PhD position in Nephrology in Freiburg, Germany

Studying mechanisms of genetic renal disease in Drosophila and mouse

The Renal Division of the University Medical Center Freiburg is offering a PhD position (DFG-funded). The position is available for three years and should be filled as soon as possible (starting in fall 2018).

Project:

• The lab is interested in studying mechanisms of genetic renal disease with a focus on monogenic causes of nephrotic syndrome.
• To this end we are utilizing the Drosophila and mouse animal models in conjunction with approaches in vitro.
• The podocyte-like Drosophila nephrocytes will be employed to characterize disease genes functionally and for whole-animal drug screening to develop novel therapeutic strategies.
• The candidate will work in diverse scientific environment with intensive supervision and support.

Requirements:

• We are looking for a highly motivated and ambitious candidate with a strong interest in basic research with clinical relevance.
• The applicant should hold a master’s degree in Biology, Molecular Medicine or an equivalent discipline.
• Experience in cell biology, mice and/or Drosophila is desirable but not mandatory.

Application: Interested candidates should send an application including a CV, a brief motivation letter and two references to

Dr. Tobias Hermle (tobias.hermle[at]uniklinik-freiburg[dot]de).

Selected References:

1. Hermle, T, Schneider, R, Schapiro, D, Braun, DA, van der Ven, AT, Warejko, JK, et al.: GAPVD1 and ANKFY1 Mutations Implicate RAB5 Regulation in Nephrotic Syndrome. J Am Soc Nephrol, 2018.

2. Helmstadter, M, Huber, TB, Hermle, T: Using the Drosophila Nephrocyte to Model Podocyte Function and Disease. Front Pediatr, 5: 262, 2017.

3. Hermle, T, Braun, DA, Helmstadter, M, Huber, TB, Hildebrandt, F: Modeling Monogenic Human Nephrotic Syndrome in the Drosophila Garland Cell Nephrocyte. J Am Soc Nephrol,28: 1521-1533, 2017.

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A postdoc position is available in the Heemskerk lab, Department of Cell and Developmental Biology at the University of Michigan Medical School.

We are looking for a postdoc that shares our excitement about using stem cells to discover the developmental mechanisms underlying embryogenesis and organogenesis. The lab is highly interdisciplinary and combines experimental and theoretical methods from biology, physics, and engineering, focusing on quantitative live-cell measurements to study spatial organization and cell fate determination in human pluripotent stem cells.

The broader institutional environment of the University of Michigan – the public university with the highest research spending in the United States – provides exceptional resources for professional development and trailblazing scientific exploration. The university is located in Ann Arbor, which is consistently named among cities with the highest quality of life in the US.

The successful candidate is a rigorous thinker with either a relevant biology background and strong interest in quantitative methods, or a quantitative background (e.g. physics, engineering, math) and strong interest in wet lab biology.

For more information see http://idseheemskerk.com.
To apply, please send a CV with publication list and three references, as well as a cover letter stating your motivation to iheemske@umich.edu.

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Welcome to our monthly selection of developmental biology (and related) preLights

preLights, the preprint highlighting service supported by The Company of Biologists, has now reached over 150 posts since launching in late February. To further promote this platform, we are now featuring preLights content in three of The Company of Biologist’s journals – including Development. In addition, complementing the Node’s monthly trawl for preprints, we are starting a monthly series where we highlight some of the exciting developmental biology (and related) preLights articles. So, on to our first post!

Flies, fish and chicks

preLighters  featured several exciting  preprints using Drosophila. A modern imaging approach to study transcriptional dynamics, combined with mathematical modelling shed new light on the generation of the famous even-skipped stripes, and was covered by Erik Clark. Mathematical modelling was also key in getting at the mechanisms of dorsal closure in a preprint that Yara Sanchez and Arnaud Monnard reviewed  together. Ivana Viktorinova’s preLight discussed how the wing epithelium responds to mechanical stress during morphogenesis, in which the mechanosensitive binding of the endocytic regulator p120 plays a major role. Drosophila embryos also have to tolerate other kind of stresses during their development, such as hypoxia; Sarah Bowling’s preLight featured a study that showed how the fat body of larvae senses low oxygen and modulates TORC1 in response.

There were plenty of exciting preprints coming from the zebrafish community, and the preLighters did their best to cover them. James Gagnon highlighted a fascinating study showing the essential role of a novel small protein for species-specific fertilization. Genes and phenotypes were studied at a much larger scale in a story ­­­­– covered by Daniel Grimes – about an impressive effort to link functions to human schizophrenia-associated loci. The strength of zebrafish in modelling complex human diseases was also nicely featured in preLights posts by Hannah Brunsdon and Giuliana Clemente. Hannah highlighted how a putative human CHD gene variant enhances the phenotype of a known CHD-associated gene, and called attention to the importance of investigating the contribution of risk alleles to existing disease-associated phenotypes. Giuliana wrote about the introduction of elements of the human immune system into zebrafish, which could allow future research to investigate how immune cells contribute to cancer progression and metastasis. It turns out that immune cells, and specifically the spatial-temporal dynamics of cytokine induction, are crucial for spinal cord regeneration, as explored in Shikha Nayar’s preLight.

Wouter Masselink and Ashrifia Adomako-Ankomah both highlighted preprints that combined chick embryology methods with modern molecular approaches to gain new insights into one of developmental biology’s ‘classical’ problems: limb development. Wouter covered a study showing that the collinear activation of Hox genes is important for controlling the position of the forelimb. Ashrifia’s post dealt with the question of how the final size of the limb is determined and a preprint showing BMP signalling-dependent regulation of proliferation rates in the limb bud.

Chromatin and genomics

The chromatin biology and genomics fields were well represented on preLights this month. Claire Simon and Sophie Morgani discussed how Sox3 and Pou5f3 act as pioneer transcription factors to open chromatin for genome activation in Xenopus, while the organization of inactive chromatin in senescent cells was the focus of Carmen Adriaens’ post. Lauren Neves’ preLight reported on a remarkable study, which showed that the histone H3-H4 tetramer – a main component of the building blocks of chromatin – also has copper reductase activity. This enzymatic function of histones may have been important for the emergence of eukaryotes. Several preLights featured the ever-increasing power of RNA-seq to answer interesting biological questions. A transcriptomic study in plants, highlighted by Martin Balczerowicz, investigated the level of transcriptional noise among genetically identical species. Rob Hynds’ preLight discussed the use of single-cell transcriptomics combined with bulk proteomics to study healthy ageing in mouse lungs. Finally, an RNA-seq study also gave insight into how a remodelled chloroplast is maintained in a non-photosynthetic alga, preLighted by Ellis O’Neill.

Tools & Technologies

Novel technologies featured heavily this month, for instance Rebekah Tillotson’s preLight on CRISPR gene drives in mouse, which could help scientists create disease models with multiple mutations. Satish Bodakuntla covered  a novel expansion microscopy technique that goes beyond the limits of super-resolution. The most popular type of method to highlight turned out to be optogenetics. Mahesh Karnani reflected on two preprints that made major advances in achieving optogenetic inhibition of neural activity by soma targeting, and the preLight includes insightful comments from both research teams. Patricia’s preLight discussed optogenetic manipulation in locust brains, while moving a bit away from neuronal function, Srivats Venkataramanan preLighted a study that used an optogenetic tool to control the formation of stress granules.

Finally, preLighters’ coverage of reproducibility (see Carmen’s earlier post and Reid Alderson’s preLight from this month) and flaws in experiments (see Fabio Liberante’s post on false detection of circular RNAs from RNA-seq) signalled the importance of preprints in rapid dissemination of studies which are extremely valuable for the community, but often more difficult to get published in journals.

Considering reading something more out of your scope? Then explore the preLights website, where you can also find out about microbes in a Mars-analogue environment, Mycobacteria on your showerheads, or drug repurposing to combat brain-eating amoebae.

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https://www.grimes-lab.com

Postdoctoral positions are available in the laboratory of Daniel T. Grimes, Institute of Molecular Biology and Department of Biology at the University of Oregon. The laboratory focuses on symmetry in the biological world.

We are a new lab opening in January 2019. We want to understand how some features of vertebrate bodies (like limbs and the skeleton) develop with left-right symmetry, while others (like the heart, liver, and gut) develop with striking left-right asymmetries. 

We use zebrafish to address these fundamental questions of developmental biology. Our main techniques include genome editing, confocal and micro-CT imaging, genetics and genomics, single-cell sequencing, and more. Current projects include: understanding how mechanical flow signals are generated and sensed by cilia in left-right patterning, investigating Polycystin signal transduction, elucidating mechanisms by which the spine remains straight during growth. We also model human diseases of aberrant (a)symmetry including heterotaxia, scoliosis, and primary ciliary dyskinesia.

We offer the opportunity to work closely with the PI, and to help build and shape lab culture. Your career and manuscripts are important; we are committed to the mentorship and long-term success of our lab members. We also offer a high quality training in zebrafish development and genetics. Zebrafish research was founded at the University of Oregon. As such, we share a large state-of-the-art aquarium with labs that use the zebrafish for diverse science. There is no better place to work with zebrafish!

The Biology Department at the University of Oregon offers an exceptional environment and a broad range of research, great core facilities and close ties to the Knight Campus, a new $1-billion initiative that brings together engineers, biologists and computational scientists to address pressing biological questions.

We are looking for ambitious candidates who hold (or be due to complete) a relevant PhD and have evidence of excellent scholarship. Experience with confocal imaging is a bonus but previous experience with zebrafish is not essential. Candidates should be able to work independently, to implement new technologies, and be productive and collaborative.

The position is fully funded but the candidate will be expected to seek external funding opportunities during their tenure.

The candidate should email (dtgrimes@princeton.edu) with a cover letter describing their career goals, previous experience, scientific interests and reasons for applying, along with a CV. Informal inquiries are welcome (see grimes-lab.com/join-us-1).

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• Develop tailored bioinformatics approaches and provide advice and assistance to DanStem and CPR researchers in their analyses, focusing in particular on the planning, processing, analysis and publication of transcriptomic and epigenomic next-generation sequencing data.
• Prepare pipelines and scripts for use by DanStem and CPR researchers.
• Provide training and design new approaches to analysis.
• Cooperate and collaborate with DanStem and CPR researchers.
• Cooperate with platform personnel and contribute to platform management.
• Network actively with the global bioinformatics community and stay up-to-date with current trends in the field.

