Applications are invited from outstanding individuals to work under the supervision of Dr Rui Monteiro, Birmingham Fellow, on a BHF funded research project to study the role of TGFb signalling in angiogenic and haemogenic endothelial cell programming. The Monteiro Lab are interested in learning how extrinsic signalling impinges on lineage fate decisions in development and how progenitors and stem cells carry out those decisions, with a particular emphasis on the Transforming Growth Factor β (TGFβ) pathway. Previous work in the lab demonstrated that TGFb1 and TGFb3 play different roles in programming haemogenic endothelium to become of blood stem cells in vivo (Monteiro et al, 2016). The Research Fellow will study the gene regulatory network that carries out the ligand-specific functions for TGFb1 and TGFb3 ligands in haemogenic and angiogenic endothelium in vivo. They will make use of several approaches, including genome editing with CRISPR/Cas9, transgenesis, fluorescence activated cell sorting and transcriptional and epigenetic profiling using zebrafish as a model.

 

The successful applicant will have a first degree and a PhD in developmental biology, molecular genetics, biology or in a related discipline relevant to the project. They will also have a strong background in molecular biology and previous experience with model organism and/or analysis of transcriptomic and epigenetic data.

 

Informal enquiries should be directed to Dr. Rui Monteiro (R.Monteiro@bham.ac.uk)

Starting salary is normally on Grade 7 according to experience.

Closing date: 10 March 2018            Reference:  58652

 

To download the details of this position and submit an electronic application online please go to https://www.birmingham.ac.uk/staff/jobs/index.aspx. Please quote the appropriate Job Ref in all enquiries, alternatively information can be obtained from www.hr.bham.ac.uk

(No Ratings Yet)
Loading...

PD2018-03 – Computational study of cell pattern emergence in embryonic and tumorigenic tissues

Project abstract – The ability of cells to self-organize into patterned tissues composed of multiple cell types is central to animal morphogenesis and relies on both biological and physical factors. We propose to investigate numerically and from a biophysical point of view the pattern formation observed in two different complex tissues respectively characterised by their stereotyped vs seemingly disorganised structure: the embryonic epithelium of Xenopus (with A. Pasini) and Drosophila brain tumors (with C. Maurange).

In Xenopus, we will study how multiciliated cells (MCCs) distribute in a regularly spaced pattern during intercalation into an epithelial layer, and explore how the pattern is established and maintained through a balance between mutual repulsion among MCCs and attraction between MCCs and epithelial layer cells. In Drosophila, we will study how clusters of brain cancer stem cells (CSCs) form and how they affect tumor progression. We will investigate how physical (tension, adhesion) and biochemical (growth and differentiation factors) cues contribute to segregate clusters of cells with different self-renewing potentials, regulate their size distribution and density, and thus determine tumor growth rate.

The computational tools envisaged for the project involve the numerical implementation of energy minimization algorithms such as the Cellular Potts Model (with R. Clément). We plan to model both systems with an energy function encompassing the different biological and physical interactions suspected to play a role in the processes. Such energy functions can comprise adhesion, tension, affinities or repulsions among cell types. Motility and cell proliferation can also be implemented at given rates, depending on cell types. Models with be implemented in light of the experimental results, and we expect that simulations will in turn guide the design of new biological experiments.

Expected profile – Candidates should have a robust background in physics and numerical simulations, and ideally be familiar with the Potts Model and its cellular version. As the project is strongly interdisciplinary and involves close collaboration with experimental biologists, previous experience in developmental biology or biophysics will be appreciated. A strong interest in biological questions, in particular in the principles of morphogenesis, is mandatory.

Scientific environment – The recruited post-doc will benefit from a world-class interdisciplinary environment, both within the IBDM (Marseilles Institute for Developmental Biology) and among the other institutes taking part into the CENTURI program.

Supervisors

Raphaël Clément (raphael.clement@univ-amu.fr)- IBDM, UMR 7288 – Cell and tissue physics – Team Lenne

Cédric Maurange (cedric.maurange@univ-amu.fr)- IBDM, UMR7288 – Neural stem cell plasticity – Team Maurange

Andrea Pasini (andrea.pasini@univ-amu.fr) – IBDM, UMR7288 – Biology of ciliated epithelia – Team Kodjabachian

Deadline for application: 28th February

Please apply online on the Centuri website.

Recruitment Form – PD2018-03 – Computational study of cell pattern emergence in embryonic and tumorigenic tissues

(No Ratings Yet)
Loading...

A postdoctoral position is available to study mechanisms of Sonic Hedgehog signal transduction in Stacey Ogden’s lab at St. Jude Children’s Research Hospital, Memphis, TN. The successful candidate will join a collaborative work group aimed at understanding how the Sonic Hedgehog pathway is regulated during development, and dissecting how its regulation is usurped in cancer. Areas of interest include biogenesis and secretion of the Hedgehog family ligands, contributions of lipid metabolism to pathway activity, regulation and signaling of the signal transducer Smoothened and investigation of the downstream effectors to which it signals. Research projects in the lab will entail use of biochemical and cell biological techniques and mouse model systems.

 

Applicants should have or expect a PhD degree at the time of application. The selected postdoctoral fellow will actively develop their own research project, perform laboratory experiments with minimal supervision, develop new procedures as needed and interact collaboratively with other members of the lab. The successful candidate will also actively participate in the publication and presentation of research results. Prior experience with signal transduction research, lipid metabolism or mouse model systems is preferred.

 

www.stjude.org/ogden

 

Email: Stacey.ogden@stjude.org

Phone: 901-595-6281

Application website: https://postdoc-stjude.icims.com/jobs

Job number: 38158

 

(No Ratings Yet)
Loading...

The San Francisco Declaration on Research Assessment (DORA) was conceived in 2012 at an ASCB meeting, and has since its launch in 2013 has garnered thousands of signatories from individuals and organisations. Its aim is to improve the way in which the quality of research output is evaluated, with a key recommendation being the elimination of journal-based metrics by funding agencies, institutions and publishers when judging research and researchers.

This year, DORA has had something of an upgrade: with the support of organisations including the Company of Biologists (the not-for-profit publisher that runs Development and funds the Node!), DORA now has a full time Community Manager Anna Hatch, a new steering committee, and a new website.

To find out more about these developments, we caught up with Stephen Curry, who chairs the DORA steering committee and is Professor of Structural Biology and Assistant Provost for Equality, Diversity and Inclusion at Imperial College London.

 

Hi Stephen! Can you tell us a bit about your science?

I’m a structural biologist and primarily use protein crystallography to work out the three-dimensional structures of interesting macromolecules. My main research efforts have been focused on virus and host-cell proteins involved in the replication of RNA viruses – principally foot-and-mouth disease virus and noroviruses. But I am in the process of winding down my research lab so that I can concentrate on other interests (discussed below) and my new role as Assistant Provost for Equality, Diversity and Inclusion at Imperial College.

 

You’re also passionate about science advocacy and communication – you are Vice Chair of the Science is Vital campaign group, contribute to The Guardian’s science blog Occam’s Corner, and have 16k followers on Twitter. Has this side of science – away from the lab bench – always been important to you?

It’s always been important but I’ve only really been properly active in this space since 2008 when I started my blog. I found that writing about science really made me think about what it means to be a scientist in 21^st century Britain and that led me to learn a lot about scientific publishing and research funding, both of which are tied in rather convoluted ways to the business of research assessment. I have enjoyed getting involved in these debates and in campaigns to bring about positive change. Being involved in Science it Vital right from the very beginning has been a fantastic lesson in what can be done with modern communication tools if you just knuckle down and get organised.

 

You were one of the original signatories to DORA – why was DORA necessary in 2013?

It was already overdue in 2013. I wasn’t involved in the formulation of the declaration but was invited to sign prior to the launch and didn’t hesitate to do so. I had already become aware of the perverting effects of journal impact factors on science and scientists’ careers. And I knew that many other people shared my concerns. My 2012 blogpost, Sick of Impact Factors, remains on of the most ‘popular’ that I have ever written. It clearly struck a nerve.

 

And what do you think has been achieved in the years since then?

DORA has been really helpful in re-focusing the conversation on how the scientific community does research assessment. Without anyone designing the system, journal metrics have been co-opted for the evaluation of individuals to such a degree that publication in certain tiles (infamously Nature, Cell and Science in the biomedical sciences) are now seen as the key to success. DORA has helped to challenge that view – though we should certainly be mindful of parallel work on the Leiden Manifesto and The Metric Tide report (on which I was a co-author). So I think there is much greater awareness of the nature of the problem now and even some tentative steps to address it.

 

So what’s new – what does DORA’s new lease of life entail?

What’s new is that DORA now has a much higher level of material and financial support (from 9 organisations: ASCB, Company of Biologists, CRUK, eLife, EMBO, F1000, Hindawi, PLoS, and Wellcome). That has allowed us to hire a full-time community manager (Dr Anna Hatch) and refresh the steering group, which I now chair. We’ve also refreshed out web-site and have a new, easy-to-find URL (sfdora.org). This will allow us to raise the profile of DORA – we mean to get the word out much more proactively – but we are also determined to make a renewed effort to ignite the discussion around what constitutes robust and effective research assessment. We know that to change practice we need to figure out practical ways to help busy reviewers sift through job and grant applications and CVs without falling back on mis-use of the JIF.

 

Personally, what has it been like to be involved with DORA – is it challenging to get consensus from such a broad group of scientists and organisations?

There’s a lot of work to do because there is always resistance to change. DORA is not out to name and shame people or organisations that haven’t signed. But we want to challenge them to think about research assessment and do what we can to help them find a way forward. We aim to do a much more comprehensive job of discovering and disseminating good practice from around the world.

 

Why (and how) should young researchers get involved in DORA?

Because bad research assessment leads to bad research. DORA’s focus on improving research assessment fits very well with the ambitions that first attracts early career researchers to research: to understand and change the world. We will do that best if we are doing a proper job of recognising and rewarding the best research. That’s not just about publishing the best science (irrespective of journal name), but also meshes with parallel concerns about open science, data and code sharing and efforts to address deepening concerns about reproducibility, which are at least partly due to our over-reliance on metrics such as the JIF for judging individuals. However, we cannot simply expect young researchers to take the responsibility for change; it is up to the old guard (people like myself) and organisations like DORA to provide real support.

---

Further DORA articles:

 

Stephen Curry’s World View in Nature

https://www.nature.com/articles/d41586-018-01642-w

 

Research Councils UK Press release:

http://www.rcuk.ac.uk/media/news/180207/

 

Research Councils UK statement on responsible metrics:

http://www.rcuk.ac.uk/documents/research/rcuk-statement-on-the-responsible-use-of-metrics-in-research-assessment-pdf/

 

Times Higher Education also wrote a story about DORA

https://www.timeshighereducation.com/news/funding-councils-sign-responsible-research-assessment#survey-answer

 

 

 

 

(2 votes)
Loading...

Primary supervisor: Professor Claudio Stern FMedSci FRS, Department of Cell and Developmental Biology, University College London

Project title: “Dynamics of cell behaviour during somite formation”

 

A studentship funded by the Anatomical Society is available in Claudio Stern’s lab. The project will study the mechanisms of somite formation, to elucidate the molecular and physical mechanisms that control somite size, shape and regional identity and the role of the “segmentation clock” and local cell-cell interactions in this process.  It is a multi-disciplinary project and will involve advanced live imaging (including super-resolution microscopy in vivo), molecular biology, biophysics and some computational modelling. The project may include travel to the labs of collaborators in the USA and/or Singapore.

