (Mariano Gabitto, Systems Biology)
-
Mariano Gabitto
Algorithms for Describing and Predicting Chromatin Remodeling during Cortical Interneuron Development (Mariano Gabitto, Systems Biology)
Mariano Gabitto
10:00 AM - 10:10 AM
Interneurons within the mature cortex are remarkably diverse in their morphology, connectivity, and transcriptional signatures. How developmental changes in chromatin structure contribute to the emergence of distinct interneuron subtypes is unknown. In recent years, single-cell ATAC-seq has become the leading assay for probing the chromatin regulatory landscape. How do we discover structure in this high-dimensional data and use it to understand interneuron development? During this talk, I will describe Bayesian state-space models to characterize chromatin information. I will use this model to describe the chromatin developmental landscape of cortical Interneurons. By focusing on two of the largest cardinal classes of interneurons, I identify three epochs during which chromatin is refined. After identifying enriched transcriptional regulators at different epochs, I harness transcriptional and chromatin information to calculate cell type-specific gene regulatory networks. I will show that remodeling of gene regulatory networks echoes chromatin reshaping during different epochs. Finally, I will briefly demonstrate that gene regulatory networks provide a framework to predict
10:10 AM
HumanBase and Sleipnir: Architectures for Large Scale Genomics (Jerry Vinokurov, Genomics)
-
Jerry Vinokurov
HumanBase and Sleipnir: Architectures for Large Scale Genomics (Jerry Vinokurov, Genomics)
Jerry Vinokurov
10:10 AM - 10:20 AM
I will be talking about the work I have done in the last year of modernizing both the HumanBase pipeline and the associated Sleipnir library. I will cover the transition to a more principled architecture for both projects and future work.
10:20 AM
Protein Structural Alignments From Sequence (Jamie Morton, Systems Biology)
-
Jamie Morton
Protein Structural Alignments From Sequence (Jamie Morton, Systems Biology)
Jamie Morton
10:20 AM - 10:30 AM
Computing sequence similarity is a fundamental task in biology, with alignment forming the basis for the annotation of genes and genomes and providing the core data structures for evolutionary analysis. Standard approaches are a mainstay of modern molecular biology and rely on variations of edit distance to obtain explicit alignments between pairs of biological sequences. However, sequence alignment algorithms struggle with remote homology tasks and cannot identify similarities between many pairs of proteins with similar structures and likely homology. Recent work suggests that using machine learning language models can improve remote homology detection. To this end, we introduce DeepBLAST, that obtains explicit alignments from residue embeddings learned from a protein language model integrated into an end-to-end differentiable alignment framework. This approach can be accelerated on the GPU architectures and outperforms conventional sequence alignment techniques in terms of both speed and accuracy when identifying structurally similar proteins.
10:30 AM
Integrated view of Posterior Patterning in Drosophila Embryo (Maria Avdeeva, Developmental Dynamics)
-
Maria Avdeeva
Integrated view of Posterior Patterning in Drosophila Embryo (Maria Avdeeva, Developmental Dynamics)
Maria Avdeeva
10:30 AM - 10:40 AM
During early Drosophila embryogenesis, a network of gene regulatory interactions orchestrates terminal patterning responsible for the subsequent formation of the gut. We have used MS2/MCP mRNA labeling system to obtain live imaging of gene expression at the posterior end of the fly embryo. We use this data to demonstrate our ability to construct an integrated view of multivariable gene expression dynamics in the embryo, with our analysis revealing low intrinsic dimensionality of posterior patterning.
10:40 AM
Mechanics of Planar Tissues with Active Surfaces (XinXin Du, Biophysical Modeling)
-
XinXin Du
Mechanics of Planar Tissues with Active Surfaces (XinXin Du, Biophysical Modeling)
XinXin Du
10:40 AM - 10:50 AM
Many biological developmental systems feature tissues that mold their own structure using active forces that live on their surfaces in the form of populations of force-producing molecules. I am presenting a 3D model of these tissues in a rectangular geometry that emphasizes tracking the internal 3D structure of how the material moves, deep into the plane of the tissue. This model benefits studying cell deformations that are non-uniform in the perpendicular direction of cells in a planar tissue.