• Fluent programming skills in R/Bioconductor.
• Experience with next generation sequencing data.
• Strong statistics skills.
• Knowledge of UNIX-like operating system.
• Experience in working with biologists and an understanding of molecular biology and genomics.
• Excellent oral and written communication skills and fluency in English.
• Successful experiences in project management, including multi-tasking.
• A service-minded and team player attitude.

• State-of-the-art computational infrastructure for data analysis, including access to cluster computing at the Danish National Supercomputer (Computerome) and excellent IT and systems administration support.
• Stimulating and multifaceted research environment of high scientific and societal impact.
• Possibility for continued education and training, especially to develop further as an expert in single cell bioinformatics.

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When reading about co-evolution of prey and predators, I stumbled across a cute new plot type: a half boxplot, half dot plot to show data distributions.

Wilson used this plot to simultaneously visualize summaries about their data (center, spread) and the actual data points. This allows us, the audience, to learn a lot about their results. That cheetahs are maybe binomially distributed and have outliers, or that zebras show a curious clustering.

Your quick guide to distribution plots:

The half-and-half, aka dox-plot (a friend), led me to explore which visuals are commonly used for showing distributions.

Raw data

To show how the raw data is distributed, we simply use dots or bars (as in barcode plots). When there are overlapping data points, we can use transparency or “jittering”. Jittering is distributing the data points in a given area, for increased clarity: the y-position remains the same, the x- position becomes random.

Summarizing the data: center and spread

Often, we are interested in summarizing statistics to judge and compare data. By convention the center (median) is indicated with a horizontal bar and the spread (variance, standard deviation) with vertical whiskers. Common plot types for this are the “star-wars rebel fighter”, the dot plot and boxplot. Bar plot used to be widely used, but are now banned by most journals for concealing most relevant information, so they are here only for completeness (see previous post). Very often these days I see boxplots that are overlaid with the data points – this works really well for up to 100 data points and is easy to implement with most software.

Show shape and unusual features

For normally distributed data, the center and the spread are highly informative. However, in life science we often have bimodal distributions, clusters, or gaps. Then boxplots become very insufficient and might even conceal interesting aspects (if not outright be misleading).

For faithfully showing distributions, histograms have a long history. Here, one has to be very careful with choosing bin sizes: too large or too small bins can greatly distort the histogram shape and result in a misleading chart. Choosing bin sizes is a science in itself, for details see wikipedia – but basically, it again depends on the data shape and sampling depth.

An alternative to histograms are density plots. Density plots show how data are distributed. They become very useful for large data sets. For large data sets individual points can’t be visualized anymore and the eye can’t anymore judge spread intuitively. A rather recent but so far “happy marriage” is the violin plot. Violin plots are a fusion of the boxplot and its summary statistics, with the density/shape of the data (Hintze and Nelson, 1998 doi: 10.1080/00031305.1998.10480559).

Further reading in a recent preLIGHT by Gautam Dey!

Pro and cons of different plot types:

All figures in one for teaching:

(11 votes)

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In LM Escudero´s group, we like developmental biology, mathematical biology and computational biology. We try to be imaginative and get inspiration from simple things… such as a toilet paper roll. Using this tool (and some computers), we claim that we have described a novel geometrical shape… You will be wondering… how do you do that??? You are going to find here: the story behind the discovery of “scutoids”.

First, you need a multidisciplinary group distributed between two buildings: “the wet lab”, with flies and their epithelial tissues, at Institute of Biomedicine of Seville, IBiS (Fig. 1); and the “computer lab” with… well… with a bit of everything (it does not fit in a simple picture… so, see Video 1) at the Faculty of Biology of University of Seville. It is ideal if the two buildings are separated by 1 km, so you can exercise everyday walking between the two labs to interact with the members of each branch.

Fig. 1. A. Tagua (at right, masterful segmenter and drosophilist) and C. Gordillo looking for more scutoids in the fly lab.

Video 1. The computational lab (that is wet if you open the tap) showing P. Gómez-Gálvez and P. Vicente-Munuera, the two first authors, working hard and listening good music.

Very important! You need also an office where both computational and Drosophila worlds can fit together (Fig. 2).

Fig. 2. Very trendy office. Please note the a/c controller, essential if you are based in Seville.

Then, you need a problem to think about while you are walking between the two labs… As animals develop, the initial simple planar epithelia of embryos must be sculpted into complex three-dimensional tissues. These cells pack together tightly. To accommodate the curving that occurs during embryonic development, it has been assumed that epithelial cells adopt either columnar or bottle-like shapes.

We thought that a very logic way to approach the problem of how curved epithelia pack in 3D was to design a computer model with the shape of a toilet paper roll (Fig. 3). The results we saw were weird. Our model predicted that, as the curvature of the tissue increases, columns and bottle-shapes were not the only forms that cells may developed. To our surprise, the discovered geometric solid didn’t even have a name in math! We were happy. Really happy. One does not normally have the opportunity to name a shape. We chose the name scutoid.

Fig. 3. The toilet paper: reality versus model.

The undescribed shape was characterised by having at least a vertex in the lateral surface (Fig. 4). This vertex confers an interesting property to the scutoid: when cells adopt this shape, they can have different neighbours in the upper and bottom surfaces (apical and basal in biology). This is exclusive of scutoids and cannot be done with the “prism”, “trunk” (frusta) or “prismatoid” shapes.

Fig. 4. The brotherhood of the cellular geometry: evolution from prisms to the undescribed scutoid geometrical shapes.

All this was amazing… but we needed help to completely understand the problem. We needed lots of collaborators (we are 16 authors), starting with Dr Grima and Dr Márquez, real mathematicians that helped us with the formal aspects of the toilet paper model.

To verify the model’s predictions, the group investigated the three-dimensional packing of different tissues in different animals. The experimental data, using Drosophila salivary glands, confirmed that epithelial cells adopted shapes and three-dimensional packing motifs similar to the ones predicted by the computational model.  This important validation required more collaborators: Dr Sotillos and Dr Martín-Bermudo groups (CABD, CSIC/JA/UPO, Seville) and Dr Cavodeassi (St. George’s University of London) all with biological background but working in other types of epithelia.

And then, the biophysics. We joined efforts with the lab of Dr Javier Buceta (Lehigh University), to study the role of scutoids in tissue architecture from a mechanical point of view. We argue that the scutoids stabilise the three-dimensional packing and make it energetically efficient. Our conclusion was that we have uncovered nature’s solution to achieving efficient epithelial bending. This was really cool… but not so much as the summary that Dr Buceta has prepared for you if you do not have time to read the whole paper… this is art and science in a single sheet (Fig. 5, click to see at full resolution).

Thanks for reading!!!

If you need more information, you can check our paper: Scutoids are a geometrical solution to three-dimensional packing of epithelia. Gómez-Gálvez P, Vicente-Munuera P, Tagua A, Forja C, Castro AM, Letrán M, Valencia-Expósito A, Grima C, Bermúdez-Gallardo M, Serrano-Pérez-Higueras Ó, Cavodeassi F, Sotillos S, Martín-Bermudo MD, Márquez A, Buceta J, Escudero LM. Nat Commun. 2018 Jul 27;9(1):2960. doi: 10.1038/s41467-018-05376-1.

Here you have the link.

(7 votes)

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An opportunity is available for a Postdoctoral position in the Cox Lab at the Peter MacCallum Cancer Centre in Melbourne, Australia. The position requires a highly motivated and enthusiastic postdoctoral scientist to investigate how metabolic reprogramming contributes to liver regeneration and cancer using zebrafish (Danio rerio) as a model organism. The successful candidate should hold a PhD in biochemistry, molecular biology, developmental biology or a related discipline. The person will be expected to conduct rigorous, valid and ethical research both independently and as part of the research team. The person will be expected to supervise undergraduate and postgraduate students, and technical staff.  For more information on recent publications and projects running in the Cox laboratory refer to: https://www.petermac.org/research/labs/andrew-cox

More information about the details of the application process can be found on the website (https://petermac.mercury.com.au/ViewPosition.aspx?id=/GrfG/WmYM8=&jbc=ere), or contact via email (Andrew.Cox@petermac.org).

(1 votes)

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Welcome to our monthly trawl for developmental biology (and other related/just plain cool) preprints. 

In one of the most contentious (at least on Twitter!) pieces of preprint news in July, Tom Sheldon, Senior Press Manager at the Science Media Center in London, voiced his concerns about the impact of preprints on public understanding of science in his ‘World View’ in Nature. Sheldon, building on an earlier SMC blog post, pictured the harm that could be done if bad science were to be deposited on preprint servers and picked up by journalists, and wondered how rigorous science would fare in a journalistic ecosystem which prioritises breaking the story first (i.e. giving credence to the preprint, not the peer reviewed article). Here’s a completely unscientific selection of the mainly negative Twitter responses to the piece, from Michael Eisen (who in fact has 3 preprints in this month’s haul!), James Fraser, Leslie Vosshall and Alejandro Sanchez Alvarado. The arguments swirled around the legitimacy of peer review, the responsibility of journalists to vet their stories properly, and the responsibility of scientists and university press offices not to oversell their results.

Away from the tumult, there was so much beautiful research deposited as preprints in July, from the molecular drivers of neurogenesis to the derivation of platypus pluripotent stem cells, cephalopod limb patterning to fern shoot development (and, right at the bottom, a truly humungous humdinger of a fungus!).

The preprints were hosted on bioRxiv, PeerJ, and arXiv. Let us know if we missed anything, and use these links to get to the section you want:

Developmental biology

| Patterning & signalling

| Morphogenesis & mechanics

| Genes & genomes

| Stem cells, regeneration & disease modelling

Evo-devo & evo

Cell biology

Modelling

Tools & resources

| Imaging etc.

| Genome tools

Research practice & education

Why not…

Developmental biology

| Patterning & signalling

Synthetic mammalian pattern formation driven by differential diffusivity of Nodal and Lefty
Ryoji Sekine, Tatsuo Shibata, Miki Ebisuya

Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?
Irepan Salvador-Martínez, Marco Grillo, Michalis Averof, Maximilian J Telford

Positional information encoded in the dynamic differences between neighbouring oscillators during vertebrate segmentation.
Marcelo Boareto, Tomas Tomka, Dagmar Iber

Activin signaling informs the graded pattern of terminal mitosis and hair cell differentiation in the mammalian cochlea
Meenakshi Prajapati-DiNubila, Ana Benito-Gonzalez, Erin J Golden, Shuran Zhang, Angelika Doetzlhofer

Notch signalling patterns retinal composition by regulating atoh7 during post-embryonic growth
Alicia Perez Saturnino, Katharina Lust, Joachim Wittbrodt

Otx2 signals from the choroid plexus to regulate adult neurogenesis
Anabelle Planques, Vanessa Oliveira Moreira, Chantal Dubreuil, Alain Prochiantz, Ariel A Di Nardo

AKT, NOTCH and GSK3β interact to trigger early myogenesis in vertebrate embryos.
Diane Lebrun, Pamela Rahal, Valerie MORIN, Christophe Marcelle

Positive-feedback defines the timing and robustness of angiogenesis
Donna J Page, Raphael Thuret, Lakshmi Venkatraman, Tokiharu Takahashi, Katie Bentley, Shane P Herbert

Thyroid hormone signaling specifies cone subtypes in human retinal organoids
Kiara C Eldred, Sarah E Hadyniak, Katarzyna A Hussey, Boris Brennerman, Pingwu Zhang, Xitiz Chamling, Valentin M Sluch, Derek S Welsbie, Samer Hattar, James Taylor, Karl Wahlin, Donald J Zack, Robert J Johnston Jr.