 

Conditions and requirements: This PhD studentship is open to British, Irish or European citizens who have spent at least three years at a British or Irish institute of higher education. It is funded by the Anatomical Society of Great Britain and Ireland and offers a stipend (tax free) of £16,553 per annum (revised annually), university fees (UK/EU rate) and a contribution to research expenses as well as funds to travel to meetings. Funding is for 3 years but it may be extended to a fourth year if necessary. Candidates should have a 2.1 (or equivalent) degree or better in a Biomedical, Physical or Computational science-related area and strong interest in developmental biology, ideally along with some laboratory experience working in a biomedicine-related research project. Experience with microscopy, programming (preferably PYTHON) and/or other computational/mathematical skills, are not essential but will be an advantage.

 

Starting date: 1 October 2018 or earlier by arrangement.

To apply (with a cover letter, CV a brief statement of your interests and the names and contact details of two academic referees), or for further information please contact Prof. Stern: c.stern@ucl.ac.uk

There is no formal closing date for applications but a student will be appointed as soon as a suitable, high quality candidate is identified.

 

(No Ratings Yet)
Loading...

For both young and established developmental biologists considering their next career move, choosing a model system with which to answer one’s research questions is a big decision. Of course, the most important thing to consider is whether or not a particular system is compatible with your research goals. But for a young scientist looking to make the move from one system to another, the ease of such a transition is an important concern. Having transitioned from sea urchin to zebrafish and then to chicken, I am often asked about my experience working with each of these three organisms, and what the practical, hands-on similarities and differences are among these creatures as model systems for development.

 

It began with the sea urchin

 

 

For my graduate research I studied skeleton formation in the sea urchin embryo. Most laboratories get adult sea urchins either by lab-organized diving trips if the lab is close enough to the ocean, or much more commonly by purchasing them from a supplier. When the sea urchins get to the lab, they need to be carefully acclimatized to the artificial sea water and the temperatures of lab aquaria, as any stress can make them spawn out their precious gametes prematurely. The maintenance of these aquaria and the monitoring of a new shipment of animals is an important and time-consuming job. Harvesting sea urchin sperm and eggs is as simple as injecting potassium chloride into the adults, after which they usually die (sad face!). In some species, however, adults can be shaken vigorously to make them spawn, and these animals can be used a few more times.

A major disadvantage of the sea urchin as a model system is the inability to establish stable transgenic lines or to easily create knockouts. Most analyses of development therefore depend on knockdown and overexpression experiments, which though easy to perform by microinjections, are not always clean. On the other hand, the ability to produce very large numbers of embryos from each round of fertilization gives the sea urchin a strong advantage for large-scale experiments. Since in situ hybridization and immunohistochemistry can be done on whole embryos, no time is spent sectioning embryos prior to analysis. Also, these embryos are very easy to analyze with several types of microscopy. Sea urchin embryonic development lasts only 2-4 days depending on the species, a definite benefit for moving a project along. An unexpected advantage of the sea urchin is the ability to replicate results in several closely-related species, which makes for a stronger case when putting together a story for publication. This also makes it an interesting model for evo-devo research especially when comparing multiple urchin species to other echinoderms.

 

Fish, fish and more fish

 

 

After my initial love affair with the sea urchin, I transitioned to zebrafish during my postdoc where I made zebrafish models for rare human diseases. Unlike the average sea urchin lab where adult animals are acquired from an external supplier, zebrafish labs often have several stable lines in-house, maintained by breeding adult fish and raising their offspring. While all this aquaculture can be time-consuming for a graduate student or postdoc, many institutions have fish core facilities and/or staff hired specifically for fish husbandry. Male and female zebrafish are usually kept separately, and to get them to breed, you only need to put them together in the same tank and they take over from there.

The zebrafish has many of the same advantages as the sea urchin, as it is easy to get large numbers of relatively transparent embryos. Adult animal and embryo care is similar to the sea urchin, as are methods of microinjection and analysis of results. The distinct advantage of the zebrafish (and indeed the main reason I found it attractive as a model system) is the immense power of transgenics in this system.  Stable transgenic lines and knockouts are standard in the zebrafish field, and this opens up a world of possibilities for a researcher.

Another advantage of this system is the ability to culture embryos into adulthood. This lets you study a phenotype throughout the lifespan of the fish. Moreover, since the zebrafish is a closer relative to humans, antibodies raised against human proteins work better in the fish than they do in sea urchins. Aside from learning about zebrafish morphology and how to make the best use of the transgenic toolkit, my transition from sea urchin to zebrafish was seamless.

 

Chicken, anyone?

 

 

My current postdoctoral work is on neural crest and placode cells in the chicken embryo, which is distinct from the first two systems described. We get our embryos by incubating fertilized chicken eggs shipped in from a supplier, and as orders for eggs must be placed relatively far in advance, a researcher’s plan for experiments can fizzle out very quickly if egg quality is poor for a specific shipment. Also, a lot of time is spent on egg prep work, and you start out with fewer eggs, which means fewer embryos for your experiments.

Unlike aquatic embryos where you can just peek into a petri dish to tell what stage of development your embryos are, chicken eggs have to be opened and sometimes stained to check embryo development. Very early embryos especially do not take too kindly to this abuse, and may stop growing. My favorite thing about chick work is that you can stop and restart development multiple times simply by changing incubation temperature. This means that you can set a timer on an incubator and have your embryos ready at the stage at which you want them, when you want them. This cuts down on those infamous late nights in the lab.

The toolkit available to a chicken embryologist is relatively large and effective, and of the three systems described, antibodies generally work best in the chick. It is possible (but not at all common) to create stable transgenic lines of chicken, and other more common gene manipulation techniques such as morpholinos also work well. Since chicken embryos are relatively large, they often must be sectioned to observe the results of experiments.

The one thing I couldn’t escape with all three systems was the fact that embryo quality changed with the weather and the seasons.

 

The verdict?

Through all these transitions, I have found that studying development is a state of mind that transcends any specific model system, and the expertise you gain from one system is very easily transferable to another. However, if forced to pick a favorite, I would confess that my heart still belongs to the sea urchin.

 

(13 votes)
Loading...

The deadline to apply for the 2018 Mouse Development, Stem Cells & Cancer course at Cold Spring Harbor Laboratory (CSHL) is March 15^th. If you don’t know much about the course or are on the fence about applying, I want to give you some background about my experiences from 2017, in hopes that I can convince you to apply, too.

The mouse course was founded in 1983 by superstar mouse wranglers Frank Costantini, Brigid Hogan, and Elizabeth Lacy. They recognized the power of emerging techniques to generate transgenic mice and knew they had to create an opportunity to pass these skills on to scientists of all levels and from around the world. Every year, the mouse course brings together 14 students at various stages of their careers and from diverse backgrounds to blast through an intense curriculum packed with hands-on lab work. The course is hosted by the historic Cold Spring Harbor Laboratory, established in 1890: the home of many major scientific discoveries that have shaped modern biology.

In June 2017, I was fortunate to take the mouse course. During my 3 weeks at the CSHL campus, I learned a host of experimental techniques and made tons of new professional contacts and friends. Exposure to these new tools and conversations with the many faculty speakers brought fresh insight into problems I face in my current research, giving me ideas for future projects and collaborations that will benefit me for the rest of my career. I emerged from the mouse course a better scientist equipped, not just with new skills, but the belief I can learn whatever I set out to learn.

Applying for the course

Who should apply for the mouse course? You! Graduate students at all levels, postdoctoral fellows, and new PIs. We had all 3 categories in our class, and we came from different backgrounds within the life sciences: genetics, neuroscience, developmental biology, cancer biology, reproductive biology, and medicine, among others. I am an early graduate student, as were several other participants. The 14 of us had different levels of experience with lab and mouse work, but everyone had the chance to learn and try each new skill, and even the more seasoned students picked up new tricks.

[An aside: If you’re worried you might not have enough experience to apply, consider my case. I had virtually no experience with most techniques taught during the course, and (have to admit), I have a fear of handling mice. As long as you’re willing to grit your teeth and really throw yourself into the course, any level of background experience (or mouse-phobia) is ok.]

For each applicant, the course has different albeit overlapping benefits. For example, junior graduate students can establish a solid experimental foundation for their graduate research. Senior graduate students and new postdocs moving into fresh projects in mouse labs can use the course to quickly gain experience with a new model system. Finally, senior postdocs and new PIs can learn more about the experimental techniques and equipment they’ll need for their new labs, not to mention learning how to design mouse protocols and experiments essential for development of their research programs. In sum: if you want to get ahead in mouse research, you should apply, regardless of your current position along whatever scientific trajectory you are following.

With an intensive, 3-week long course like this, you might find reasons to talk yourself out of applying. Maybe you worry about being away from your regular work schedule for 3 weeks. Sure, 3 weeks away can be disruptive, but in my opinion it’s worth it, and you can plan around it. The mouse course only happens once a year, and your lab will still be there when you come back! Plus, you’ll be returning with way more expertise and new ideas than when you left. If you’re worried about the cost of the course, remember that many institutions offer travel awards and funds to cover the costs. CSHL also provides generous financial aid to students who need it, so there’s no need to worry about funding, and financial concerns should not stop you from applying. Finally, if you’re pretty convinced the mouse course is a good idea, but you don’t know whether this is the right year, or maybe next year would be more convenient, here’s the truth: it will never be perfectly convenient (because science is busy!). That said, applying to the mouse course this year can provide you with the expertise and networking opportunities that will strongly affect how you tackle and succeed next year. So don’t wait.

Taking the course

                The mouse course is jam-packed with experiments, some lasting several days, and all requiring specific lab supplies and equipment. The course instructors and teaching assistants lovingly and painstakingly organize all the protocols into a tight schedule that flows smoothly and follows evolving themes over the course of the 3 weeks. At the beginning of the course, the experimental focus is on the tools required to create a transgenic mouse; specifically, work with very early embryos. This section includes techniques like electroporation and microinjection of 1- and 2-cell embryos, as well as CRISPR workshops. During my course, we moved along the developmental timeline and towards tools required to manipulate and characterize older embryos, including roller bottle culture and electroporation of mid-gestation embryos, tissue sectioning and staining, and fluorescence-activated cell sorting (FACS). Aside from the lab work, there were guest lectures once or twice a day. Each speaker would cover background topics related to the day’s lab work, and then talk about new research being carried out by their group(s). Usually, the guest speaker would also join us in the lab, and sometimes even show off their skills by demonstrating experiments and giving students hands-on help.

The course also included great ways to connect with other students and faculty. Students presented their work in a mini-seminar early on in the course, which allowed us to get to know each other and understand our various backgrounds and scientific inclinations. We enjoyed weekly social events organized either by the instructors or the students, as well, providing a perfect place to unwind (and sing karaoke, if that’s your thing). One of my favorite parts of the course was the opportunity to meet the guest lecturers. Students would sign up to take speakers out for their “first drink” at the bar; basically, this was a chance to sit down and get to know each other in an informal setting. These get-togethers at the campus pub were a fantastic way to relax after a long day in the lab, not to mention giving us a chance to chat about anything from science and careers to English bulldogs and pink fairy armadillos. (Don’t ask.)