10:50 AM
AutoML for Genomics (Frank [Zijun] Zhang, Genomics)
-
Frank (Zijung) Zhang
AutoML for Genomics (Frank [Zijun] Zhang, Genomics)
Frank (Zijung) Zhang
10:50 AM - 11:00 AM
AMBER is a fully automated framework to efficiently design and apply CNNs for genomic sequences. Interpretation of AMBER architecture search revealed its design principles of utilizing the full space of computational operations for accurately modelling genomic sequences. We illustrated the use of AMBER to accurately discover functional genomic variants in allele-specific binding and disease heritability enrichment.
11:00 AM
What is hiding in chromosome conformation capture data? Searching for overlooked mechanisms that organize DNA
-
Adam Lamson
What is hiding in chromosome conformation capture data? Searching for overlooked mechanisms that organize DNA
Adam Lamson
11:00 AM - 11:10 AM
Chromosome conformation capture technologies(3C, Hi-C, Micro-C, etc.), assays that map nucleotide separation of genomic regions to their average proximity in space, have greatly increased our understanding of how DNA is organized. However, a full picture of the physical mechanisms behind the hierarchical and dynamic structures of chromosomes remains elusive. I am developing methods from Multi-View Convolutional Neural Networks (MVCNN) to more efficiently search high-resolution 3C data for overlooked topological features. These features then inform physical theories on how chromosomes organize, why they follow certain principles, and what may drive organization in the first place.
11:10 AM
Axisymmetric Membranes with Edges under External Force (Leroy Jia, Biophysical Modeling)
-
Leroy Jia
Axisymmetric Membranes with Edges under External Force (Leroy Jia, Biophysical Modeling)
Leroy Jia
11:10 AM - 11:20 AM
A time-honored problem in the calculus of variations is to show that a soap film suspended between two symmetric rings forms a catenoid. Inspired by experiments from the Dogic (UCSB) and Sharma (IIS) Labs, we will explore the shapes of a membrane with a resistance to bending and a fixed area in this geometry. In so doing, we unify various classic shapes such as catenoids, thin tethers, and elastica as different limits of a single system.
11:20 AM
Common Coordinate Registration of High-Resolution Histology Images (Aidan Daly, Systems Biology)
-
Aidan Daly
Common Coordinate Registration of High-Resolution Histology Images (Aidan Daly, Systems Biology)
Aidan Daly
11:20 AM - 11:30 AM
Registration of histology images from multiple sources is a pressing problem in large-scale studies of spatial -omics data. Researchers often perform ``common coordinate registration,'' akin to segmentation, in which samples are partitioned based on tissue type to allow for quantitative comparison of similar regions across samples. I will present on a novel CNN architecture designed to address this problem and motivated in particular by the data acquired from spatial transcriptomics experiments.
11:30 AM
A Theoretical Framework for Active Chiral Filaments (Aleks Plochocka, Biophysical Modeling)
-
Aleks Plochocka
A Theoretical Framework for Active Chiral Filaments (Aleks Plochocka, Biophysical Modeling)
Aleks Plochocka
11:30 AM - 11:40 AM
The cell cytoskeleton - the active structure that drives cellular motion - is an active chiral fluid. Chirality refers to the breaking of left-right symmetry and can be observed experimentally. We develop a framework for coarse graining chiral filament-filament interactions to obtain an active gel theory for living chiral materials.