Spontaneous symmetry breaking and pattern formation of organoids

Keisuke Ishihara, Elly M. Tanaka

A transition from SoxB1 to SoxE transcription factors is essential for progression from pluripotent blastula cells to neural crest cells
Elsy Buitrago-Delgado, Elizabeth Schock, Kara Nordin, Carole LaBonne

Lmx1a drives Cux2 expression in the cortical hem through activation of a conserved intronic enhancer.
Santiago P Fregoso, Brett E Dwyer, Santos J Franco

Conserved and divergent development of brainstem vestibuloacoustic nuclei
Marcela Lipovsek, Richard JT Wingate

Tissue-specific actions of Pax6 on proliferation-differentiation balance in the developing forebrain are Foxg1-dependent
Idoia Quintana-Urzainqui, Zrinko Kozić,, Soham Mitra, Tian Tian, Martine Manuel, John O. Mason, David J. Price

Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error
Ross F Collery, Brian A Link

Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice
Wendi A Bacon, Russell S Hamilton, Ziyi Yu, Jens Kieckbuscha, Delia Hawkesa, Ada Krzaka, Christopher Abell, Francesco Colucci, D. Stephen Charnock-Jones

G protein-coupled estrogen receptor is not required for sex determination or ovary function in zebrafish
Camerron M Crowder, Shannon N Romano, Daniel A Gorelick

Nuclear polymorphism and non-proliferative adult neurogenesis in human neural crest-derived cells.
Carlos Bueno, Marta Martinez-Morga, Salvador Martinez

Expression and role of Galectin-3 in the postnatal development of the cerebellum
Ines Gonzalez-Calvo, Fekrije Selimi

Ral signals through a MAP4 Kinase-p38 MAP kinase cascade in C. elegans cell fate patterning.
Hanna Shin, Rebecca E.W. Kaplan, Tam Duong, Razan Fakieh, David J Reiner

Multiple Mechanisms Inactivate the LIN-41 RNA-Binding Protein to Ensure A Robust Oocyte-to-Embryo Transition in Caenorhabditis elegans
David I. Greenstein, Caroline Spike, Gabriela Huelgas-Morales, Tatsuya Tsukamoto

A re-inducible gap gene cascade patterns the anterior-posterior axis of insects in a threshold-free fashion
Alena Boos, Jutta Distler, Heike Rudolf, Martin Klingler, Ezzat El-Sherif

Drosophila ovarian germline stem cell cytocensor projections dynamically receive and attenuate BMP signalling
Scott G Wilcockson, Hilary L Ashe

Choline Transporter in α/β core neurons of Drosophila mushroom body non-canonically regulates pupal eclosion and maintains neuromuscular junction integrity
Runa Hamid, Nikhil Hajirnis, Shikha Kushwaha, Sadaf Saleem, Vimlesh Kumar, Rakesh K Mishra

Blimp-1 mediates tracheal lumen maturation in Drosophila melanogaster
Arzu Ozturk-Colak, Camille Stephan-Otto Attolini, Jordi Casanova, Sofia J. Araujo

Cell-type specific patterned stimulus-independent neuronal activity in the Drosophila visual system during synapse formation
Orkun Akin, Bryce T. Bajar, Mehmet F. Keles, Mark A. Frye, S. Lawrence Zipursky

The Mediator CDK8-Cyclin C complex modulates vein patterning in Drosophila by stimulating Mad-dependent transcription
Xiao Li, Mengmeng Liu, Xingjie Ren, Nicolas Loncle, Qun Wang, Rajitha-Udakara-Sampath Hemba-Waduge, Muriel Boube, Henri-Marc G Bourbon, Jian-Quan Ni, Jun-Yuan Ji

Drosophila ZDHHC8 palmitoylates scribble and Ras64B and controls growth and viability
Katrin Strassburger, Evangeline Kang, Aurelio A Teleman

The Drosophila chromodomain protein Kismet activates steroid hormone receptor transcription to govern axon pruning and memory in vivo.
Nina K Latcheva, Jennifer M Viveiros, Daniel R Marenda

High JNK following Ras/Rpr/Tak1 over-expression in imaginal discs of Drosophila reduces post-pupariation ecdysone via Dilp8 resulting in early pupal death
Mukulika Ray, Subhash C. Lakhotia

Of puzzles and pavements: a quantitative exploration of leaf epidermal cell shape
Roza V Vofely, Joseph Gallagher, Grace D Pisano, Madelaine Bartlett, Siobhan A Braybrook

High-resolution 4D spatiotemporal analysis reveals the contributions of local growth dynamics to contrasting maize root system architectures
Ni Jiang, Eric Floro, Adam L Bray, Benjamin Laws, Christopher N Topp

Lateral root priming synergystically arises from root growth and auxin transport dynamics
Thea van den Berg, Kirsten H. ten Tusscher

Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development
Thomas Vain, Sara Raggi, Noel Ferro, Deepak Kumar Barange, Martin Kieffer, Qian Ma, Siamsa Melina Doyle, Mattias Thelander, Barbora Pařízková, Ondřej Novák, Alexandre Ismail, Per Anders Enquist, Adeline Rigal, Małgorzata Łangowska, Sigurd Ramans Harborough, Yi Zhang, Karin Ljung, Judy Callis, Fredrik Almqvist, Stefan Kepinski, Mark Estelle, Laurens Pauwels, Stéphanie Robert

LEAFY maintains apical stem cell activity during shoot development in the fern Ceratopteris richardii
Jane Langdale, Veronica S Di Stilio, Andrew R.G. Plackett, Stephanie J Conway, Kristen D Hewett Hazelton, Ester H Rabbinowitsch

Ethylene inhibits stem trichome formation in Arabidopsis

Susan I Gibson

The role of UV-B light on small RNA activity during grapevine berry development
Sukumaran Sunitha, Rodrigo Loyola, Jose Antonio Alcalde, Patricio Arce-Johnson, Tomas Matus, Christopher Dale Rock

| Morphogenesis & mechanics

Neural crest cells regulate optic cup morphogenesis by promoting extracellular matrix assembly
Chase Dallas Bryan, Rebecca Lynne Pfeiffer, Bryan William Jones, Kristen Marie Kwan

YAP/TAZ-TEAD Activity Links Mechanical Cues To Specific Cell Fate Within The Hindbrain Boundaries
Adria Voltes, Covadonga F Hevia, Chaitanya Dingare, Simone Calzolari, Javier Terriente, Caren Norden, Virginie Lecaudey, Cristina Pujades

Tissue flow induces cell shape changes during organogenesis
Gonca Erdemci-Tandogan, Madeline J Clark, Jeffrey D Amack, M. Lisa Manning

N-Cadherin Provides a Cis and Trans Ligand for Astrotactin that Functions in Glial-Guided Neuronal Migration
Zachi Horn, Hourinaz Behesti, Mary E. Hatten

Blood flow-induced Notch activation and endothelial migration enable embryonic vascular remodeling.
Bart Weijts, Edgar Gutierrez, Semion K Saikin, Ararat J Ablooglu, David Traver, Alex Groisman, Eugene Tkachenko

Positive-feedback defines the timing and robustness of angiogenesis
Donna J Page, Raphael Thuret, Lakshmi Venkatraman, Tokiharu Takahashi, Katie Bentley, Shane P Herbert

mRNA localisation in endothelial cells regulates blood vessel sprouting
Guilherme Costa, Nawseen Tarannum, Shane Herbert

Morphogenesis of the Sternum in Quail Embryos

Nashwa Araby, Soha Soliman, Eman Abdel Raheem, Yasser Ahmed

Radial F-actin Organization During Early Neuronal Development
Durga Praveen Meka, Robin Scharrenberg, Bing Zhao, Theresa Koenig, Irina Schaefer, Birgit Schwanke, Oliver Kobler, Sergei Klykov, Melanie Richter, Dennis Eggert, Sabine Windhorst, Carlos G. Dotti, Michael R. Kreutz, Marina Mikhaylova, Froylan Calderon de Anda

Multiscale analysis of 3D nuclear morphology reveals new insights into growth plate organization in mice
Sarah Rubin, Tomer Stern, Paul Villoutreix, Johannes Stegmaier, Yoseph Addadi, Elazar Zelzer

Modulation of corneal tissue mechanics influences epithelial cell phenotype
Ricardo M Gouveia, Guillaume Lepert, Suneel Gupta, Rajiv R Mohan, Carl Paterson, Che J Connon

Pkd2l1 is required for mechanoception in cerebrospinal fluid-contacting neurons and maintenance of spine curvature
Jenna Sternberg, Andrew E Prendergast, Lucie Brosse, Yasmine Cantaut-Belarif, Olivier Thouvenin, Adeline Orts-Del’Immagine, Laura Castillo, Lydia Djenoune, Shusaku Kurisu, Jonathan R McDearmid, Pierre-Luc Bardet, Claude Boccara, Hitoshi Okamoto, Patrick Delmas, Claire Wyart

Balance of Mechanical Forces Drives Endothelial Gap Formation and May Facilitate Cancer and Immune-Cell Extravasation
Jorge Escribano, Michelle Chen, Emad Moeendarbary, Xuan Cao, Vivek Shenoy, Jose Manuel Garcia-Aznar, Roger Kamm, Fabian Spill