After the course (and some final reasons why you should apply if you aren’t already convinced)

After my 3 weeks at CSHL, I was mentally and physically exhausted, but excited about my work in a way I hadn’t felt before. I left the course equipped with new skills and heaps of reading materials and protocols, all of which I was enthused to share with my labmates back home. In the months since the course, I’ve had the chance to apply protocols taught by the instructors and to follow up on ideas that came up in conversations with guest lecturers. I’ve even spent some idle time dreaming about and planning out a potential post-doc project (which is still several years away for me), based on discussions that took place during the course. The many benefits I reaped overall extended beyond just my own feelings about research; the course was also a place I could start to build a network of scientific contacts and friends. At conferences since my time at CSHL, I have encountered so many familiar faces and reconnected with fellow students, teaching assistants, and guest lecturers. My experiences and friendships from the mouse course have helped me become a part of and feel at home within a larger scientific community.

So: if you want to add an injection of energy and excitement to your scientific research and career that will last for years (and why wouldn’t you?!), then apply. You won’t regret it.

(4 votes)
Loading...

Our latest monthly trawl for developmental biology (and other cool) preprints. Let us know if we missed anything.

---

Here at the Company of Biologists we are very excited about our soon to launch biology preprints highlighting service, preLights. Before the site goes live, you can sign up for email updates here and follow preLights on Twitter here.

This month was notable for its plant content (see the many beautiful images below), plus a bumper ‘Research practice’ section with discussion of gender, ethics, education, and the future of US science.

The preprints were hosted on bioRxiv, PeerJ, and arXiv. 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

Chiral cilia orientation in the left-right organizer. Rita Rua Ferreira, Guillaume Pakula, Andrej Vilfan, Willy Supatto,Julien Vermot

 

 

Mutations in Bcl9 and Pygo genes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling. Claudio Cantu, Anastasia Felker, Dario Zimmerli, Elena Chiavacci, Elena Maria Cabello, Lucia Kirchgeorg, Tomas Valenta, George Hausmann, Jorge Ripoll, Natalie Vilain, Michel Aguet, Konrad Basler, Christian Mosimann

 

Multiple sources of variability drive a stochastic cell fate decision in C. elegans. Jason R Kroll, Jasonas Tsiaxiras, Jeroen S van Zon

 

Noise-resistant developmental reproducibility in vertebrate somite formation. Honda Naoki, Ryutaro Akiyama, Shin Ishii, Yasumasa Bessho, Takaaki Matsui

 

 

CDK1 and CDK2 regulate phosphorylation-dependent NICD1 turnover and the periodicity of the segmentation clock. J Kim Dale, Francesca Anna Carrieri, Philip Murray, Paul Davies

 

PIN7 auxin carrier is a terminator of radial root expansion in Arabidopsis thaliana. Michel Ruiz Rosquete, Jurgen Kleine-Vehn

 

PILS6 is a temperature-sensitive regulator of nuclear auxin input and organ growth in Arabidopsis thaliana. Elena Feraru, Mugurel I. I Feraru, Elke Barbez, Lin Sun, Angelika Gaidora, Juergen Kleine-Vehn

 

Arabidopsis HB52 mediates the crosstalk between ethylene and auxin signaling pathways by regulating PIN2, WAG1, and WAG2 during primary root elongation. Zi-Qing Miao, Ping_Xia Zhao, Jie-Li Mao, Lin-Hui Yu, Yang Yuan, Hui Tang, Chengbin Xiang

 

SlARF10, an auxin response factor, is required for chlorophyll and sugar accumulation during tomato fruit development. Lihua Mei, Yujin Yuan, Mengbo Wu, Zehao Gong, Qiang Zhang, Fengqing Yang, Qian Zhang, Yingqing Luo, Xin Xu, Wenfa Zhang, Mingjun Miao, Zhengguo Li, Wei Deng

 

Branch angle responses to photosynthesis are partially dependent on TILLER ANGLE CONTROL 1. Jessica Marie Guseman, Chris Dardick

 

Integration of Brassinosteroid and Phytosulfokine Signalling Controls Vascular Cell Fate in the Arabidopsis Root. Eleonore Holzwart, Apolonio Ignacio Huerta, Nina Gloeckner, Borja Garnelo Gomez, Friederike Ladwig, Sebastian Augustin, Jana Christin Askani, Ann-Kathrin Schuerholz, Klaus Harter, Sebastian Wolf

 

Root Responses to Heterogeneous Nitrate Availability are Mediated by trans-Zeatin in Arabidopsis Shoots. Arthur Poitout, Amandine Crabos, Ivan Petřík, Ondrej Novák, Gabriel Krouk, Benoît Lacombe, Sandrine Ruffel

 

CONFLICTING AUXIN-PHOSPHATE SIGNALS IMPACT ON RSL2 EXPRESSION AND ROS-HOMEOSTASIS LINKED TO ROOT HAIR GROWTH IN ARABIDOPSIS. Silvina Mangano, Silvina Denita Juarez, Eliana Marzol, Cecilia Borassi, Jose Estevez

 

Root meristem growth factor 1 controls root meristem size through reactive oxygen species signaling. Masashi Yamada, Xinwei Han, Philip N Benfey

 

 

C. elegans Multidrug Resistance Protein 5 (MRP-5) Transports Vitamin B12 from the Intestine to the Gonad to Support Embryonic Development. Huimin Na, Olga Ponomarova, Gabrielle E. Giese, Marian J. M. Walhout

 

miR-132 controls mouse pancreatic beta cell proliferation and survival through the Pten/Akt/Foxo3 signaling. HASSAN MZIAUT, Georg Henniger, Katharina Ganss, Sebastian Hempel, Steffen Wolk, Johanna McChord, Kamal Chowdhury Chowdhury, Klaus Peter Knoch, Jurgen Weitz, Robert Grutzmann, Christian Pilarsky, Michele Solimena, Stephan Kersting

 

 

Planar cell polarity: the prickle gene acts independently on both the Ds/Ft and the Stan systems. Jose Casal, Beatriz Ibanez-Jimenez, Peter A. Lawrence

 

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

 

Radial glial lineage progression and differential intermediate progenitor amplification underlie striatal compartments and circuit organization. Sean Michael Kelly, Miao He, Jannifer Lee, Yongsoo Kim, Leif Garrison Gibb, Priscilla Wu, Katie Matho, Pavel Osten, Ann Martin Graybiel, Z. Josh Huang

 

In vivo clonal analysis reveals spatiotemporal regulation of thalamic nucleogenesis. Samuel Wong, Earl Parker Scott, Ella Borgenheimer, Madeline Freeman, Guo-li Ming, Qing-Feng Wu, Hongjun Song, Yasushi Nakagawa

 

HIF-2α is essential for carotid body development and function. Randall Johnson, David Macias, José López-Barneo, Andrew S Cowburn, Hortensia Torres-Torrelo, Patricia Ortega-Saenz

 

Neonate gut and respiratory microbiota: coordinated development through time and space. Alex Grier, Andrew McDavid, Bokai Wang, Xing Qui, James Java, Sanjukta Bandyopadhyay, Jeanne Holden-Wiltse, Haeja A Kessler, Ann L Gill, Heidie Huyck, Ann R Falsey, David J Topham, Kristin M Scheible, Mary T Caserta, Gloria S Pryhuber, Steven R Gill

 

 

Heat shock factor 5 is conserved in vertebrates and essential for spermatogenesis in zebrafish. László Orbán, Jolly M Saju, Mohammed Sorowar Hossain, Woei C Liew, Ajay Pradhan, Natascha M Thevasagayam, Amit Anand, Per-Erik Olsson

 

Comprehensive characterization of transcript diversity at the human NODAL locus. Scott D Findlay, Lynne-Marie Postovit

 

BMP Signaling Downstream of the Highwire E3 Ligase Sensitizes Nociceptors. Ken Honjo, W. Daniel Tracey

 

HMGA1 zebrafish co-orthologue hmga1b can modulate p53-dependent cellular responses but is unable to control the alternative splicing of psen1. Seyyed Hani Moussavi Nik, Morgan Newman, Amanda Lumsden, Tanya Jayne, eMichael Lardelli

 

Increased PHGDH expression uncouples hair follicle cycle progression and promotes inappropriate melanin accumulation. Katherine R Mattaini, Mark R Sullivan, Allison N Lau, Brian P Fiske, Roderick T Bronson, Matthew G Vander Heiden

 

Loss of PRMT5 promotes PDGFRα degradation during oligodendrocyte differentiation and myelination. Sara Calabretta, Gillian Vogel, Zhenbao Yu, Karine Choquet, Lama Darbelli, Thomas B. Nicholson, Claudia L. Kleinman, Stéphane Richard

 

Loss of Trem2 in microglia leads to widespread disruption of cell co-expression networks in mouse brain. Guillermo Carbajosa, Karim Malki, Nathan Lawless, Hong Wang, John W. Ryder, Eva Wozniak, Kristie Wood, Charles A. Mein, Richard J. B. Dobson, David A. Collier, Michael J. O’Neill, Angela K. Hodges, Stephen J. Newhouse

 

 

Visualizing BDNF cell-to-cell transfer reveals astrocytes are the primary recipient of neuronal BDNF. Markus A. Stahlberg, Sebastian Kuegler, Camin Dean

 

 

In addition to being a marker for muscle connective tissue, Odd skipped-related 2 (OSR2) is expressed in differentiated muscle cells during chick development. Sonya Nassari, Mickael Orgeur, Cedrine Blavet, Sigmar Stricker, Claire Fournier-Thibault, Delphine Duprez

 

 

Odd skipped-related 1 (Osr1) identifies muscle-interstitial fibro-adipogenic progenitors (FAPs) activated by acute injury. Juergen Stumm, Pedro Vallecillo Garcia, Sophie vom Hofe-Schneider, David Ollitrault, Heinrich Schrewe, Aris Economides, Giovanna Marazzi, David Sassoon, Sigmar Stricker

 

An FGF-driven feed-forward circuit patterns the cardiopharyngeal mesoderm in space and time. Florian Razy-Krajka, Basile Gravez, Nicole Kaplan, Claudia Racioppi, Wei Wang, Lionel Christiaen

 

Unbiased construction of a temporally consistent morphological atlas of neonatal brain development. Andreas Schuh, Antonios Makropoulos, Emma C. Robinson, Lucilio Cordero-Grande, Emer Hughes, Jana Hutter, Anthony N Price, Maria Murgasova, Rui Pedro A. G. Teixeira, Nora Tusor, Johannes K. Steinweg, Suresh Victor, Mary A. Rutherford, Joseph V. Hajnal, A. David Edwards, Daniel Rueckert

 

Gradual repression of selenoprotein W ensures physiological bone remodelling. Hyunsoo Kim, Kyunghee Lee, Jin Man Kim, Jae-Ryong Kim, Han-Woong Lee, Youn Wook Chung, Hong-In Shin, Eui-Soon Park, Jaerang Rho, Seoung Hoon Lee, Nacksung Kim, Soo Young Lee, Yongwon Choi, Daewon Jeong

 

 

Lrfn2-mutant mice display suppressed synaptic plasticity and inhibitory synapse development and abnormal social communication and startle response. Yan Li, Ryunhee Kim, Yi Sul Cho, Doyoun Kim, Kyungdeok Kim, Junyeop Daniel Roh, Hanwool Park, Esther Yang, Soo-Jeong Kim, Jaewon Ko, Hyun Kim, Yong-Chul Bae, Eunjoon Kim

 