11:40 AM
Longitudinal Data Analysis of COVID-19 (Natalie Sauerwald, Genomics)
-
Natalie Sauerwald
Longitudinal Data Analysis of COVID-19 (Natalie Sauerwald, Genomics)
Natalie Sauerwald
11:40 AM - 11:50 AM
I will share some preliminary results from data analysis work searching for patterns in gene expression data from a longitudinal COVID-19 study. Time permitting, I will also discuss other avenues for my future work here.
11:50 AM
Learning to Count: The Problem of Transit Amplification (Hayden Nunley, Developmental Dynamics)
-
Hayden Nunley
Learning to Count: The Problem of Transit Amplification (Hayden Nunley, Developmental Dynamics)
Hayden Nunley
11:50 AM - 12:00 PM
Both in the germline and in embryos, proper development depends on the control of when cells start dividing, which cells divide in synchrony, and when divisions halt. The genesis of germline cysts via rounds of incomplete cytokinesis inspires a minimal model of cells that divide only a finite number of times and that remain coupled to their progeny.
12:00 PM
Active Nuclear Transport in Living Cells (Alex Rautu, Biophysical Modeling)
-
Alex Rautu
Active Nuclear Transport in Living Cells (Alex Rautu, Biophysical Modeling)
Alex Rautu
12:00 PM - 12:10 PM
The transport of cargo into and out of the nucleus is crucial for the functioning of all eukaryotes cells. Although the migration of ions and small molecules can occur diffusively, the nuclear transport of larger macromolecules generally require an active process. Here, a physical model of this mechanism is discussed that allows us to describe the temporal and spatial distribution of cargo within the nucleus, and its role in the regulation of other cellular processes such as chromatin remodeling and transcription.
12:10 PM
Building Tools For Biologists on the Web (Julien Funk, Genomics)
-
Julien Funk
Building Tools For Biologists on the Web (Julien Funk, Genomics)
Julien Funk
12:10 PM - 12:20 PM
I will share my work and process of designing, deploying and maintaining the tools of HumanBase.
12:20 PM
A Minimal Model for Ciliary Coordination (Brato Chakrabarti, Biophysical Modeling)
-
Brato Chakrabarti
A Minimal Model for Ciliary Coordination (Brato Chakrabarti, Biophysical Modeling)
Brato Chakrabarti
12:20 PM - 12:30 PM
I will talk about a one dimensional reduced model for ciliary beating. This model captures some salient features of hydrodynamic synchronization in ciliary arrays and also highlights the role of heterogeneity in metachronal coordination.
12:30 PM
Sticky, Stretchy, Sliding Cells: A Minimal Model for Cell Intercalation (Tatyana Gavrilchenko, Developmental Dynamics)
-
Tatyana Gavrilchenko
Sticky, Stretchy, Sliding Cells: A Minimal Model for Cell Intercalation (Tatyana Gavrilchenko, Developmental Dynamics)
Tatyana Gavrilchenko
12:30 PM - 12:40 PM
Tissue morphogenesis is driven by cell rearrangements, which stem from mechanical forces generated at membrane interfaces and stabilized by tricellular junctions. Existing vertex models are successful in describing bulk tissue flow, but do not resolve cellular interfaces consisting of two separate membranes. We present our progress on a model that captures single-cell-level dynamics during rearrangements in small clusters of cells, driven by adhesions between neighboring cell membranes.