CBD-1 scaffolds two independent complexes required for eggshell vitelline layer formation and egg activation in C. elegans
Delfina P González, Helen V. Lamb, Diana Partida, Zachary T. Wilson, Marie-Claire Harrison, Julián A. Prieto, James J. Moresco, Jolene K. Diedrich, John R. Yates III, Sara K. Olson

Excitable RhoA dynamics drive pulsed contractions in the early C. elegans embryo.
Jonathan B Michaux, Francois B Robin, William M McFadden, Edwin M Munro

Extracellular matrix regulates morphogenesis and function of ciliated sensory organs in Caenorhabditis elegans
Maureen M. Barr, Deanna M De Vore, Karla M Knobel, Ken C.Q. Nguyen, David H Hall

Novel exc Genes Involved in Formation of the Tubular Excretory Canals of C. elegans
Hikmat Al-Hashimi, Travis Chiarelli, Erik A. Lundquist, Matthew Buechner

Curvature Dependent constraints drive remodeling of epithelia
Florian Maechler, Cedric Allier, Aurelien Roux, Caterina Tomba

The C-type lectin Schlaff ensures epidermal barrier compactness in Drosophila
Renata Zuber, Khaleelula Saheb Shaik, Frauke Meyer, Hsin-Ning Ho, Anna Speidel, Nicole Gehring, Slawomir Bartoszewski, Heinz Schwarz, Bernard Moussian

microRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis
Albertomaria Moro, Tristan Driscoll, William Armero, Liana C. Boraas, Dionna Kasper, Nicolas Baeyens, Charlene Jouy, Venkatesh Mallikarjun, Joe Swift, Sang Joon Ahn, Donghoon Lee, Jing Zhang, Mengting Gu, Mark Gerstein, Martin Schwartz, Stefania Nicoli

| Genes & genomes

Long non-coding RNAs are largely dispensable for zebrafish embryogenesis, viability and fertility
Mehdi Goudarzi, Kathryn Berg, Lindsey M Pieper, Alexander F Schier

Compensatory mechanisms render Tcf7l1a dispensable for eye formation despite its requirement in eye field specification
Rodrigo M Young, Florencia Cavodeassi, Thomas A Hawkins, Heather L Stickney, Quenten Schwarz, Lisa M Lawrence, Claudia Wierzbicki, Gaia Gestri, Elizabeth Mayela Ambrosio, Allison Klosner, Jasmine Rowell, Isaac H. Bianco, Miguel L Allende, Stephen W Wilson

Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns
Jamie C Kwasnieski, Terry L Orr-Weaver, David P Bartel

Brd4 and P300 regulate zygotic genome activation through histone acetylation
Shun Hang Chan, Yin Tang, Liyun Miao, Hiba Darwich-Codore, Charles E. Vejnar, Jean-Denis Beaudoin, Damir Musaev, Juan P. Fernandez, Miguel A. Moreno-Mateos, Antonio J. Giraldez

A cell cycle-coordinated nuclear compartment for Polymerase II transcription encompasses the earliest gene expression before global genome activation
Yavor Hadzhiev, Haseeb Qureshi, Lucy Wheatley, Ledean Cooper, Aleksandra Jasiulewicz, Huy Van Nguyen, Joseph Wragg, Divyasree Poovathumkadavil, Sacha Conic, Sarah Bajan, Attila Sik, Gyorgy Hutvagner, Laszlo Tora, Agnieszka Gambus, John S Fossey, Ferenc Mueller

Heterogeneity of transposon expression and activation of the repressive network in human fetal germ cells
Boris Reznik, Steven A. Cincotta, Rebecca G. Jaszczak, Leslie J. Mateo, Joel Shen, Mei Cao, Laurence Bascin, Ping Ye, Wenfeng An, Diana Laird

Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos
Mustafa Mir, Michael R Stadler, Stephan A Ortiz, Melissa M Harrison, Xavier Darzacq, Michael B Eisen

Zelda potentiates transcription factor binding to zygotic enhancers by increasing local chromatin accessibility during early Drosophila melanogaster embryogenesis.
Xiao-Yong Li, Michael B Eisen

Mutation of sequences flanking and separating transcription factor binding sites in a Drosophila enhancer significantly alter its output
Xiao-Yong Li, Michael Eisen

cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg.
Susan Newcomb, Roumen Voutev, Aurelie Jory, Rebecca K Delker, Matthew Slattery, Richard S Mann

Drosophila small ovary encodes a zinc-finger repressor required for ovarian differentiation
Leif Benner, Elias A Castro, Cale Whitworth, Koen JT Venken, Haiwang Yang, Brian Oliver, Kevin R Cook, Dorothy A Lerit

The mirtron miR-1010 functions in concert with its host gene SKIP to maintain synaptic homeostasis
Christopher Amourda, Timothy E Saunders

Transposon silencing in the Drosophila female germline ensures genome stability in progeny embryos
Anne Ephrussi, Zeljko Durdevic, Ramesh S Pillai

Muscleblind regulates Drosophila Dscam2 cell-type-specific alternative splicing
Joshua Shing Shun Li, S Sean Millard

The cis-regulatory logic underlying abdominal Hox-mediated repression versus activation of regulatory elements in Drosophila
Arya Zandvakili, Juli Uhl, Ian Campbell, Yuntao Charlie Song, Brian Gebelein

Disparate expression specificities coded by a shared Hox-C enhancer
Steven W Miller, James W. Posakony

CONSERVATION AND VARIATIONS OF BIMODAL HoxD GENE REGULATION DURING TETRAPOD LIMB DEVELOPMENT
Nayuta Yakushiji-Kaminatsui, Lucille Lopez-Delisle, Christopher Chase Bolt, Guillaume Andrey, Leonardo Beccari, Denis Duboule

Ectopic expression of Hoxb1 induces cardiac and craniofacial malformations
Stéphane Zaffran, Gaëlle Odelin, Sonia Stefanovic, Fabienne Lescroart, Heather C Etchevers

Tbx1 and Foxi3 genetically interact in the third pharyngeal pouch endoderm required for thymus and parathyroid development
Erica Hasten, BERNICE E MORROW

Single-cell transcriptome analysis during cardiogenesis reveals basis for organ level developmental anomalies
Tarja Yvanka de Soysa, Sanjeev Ranade, Satoshi Okawa, Srikanth Ravichandran, Yu Huang, Hazel Salunga, Amelia Schricker, Antonio del Sol, Casey Gifford, Deepak Srivastava

Specific histone modifications associate with alternative exon selection during mammalian development
Qiwen Hu, Casey Greene, Elizabeth Heller

Rewiring of transcription factor binding in differentiating human embryonic stem cells is constrained by DNA sequence repeat symmetry
Matan Goldshtein, David B. Lukatsky

Genome-wide maps of distal gene regulatory regions active in the human placenta
Joanna Zhang, Corinne N. Simonti, John Anthony Capra

Molecular Diversity of Intrinsically Photosensitive Ganglion Cells
Daniel Berg, Katherine Kartheiser, Megan Leyrer, Alexandra Saali, David Berson

The Nucleome of Developing Murine Rod Photoreceptors
Issam Al Diri, Marc Valentine, Beisi Xu, Daniel Putnam, Lyra Griffiths, Marybeth Lupo, Jackie Norrie, Jiakun Zhang, Dianna Johnson, John Easton, Abbas Shirinifard, Ying Shao, Victoria Honnell, Sharon Frase, Shondra Miller, Valerie Stewart, Xiang Chen, Michael Dyer

Comprehensive analysis of retinal development at single cell resolution identifies NFI factors as essential for mitotic exit and specification of late-born cells
Brian Clark, Genevieve Stein-O’Brien, Fion Shiau, Gabrielle Cannon, Emily Davis, Thomas Sherman, Fatemeh Rajaii, Rebecca James-Esposito, Richard Gronostajski, Elana Fertig, Loyal Goff, Seth Blackshaw

Living Neural Networks: Dynamic Network Analysis of Developing Neural Progenitor Cells
Arun S Mahadevan, Nicolas E Grandel, Jacob T Robinson, Kevin R Francis, Amina A Qutub

Quantitative, real-time, single cell analysis in tissue reveals expression dynamics of neurogenesis
Cerys S Manning, Veronica Biga, James Boyd, Jochen Kursawe, Bodvar Ymisson, David G Spiller, Christopher M Sanderson, Tobias Galla, Magnus Rattray, Nancy Papalopulu

Simultaneous production of diverse neuronal subtypes during early corticogenesis
Elia Magrinelli, Robin Jan Wagener, Denis Jabaudon

Transcriptome analysis of early stage of neurogenesis reveals temporal-specific gene network for preplate neuron differentiation and Cajal-Retzius cell specification
Jia Li, Lei Sun, Xue-Liang Peng, Xiao-Ming Yu, Shao-Jun Qi, Zhi John Lu, Jing-Dong J. Han, Qin Shen

Bcl6 promotes neurogenic conversion through transcriptional repression of multiple self-renewal-promoting extrinsic pathways.
Jerome Bonnefont, Luca Tiberi, Jelle van den Ameele, Delphine Potier, Zachary Gaber, Xionghui Lin, Angeline Bilheu, Adele Herpoel, Fausto Velez Bravo, Francois Guillemot, Stein Aerts, Pierre Vanderhaeghen

Fine-scale excitatory cortical circuits reflect embryonic progenitor pools
Tommas J Ellender, Sophie V Avery, Kashif Mahfooz, Alexander von Klemperer, Sophie L Nixon, Matthew J Buchan, Joram J van Rheede, Aleksandra Gatti, Cameron Waites, Sarah E Newey, Colin J Akerman

Single-cell transcriptomics characterizes cell types in the subventricular zone and uncovers molecular defects underlying impaired adult neurogenesis
Vera Zywitza, Aristotelis Misios, Lena Bunatyan, Thomas E. Willnow, Nikolaus Rajewsky

Regulation of cell fate in neurodevelopment and oligodendroglioma by the transcriptional repressor Capicua
Sheikh Tanveer Ahmad, Alexandra D Rogers, Myra J Chen, Rajiv Dixit, Lata Adnani, Luke Frankiw, Samuel O Lawn, Michael D Blough, Mana Alshehri, Wei Wu, Stephen M Robbins, Gregory Cairncross, Carol Schuurmans, Jennifer Chan

The regulatory control of Cebpa enhancers and silencers in the myeloid and red-blood cell lineages
Andrea Repele, Shawn Krueger, Michelle Y. Tuineau, Manu Manu