Pericyte ontogeny: the use of chimeras to track a cell lineage of diverse germ line origins. Heather Corbett Etchevers

 

A compromised gsdf signaling leads to gamatogenesis confusion and subfertility in medaka. Guijun Guan, Shumei Xu, Anning Guo, Xiaomiao Zhao, Yingqing Zhang, Kaiqing Sun, Yi Kang, Yuyang Chang, Xiaowen Wu, Liangbiao Chen

 

Aged blood inhibits hippocampal neurogenesis and activates microglia through VCAM1 at the blood-brain barrier. Hanadie Yousef, Cathrin J Czupalla, Davis Lee, Ashley Burke, Michelle Chen, Judith Zandstra, Elisabeth Berber, Benoit Lehallier, Vidhu Mathur, Ramesh V Nair, Liana Bonanno, Taylor Merkel, Markus Schwaninger, Stephen Quake, Eugene C Butcher, Tony Wyss-Coray

 

 

| Morphogenesis & mechanics

 

Quantification of gene expression patterns to reveal the origins of abnormal morphogenesis. Neus Martinez-Abadias, Roger Mateu Estivill, Jaume Sastre Tomas, Susan Motch Perrine, Melissa Yoon, Alex Robert-Moreno, Jim Swoger, Lucia Russo, Kazuhiko Kawasaki, Joan Richtsmeier, James Sharpe

 

A three-dimensional staging system of mouse endometrial gland morphogenesis. Zer Vue, Gabriel Gonzalez, C. Allison Stewart, Shyamin Mehra, Richard R. Behringer

 

Pcdh18a-positive tip cells instruct notochord formation in zebrafish. Bernadett Bosze, Benjamin Mattes, Claude Sinner, Kathrin Stricker, Victor Gourain, Thomas Thumberger, Sham Tlili, Sabrina Weber, Joachim Wittbrodt, Timothy E Saunders, Uwe Straehle, Alexander Schug, Steffen Scholpp

 

In vivo topology converts competition for cell-matrix adhesion into directional migration. Fernanda Bajanca, Nadege Gouignard, Charlotte Colle, Maddy Parsons, Roberto Mayor, Eric Theveneau

 

Mechanical mapping of spinal cord development and repair in living zebrafish larvae using Brillouin microscopy. Raimund Schlüßler, Stephanie Möllmert, Shada Abuhattum, Gheorghe Cojoc, Paul Müller, Kyoohyun Kim, Conrad Möckel, Conrad Zimmermann, Jürgen Czarske, Jochen Guck

 

 

Optochemical control of cell contractility at single cell resolution during tissue morphogenesis. Deqing Kong, Fred Wolf, Joerg Grosshans

 

Coupling of Rho family GTPases during mesenchymal-to-epithelial-like transitions. Christopher Toret, Pruthvi Shivakumar, Pierre-Francois Lenne, Andre LE BIVIC

 

Non-canonical apical constriction shapes emergent matrices in C. elegans. Sophie S Katz, Alison Renee Frand

 

Mechanical strain can increase segment number in live chick embryos. Ben K. A. Nelemans, Manuel Schmitz, Hannan Tahir, Roeland M. H. Merks, Theodoor H. Smit

 

E-cadherin bridges cell polarity and spindle orientation to ensure prostate epithelial integrity and prevent carcinogenesis in vivo. Xue Wang, Kai Zhang, Zhongzhong Ji, Chaping Cheng, Huifang Zhao, Yaru Sheng, Xiaoxia Li, Liancheng Fan, Baijun Dong, Wei Xue, Wei-Qiang Gao, Helen Zhu

 

Two contractile pools of actomyosin distinctly load and tune E-cadherin levels during morphogenesis. Girish R Kale, Xingbo Yang, Jean-Marc Philippe, Madhav Mani, Pierre-Francois Lenne, Thomas Lecuit

 

Basal constriction during midbrain-hindbrain boundary morphogenesis is mediated by Wnt5b and Focal Adhesion Kinase. Jennifer H Gutzman, Ellie Graeden, Isabel Brachmann, Sayumi Yamazoe, James K Chen, Hazel Sive

 

GSK3 Controls Migration of the Neural Crest Lineage. Sandra G Gonzalez Malagon, Anna Lopez Munoz, Daniel Doro, Triona Bolger, Evan Poon, Elizabeth Tucker, Hadeel Adel Al-Lami, Matthias Krause, Christopher Phiel, Louis Chesler, Karen J Liu

 

 

Feedback control of neurogenesis by tissue packing. Tom W. Hiscock, Joel B. Miesfeld, Kishore R. Mosaliganti, Brian A. Link, Sean G. Megason

 

Spindle assembly in egg extracts of the Marsabit clawed frog, Xenopus borealis. Maiko Kitaoka, Rebecca Heald, Romain Gibeaux

 

 

The expa1-1 mutant reveals a new biophysical lateral root organogenesis checkpoint. Priya Ramakrishna, Graham A. Rance, Lam D. Vu, Evan Murphy, Kamal Swarup, Kamaljit Moirangthem, Bodil Jorgensen, Brigitte van de Cotte, Tatsuaki Goh, Zhefeng Lin, Ute Voss, Tom Beeckman, Malcolm J. Bennett, Kris Gevaert, Ive De Smet

 

Microtubule acetylation is required for mechanosensation in Drosophila. Connie Yan, Fei Wang, Yun Peng, Claire R Williams, Brian Jenkins, Jill Willdonger, John C Tuthill, Yang Xiang, Stephen L Rogers, Jay Z Parrish

 

Bovine mammary gland development: new insights into the epithelial hierarchy. Laurence Finot, Eric Chanat, Frederic Dessauge

 

Development of High-Order Organization of Guanine-Based Reflectors Underlies the Dual Functionality of the Zebrafish Iris. Dvir Gur, Jan-David Nicolas, Vlad Brumfeld, Omri Bar-Elli, Dan Oron, Gil Levkowitz

 

Morphohistological development of the somatic embryo of Typha domingensis. Guadalupe Hernández-Piedra​, Violeta Ruiz-Carrera, Alberto J Sánchez, Arlette Hernández-Franyutti​,Alfonso Azpeitia-Morales

 

| Genes & genomes

PRC1-dependent compaction of Hox gene clusters prevents transcriptional derepression during early Drosophila embryogenesis. Thierry Cheutin, Giacomo Cavalli

 

Phenotypic convergence in the brain: distinct transcription factors regulate common terminal neuronal characters. Nikolaos Konstantinides, Katarina Kapuralin, Chaimaa Fadil, Luendreo Barboza, Rahul Satija, Claude Desplan

 

 

The age-regulated zinc finger factor ZNF367 is a new modulator of embryonic neurogenesis. Valentina Naef, Sara Monticelli, Debora Corsinovi, Maria Teresa Mazzetto, Alessandro Cellerino, Michela Ori

 

Fragile X mental retardation protein is a size-dependent translational activator. Ethan J Greenblatt, Allan C Spradling

 

Precise temporal regulation of alternative splicing during neural development. Sebastien M Weyn-Vanhentenryck, Huijuan Feng, Dmytro Ustianenko, Rachel Duffie, Qinghong Yan, Martin Jacko, Jose C Martinez, Marianne Goodwin, Xuegong Zhang, Ulrich Hengst, Stavros Lomvardas, Maurice S Swanson, Chaolin Zhang

 

Differential 3′ Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types. Sasa Jereb, Hun-Way Hwang, Eric Van Otterloo, Eve-Ellen Govek, John J Fak, Yuan Yuan, Mary E Hatten, Robert B Darnell

 

 

Chromosome Removal Via Cellular Fragmentation and Aneuploid Blastomere Exclusion in Primate Embryos. Brittany L. Daughtry, Jimi L Rosenkrantz, Nathan H. Lazar, Suzanne S. Fei, Nash Redmayne, Kristof A. Torkenczy, Andrew Adey, Lina Gao, Byung Park, Kimberly A. Nevonen, Lucia Carbone, Shawn L. Chavez

 

HMGA1 zebrafish co-orthologue hmga1b can modulate p53-dependent cellular responses but is unable to control the alternative splicing of psen1. Seyyed Hani Moussavi Nik, Morgan Newman, Amanda Lumsden, Tanya Jayne, Michael Lardelli

 

 

OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development. Joel Hrit, Cheng Li, Elizabeth Allene Martin, Eric Simental, Mary Goll, Barbara Panning

 

Male mice with large inversions or deletions of X-palindrome arms are fertile and express their associated genes post-meiosis. Alyssa N Kruger, Quinn Ellison, Michele A Brogley, Emma R Gerlinger, Jacob L Mueller

 

The repressive and alleviating nature of FACT shapes the transcriptional landscape in ES cells. Peter Tessarz, Constantine Mylonas

 

Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster. Michael P.  Meers, Karen Adelman, Robert J. Duronio, Brian D. Strahl, Daniel J. McKay, A. Gregory Matera

 

Shared Genetic Requirements for Atf5 Translation in the Vomeronasal Organ and Main Olfactory Epithelium. Ryan P Dalton

 

 

The Trithorax group protein dMLL3/4 instructs the assembly of the zygotic genome at fertilization. Pedro Prudêncio, Leonardo G. Guilgur, João Sobral, Jörg D. Becker, Rui Gonçalo Martinho, Paulo Navarro-Costa

 

 

A molecular framework for functional versatility of HECATE transcription factors. Christophe Gaillochet, Suraj Jamge, Froukje van der Wal, Gerco Angenent, Richard Immink, Jan U. Lohmann

 

 

Expression of SULTR2;2 in the Arabidopsis bundle sheath is mediated by a highly conserved positive regulator. Sandra Kirschner, Helen Woodfield, Katharina Prusko, Maria Koczor, Udo Gowik, Julian M Hibberd, Peter Westhoff

 

The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis. E. Shannon Torres, Roger B. Deal

 

 

Mapping and dynamics of regulatory DNA during seed development. Alessandra M Sullivan, Andrej A Arsovski, Agnieszka Thompson, Richard Sandstrom, Robert E Thurman, Shane Neph, Audra K Johnson, Shawn T Sullivan, Peter J Sabo, Fidencio V Neri III, Molly Weaver, Morgan Diegel, Jennifer L Nemhauser, John A Stamatoyannopoulos, Kerry L Bubb, Christine Queitsch

 

Developmental genetics of corolla tube formation: role of the tasiRNA-ARF pathway. Baoqing Ding, Rui Xia, Vandana Gurung, Janelle M. Sagawa, Lauren E. Stanley, Matthew Strobel, Qiaoshan Lin, Pamela K. Diggle, Blake C. Meyers, Yao-Wu Yuan

 

RNA helicase, DDX27 regulates skeletal muscle growth and regeneration by modulation of translational processes. Alexis H Bennett, Marie Francoise O’Donohue, Stacey R Gundry, Aye T Chan, Jeffery Widrick, Isabelle Draper, Anirban Chakraborty, Yi Zhou, Leonard I Zon, Pierre-Emmanuel Gleizes, Alan H Beggs, Vandana A Gupta

 

Ventricular chamber-specific Pitx2 insufficiency leads to cardiac hypertrophy and arrhythmias. Ana Chinchilla, Francisco J Esteban, Estefania Lozano-Velasco, Francisco Hernandez-Torres, Jorge N Dominguez, Amelia E Aranega, Diego Franco

 