12:40 PM
Lunch/Break
Lunch/Break
12:40 PM - 2:00 PM
1:00 PM
Trivia Challenge
Trivia Challenge
1:00 PM - 2:00 PM
2:00 PM
Keynote Speaker: Katie Pollard, PhD
-
Katie Pollard
Keynote Speaker: Katie Pollard, PhD
Katie Pollard
2:00 PM - 3:30 PM
Katie Pollard, PhD is the Director of the Gladstone Institute of Data Science and Biotechnology, Professor of Epidemiology and Biostatistics at UC San Francisco, Director of the Biomedical Informatics Graduate Program at UC San Francisco, and an Investigator, Chan Zuckerberg Biohub. Katie Pollard earned her BA at Pomona College and her master’s degree and PhD in biostatistics from UC Berkeley. At Berkeley, she developed computationally intensive statistical methods for the analysis of microarray data with applications in cancer biology. She implemented these approaches in Bioconductor, an open-source software program used with high-throughput genomic data. As a comparative genomics postdoctoral fellow at UC Santa Cruz, Pollard participated in the Chimpanzee Genome Project and used this sequence to identify the fastest-evolving regions in the human genome, known as Human Accelerated Regions. Before joining Gladstone, Pollard was an assistant professor in the Genome Center and Department of Statistics at UC Davis. She was awarded the Thomas J. Watson Fellowship in 1995 and the Sloan Research Fellowship in 2008. Pollard is a fellow of the California Academy of Sciences and a Chan Zuckerberg Biohub Investigator. In 2018, she became the founding director of the Gladstone Institute of Biotechnology and Data Science. Pollard is a member of the American Society of Human Genetics, the American Statistical Association, and the International Society for Computational Biology.
3:30 PM
BREAKOUT SESSIONS
BREAKOUT SESSIONS
3:30 PM - 5:00 PM
(1) Interpretability of Machine Learning (2) Cells and Tissues (3) Molecular Dynamics
Friday, January 22, 2021
9:30 AM
Computational Platform for Simulation of Cellular Mechanics (Gokberk Kabacaoglu, Biophysical Modeling)
-
Gokberk Kabacaoglu
Computational Platform for Simulation of Cellular Mechanics (Gokberk Kabacaoglu, Biophysical Modeling)
Gokberk Kabacaoglu
9:30 AM - 9:40 AM
I will review our computational platform for the large-scale three-dimensional simulations of flexible filaments, motor proteins and rigid bodies in a Stokesian fluid.
9:40 AM
Biophysics of Arrested Cytokinesis (Jaspreet Singh, Developmental Dynamics)
-
Jaspreet Singh
Biophysics of Arrested Cytokinesis (Jaspreet Singh, Developmental Dynamics)
Jaspreet Singh
9:40 AM - 9:50 AM
Incomplete cytokinesis leads to the formation of daughter cells that are connected through arrested cleavage furrows. These develop into stable intercellular bridges that are critical for processes such as cell differentiation and cell cycle synchronization. We show that precise control of the magnitude and duration of contractility, together with the evolving stiffness of the F-actin ring is essential for assembling intercellular bridges with experimentally observed aspect ratios.
9:50 AM
Pseudotemporal Ordering and Network Inference from Single Cell Technologies (Anders Rasmussen, Systems Biology)
-
Anders Rasmussen
Pseudotemporal Ordering and Network Inference from Single Cell Technologies (Anders Rasmussen, Systems Biology)
Anders Rasmussen
9:50 AM - 10:00 AM
Single cell RNA-seq and ATAC-seq provide a means to capture transcriptomic and epigenomic information from individual cells. In cell populations undergoing dynamic processes, pseudotemporal ordering aims to arrange cells by their progression through this process. Many algorithms have been developed for this task, employing techniques in dimensionality reduction and graph construction, however, approaches to infer gene regulatory networks (GRNs) across cellular trajectories remain limited. In this brief talk, I will discuss prospects of learning GRNs in low-dimensional representations of pseudotemporally ordered transcriptomic and epigenomic data.
10:00 AM
Symmetry Breaking Mechanisms in Cell Polarization (Pearson Miller, Developmental Dynamics)
-
Pearson Miller
Symmetry Breaking Mechanisms in Cell Polarization (Pearson Miller, Developmental Dynamics)
Pearson Miller
10:00 AM - 10:10 AM
Using numerical methods, we explore spatial-symmetry breaking in reaction diffusion processes in a model cell, with an emphasis on the role cell geometry plays in localizing steady state patterns. These results provide greater insight into mechanisms of cell polarization during development.