Characterization of Telomeric Repeat-Containing RNA (TERRA) localization and protein interactions in Primordial Germ Cells of the mouse
Miguel Angel Brieno-Enriquez, Stefannie L. Moak, Anyul Abud-Flores, Paula Elaine Cohen

Role of Cnot6l in maternal mRNA turnover
Filip Horvat, Helena Fulka, Radek Jankele, Radek Malik, Jun Ma, Katerina Solcova, Radislav Sedlacek, Kristian Vlahovicek, Richard M Schultz, Petr Svoboda

Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons
Chongyuan Luo, Qian Yi Lee, Orly L Wapinski, Rosa Castanon, Joseph R Nery, Sean M Cullen, Margaret A. Goodell, Howard Chang, Marius Wernig, Joseph R. Ecker

Gene-regulatory independent functions for insect DNA methylation
Adam J. Bewick, Zachary Sanchez, Elizabeth C. Mckinney, Allen J. Moore, Patricia J. Moore, Robert J. Schmitz

PIF transcription factors link a neighbor threat cue to accelerated reproduction in Arabidopsis
Vinicius Costa Galvao, Anne-Sophie Fiorucci, Martine Trevisan, Jose Manuel Franco-Zorrilla, Anupama Goyal, Emanuel Schmid-Siegert, Roberto Solano, Christian Fankhauser

A single cis-element that controls cell-type specific expression in Arabidopsis
Jana Knerova, Patrick J Dickinson, Marek Szecowka, Steven J Burgess, Hugh Mulvey, Anne-Maarit Bagman, Allison Gaudinier, Siobhan M Brady, Julian M Hibberd

Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of Arabidopsis originome
Joana Sequeira-Mendes, Zaida Vergara, Ramon Peiro, Jordi Morata, Irene Araguez, Celina Costas, Raul Mendez-Giraldez, Josep Casacuberta, Ugo Bastolla, Crisanto Gutierrez

Loss of CG methylation in Marchantia polymorpha causes disorganization of cell division and reveals unique DNA methylation regulatory mechanisms of non-CG methylation.
Yoko Ikeda, Ryuichi Nishihama, Shohei Yamaoka, Mario A. Arteaga-Vazquez, Adolfo Aguilar-Cruz, Daniel Grimanelli, Romain Pogorelcnik, Robert A Martienssen, Katsuyuki T Yamato, Takayuki Kohchi, Takashi Hirayama, Olivier Mathieu

Isolation and characterization of mutants with altered seminal root numbers in hexaploid wheat
Oluwaseyi Shorinola, Ryan Kaye, Stefan Kepinski, CRISTOBAL UAUY

Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing
Nowlan H Freese, April R. Estrada, Ivory C. Blakley, Jinjie Duan, Ann E. Loraine

The USTC complex co-opts an ancient machinery to drive piRNA transcription in C. elegans
Chenchun Weng, Asia Kosalka, Ahmet C. Berkyurek, Przemislaw Stempor, Xuezhu Feng, Hui Mao, Chenming Zeng, Wen-Jun Li, Yong-Hong Yan, Meng-Qiu Dong, Cecilia Zuliani, Orsolya Barabas, Julie Ahringer, Shouhong Guang, Eric Miska

| Stem cells, regeneration & disease modelling

Platypus Induced Pluripotent Stem Cells: the Unique Pluripotency Signature of a Monotreme
Deanne J Whitworth, Ioannis Limnios, Maely Gauthier, Prasanna Weeratunga, Dmitry Ovchinnikov, Gregory Baillie, Sean Grimmond, Jennifer Graves, Ernst J Wolvetang

Regulating prospero mRNA Stability Determines When Neural Stem Cells Stop Dividing
Lu Yang, Tamsin J. Samuels, Yoav Arava, Francesca Robertson, Aino I. Järvelin, Ching-Po Yang, Tzumin Lee, David Ish-Horowicz, Ilan Davis

Axin proteolysis by Iduna is required for the regulation of stem cell proliferation and intestinal homeostasis in Drosophila
Yetis Gultekin, Hermann Steller

The creation of sexual dimorphism in Drosophila gonad stem cell niches
Nicole Camara, Cale Whitworth, Mark Van Doren

Subunit redundancy within the NuRD complex ensures fidelity of ES cell lineage commitment
Thomas Burgold, Michael Barber, Susan Kloet, Julie Cramard, Sarah Gharbi, Robin Floyd, Masaki Kinoshita, Meryem Ralser, Michiel Vermeulen, Nicola Reynolds, Sabine Dietmann, Brian Hendrich

The molecular logic of Nanog-induced self-renewal
Victor Heurtier, Nick Owens, Inma Gonzalez, Florian Mueller, Caroline Proux, Damien Mornico, Philippe Clerc, Agnes Dubois, Pablo Navarro

Signalling pathways drive heterogeneity of ground state pluripotency
Kirsten R McEwen, Sarah Linnett, Harry G Leitch, Prashant Srivastava, Lara Al-Zouabi, Tien-Chi Huang, Maxime Rotival, Alex Sardini, Thalia E Chan, Sarah Filippi, Michael Stumpf, Enrico Petretto, Petra Hajkova

Non-adhesive alginate hydrogels support growth of pluripotent stem cell-derived intestinal organoids
Meghan M. Capeling, Michael Czerwinski, Sha Huang, Yu-Hwai Tsai, Angeline Wu, Melinda S. Nagy, Benjamin Juliar, Yang Song, Nambirajan Sundaram, Shuichi Takayama, Eben Alsberg, Michael Helmrath, Andrew J. Putnam, Jason R Spence

In Vitro Assay for the Detection of Network Connectivity in Embryonic Stem Cell-Derived Cultures
Jeffrey R Gamble, Eric T Zhang, Nisha Iyer, Shelly Sakiyama-Elbert, Dennis L. Barbour

Towards an autologous iPSC-derived patient-on-a-chip
Anja Patricia Ramme, Leopold Koenig, Tobias Hasenberg, Christine Schwenk, Corinna Magauer, Daniel Faust, Alexandra K. Lorenz, Anna-Catharina Krebs, Christopher Drewell, Kerstin Schirrmann, Alexandra Vladetic, Grace-Chiaen Lin, Stephan Pabinger, Winfried Neuhaus, Frederic Bois, Roland Lauster, Uwe Marx, Eva-Maria Dehne

Need for high-resolution Genetic Analysis in iPSC: Results and Lessons from the ForIPS Consortium
Bernt Popp, Mandy Krumbiegel, Janina Grosch, Annika Sommer, Steffen Uebe, Zacharias Kohl, Sonja Ploetz, Michaela Farrell, Udo Trautmann, Cornelia Kraus, Arif B Ekici, Reza Asadollahi, Martin Regensburger, Katharina Guenther, Anita Rauch, Frank Edenhofer, Juergen Winkler, Beate Winner, Andre Reis

Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs
Emily E Burke, Joshua G Chenoweth, Joo Heon Shin, Leonardo Collado-Torres, Suel Kee Kim, Nicola Micali, Yanhong Wang, Richard E Straub, Daniel J Hoeppner, Huei-Ying Chen, Alana Lescure, Kamel Shibbani, Gregory R Hamersky, BaDoi N Phan, William S Ulrich, Cristian Valencia, Amritha Jaishankar, Amanda J Price, Anandita Rajpurohit, Stephen A Semick, Roland Bürli, James C Barrow, Daniel J Hiler, Stephanie Cerceo Page, Keri Martinowich, Thomas M Hyde, Joel E Kleinman, Karen F Berman, José A Apud, Alan J Cross, Nick J Brandon, Daniel R Weinberger, Brady J Maher, Ronald DG McKay, Andrew E Jaffe

Continuous single cell transcriptome dynamics from pluripotency to hemangiogenic lineage
Haiyong Zhao, Kyunghee Choi

Alternative splicing links histone modifications to stem cell fate decision
Yungang Xu, Weilling Zhao, Scott D. Olson, Karthik S. Prabhakara, Xiaobo Zhou

Soft Substrate Maintains Proliferative and Multi-lineage Potential of Human Mesenchymal Stem Cells on Long Term Expansion
Sanjay Kumar Kureel, Pankaj Mogha, Akshada Khadpekar, Vardhman Kumar, Rohit Joshi, Siddhartha Das, Jayesh Bellare, Abhijit Majumder

Dynamic Distribution Decomposition for Single-Cell Snapshot Time Series Identifies Subpopulations and Trajectories during iPSC Reprogramming
Jake Taylor-King, Asbjorn Riseth, Manfred Claassen

Gfi1-expressing Paneth cells revert to stem cells following intestinal injury
Min-Shan Chen, Yuan-Hung Lo, Joann Butkus, Winnie Zou, Yu-Jung Tseng, Hsin-I Jen, Shreena Patel, Andrew Groves, Mary Estes, Ergun Sahin, Mark Frey, Peter Dempsey, Noah Shroyer

JNK-mediated spindle reorientation in stem cells promotes dysplasia in the aging intestine
Daniel Hu, Heinrich Jasper

Regeneration of dopaminergic neurons in adult zebrafish depends on immune system activation and differs for distinct populations
Lindsey J. Caldwell, Nick O. Davies, Leonardo Cavone, Karolina S. Mysiak, Svetlana A. Semenova, Pertti Panula, J. Douglas Armstrong, Catherina G. Becker, Thomas Becker

Damage-induced reactive oxygen species enable regenerative signalling by the rapid repositioning of Hedgehog expressing cells.
Henry Roehl, Montserrat Garcia Romero, Gareth McCathie, Philip Jankun

Regeneration of the zebrafish retinal pigment epithelium after widespread genetic ablation
Nicholas Hanovice, Lyndsay Leach, Kayleigh Slater, Ana Gabriel, Dwight Romanovicz, Enhua Shao, Ross Collery, Edward Burton, Kira Lathrop, Brian Link, Jeff Gross

CNTN5-/+ or EHMT2-/+ iPSC-Derived Neurons from Individuals with Autism Develop Hyperactive Neuronal Networks
Eric Deneault, Muhammad Faheem, Sean H White, Deivid C Rodrigues, Song Sun, Wei Wei, Alina Piekna, Tadeo Thompson, Jennifer L Howe, Leon Chalil, Vickie Kwan, Susan Walker, Peter Pasceri, Frederick P Roth, Ryan KC Yuen, Karun K Singh, James Ellis, Stephen W Scherer

TUBA1A mutations identified in lissencephaly patients dominantly disrupt neuronal migration and impair dynein activity
Jayne Aiken, Jeffrey Moore, Emily Anne Bates