Caenorhabditis elegans heterochromatin factor SET-32 plays an essential role in transgenerational establishment of nuclear RNAi-mediated epigenetic silencing. Natallia Kalinava, Julie Ni, Zoran Gajic, Helen Ushakov, Sam Gu

 

The chromatin modifiers SET-25 and SET-32 are required for initiation but not long-term maintenance of transgenerational epigenetic inheritance. Rachel M Woodhouse, Gabrielle Buchmann, Matthew Hoe, Dylan Harney, Mark Larance, Peter R Boag, Alyson Ashe

 

Transgenerational Epigenetic Inheritance Factors Localize to Spatially and Temporally Ordered Liquid Droplet Assemblages. Gang Wan, Brandon Fields, George Spracklin, Carolyn Phillips, Scott Kennedy

 

NRSF−mediated repression of neuronal genes in developing brain persists in the absence of NRSF−Sin3 interaction. Alicia M Hall, Annabel K Short, Akanksha Singh-Taylor, Jennifer Daglian, Tadashi Mishina, William K Schmidt, Hiroyuki Kouji, Tallie Z Baram

 

Growing oocyte specific transcription-dependent de novo DNA methylation at the imprinted Zrsr1-DMR. Keiichiro Joh, Fumikazu Matsuhisa, Shuji Kitajima, Kenichi Nishioka, Ken Higashimoto, Hitomi Yatsuki, Tomohiro Kono, Haruhiko Koseki, Hidenobu Soejima

 

Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures. Federico Comoglio, Hyun Jung Park, Stefan Schoenfelder, Iros Barozzi, Daniel Bode, Peter Fraser, Anthony R Green

 

HOTAIR ancient sequence suggests regulatory roles both in cis and trans. Chirag Nepal, Yavor Hadzheiv, Sachin Pundhir, Piotr Mydel, Boris Lenhard, Ferenc Mueller, Jesper B Andersen

 

The contribution of non-canonical splicing mutations to severe dominant developmental disorders. Jenny Lord, Giuseppe Gallone, Patrick J. Short, Jeremy F. McRae, Holly Ironfield, Elizabeth H. Wynn, Sebastian S. Gerety, Liu He, Bronwyn Kerr, Diana S. Johnson, Emma McCann, Esther Kinning, Frances Flinter, I. Karen Temple, Jill Clayton-Smith, Meriel McEntagart, Sally Ann Lynch, Shelagh Joss, Sofia Douzgou, Tabib Dabir, Virginia Clowes, Vivienne P. M. McConnell, Wayne Lam, Caroline F. Wright, David R. FitzPatrick, Helen V. Firth, Jeffrey C. Barrett, Matthew E. Hurles, on behalf of the DDD study

 

HSF2 Co-regulates Protein-coding and Long Non-coding RNA Genes Specific to Black Tissues of the Black Chicken, Yeonsan Ogye. Hyosun Hong, Han-Ha Chai, Kyoungwoo Nam, Dajeong Lim, Kyung-Tai Lee, Yoon Jung Do, Chang-Yeon Cho, Jin-Wu Nam

 

Functional mapping of the mouse hairless gene promoter region. Eric G Folco, Stefan Nonchev

 

Gemin4 is an essential gene in mice, and its overexpression in human cells causes relocalization of the SMN complex to the nucleoplasm. Ingo D. Meier, Michael P. Walker, A. Gregory Matera

 

| Stem cells, regeneration & disease modelling

Three-dimensional human axon tracts derived from cerebral organoids. D. Kacy Cullen, Laura A. Struzyna, Dennis Jgamadze, Wisberty J. Gordián-Vélez, James Lim, Kathryn L. Wofford, Kevin D. Browne, H. Isaac Chen

 

 

Spatiotemporal mosaic patterning of pluripotent stem cells using CRISPR interference. Ashley R.G. Libby, David A. Joy, Po-Lin So, Mohammad A. Mandegar, Jonathon M. Muncie, Valerie M. Weaver, Bruce R. Conklin, Todd C. McDevitt

 

Efficient production of erythroid, megakaryoid and myeloid cells, using single cell-derived iPSC colony differentiation. Marten Hansen, Eszter Varga, Cathelijn Aarts, Tatjana Wust, Taco Kuijpers, Marieke von Lindern, Emile van den Akker

 

Highly efficient chondrogenic differentiation of human iPSCs and purification via a reporter allele generated by CRISPR-Cas9 genome editing. Shaunak S Adkar, Chia-Lung Wu, Vincent P Willard, Amanda Dicks, Adarsh Ettyreddy, Nancy Steward, Nidhi Bhutani, Charles A Gersbach, Farshid Guilak

 

The chick caudo-lateral epiblast acts as a permissive niche for generating neuromesodermal progenitor behaviours. Peter Baillie-Johnson, Octavian Voiculescu, Penny Hayward, Benjamin Steventon

 

 

An Epiblast Stem Cell derived multipotent progenitor population for axial extension. Shlomit Edri, Penelope Hayward, Peter Baillie-Johnson, Benjamin Steventon, Alfonso Martinez Arias

 

Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized fates and patterning. Sophie Morgani, Jakob J Metzger, Jenny Nichols, Eric Siggia, Anna-Katerina Hadjantonakis

 

Inter-cellular Interactions and Patterns: Vertebrate Development and Embryonic Stem Cells. Eric D. Siggia

 

Inheritance of OCT4 predetermines fate choice in human embryonic stem cells. Samuel C. Wolff, Raluca Dumitru, Kasia M. Kedziora, Cierra D. Dungee, Tarek M. Zikry, Rachel A. Haggerty, JrGang Cheng, Adriana S. Beltran, Jeremy E. Purvis

 

Hematopoietic stem cells differentiate into restricted myeloid progenitors before cell division. Tatyana Grinenko, Anne Eugster, Lars Thielecke, Beata Ramasz, Anja Krueger, Sevina Dietz, Ingmar Glauche, Alexander Gerbaulet, Malte von Bonin, Onur Basak, Hans Clevers, Triantafyllos Chavakis, Ben Wielockx

 

Interrogation of human hematopoiesis at single-cell and single-variant resolution. Caleb A Lareau, Jacob C Ulirsch, Erik L Bao, Leif S Ludwig, Michael H Guo, Christian Benner, Ansuman T Satpathy, Rany Salem, Joel N Hirschhorn, Hilary K Finucane, Martin J Aryee, Jason D Buenrostro, Vijay G Sankaran

 

 

Muscle stem cell intramuscular delivery within hyaluronan methylcellulose improves engraftment efficiency and dispersion. Sadegh Davoudi, Chih-Ying Chin, Michael C. Cooke, Roger Y. Tam, Molly S. Shoichet, Penney M. Gilbert

 

Behavior and biocompatibility of rabbit bone marrow mesenchymal stem cells with bacterial cellulosic membrane. Marcello Silva Alencar, Yulla Klinger Carvalho, Camila Ernanda Carvalho, Matheus Tajra Feitosa, Michel Muálem Alves​, Fernando Aécio de Amorim Carvalho, Bartolomeu Cruz Viana, Maria Angélica Miglino, Ângela Faustino Jozala​, Maria Acelina Carvalho

 

RNA polymerase II pausing regulates a quiescence-dependent transcriptional program, priming cells for cell cycle reentry. Hardik P Gala, Debarya Saha, Nisha Venugopal, Ajoy Aloysius, Jyotsna Dhawan

 

Elongator is required for root stem cell maintenance by regulating SHORT ROOT transcription. Qian Chen, Chuanyou Li, Linlin Qi, Xiaoyue Zhang, Huawei Zhai, Jian Liu, Fangming Wu

 

Mono-Association with Lactobacillus plantarum Disrupts Intestinal Homeostasis in adult Drosophila. David Fast, Aashna Duggal, Edan Foley

 

A centrosome asymmetry switch in fly neural stem cells. Emmanuel Gallaud, Anjana Ramdas Nair, Arnaud Monnard, Priyanka Singh, Tri Pham, David Salvador Garcia, Alexia Ferrand, Clemens Cabernard

 

Asymmetric histone incorporation during DNA replication in Drosophila male germline stem cells. Matthew Wooten, Zehra Nizami, Xinxing Yang, Jonathan Snedeker, Rajesh Ranjan, Jee Min Kim, Elizabeth Urban, Vuong Tran, Jackson Buss, Joseph Gall, Jie Xiao, Xin Chen

 

Wolbachia control stem cell behavior and stimulate germline proliferation in filarial nematodes. Vincent Foray, Mercedes M Perez-Jimenez, Nour Fattouh, Frederic Landmann

 

Combinatorial Tissue Engineering Partially Restores Function after Spinal Cord Injury. Jeffrey Hakim, Brian Rodysill, Bingkun K Chen, Ann Schmeichel, Michael J Yaszemski, Anthony Windebank, Nicolas Madigan

 

 

Transient fibrosis resolves via fibroblast inactivation in the regenerating zebrafish heart. Héctor Sánchez-Iranzo, María Galardi-Castilla, Andrés Sanz-Morejón, Juan Manuel González-Rosa, Ricardo Costa, Alexander Ernst, Julio Sainz de Aja, Javier Langa, Nadia Mercader

 

 

KLF6 activates complementary gene modules relevant to axon growth and promotes corticospinal tract regeneration after spinal injury. Zimei Wang, Ishwariya Venkatesh, Vatsal Mehra, Matthew Simpson, Brian Maunze, Erik Eastwood, Lyndsey Holan, Murray Blackmore

 

 

RNA sequencing of Stentor cell fragments reveals key processes underlying cellular regeneration. Henning Onsbring Gustafson, Mahwash Jamy, Thijs J. G. Ettema

 

Chronic inflammation delays cell migration to villi in the intestinal epithelium. Daniele Muraro, Aimee Parker, Laura Vaux, Sarah Filippi, Alexander Fletcher, Alastair Watson, Carmen Pin, Philip Maini, Helen Byrne

 

Drosophila Toll links systemic immunity to long-term intestinal epithelial integrity. Magda Atilano, Marcus Glittenberg, Anna Hoyle, Petros Ligoxygakis

 

Allele-specific CRISPR/Cas9 genome editing of the single-base P23H mutation for rhodopsin associated dominant retinitis pigmentosa. Pingjuan Li, Benjamin P. Kleinstiver, Mihoko Y. Leon, Michelle S. Prew, Daniel Navarro-Gomez, Scott H. Greenwald, Eric A. Pierce, J. Keith Joung, Qin Liu

 

 

Zebrafish type I collagen mutants faithfully recapitulate human type I collagenopathies. Charlotte Gistelinck, Ronald Y Kwon, Fransiska Malfait, Sofie Symoens, Matthew P Harris, Katrin Henke, Shannon Fisher, Patrick Sips, Brecht Guillemyn, Jan Willem Beck, Petra Vermassen, Hanna De Saffel, MaryAnn Weis, Anne De Paepe, David R Eyre, Andy Willaert, Paul Coucke

 

Effects of Parathyroid Hormone, Alendronate and Odanacatib on the mineralisation process in intracortical and endocortical Haversian bone of ovariectomized rabbits. Christina Vrahnas, Pascal Buenzli, Thomas A Pearson, Brenda L Pennypacker, Mark J Tobin, Keith R Bambery, Le T Duong, Natalie A Sims

 

Severely impaired bone material quality in Chihuahua zebrafish resembles classical dominant human osteogenesis imperfecta. Imke Astrid Kristina Fiedler, Felix Nikolai Schmidt, Christine Plumeyer, Petar Milovanovic, Roberta Gioia, Francesca Tonelli, Antonella Forlino, Bjoern Busse