10:10 AM
Break/Overflow Time
Break/Overflow Time
10:10 AM - 10:20 AM
10:20 AM
Inferring Single-Cell Gene Regulatory Networks in the Developing Drosophila Optic Lobe (Claudia Skok Gibbs, Systems Biology)
-
Claudia Skok Gibbs
Inferring Single-Cell Gene Regulatory Networks in the Developing Drosophila Optic Lobe (Claudia Skok Gibbs, Systems Biology)
Claudia Skok Gibbs
10:20 AM - 10:30 AM
Methods to elucidate single-cell gene regulatory networks must incorporate several orthogonal genomic datatypes. In my talk I will present gene regulatory networks inferred within the developing Drosophila Optic Lobe using the network inference method, the Inferelator.
10:30 AM
Networks in Inflammation (Danxun Li, Systems Biology)
-
Danxun Li
Networks in Inflammation (Danxun Li, Systems Biology)
Danxun Li
10:30 AM - 10:40 AM
Infiltration of CD4+ T cells into the inflamed intestines of inflammatory bowel disease (IBD) patients is important for disease pathogenesis. Despite many efforts to understand priming and differentiation of CD4+ T cells in IBD, epigenetic characterization of primary CD4+ T cells isolated from intestinal tissues in IBD patient samples is lacking. We integrated ATAC-seq and RNA-seq profiles from primary CD4+ T cells isolated from intestinal pinch biopsies of IBD patients to characterize regulatory networks in inflammation.
10:40 AM
Identifying Turbunance Driving Scales using the Bicoherence (Michael O'Brien, Biophysical Modeling)
-
Michael O'Brien
Identifying Turbunance Driving Scales using the Bicoherence (Michael O'Brien, Biophysical Modeling)
Michael O'Brien
10:40 AM - 10:50 AM
Higher-order spectral statistics like the bispectrum have proven to be a natural tools for analysing magnetohydrodynamic turbulence by identifying non-linear scaling correlations and breaking degeneracy in lower order statistics like the power spectrum. We have found that the bicoherence, a related statistic, is able to pick out driving scales in supersonic turbulence with the potential to be used on galaxy observational data. These statistics can shed light on the parallels between classical turbulence and turbulence in living fluids such as active nematics.
11:00 AM
Keynote Speaker: Apoorva Mandavilli
-
Apoorva Mandavilli
Keynote Speaker: Apoorva Mandavilli
Apoorva Mandavilli
11:00 AM - 12:30 PM
Apoorva Mandavilli is a health and science reporter at The New York Times, where she write mostly about infectious diseases. She has also written for The Atlantic, The New Yorker online, Slate, Nature, Scientific American and others. Apoorva is the 2019 winner of the Victor Cohn Prize for Excellence in Medical Reporting. She likes to tell stories about complex science through the lives of people directly affected by it — whether that’s the second person ever to be cured of H.I.V., women with autism, the people who live near the abandoned Bhopal factory or a man recovering from a traumatic brain injury. Apoorva was the founding editor and editor-in-chief of the autism news site Spectrum from its launch in 2008 through May 2020. With her colleague Nidhi Subbaraman, she launched Culture Dish, a nonprofit dedicated to enhancing diversity in science journalism. For four years, she also served as an adjunct professor at New York University’s Science Health and Environmental Reporting Program.
12:30 PM
Lunch/Break
Lunch/Break
12:30 PM - 2:00 PM
1:00 PM
Meditation
Meditation
1:00 PM - 1:30 PM
2:00 PM
BREAKOUT SESSIONS
BREAKOUT SESSIONS
2:00 PM - 3:30 PM
(1) Combining Machine Learning and Dynamical Biophysical Models (2) Reproducibility, Software Development, and Benchmarking (3) CCB Group Activities
3:30 PM
Closing Remarks
-
Michael J. Shelley
Closing Remarks
Michael J. Shelley
3:30 PM - 3:40 PM