APP-induced patterned neurodegeneration exacerbated by APOE4 in C. elegans
Wisath Sae-Lee, Luisa L Scott, Aliyah J Encarnacion, Pragati Kore, Lashaun O Oyibo, Congxi Ye, Jonathan T. Pierce

Zebrafish duox mutations provide a model for human congenital hypothyroidism
Kunal Chopra, Shoko Ishibashi, Enrique Amaya

Intracellular calcium dysregulation precedes muscle decline in C. elegans modeling Duchenne muscular dystrophy
Anjelica Rodriguez, Kiley Hughes, Andrew Schuler, Brian Rodemoyer, Chance Bainbridge, Lucas Barickman, Kori Cuciarone, Alex Kullman, Calis Lim, Neha Gutta, Yazmine Giliana, Lavanya Sathyamurthy, Sruthi Singaraju, Samantha Vemuri, Victoria Andriulis, Dana Niswonger, Andres G Vidal-Gadea

PRSS56 is required for the developmental positioning of ocular angle structures
Cassandre Labelle-Dumais, Nicholas G Tolman, Seyyedhassan Paylakhi, Simon WM John, K Saidas Nair

The mechanical impact of col11a2 loss on joints; col11a2 mutant zebrafish show changes to joint development and function which lead to early onset osteoarthritis
Elizabeth A Lawrence, Erika Kague, Jessye A Aggleton, Robert L Harniman, Karen A Roddy, Chrissy L Hammond

Evo-devo & evo

Evolution of limb development in cephalopod mollusks
Oscar A. Tarazona, Davys H. Lopez, Leslie A Slota, Martin J. Cohn

Breaking the ladder: Evolution of the ventral nerve cord in Annelida
Conrad Helm, Patrick Beckers, Thomas Bartolomaeus, Stephan H. Drukewitz, Ioannis Kourtesis, Anne Weigert, Guenter Purschke, Katrine Worsaae, Torsten H. Struck, Christoph Bleidorn

Evolution of Endothelin signaling and diversification of adult pigment pattern in Danio fishes
Jessica Spiewak, Emily Bain, Jin Liu, Kellie Kou, Samantha Sturiale, Larissa Patterson, Parham Diba, Judith Eisen, Ingo Braasch, Julia Ganz, David M. Parichy

Quantitative comparison of the anterior-posterior patterning system in the embryos of five Drosophila species
Zeba Wunderlich, Charless C. Fowlkes, Kelly B. Eckenrode, Meghan D. J. Bragdon, Arash Abiri, Angela H. DePace

Zelda and the evolution of insect metamorphosis
Alba Ventos-Alfonso, Guillem Ylla, Xavier Belles

Myoglianin triggers the pre-metamorphosis stage in hemimetabolan insects
Orathai Kamsoi, Xavier Belles

A test of the general occurrence and predictive utility of isochronal, equiproportional, ‘variable proportional’, and ‘mixed’ development among arthropods
Brady Quinn

Divergent genetic mechanisms lead to spiny hair in mammals
Gislene L. Goncalves, Renan Maestri, Gilson R.P. Moreira, Marly A.M. Jacobi, Thales R.O. Freitas, Hopi E. Hoekstra

Sexually dimorphic gene expression and transcriptome evolution provides mixed evidence for a fast-Z effect in Heliconius
Ana Pinharanda, Marjolaine Rousselle, Simon H Martin, Joseph J Hanly, John W Davey, Sujai Kumar, Nicolas Galtier, Chris D Jiggins

Step-wise evolution of temperature-mediated phenotypic plasticity in eyespot size across nymphalid butterflies
Shivam Bhardwaj, Lim Si Hui Jolander, Markus R. Wenk, Jeffrey C. Oliver, H. Frederik Nijhout, Antonia Monteiro

Evolution of the embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians.
Alicia Madgwick, Marta Silvia Magri, Christelle Dantec, Damien Gailly, Ulla-Maj Fiuza, Leo Guignard, Sabrina Hettinger, Jose Luis Gomez-Skarmeta, Patrick Lemaire

Rampant hybrid misexpression in craniofacial tissues within a recent adaptive radiation of Cyprinodon pupfishes
Joseph Alan McGirr, Christopher Herbert Martin

Did position-effect guide the evolutionary dynamics of developmental gene expression?
Meenakshi Bagadia, Keerthivasan Raanin Chandradoss, Yachna Jain, Harpreet Singh, Mohan Lal, Kuljeet Singh Sandhu

Correlated Evolution of two Sensory Organs via a Single Cis-Regulatory Nucleotide Change
Olga Nagy, Isabelle Nuez, Rosina Savisaar, Alexandre Erwan Peluffo, Amir Yassin, Michael Lang, David L. Stern, Daniel Matute, Jean R. David, Virginie Courtier-Orgogozo

Evolution of salivary glue genes in Drosophila species
Jean-Luc Da Lage, Gregg W. C. Thomas, Magalie Bonneau, Virginie Courtier-Orgogozo

Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 33 primate species
Katja Heuer, Omer Faruk Gulban, Pierre-Louis Bazin, Anastasia Osoianu, Romain Valabregue, Mathieu Santin, Marc Herbin, Roberto Toro

Evolutionary parallelisms of pectoral and pelvic network-anatomy from fins to limbs
Borja Esteve-Altava, Stephanie E Pierce, Julia L Molnar, Peter Johnston, Rui Diogo, John R Hutchinson

Subdivision of ancestral scale genetic program underlies origin of feathers and avian scutate scales
Jacob M Musser, Gunter P Wagner, Cong Liang, Frank A Stabile, Alison Cloutier, Allan J Baker, Richard O Prum

Climate, habitat, and geographic range overlap drive plumage evolution
Eliot T Miller, Gavin M Leighton, Benjamin G Freeman, Alexander C Lees, Russell A Ligon

Base-pairing requirements for small RNA-mediated gene silencing of recessive self-incompatibility alleles in Arabidopsis halleri.
Nicolas Burghgraeve, Samson Simon, Simon Barral, Isabelle Fobis-Loisy, Anne-Catherine Holl, Chloe Ponitzki, Eric Schmitt, Xavier Vekemans, Vincent Castric

Genes involved in the convergent evolution of asexuality in stick insects
Darren J Parker, Jens Bast, Kirsten Jalvingh, Zoé Dumas, Marc Robinson-Rechavi, Tanja Schwander

The many nuanced evolutionary consequences of duplicated genes
Ashley I Teufel, Mackenzie M Johnson, Jon M Laurent, Aashiq H Kachroo, Edward M Marcotte, Claus O Wilke

Sexual Dichromatism Drives Diversification Within a Major Radiation of African Amphibians
Daniel M Portik, Rayna C Bell, David C Blackburn, Aaron M Bauer, Christopher D Barratt, William R Branch, Marius Burger, Alan Channing, Timothy J Colston, Werner Conradie, J. Maximillian Dehling, Robert C Drewes, Raffael Ernst, Eli Greenbaum, Václav Gvoždík, James Harvey, Annika Hillers, Mareike Hirschfeld, Gregory Jongsma, Jos Kielgast, Marcel T Kouete, Lucinda P Lawson, Adam D Leaché, Simon P Loader, Stefan Lötters, Arie van der Meijden, Michele Menegon, Susanne Müller, Zoltán T Nagy, Caleb Ofori-Boateng, Annemarie Ohler, Theodore J Papenfuss, Daniela Rößler, Ulrich Sinsch, Mark-Oliver Rödel, Michael Veith, Jens Vindum, Ange-Ghislain Zassi-Boulou, Jimmy A McGuire

The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle
Lucas Leclère, Coralie Horin, Sandra Chevalier, Pascal Lapébie, Philippe Dru, Sophie Peron, Muriel Jager, Thomas Condamine, Karen Pottin, Séverine Romano, Julia Steger, Chiara Sinigaglia, Carine Barreau, Gonzalo Quiroga-Artigas, Antonella Ruggiero, Cécile Fourrage, Johanna Kraus, Julie Poulain, Jean-Marc Aury, Patrick Wincker, Eric Quéinnec, Ulrich Technau, Michaël Manuel, Tsuyoshi Momose, Evelyn Houliston, Richard Copley

The draft genome sequence of mandrill (Mandrillus sphinx)
Ye Yin, Ting Yang, Huan Liu, Ziheng Huang, Yaolei Zhang, Yue Song, Wenliang Wang, Karsten Kristiansen

De Novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole genome duplication
Zelin Chen, Yoshihiro Omori, Sergey Koren, Takuya Shirokiya, Takuo Kuroda, Atsushi Miyamoto, Hironori Wada, Asao Fujiyama, Atsushi Toyoda, Suiyuan Zhang, Tyra G Wolfsberg, Koichi Kawakami, Adam M. Phillippy, NISC Comparative Sequencing Program, James C Mullikin, Shawn M Burgess

A Chromosome-Scale Assembly of the Enormous (32 Gb) Axolotl Genome
Jeramiah J. Smith, Nataliya Timoshevskaya, Vladimir A. Timoshevskiy, Melissa C. Keinath, Drew Hardy, S. Randal Voss

A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds
Andreas Wallberg, Ignas Bunikis, Olga Vinnere Pettersson, Mai-Britt Mosbech, Anna K Childers, Jay D Evans, Alexander S Mikheyev, Hugh M Robertson, Gene E Robinson, Matthew T Webster

Stout camphor tree genome fills gaps in understanding of flowering plant genome and gene family evolution
Shu-Miaw Chaw, Yu-Ching Liu, Han-Yu Wang, Yu-Wei Wu, Chan-Yi Ivy Lin, Chung-Shien Wu, Huei-Mien Ke, Lo-Yu Chang, Chih-Yao Hsu, Hui-Ting Yang, Edi Sudianto, Ming-Hung Hsu, Kun-Pin Wu, Ning-Ni Wang, James Leebens-Mack, Isheng Jason J Tsai

Genome sequence of the wheat stem sawfly, Cephus cinctus, a primitive hymenopteran and wheat pest, illuminates evolution of hymenopteran chemoreceptors
Hugh M Robertson, Robert M Waterhouse, Kimberly KO Walden, Livio Ruzzante, Maarten JMF Reijnders, Brad S Coates, Fabrice Legeai, Joanna C Gress, Sezgi Biyiklioglu, David K Weaver, Kevin W Wanner, Hikmet Budak

Cell biology

Cell morphological motif detector for high-resolution 3D microscopy images
Meghan K Driscoll, Erik S Welf, Kevin M Dean, Reto Fiolka, Gaudenz Danuser

Extreme nuclear branching in healthy epidermal cells of the Xenopus tail fin
Hannah E. Arbach, Marcus Harland-Dunaway, Jessica K. Chang, Andrea E. Wills

Analysis of P granules in vivo and ex vivo
Andrea Putnam, Madeline Cassani, Jarrett Smith, Geraldine Seydoux

Live tracking of inter-organ communication by endogenous exosomes in vivo
Frederik J Verweij, Celine Revenu, Guillaume Arras, Florent Dingli, Loew Damarys, Gautier Follain, Guillaume Allio, Jacky Goetz, Philippe Herbomel, Filippo Del Bene, Graca Raposo, Guillaume van Niel

Filopodome mapping identifies p130Cas as a mechanosensitive regulator of filopodia stability
Guillaume Jacquemet, Rafael Saup, Hellyeh Hamidi, Mitro Miihkinen, Johanna Ivaska

Tissue-specific degradation of essential centrosome components reveals distinct microtubule populations at microtubule organizing centers
Maria D Sallee, Jenny C Zonka, Taylor D Skokan, Brian C Raftrey, Jessica L Feldman

Ancestral Roles of the Fam20C Family of Secreted Protein Kinases Revealed by Functional Analysis in C. elegans
Adina Gerson-Gurwitz, Carolyn A Worby, Kian-Yong Lee, Renat Khaliullin, Jeff Bouffard, Dhanya Cheerambathur, Erin J Cram, Karen Oegema, Jack E Dixon, Arshad Desai

Exocyst subunit Sec6 is positioned by microtubule overlaps in the moss phragmoplast prior to the arrival of cell plate membrane
Han Tang, Jeroen de Keijzer, Elysa Overdijk, Els Sweep, Maikel Steentjes, Joop Vermeer, Marcel Janson, Tijs Ketelaar

EphB2 and ERK signaling are required for heterotypic contact inhibition of locomotion to drive cell sorting
Simon Brayford, Eduardo Serna-Morales, Andrei Luchici, Toru Hiratsuka, Brian Stramer

Developmental Regulation of an Organelle Tether Coordinates Mitochondrial Remodeling in Meiosis
Eric Sawyer, Pallavi Joshi, Luke Berchowitz, Elcin Unal

Loss of vimentin intermediate filaments decreases peri-nuclear stiffness and enhances cell motility through confined spaces
Alison Elise Patteson, Katarzyna Pogoda, Fitzroy J. Byfield, Elisabeth E. Charrier, Peter A. Galie, Piotr Deptuła, Robert Bucki, Paul A. Janmey

p130Cas contributes to cellular mechanosensing and force exertion.
Hedde van Hoorn, Dominique M Donato, H. Emrah Balcioglu, Erik H Danen, Thomas Schmidt

Functional characterization of peroxisome biogenic proteins Pex5 and Pex7 of Drosophila
Francesca Di Cara, Richard A Rachubinski, Andrew J Simmonds

A positive feedback loop drives centrosome maturation in flies
Ines Alvarez Rodrigo, Paul T Conduit, Janina Baumbach, Zsofia A Novak, Mustafa G Aydogan, Alan Wainman, Jordan W Raff

Mechanisms of Kinesin-1 activation by Ensconsin/MAP7 in vivo
Mathieu Metivier, Brigette Monroy, Emmanuel Gallaud, Renaud Caous, Aude Pascal, Laurent Richard-Parpaillon, Antoine Guichet, Kassandra Ori-McKenney, Regis Giet

A centrosome calcium signal is essential for mammalian cell mitosis
Nordine Helassa, Charlotte Nugues, Robert D Burgoyne, Lee P Haynes

Drosophila kinesin-8 stabilises kinetochore-microtubule interaction
Tomoya Edzuka, Gohta Goshima

Atypical septate junctions maintain the somatic enclosure around maturing spermatids and prevent premature sperm release in Drosophila testis.
Pankaj Dubey, Tushna Kapoor, Samir Gupta, Seema Shirolikar, Krishanu Ray

The Drosophila Cortactin Binding Protein 2 homolog, Nausicaa, regulates lamellipodial actin dynamics in a Cortactin-dependent manner.
Meghan E O’Connell, Divya Sridharan, Tristan Driscoll, Ipsita Krishnamurthy, Wick G Perry, Derek A Applewhite

Lysosome exocytosis is required for mitosis
Charlotte Nugues, Nordine Helassa, Lee Haynes

Nuclear pore density controls heterochromatin reorganization during senescence
Wendy Bickmore, Charlene Boumendil, Priya Hari, Karl Olsen, Juan-Carlos Acosta

Mother centrioles are dispensable for deuterosome formation and function during basal body amplification
Huijie Zhao, Qingxia Chen, Qiongping Huang, Xiumin Yan, Xueliang Zhu

Mechanosensitive clathrin platforms anchor desmin intermediate filaments in skeletal muscle
Agathe Franck, Jeanne Laine, Gilles Moulay, Michael Trichet, Christel Gentil, Anais Fongy, Anne Bigot, Sofia Benkhelifa-Ziyyat, Emmanuelle Lacene, Mai Thao Bui, Guy Brochier, Pascale Guicheney, Sabrina Sacconi, Vincent Mouly, Norma Beatriz Romero, Catherine Coirault, Marc Bitoun, Stephane Vassilopoulos

The cytoskeleton as a smart composite material: A unified pathway linking microtubules, myosin-II filaments and integrin adhesions
Nisha Mohd Rafiq, Yukako Nishimura, Sergey V. Plotnikov, Visalatchi Thiagarajan, Zhen Zhang, Meenubharathi Natarajan, Shidong Shi, Virgile Viasnoff, Gareth E. Jones, Pakorn Kanchanawong, Alexander D. Bershadsky

Rudhira/BCAS3 couples microtubules and intermediate filaments to promote cell migration for angiogenic remodeling
Divyesh Joshi, Maneesha S Inamdar

Modelling

Predicting division planes of three-dimensional cells by soap-film minimization
Pablo Martinez, Lindy Allsman, Kenneth A Brakke, Christopher Hoyt, Jordan Hayes, Hong Liang, Wesley Neher, Yue Rui, Allyson Roberts, Amir Moradifam, Bob Goldstein, Charles Anderson, Carolyn G Rasmussen

Dynamics of PAR proteins explain the oscillation and ratcheting mechanisms in dorsal closure
Clinton H. Durney, Tony J. C. Harris, James J. Feng

Tensional homeostasis in multicellular clusters: effects of geometry and traction force dynamics
Dimitrije Stamenovic, Juanyong Li, Paul E. Barbone, Michael L. Smith

Pulling in models of cell migration
Christian A. Yates, George Chappelle

Modifying Reaction Diffusion: A Numerical Model for Turing Morphogenesis, Ben Jacob Patterns, and Cancer Growth
Kai Trepka

Toward deciphering developmental patterning with deep neural network
Jingxiang Shen, Feng Liu, Chao Tang

Long-range memory of growth and cycle progression correlates cell cycles in lineage trees
Erika E Kuchen, Nils Becker, Nina Claudino, Thomas Hofer

Noise-driven Cell Differentiation and the Emergence of Organization
Hadiseh Safdari, Ata Kalirad, Cristian Picioreanu, Rouzbeh Tusserkani, Bahram Goliaei, Mehdi Sadeghi

Tools & resources

| Imaging etc.

se

Panoptic vDISCO imaging reveals neuronal connectivity, remote trauma effects and meningeal vessels in intact transparent mice
Ruiyao Cai, Chenchen Pan, Alireza Ghasemigharagoz, Mihail I. Todorov, Benjamin Foerstera, Shan Zhao, Harsharan S. Bhatia, Leander Mrowka, Delphine Theodorou, Markus Rempfler, Anna Xavier, Benjamin T. Kress, Corinne Benakis, Arthur Liesz, Bjoern Menze, Martin Kerschensteiner, Maiken Nedergaard, Ali Erturk

Cortical Column and Whole Brain Imaging of Neural Circuits with Molecular Contrast and Nanoscale Resolution
Ruixuan Gao, Shoh M Asano, Srigokul Upadhyayula, Igor Pisarev, Daniel E Milkie, Tsung-Li Liu, Ved Singh, Austin Graves, Grace H Huynh, Yongxin Zhao, John Bogovic, Jennifer Colonell, Carolyn M Ott, Christopher Zugates, Susan Tappan, Alfredo Rodriguez, Kishore R Mosaliganti, Sean G Megason, Jennifer Lippincott-Schwartz, Adam Hantman, Gerald M Rubin, Tom Kirchhausen, Stephan Saalfeld, Yoshinori Aso, Edward S Boyden, Eric Betzig

Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy
Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, Siân Culley, Maurício Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, Ricardo Henriques, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, Eugene W. Myers

Tiling light sheet selective plane illumination microscopy using discontinuous light sheets
Liang Gao

MemBright: a Family of Fluorescent Membrane Probes for Advanced Cellular Imaging and Neuroscience
Mayeul Collot, pichandi ashokkumar, Halina Anton, Emmanuel Boutant, Orestis Faklaris, Thierry Galli, Yves Mely, Lydia Danglot, Andrey S. Klymchenko

Self-healing dyes for super-resolution microscopy
Jasper van der Velde, Jochem Smit, Michel Punter, Thorben Cordes

Accelerated FRET-PAINT Microscopy
Jongjin Lee, Sangjun Park, Sungchul Hohng

Commonly-used FRET fluorophores promote collapse of an otherwise disordered protein.
Joshua A Riback, Micayla A Bowman, Adam M Zmyslowski, Kevin W Plaxco, Patricia L Clark, Tobin R Sosnick

Solid immersion microscopy readily and inexpensively enables 12 nm resolution on plunge-frozen cells
Marisa Luisa Martin-Fernandez, Lin Wang, Benji Bateman, Laura Carolina Zanetti-Domingues, Amy Moores, Sarah Rebecca Needham, Daniel Rolfe, Sam Astbury, Christopher Spindloe, Michelle Darrow, Maria Romano, Konstantinos Beis, David Clarke

Super-resolution fight club: A broad assessment of 2D & 3D single-molecule localization microscopy software
Daniel Sage, Thanh-An Pham, Hazen Babcock, Tomas Lukes, Thomas Pengo, Jerry Chao, Ramraj Velmurugan, Alex Herbert, Anurag Agrawal, Silvia Colabrese, Ann Wheeler, Anna Archetti, Bernd Rieger, Raimund Ober, Guy M. Hagen, Jean-Baptiste Sibarita, Jonas Ries, Ricardo Henriques, Michael Unser, Seamus Holden

Development of a genetically encoded sensor for endogenous CaMKII activity
Goli Ardestani, Megan West, Thomas J Maresca, Rafael A Fissore, Margaret M Stratton

Systematic assessment of GFP tag position on protein localization and growth fitness in yeast
Dan Davidi, Uri Weill, Gat Krieger, Zohar Avihou, Ron Milo, Maya Schuldiner

3D-printable tools for developmental biology: Improving embryo injection and screening techniques through 3D-printing technology
Marta Truchado-Garcia, Richard M Harland, Michael J Abrams

Coherent-hybrid STED: a tunable photo-physical pinhole for super-resolution imaging at high contrast
Antonio J Pereira, Mafalda Sousa, Ana C Almeida, Luisa T Ferreira, Ana Rita Costa, Marco Novais-Cruz, Cristina Ferras, Monica Mendes Sousa, Paula Sampaio, Michael Belsley, Helder Maiato

| Genome tools

Super-Mendelian inheritance mediated by CRISPR/Cas9 in the female mouse germline
Hannah A. Grunwald, Valentino M. Gantz, Gunnar Poplawski, Xiang-ru S. Xu, Ethan Bier, Kimberly L. Cooper

SANe: The Seed Active Network for Discovering Transcriptional Regulatory Programs of Seed Development.
Chirag Gupta, Arjun Krishnan, Andrew Schneider, Cynthia Denbow, Eva Collakova, Pawel Wolinski, Andy Pereira

Short hairpin RNAs artifactually impair cell growth and suppress clustered microRNA expression.
John Powers, Edrualdo da Rocha, Daniel Pearson, Pavlos Missios, Tarja Yvanka de Soysa, Jessica Barragan, Patrick Cahan, George Daley

RNAlater and flash freezing storage methods nonrandomly influence observed gene expression in RNAseq experiments
Courtney N. Passow, Thomas J. Y. Kono, Bethany A. Stahl, James B. Jaggard, Alex C. Keene, Suzanne E. McGaugh

CRISPR-Cas9 human gene replacement and phenomic characterization in Caenorhabditis elegans to understand the functional conservation of human genes and decipher variants of uncertain significance
Troy A McDiarmid, Vinci Au, Aaron Loewen, Joseph J.H. Liang, Kota Mizumoto, Donald G Moerman, Catharine H Rankin

Optimizing guide RNA selection and CRISPR/Cas9 methodology for efficient generation of deletions in C. elegans.
Vinci Au, Erica Li-Leger, Greta Raymant, Stephane Flibotte, George Chen, Kiana Martin, Lisa Fernando, Claudia Doell, Federico Rosell, Su Wang, Mark Edgley, Ann Rougvie, Harald Hutter, Donald G. Moerman

Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting
Francesco Iorio, Fiona M Behan, Emanuel Goncalves, Shriram Bhosle, Elisabeth Chen, Rebecca Shepherd, Charlotte Beaver, Rizwan Ansari, Rachel Pooley, Piers Wilkinson, Sarah Harper, Adam P Butler, Euan Stronach, Julio Saez-Rodriguez, Kosuke Yusa, Mathew J Garnett

A total synthetic approach to CRISPR/Cas9 genome editing and homology directed repair
Sara E. DiNapoli, Raul Martinez-McFaline, Caitlin K. Gribbin, Courtney A. Balgobin, Isabel Nelson, Abigail Leonard, Darya Mailhiot, Clara Kao, Sean McDonnell, Jill L.O. de Jong, Yariv Houvras

Up, down, and out: optimized libraries for CRISPRa, CRISPRi, and CRISPR-knockout genetic screens
Kendall R Sanson, Ruth E Hanna, Mudra Hegde, Katherine F Donovan, Christine Strand, Meagan E Sullender, Emma W Vaimberg, Amy Goodale, David E Root, Federica Piccioni, John G Doench

Highly efficient scarless knock-in of reporter genes into human and mouse pluripotent stem cells via transient antibiotic selection
Valentin M Sluch, Xitiz Chamling, Claire Wenger, Yukan Duan, Dennis S Rice, Donald J Zack

CRISPR/Cas9 Targeted Capture Of Mammalian Genomic Regions For Characterization By NGS
Alexei Slesarev, Lakshmi Viswanathan, Yitao Tang, Trissa Borgschulte, Katherine Achtien, David Razafsky, David Onions, Audrey Chang, Colette Cote

A neuron-optimized CRISPR/dCas9 activation system for robust and specific gene regulation
Katherine E. Savell, Svitlana V. Bach, Morgan E. Zipperly, Jasmin S. Revanna, Nicholas A. Goska, Jennifer J. Tuscher, Corey G. Duke, Faraz A. Sultan, Julia N. Burke, Derek M. Williams, Lara Ianov, Jeremy J Day

Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
Joseph W Foley, Chunfang Zhu, Philippe Jolivet, Shirley X Zhu, Peipei Lu, Michael J Meaney, Robert B West

Web-based design and analysis tools for CRISPR base editing
Gue-ho Hwang, Jeongbin Park, Kayeong Lim, Sunghyun Kim, Jihyeon Yu, Sang-Tae Kim, Roland Eils, Jin-Soo Kim, Sangsu Bae

DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors
Christopher S McGinnis, Lyndsay M Murrow, Zev J Gartner

CRISPR-bind: a simple, custom CRISPR/dCas9-mediated labeling of genomic DNA for mapping in nanochannel arrays
Denghong Zhang, Saki Chan, Kenneth Sugerman, Joyce Lee, Ernest T Lam, Sven Bocklandt, Han Cao, Alex R Hastie

A simple and effective method to isolate germ nuclei from C. elegans for genomic assays.
Mei Han, Guifeng Wei, Catherine E McManus, Valerie Reinke

Panoramic stitching of heterogeneous single-cell transcriptomic data
Brian L Hie, Bryan Bryson, Bonnie Berger

Ultra-sensitive proteome profiling of FACS-isolated cell populations by data-independent acquisition-MS: Application to human hematopoietic stem and progenitor cells
Sabine Amon, Fabienne Meier-Abt, Ludovic C Gillet, Slavica Dimitrieva, Alexandre PA Theocharides, Markus G Manz, Ruedi Aebersold

High-throughput yeast two-hybrid library screening using next generation sequencing
Alain Goossens, Marie-Laure Erffelinck, Bianca Ribeiro, Maria Perassolo, Laurens Pauwels, Jacob Pollier, Veronique Storme

A GAL80 collection to inhibit GAL4 transgenes in Drosophila olfactory sensory neurons
Jessica Eliason, Ali Afify, Christopher Potter, Ichiro Matsumura

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing
Kenta Sato, Koki Tsuyuzaki, Kentaro Shimizu, Itoshi Nikaido

Research practice & education

High cost of bias: Diminishing marginal returns on NIH grant funding to institutions
Wayne P. Wahls

The GRE Over the Entire Range of Scores Lacks Predictive Ability for PhD Outcomes in the Biomedical Sciences
Linda Sealy, Christina Saunders, Jeffery Blume, Roger Chalkley

Long term impact of intensive post graduate laboratory training at the Cold Spring Harbor Neurobiology of Drosophila summer course
Sarah Ly, Karla Kaun, Chi-hon Lee, David Stewart, Stefan R Pulver, Alex C Keene

Manipulating the alpha level cannot cure significance testing

Trafimow D, Amrhein V, Areshenkoff CN, Barrera-Causil C, Beh EJ, Bilgiç Y, Bono R, Bradley MT, Briggs WM, Cepeda-Freyre HA, Chaigneau SE, Ciocca DR, Carlos Correa J, Cousineau D, de Boer MR, Dhar SS, Dolgov I, Gómez-Benito J, Grendar M, Grice J, Guerrero-Gimenez ME, Gutiérrez A, Huedo-Medina TB, Jaffe K, Janyan A, Karimnezhad A, Korner-Nievergelt F, Kosugi K, Lachmair M, Ledesma R, Limongi R, Liuzza MT, Lombardo R, Marks M, Meinlschmidt G, Nalborczyk L, Nguyen HT, Ospina R, Perezgonzalez JD, Pfister R, Rahona JJ, Rodríguez-Medina DA, Romão X, Ruiz-Fernández S, Suarez I, Tegethoff M, Tejo M, van de Schoot R, Vankov I, Velasco-Forero S, Wang T, Yamada Y, Zoppino FC, Marmolejo-Ramos F

Inferential statistics are descriptive statistics

Valentin Amrhein, David Trafimow, Sander Greenland

Making headlines: An analysis of US government-funded cancer research mentioned in online media

Lauren A Maggio, Chelsea L Ratcliff, Melinda Krakow, Laura L Moorhead, Asura Enkhbayar, Juan Pablo Alperin

Why not…

The humungous fungus of Michigan three decades on
James B Anderson, Johann N Bruhn, Dahlia Kasimer, Hao Wang, Nicolas Rodrigue, Myron L Smith

How do your genetics compare to the world’s elite marathoners?
Gregory E Sims, Xiang-Pei Zheng, Jeffrey Falk, Michael Nova

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Deadline extended ! 26 Aug. 2018

Conference Jacques Monod in Developmental Biology, « Modeling Cell Fate »

Program

Students and postdocs are encouraged to apply.
The conference is eligible for tebu-bio travel grants (see https://www.tebu-bio.com/cms/1081/Get_your_400EUR_tebu_bio_Travel_Grant.html for the next draws).

Please spread the news!

Looking forward to seeing you in Roscoff soon,

laure Bally-Cuif & Claude Desplan, conference organizers

Invited speakers:

Geneviève Almouzni
Alexander Aulehla
Allison Bardin
Dominique Bergmann
Florence Besse
Sarah Bray
Claire Chazaud
Enrico Coen
Michèle Crozatier
Alain Goriely
Thomas Gregor
Laura Johnston
Frank Jülicher
Ryoichiro Kageyama
Bill Keyes
Thomas Lecuit
Andrew Oates
Patrick O’Farrell
Ewa Paluch
Nancy Papalopulu
Catherine Rabouille
Jody Rosenblatt
François Schweisguth
Benjamin Simons
Claudio Stern
Julien Vermot
Jean-Paul Vincent
Magdalena Zernicka-Goetz

(1 votes)

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