 

 

Microglia inhibition rescues developmental hypofrontality in a mouse model of mental illness. Mattia Chini, Christoph Lindemann, Jastyn A. Poepplau, Xiaxia Xu, Joachim Ahlbeck, Sebastian H. Bitzenhofer, Christoph Mulert, Ileana L. Hanganu-Opatz

 

Aberrant calcium signaling in astrocytes inhibits neuronal excitability in a human Down syndrome stem cell model. Lin Tian, Grace Or, Yinxue Wang, Guilai Shi, Yizhi Wang, Junqing Sun, Stelios Papadopoulos, Gerard Broussard, Elizabeth Unger, Wenbin Deng, Jason Weick, Anita Bhattacharyya, Chao-Yin Chen, Guoqiang Yu, Loren Looger

 

Systematic Functional Characterization Of Human 21st Chromosome Orthologs In Caenorhabditis elegans. Sarah Nordquist, Sofia R Smith, Jonathan Pierce

 

Basal mitophagy is widespread in Drosophila but minimally affected by loss of Pink1 or parkin. Juliette J. Lee, Alvaro Sanchez-Martinez, Aitor Martinez Zarate, Cristiane Beninca, Ugo Mayor, Michael J. Clague, Alexander J. Whitworth

 

Defects in the neuroendocrine axis cause global development delay in a Drosophila model of NGLY1 Deficiency. Tamy Rodriguez, Joshua Mast, Tom Hartl, Ethan Perlstein

 

Evo-devo & evo

 

De novo origin of multicellularity in response to predation. Matthew D. Herron, Josh M. Borin, Jacob C. Boswell, Jillian Walker, Charles A. Knox, Margrethe Boyd, Frank Rosenzweig, William C. Ratcliff

 

Ecological advantages and evolutionary limitations of aggregative multicellular development. Jennifer T Pentz, Pedro Márquez-Zacarías, Peter J Yunker, Eric Libby, William C Ratcliff

 

 

Protein-coding variation and introgression of regulatory alleles drive plumage pattern diversity in the rock pigeon. Anna Vickrey, Rebecca Bruders, Zev Kronenberg, Emma Mackey, Ryan J Bohlender, Emily Maclary, Edward J Osborne, Kevin P Johnson, Chad D Huff, Mark Yandell, Michael Shapiro

 

 

Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors. Hane Ryu, Fumitaka Inoue, Sean Whalen, Alex Williams, Martin Kircher, Beth Martin, Beatriz Alvarado, Md. Abul Hassan Samee, Kathleen Keough, Sean Thomas, Arnold Kriegstein, Jay Shendure, Alex Pollen, Nadav Ahituv, Katherine Pollard

 

NvERTx: A gene expression database to compare Embryogenesis and Regeneration in the sea anemone Nematostella vectensis. Jacob Warner, Vincent Guerlais, Aldine Amiel, Hereroa Johnston, Karine Nedoncelle, Eric Rottinger

 

Insect wings and body wall evolved from ancient leg segments. Heather S Bruce, Nipam H Patel

 

Comparison of village dog and wolf genomes highlights the pivotal role of the neural crest in dog domestication. Amanda L. Pendleton, Feichen Shen, Angela M. Taravella, Sarah Emery, Krishna R. Veeramah, Adam R. Boyko, Jeffrey M. Kidd

 

The mammalian decidual cell evolved from a cellular stress response. Eric M Erkenbrack, Jamie D Maziarz, Oliver W Griffith, Cong Liang, Arun R Chavan, Gunter P Wagner

 

 

Metabolic co-dependence drives the evolutionary ancient Hydra-Chlorella symbiosis. Mayuko Hamada, Katja Schröder, Jay Bathia, Ulrich Kürn, Sebastian Fraune, Mariia Khalturina, Konstantin Khalturin, Chuya Shinzato, Nori Satoh, Thomas C.G. Bosch

 

In toto live imaging in scuttle fly Megaselia abdita reveals transitions towards a novel extraembryonic architecture. Francesca Caroti, Everado González Avalos, Paula González Avalos, Dimitri Kromm, Viola Noeske, Maike Wosch, Lucas Schütz, Lars Hufnagel, Steffen Lemke

 

Conserved noncoding elements influence the transposable element landscape in Drosophila. Manee M. Manee, John Jackson, Casey M. Bergman

 

Adaptive evolution of animal proteins over development: support for the Darwin hypothesis of Evo-Devo. Jialin Liu, Marc Robinson-Rechavi

 

Developmental constraints on genome evolution in four bilaterian model species. Jialin Liu, Marc Robinson-Rechavi

 

Chromosome evolution at the origin of the ancestral vertebrate genome. Christine Sacerdot, Alexandra Louis, Celine Bon, Hugues ROEST CROLLIUS

 

Functional repurposing of regulatory element activity during mammalian evolution. Francesco N Carelli, Angelica Liechti, Jean Halbert, Maria Warnefors, Henrik Kaessmann

 

Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution. Catriona Munro, Stefan Siebert, Felipe Zapata, Mark Howison, Alejandro Damian-Serrano, Samuel H. Church, Freya E. Goetz, Philip R. Pugh, Steven H.D. Haddock, Casey W. Dunn

 

Conserved and ubiquitous expression of piRNAs and PIWI genes in mollusks antedates the origin of somatic PIWI/piRNA expression to the root of bilaterians. Julia Jehn, Daniel Gebert, Frank Pipilescu, Sarah Stern, Julian Simon Thilo Kiefer, Charlotte Hewel, David Rosenkranz

 

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity. David Lopez-Escardo, Jordi Paps, Colomban de Vargas, Ramon Massana, Inaki Ruiz-Trillo, Javier del Campo

 

Frequent Non-random Shifts in the Temporal Sequence of Developmental Landmark Events during Fish Evolutionary Diversification. Fumihiro Ito, Tomotaka Matsumoto, Tatsumi Hirata

 

Inferring the probability of the derived versus the ancestral allelic state at a polymorphic site. Peter D. Keightley, Benjamin Jackson

 

Genome-wide selection scans integrated with association mapping reveal mechanisms of physiological adaptation across a salinity gradient in killifish. Reid S. Brennan, Timothy M. Healy, Heather J. Bryant, Man Van La, Patricia M. Schulte, Andrew Whitehead

 

Transcriptomic analyses reveal tissue-specific selection on genes related to apoptotic processes in the subterranean rodent, Ctenomys sociabilis. Andrew Lang, Lauren Kordonowy, Eileen Lacey, Matthew MacManes

 

 

The evolution of nesting behaviour in Peromyscus mice. Caitlin L. Lewarch, Hopi E. Hoekstra

 

Evolution at two time frames: polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution. Steven Van Belleghem, Carl Vangestel, Katrien De Wolf, Zoe De Corte, Markus Moest, Pasi Rastas, Luc De Meester, Frederik Hendrickx

 

Strong hybrid male incompatibilities impede the spread of a selfish chromosome between populations of a fly. Rudi Verspoor, Jack ML Smith, Natasha LM Mannion, Gregory DD Hurst, Tom Price

 

 

Multiple large-scale gene and genome duplications during the evolution of hexapods. Zheng Li, George Tiley, Sally Galuska, Chris Reardon, Thomas Kidder, Rebecca Rundell, Michael S. Barker

 

A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits. Laurence Hibrand, Tom Ruttink, Latifa Hamama, Ilya Kirov, Deepika Lakhwani, Ning-Ning Zhou, Peter Bourke, Nicolas Daccord, Leen Leus, Dietmar Schulz, Henri Van deGeest, Thamara Hesselink, Katrijn Van Laere, Sandrine Balzergue, Tatiana Thouroude, Annie Chastellier, Julien Jeauffre, Linda Voisine, Sylvain Gaillard, Theo Borm, Paul Arens, Roeland Voorrips, Chris Maliepaard, Enzo Neu, Marcus Linde, Marie-Christine Le Paslier, Aurelie Berard, Remi Bounon, Jeremy Clotault, Nathalie Choisne, Hadi Quesneville, Koji Kawamura, Sebastien Aubourg, Soulaiman Sakr, Rene Smulder, Elio Schijlen, Etienne Bucher, Thomas Debener, Jan De Riek, Fabrice Foucher

 

Patterns of microsatellite distribution reflect the evolution of biological complexity. Surabhi Surabhi, Akshay Kumar Avvaru, Divya Tej Sowpati, Rakesh K Mishra

 

The soft explosive model of placental mammal evolution. Matthew J Phillips, Carmelo Fruciano

 

Genetic Signatures of Lipid Metabolism Evolution in Cetacea. Yoshinori Endo, Ken-ichiro Kamei, Miho Inoue-Murayama

 

A butterfly chromonome reveals selection dynamics during extensive and cryptic chromosomal reshuffling. Jason A Hill, Ramprasad Neethiraj, Pasi Rastas, Nathan Clark, Nathan Morehouse, Maria de la Paz Celorio-Mancera, Jofre Carnicer Cols, Heinrich Dircksen, Camille Meslin, Kristin Sikkink, Maria Vives, Heiko Vogel, Christer Wiklund, Carol L Boggs, Soren Nylin, Christopher Wheat

 

The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water.David Armisen, Rajendhran Rajakumar, Markus Friedrich, Joshua B Benoit, Hugh M Robertson, Kristen A Panfilio, Seung-Joon Ahn, Monica F Poelchau, Hsu Chao, Huyen Dinh, HarshaVardhan Doddapaneni, Shannon Dugan-Perez, Richard A Gibbs, Daniel ST Hughes, Yi Han, Sandra L Lee, Shwetha C Murali, Donna M muzny, Jiaxin Qu, Kim C Worley, Monica Munoz-Torres, Ehab Abouheif, Francois Bonneton, Travis Chen, Christopher Childers, Andrew G Cridge, Antonin JJ Crumiere, Amelie Decaras, Elise M Didion, Elizabeth Duncan, Elena N Elpidina, Marie-Julie Fave, Cedric Finet, Chris GC Jacobs, Alys Jarvela, Emily J Jennings, Jeffery W Jones, Maryna P Lesoway, Mackenzie Lovegrove, Alexander Martynov, Brenda Oppert, Angelica Lilico-Ouachour, Arjuna Rajakumar, Peter N Refki, Andrew J Rosendale, Maria Emilia Santos, William Toubiana, Maurijn van der Zee, Iris M Vargas Jentzsch, Aidamalia Vargas Lowman, Severine Viala, Stephen Richards, Abderrahman Khila

 

Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1. Timothy H Webster​​, Greer A Dolby​​, Melissa A Wilson Sayres, Kenro Kusumi

 

Embracing heterogeneity: Building the Tree of Life and the future of phylogenomics. Gustavo A Bravo​, Alexandre Antonelli, Christine D Bacon, Krzysztof Bartoszek, Mozes Blom, Stella Huynh, Graham Jones, L. Lacey Knowles, Sangeet Lamichhaney, Thomas Marcussen, Hélène Morlon, Luay Nakhleh, Bengt Oxelman, Bernard Pfeil, Alexander Schliep, Niklas Wahlberg, Fernanda Werneck, John Wiedenhoeft, Sandi Willows-Munro, Scott V Edwards

 

Gene flow mediates the role of sex chromosome meiotic drive during complex speciation. Colin D Meiklejohn, Emily L. Landeen, Kathleen E. Gordon, Thomas Rzatkiewicz, Sarah B. Kingan, Anthony J. Geneva, Jeffrey P. Vedanayagam, Christina A. Muirhead, Daniel Garrigan, David L. Stern, Daven C. Presgraves

 

Cell biology

The actin cytoskeleton of the mouse sperm flagellum is organized in a helical structure. Maria Gracia Gervasi, Xinran Xu, Blanca Carbajal-Gonzalez, Mariano G Buffone, Pablo Visconti, Diego Krapf

 

A Critical-like Collective State Leads to Long-range Cell Communication in Dictyostelium discoideum Aggregation. Giovanna De Palo, Darvin Yi, Robert G. Endres

 

 

Heterochromatin drives organization of conventional and inverted nuclei. Martin Falk, Yana Feodorova, Natasha Naumova, Maxim Imakaev, Bryan R. Lajoie, Heinrich Leonhardt, Boris Joffe, Job Dekker, Geoffrey Fudenberg, Irina Solovei, Leonid Mirny

 

A non-canonical role for dynamin-1 in regulating early stages of clathrin-mediated endocytosis in non-neuronal cells. Saipraveen Srinivasan, Christoph J. Burckhardt, Madhura Bhave, Zhiming Chen, Ping-Hung Chen, Xinxin Wang, Gaudenz Danuser, Sandra L. Schmid

 

 

Dynein-2 is required for a functional transition zone and bidirectional ciliary trafficking. Laura Vuolo, Nicola L Stevenson, Kate Heesom, David J Stephens

 

Src-transformed cells hijack mitosis to extrude from the epithelium. Katarzyna A Anton, Mihoko Kajita, Rika Narumi, Yasuyuki Fujita, Masazumi Tada

 

Transcription factor dynamics reveals a circadian code for fat cell differentiation. Zahra Bahrami-Nejad, Michael L Zhao, Stefan Tholen, Devon Hunerdosse, Karen E Tkach, Sabine van Schie, Mingyu Chung, Mary N Teruel

 

Phosphorylation of GMFγ by c-Abl coordinates lamellipodial and focal adhesion dynamics. Brennan D Gerlach, Guoning Liao, Kate Tubbesing, Alyssa C. Rezey, Ruping Wang, Margarida Barroso, Dale D Tang

 

Spindly is Required for Rapid Migration of Human Cells. Claudia Conte, Michelle Baird, Michael W Davidson, Eric Ross Griffis

 

FRMD8 promotes inflammatory and growth factor signalling by stabilising the iRhom/ADAM17 sheddase complex. Ulrike Künzel, Adam Graham Grieve, Yao Meng, Sally A Cowley, Matthew Freeman

 

iTAP, a novel iRhom interactor, controls TNF secretion by policing the stability of iRhom/TACE. Ioanna Oikonomidi, Emma Burbridge, Miguel Cavadas, Graeme Sullivan, Danielle Clancy, Blanka Collis, Jana Brezinova, Jana Humpolickova, Tianyi Hu, Andrea Bileck, Christopher Gerner, Alfonso Bolado, Alex von Kriegsheim, Kvido Strisovsky, Seamus J Martin, Colin Adrain

 

Contact inhibitory Eph signaling suppresses EGF-promoted cell migration by decoupling EGFR activity from vesicular recycling. Wayne Stallaert, Ola Sabet, Yannick Bruggemann, Lisa Baak, Philippe Bastiaens

 

Microtubule dynamics regulates mitochondrial fission. Kritika Mehta, Manjyot Kaur Chug, Siddharth Jhunjhunwala, Vaishnavi Ananthanarayanan

 

Deconvolution Of Subcellular Protrusion Heterogeneity And The Underlying Actin Regulator Dynamics From Live Cell Imaging. Chuangqi Wang, Hee June Choi, Sung-Jin Kim, Aesha Desai, Namgyu Lee, Dohoon Kim, Yongho Bae, Kwonmoo Lee

 

Stopping Transformed Growth with Cytoskeletal Proteins: Turning a Devil into an Angel. Bo Yang, Haguy Wolfenson, Naotaka Nakazawa, Shuaimin Liu, Junqiang Hu, Michael Sheetz

 

Antagonism between the dynein and Ndc80 complexes at kinetochores controls the stability of kinetochore-microtubule attachments during mitosis. Mohammed A. Amin, Richard J. McKenney, Dileep Varma

 

A saturation mutagenesis approach to understanding PTEN lipid phosphatase activity and genotype-phenotypes relationships. Taylor L Mighell, Sara Evans-Dutson,  Brian J O’Roak

 

ECM cross-linking regulates invadopodia dynamics. Kamyar Esmaeili Pourfarhangi, Aviv Bergman, Bojana Gligorijevic

 

Regulation of global translation during the cell cycle. Vilte Stonyte, Erik Boye, Beata Grallert

 

Membrane bending energy and tension govern mitochondrial division. Lina Carlini, Dora Mahecic, Tatjana Kleele, Aurelien Roux, Suliana Manley

 

Core Proteome and Architecture of COPI Vesicles. Manuel Rhiel, Bernd Hessling, Qi Gao, Andrea Hellwig, Frank Adolf, Felix T. Wieland

 

 

ESCRT-III acts in scissioning new peroxisomes from the ER. Fred D Mast, Thurston Herricks, Kathleen M Strehler, Leslie R Miller, Ramsey A Saleem, Richard A Rachubinski, John D Aitchison

 

Modelling

 

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

 

A Toolbox for Discrete Modelling of Cell Signalling Dynamics. Yasmin Z Paterson, David Shorthouse, Markus W Pleijzier, Nir Piterman, Claus Bendtsen, Benjamin A Hall, Jasmin Fisher

 

A Three-Dimensional Mathematical Model of Collagen Contraction. Emily Jennings Evans, John C. Dallon

 

 

Stochastic methods for inferring states of cell migration. Richard J Allen, Christopher Welch, Neha Pankow, Klaus Hahn, Timothy C Elston

 

 

Deep Reinforcement Learning of Cell Movement in the Early Stage of C. elegans Embryogenesis. Zi Wang, Dali Wang, Chengcheng Li, Yichi Xu, Husheng Li, Zhirong Bao

 

Modeling cell size regulation: From single-cell level statistics to molecular mechanisms and population level effects. Po-Yi Ho, Jie Lin, Ariel Amir

 

A model of dynamic stability of H3K9me3 heterochromatin to explain the resistance to reprogramming of differentiated cells. Charly Jehanno, Gilles Flouriot, Pascale Le Goff, Denis Michel

 

How Criticality of Gene Regulatory Networks Affects the Resulting Morphogenesis under Genetic Perturbations. Hyobin Kim, Hiroki Sayama

 

Complexity, Development, and Evolution in Morphogenetic Collective Systems. Hiroki Sayama

 

Statistical mechanics of cell decision-making: the cell migration force distribution. Haralampos Hatzikirou

 

Approximate Bayesian computation reveals the importance of repeated measurements for parameterising cell-based models of growing tissues. Jochen Kursawe, Ruth E. Baker, Alexander George Fletcher

 

A Reactive Inelasticity Theoretical Framework for modeling Viscoelasticity, Plastic Deformation, and damage in Soft Tissue. Babak N. Safa, Michael H. Santare, Dawn M. Elliott

 

 

Quantifying Waddington’s epigenetic landscape: a comparison of single-cell potency measures. Jifan Shi, Andrew Teschendorff, Weiyan Chen, Luonan Chen, Tiejun Li

 

Modelling mitosis with multiple phenotypes: relation to Haeckel’s biogenetic recapitulation law. Yuriy Alexandrov

 

Ontology-based validation and identification of regulatory phenotypes. Maxat Kulmanov, Paul N Schofield, Georgios V Gkoutos, Robert Hoehndorf

 

The importance of geometry in the corneal micropocket angiogenesis assay. James A Grogan, Anthony J Connor, Joe M Pitt-Francis, Philip K Maini, Helen M Byrne

 

Euplotid: A quantized geometric model of the eukaryotic cell. Diego Borges-Rivera

 

Enhanced Waddington Landscape Model with Cell-Cell Communication Can Explain Molecular Mechanisms of Self-Organization. Hosein Fooladi, Parsa Moradi, Ali Sharifi-Zarchi, Babak Hossein Khalaj

 

Tools & resources

| Imaging etc.

Observing the Cell in Its Native State: Imaging Subcellular Dynamics in Multicellular Organisms.Tsung-li Liu, Srigokul Upadhyayula, Daniel E Milkie, Ved Singh, Kai Wang, Ian A Swinburne, Kishore R Mosaliganti, Zach M Collins, Tom W Hiscock, Jamien Shea, Abraham Q Kohrman, Taylor N Medwig, Daphne Dambournet, Ryan Forster, Brian Cunniff, Yuan Ruan, Hanako Yashiro, Steffen Scholpp, Elliot M Meyerowitz, Dirk Hockemeyer, David G Drubin, Benjamin L Martin, David Q Matus, Minoru Koyama, Sean G Megason, Tom Kirchhausen, Eric Betzig

 

Sub-voxel light-sheet microscopy for high-resolution, high-throughput volumetric imaging of large biomedical specimens. Peng Fei, Jun Nie, Juhyun Lee, Yichen Ding, Shuoran Li, Zhilong Yu, Hao Zhang, Masaya Hagiwara, Tingting Yu, Tatiana Segura, Chih-Ming Ho, Dan Zhu, Tzung K. Hsiai

 

Single-cell diffraction tomography with optofluidic rotation about a tilted axis. Paul Müller, Mirjam Schürmann, Chii J. Chan, Jochen Guck

 

 

SSPIM: a beam shaping toolbox for structured selective plane illumination microscopy. Mostafa Aakhte, Ehsan A. Akhlaghi, Hans-Arno J Muller

 

Three-photon fluorescence microscopy with an axially elongated Bessel focus. Cristina Rodriguez, Yajie Liang, Rongwen Lu, Na Ji

 

Enhanced photon collection enables four dimensional fluorescence nanoscopy of living systems. Luciano Masullo, Andreas Boden, Francesca Pennacchietti, Giovanna Coceano, Michael Ratz, Ilaria Testa

 

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

 

X10 Expansion Microscopy Enables 25 nm Resolution on Conventional Microscopes. Sven Truckenbrodt, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda Kabatas, Silvio O. Rizzoli

 

Multicolor single particle reconstruction of protein complexes. Christian Sieben, Niccolo Banterle, Kyle Douglass, Pierre Gonczy, Suliana Manley

 

 

Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors. Tomas Lukes, Jakub Pospisil, Karel Fliegel, Theo Lasser, Guy M Hagen

 

In vivo monitoring of plant small GTPase activation using a Förster resonance energy transfer biosensor. Hann Ling Won, Akira Akamatsu, Qiong Wang, Masayuki Higuchi, Tomonori Matsuda, Jun Okuda, Ken-ichi Kosami, Noriko Inada, Tsutomu Kawasaki, Shingo Nagawa, Li Tan, Yoji Kawano, Ko Shimamoto

 

Exploring morphological motifs for a single neuron based on multiple 3D reconstructions. Jian Yang, Yishan He, Zhi Zhou, Ning Zhong, Hanchuan Peng

 

 

Sampling Neuron Morphologies. Roozbeh Farhoodi, Konrad P Kording

 

DeepNeuron: An Open Deep Learning Toolbox for Neuron Tracing. Zhi Zhou, Hsien-Chi Kuo, Hanchuan Peng, Fuhui Long

 

High precision automated detection of labeled nuclei in terabyte-scale whole-brain volumetric image data of mouse. Girraj Pahariya, Sukhendu Das, Jaikishan Jayakumar, Samik Bannerjee, Venu Vangala, Keerthi Ram, Partha P Mitra

 

High-resolution wide-field human brain tumor margin detection and in vivo murine neuroimaging. Derek Yecies, Orly Liba, Elliott SoRelle, Rebecca Dutta, Edwin Yuan, Hannes Vogel, Gerald Grant, Adam de la Zerda

 

FlowPot axenic plant growth system for microbiota research. James M. Kremer, Bradley C. Paasch, David Rhodes, Caitlin Thireault, John E. Froehlich, Paul Schulze-Lefert, James M. Tiedje, Sheng Yang He

 

Genetically encoded ratiometric indicators for potassium ion. Yi Shen, Sheng-Yi Wu, Vladimir Rancic, Yong Qian, Shin-Ichiro Miyashita, Klaus Ballanyi, Robert E. Campbell, Min Dong

 

A compact head-mounted endoscope for in vivo calcium imaging in freely-behaving mice. Alexander D Jacob, Adam I Ramsaran, Andrew J Mocle, Lina M Tran, Chen Yan, Paul W Frankland, Sheena A Josselyn

 

Transcranial in vivo recording of neural activity in the rodent brain with near-infrared photoacoustic voltage-sensitive dye imaging. Jeeun Kang, Haichong K. Zhang, Shilpa D. Kadam, Julie Fedorko, Heather Valentine, Ping Yan, Jin U. Kang, Arman Rahmim, Albert Gjedde, Leslie M. Loew, Dean F. Wong, Emad M. Boctor

 

Parallel holographic illumination enables sub-millisecond two-photon optogenetic activation in mouse visual cortex in vivo. I-Wen Chen, Emiliano Ronzitti, Brian R. Lee, Tanya L. Daigle, Hongkui Zeng, Eirini Papagiakoumou, Valentina Emiliani

 

In vivo multiphoton microscopy of cardiomyocyte calcium dynamics in the beating mouse heart. David M Small, Jason S Jones, Nozomi Nishimura

 

Imaging neural activity in the ventral nerve cord of behaving adult Drosophila. Chin-Lin Chen, Laura Hermans, Meera C Viswanathan, Denis Fortun, Michael Unser, Anthony Cammarato, Michael H Dickinson, Pavan Ramdya

 

Microfluidic device for on-chip mixing and encapsulation of lysates. Jui-Cha Chang, Zoe Swank, Oliver Keiser, Sebastian Josef Maerkl, Esther Amstad

 

 

Enzyme-based synthesis of single molecule RNA FISH probes. Christian Lanctôt

 

 

Fluorescent reporter lines for auxin and cytokinin signalling in barley (Hordeum vulgare). Gwendolyn Kristin Kirschner, Yvonne Stahl, Jafargholi Imani, Maria von Korff, Ruediger Simon

 

A Multi-layer, Self-aligning Hydrogel Micro-molding Process Offering a Fabrication Route to Perfusable 3D In-Vitro Microvasculature. Hossein Heidari, Hayden Taylor

 

Zebrabase: An intuitive tracking solution for aquatic model organisms. Jana Oltova, Jindrich Jindrich, Ctibor Skuta, Ondrej Svoboda, Olga Machonova, Petr Bartunek

 

An Automated Workflow for Segmenting Single Adult Cardiac Cells from Large-Volume Serial Block-Face Scanning Electron Microscopy Data. Akter Hussain, Shouryadipta Ghosh, Siavash Beikoghli Kalkhoran, Derek Hausenloy, Eric Hanssen, Vijay Rajagopal

 

Digital museum of retinal ganglion cells with dense anatomy and physiology. J. Alexander Bae, Shang Mu, Jinseop S. Kim, Nicholas L. Turner, Ignacio Tartavull, Nico Kemnitz, Chris S. Jordan, Alex D. Norton, William M. Silversmith, Rachel Prentki, Marissa Sorek, Celia David, Devon L. Jones, Doug Bland, Amy L. R. Sterling, Jungman Park, Kevin L. Briggman, H. Sebastian Seung, the EyeWirers

 

| Genome tools

 

An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein. Pooran Singh Dewari, Benjamin Southgate, Katrina Mccarten, German Monogarov, Eoghan O’Duibhir, Niall Quinn, Ashley Tyrer, Colin Plumb, Carla Blin, Rebecca Finch, Raul Bardini Bressan, Gillian Morrison, Ashley M Jacobi, Mark A Behlke, Alex von Kriegsheim, Simon Tomlinson, Jeroen Krijgsveld, Steven M Pollard

 

Identification of Pre-Existing Adaptive Immunity to Cas9 Proteins in Humans. Carsten Trevor Charlesworth, Priyanka S Deshpande, Daniel P Dever, Beruh Dejene, Natalia Gomez-Ospina, Sruthi Mantri, Mara Pavel-Dinu, Joab Camarena, Kenneth I Weinberg, Matthew H Porteus

 

On the design of CRISPR-based single cell molecular screens. Andrew J Hill, José L McFaline-Figueroa, Lea M Starita, Molly J Gasperini, Kenneth A Matreyek, Jonathan Packer, Dana Jackson, Jay Shendure, Cole Trapnel

 

Selection-free, high frequency genome editing by homologous recombination of human pluripotent stem cells using Cas9 RNP and AAV6. Renata Martin, Kazuya Ikeda, Nobuko Uchida, M. Kyle Cromer, Toshinobu Nishimura, Daniel P Dever, Joab Camarena, Rasmus Bak, Anders Lausten, Martin R Jakobsen, Volker Wiebking, Vittorio Sebastiano, Hiromitsu Nakauchi, Matthew H Porteus

 

Hi-TOM: a platform for high-throughput tracking of mutations induced by CRISPR/Cas systems. Qing Liu, Chun Wang, Xiaozhen Jiao, Huawei Zhang, Lili Song, Yanxin Li, Caixia Gao, Kejian Wang

 

Engineering Plant Architecture via CRISPR/Cas9-mediated Alteration of Strigolactone Biosynthesis. Haroon Butt, Muhammad Jamil, Jian You Wang, Salim Al-Babili, Magdy Mahfouz

 

Optimizing CRISPR/Cas9 System to Precisely Model Plasminogen Activator Inhibitor-1 Point Mutations in Mice. Yang Liu, Thomas L Saunders, Thomas Sisson, Robert Blackburn, David S Ginsberg, Duane Day

 

Next generation CRISPR/Cas9 transcriptional activation in Drosophila using flySAM. Yu Jia, Rong-Gang Xu, Xingjie Ren, Ben Ewen-Campen, Rajendhran Rajakumar, Jonathan Zirin, Donghui Yang-Zhou, Ruibao Zhao, Fang Wang, Decai Mao, Ping Peng, Huan-Huan Qiao, Xia Wang, Lu-Ping Liu, Bowen Xu, Jun-Yuan Ji, Qingfei Lu, Jin Sun, Norbert Perrimon, Jian-Quan Ni

 

Programmable RNA recognition using a CRISPR-associated Argonaute. Audrone Lapinaite, Jennifer A. Doudna, Jamie Cate

 

Efficient Homology Directed Repair by Cas9:DNA Localization and Cationic Polymeric Transfection in Mammalian Cells. Philip JR Roche, Heidi Gytz, Faiz Hussain, Christopher JF Cameron, Denis Paquette, Mathieu Blanchette, Josée Dostie, Bhushan Nagar, Uri David Akavia

 

Accurate analysis of genuine CRISPR editing events with ampliCan. Kornel Labun, Xiaoge Guo, Alejandro Chavez, George Church, James A Gagnon, Eivind Valen

 

Reducing False Positives in CRISPR/Cas9 Screens from Copy Number Variations. Alexander Wu, Tengfei Xiao, Teng Fei, Shirley X Liu, Wei Li

 

Manipulation of chromatin to enhance CRISPR activity. René Daer, Cassandra M Barrett, Karmella A Haynes

 

Targeted genome fragmentation with CRISPR/Cas9 improves hybridization capture, reduces PCR bias, and enables efficient high-accuracy sequencing of small targets. Daniela Nachmanson, Shenyi Lian, Elizabeth K. Schmidt, Michael J. Hipp, Kathryn T. Baker, Yuezheng Zhang, Maria Tretiakova, Kaitlyn Loubet-Senear, Brendan F. Kohrn, Jesse J. Salk, Scott R. Kennedy, Rosa Ana Risques

 

Efficacy and dynamics of self-targeting CRISPR/Cas constructs for gene editing in the retina. Fan Li, Sandy SC Hung, Jiang-Hui Wang, Vicki Chrysostomou, Vickie HY Wong, James A Bender, Leilei Tu, Alice Pébay, Anna E King, Anthony L Cook, Raymond CB Wong, Bang V Bui, Alex Hewitt, Guei-Sheung Liu

 

Efficient lentiviral transduction of different human and mouse cells. Gang Zhang, Taihua Wang

 

 

Generation and validation of homozygous fluorescent knock-in cells using genome editing. Birgit Koch, Bianca Nijmeijer, Moritz Kueblbeck, Yin Cai, Nike Walther, Jan Ellenberg

 

Transgenic mouse lines expressing the 3xFLAG-dCas9 protein for enChIP analysis. Toshitsugu Fujita, Fusako Kitaura, Asami Oji, Naoki Tanigawa, Miyuki Yuno, Masahito Ikawa, Ichiro Taniuchi, Hodaka Fujii

 

A MinION-based pipeline for fast and cost-effective DNA barcoding. Amrita Srivathsan, Bilgenur Baloğlu, Wendy Wang, Wei Xin Tan, Denis Bertrand, Amanda Hui Qi Ng, Esther Jia Hui Boey, Jayce Jia Yu Koh, Niranjan Nagarajan, Rudolf Meier

 

Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform. Shan Wei, Zev Williams, Zachary R Weiss

 

Resolving the Full Spectrum of Human Genome Variation using Linked-Reads. Patrick Marks, Sarah Garcia, Alvaro Martinez Barrio, Kamila Belhocine, Jorge Bernate, Rajiv Bharadwaj, Keith Bjornson, Claudia Catalanotti, Josh Delaney, Adrian Fehr, Brendan Galvin, Haynes Heaton, Jill Herschleb, Christopher Hindson, Esty Holt, Cassandra B. Jabara, Susanna Jett, Nikka Keivanfar, Sofia Kyriazopoulou-Panagiotopoulou, Monkol Lek, Bill Lin, Adam Lowe, Shazia Mahamdallie, Shamoni Maheshwari, Tony Makarewicz, Jamie Marshall, Francesca Meschi, Chris O’keefe, Heather Ordonez, Pranav Patel, Andrew Price, Ariel Royall, Elise Ruark, Sheila Seal, Michael Schnall-Levin, Preyas Shah, Stephen Williams, Indira Wu, Andrew Wei Xu, Nazneen Rahman, Daniel MacArthur, Deanna M. Church

 

The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. Olga Dudchenko, Muhammad S. Shamim, Sanjit Batra, Neva C. Durand, Nathaniel T. Musial, Ragib Mostofa, Melanie Pham, Brian Glenn St Hilaire, Weijie Yao, Elena Stamenova, