Background (mostly optional) readings

Date / Topic                            



Session 1


for an overview read: On teaching developmental biology in the 21st centrury
Gerhart & Kirscher, Cells, Embryos & Evolution-Chapter 1

videos: Richard Feynmann "Understanding magnetic attraction"
Sabine Hossenfelder's "Heisenberg's microscope

a useful reference: Milestones in developmental biology (Nature)


Session 2


The evolving definition of the term “gene” - Portin & Wilkins 2017
Your Cancer Targets may not be real - Lowe. 2019
Biological plasticity rescues target activity in CRISPR knock outs - Smits et al 2019
Genetic paradox explained by nonsense - Wilkinson, 2019


WEEK 2 Session 3


background reading: Aggregative and clonal metazoans
bacground video: The social life of bacteria: collapse of a culture
reading: Biologists rethink the logic behind cells’ molecular signals

Stochastic gene expression in a single cell - Elowitz et al 2002 
Stochastic Pulse Regulation in Bacterial Stress Response: Locke et al 2011
Programmed cell death in bacteria - Allocati et al 2015
Modeling network dynamics: the lac operon, a case study - Vilar et al 2003
Global quantification – mammalian gene expression control  - Schwanhäusser et al 2011Communication codes in developmental signaling pathways - Li & Elowitz 2019.
Saka & Smith


Session 4


Aggregative & clonal metazoans
(and review: On teaching developmental biology in the 21st centrury)
Aggregative multicellular & cell-cell communication in Dictyostelia - Du et al 2015
Cell competition and its role in the regulation - Di Gregorio et al 2016
Collective behaviour ... in slime moulds– Read & Latty 2016
Cell signaling during development of Dictyostelium – Loomis 2014


WEEK 3 Session 5


overview video: The transition to multicellular life may not have been so hard after all

Evolution of individuality during the transition
from unicellular to multicellular life
- Michod 2007
Phagotrophy by a flagellate selects of colonial prey: a possible
origin of multicellularity
- Boraas et al 1998
The multiple origins of complex multicellularity - Knoll 2011
The origin of animal multicellularity - Brunet & King 2017


Session 6


Dividing cellular asymmetry - Neumuller & Knoblich. 2009
Remodeling epithelial cell organization: front-read and apical-basal polarity - Nelson 2009
Front–Rear Polarization by mechanical cues - Ladoux et al 2016
Orienting muscle stem cells - Feige et al. 2018
The in(side) & outs(ide) of asymmetric stem cell division. - Chen et al 2016


WEEK 4 Session 7


Animal left-right asymmetry

Molecular to organismal chirality ... conserved myosin 1D - Lebreton et al., 2018
Daughter 3T3 cells: Are they mirror images of each other? - Albrecht-Buehler 1977
From cytoskeletal dynamics to organ asymmetry: a non-linear, regulative pathway underlies left-right patterning - McDowell et al 2016
Cellular chirality arising from the self-organization of the
actin cytoskeleton
- Tee et al., 2015


Session 8


A mechanism for the sharp transition of morphogen gradient interpretation
-Saka & Smith 2017
A role for actomyosin contractility in notch signaling - Hunter et al., 2019
Cell competition shape mammalian morphogenesis - Ellis et al., 2019
Cellular competition corrects noisy Wnt morphogen gradients to achieve
robust ratterning in the zebrafish embryo
– Akieda et al., 2019


Weeek 5 Session 9


Constrained architecture of mammalian Hox gene clusters
- Darbelley et al 2019.
On the evolution of bilaterality - Genikhovish & Technau. 2017
Hox genes – no need for hopeless monsters - Akam 1998
The rise and fall of Hox gene clusters -Duboule 2007


Session 10

  Watch (from last time): Homeotic Transformation - Michael Levine (UC Berkeley)(1 min)
and Hox genes and the evolution of animal body plans - Dennis Sun (UC Berkeley)(2 min)


Session 11



Session 12


reading → What’s not in the news headlines or titles of Alzheimer disease articles?
Mouse models of human disease: an evolutionary perspective - Perlman 2016.
Mice fall short as test subjects - McGlinn 2013
False analogies & logical fallacies in animal models - Sjoberg 2016
Gene losses during human origins - Wang et al 2006
Recent de novo origin of human protein-coding genes
- Knowles & McLysaght 2009
Human accelerated regions in neural progenitors - Ryu et al 2019


WEEK 7 Session 13


Richard Harland on Xenopus: parts 1 + 2 through [link] to ~12:30
Cellular basis of gastrulation: part 2
Spemann organizaton (twins): part 3
A matched set of frog sequences - Burgess 2016
Evidence that fold-change not absolute level of β-catenin dictates
Wnt signaling
- Goentoro & Kirscher 2009
Cortical rotation and mRNA localization in axis formation. - Houston, 2010
Fold-change detection in biological systems. - Adler & Alon 2018


Single cell RNA sequencing and data analysis


Watch: Drop-seq: Droplet barcoding of single cells
+Klein + Kirschner: single cell RNA seq in Xenopus
The dynamics of gene expression in vertebrate embryogenesis at single-cell
- Briggs et al. 2018
Single-cell mapping of gene expression landscapes and lineage
in the zebrafish embryo
- Wagner et al 2018

Principle Component Analysis, explained simply - BioTurning
Volcabo plot | Violin plot - Wikipedia
An introduction to UMAP:  Understanding UMAP


WEEK 8: Session 15


Levin: Transcriptional Precision: Enhancers
Patel: Anterior-Posterior Axis Patterning: Homeotic (Hox) Genes
Wieschaus - Patterning development in the embryo
How the dorsal gradient works: insights from postgenome
- Hong et al., 2008
Drosophila as a model organism - Yamaguchi & Yoshida 2018
Understanding the Effect of Gene Expression Noise in Biological Development - Holloway 2018


Session 16


The Heidelberg screen for pattern mutants of Drosophila: a personal account
- Wieschaus & Nusslein-Volhard 2016
A short history and description of Drosophila melanogaster classical genetics - Kaufman 2017


WEEK 9 Session 17


A transparent window into biology: Caenorhabditis elegans - Corsi et al 2015
Nobel lectures Sydney Brener | John Sulston | Robert Horowitz
The natural history of Caenorhabditis elegans
- Felix & Braendle 2010
Cell Death C. elegans development
- Malin & Shaham 2015


Session 18


Polarity and cell division orientationin the cleavage embryo: from worm
to human
- Ajduk & Zernicka-Goetz 2016
Cell fate decisions and axis determination in the early mouse embryo
- Takaoka & Hamada 2012
watch : mouse embryo imaging


WEEK 10: Session 19



Session 20


Spring Break    

WEEK 11 Session 21    


Thurs, Session 22



WEEK 12: Session 23


The mechanism of somite formation in mice– Saga 2012.
Patterning embryos with oscillations: structure, function anddynamics of the vertebrate segmentation clock - Oates et al 2012


Session 24


Establishing neuronal diversity in the spinal cord - Sagner & Briscoe 2019
  in vitro neural tube patterning with a microfluidic device - Demers etal, 2016
Wnt/β-catenin signaling during early Vertebrate Neural development
- Brafman & Willert 2017


WEEK 13: Session 25


The neural crest migrating into the twenty-first century - Bronner & Simoes-Costa. 2016
What can vertebrates tell us about segmentation? - Graham et al 2014


Session 26


On the formation of digits and joints during limb development - Hiscock et al 2017
A regulatory archipelago controls Hox genes transcription in digits - Montave et al 2011


WEEK 14 Session 27


On the formation of digits and joints during limb development - Hiscock et al., 2017
Shh and Gli3 are dispensable for limb skeleton formation but regulate digit number and identity – Litingtun et al 2002
BMP signals control limb bud interdigital programmed cell death by regulating FGF - Panji-Underwood et al., 2017


Session 28


Brain organoids: advances, applications and challenges- Qian et al 2019
Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in
- Schiebinger, et al 2019
The transcriptional legacy of developmental stochasticity-
Ballouz et al 2020
Cell types of the human retina and its organoids at single-cell resolution: developmental
- Cowan et al 2019
Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids - Beccari et al. 2018.


WEEK 15: Session 29


Impact of fetal alcohol syndrowm on body systems: a systemtic review - Caputo et al 2016
Did CRISPR help—or harm—the first-ever gene-edited babies? - Cohen 2019
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution - Pollan et al 2019


Session 30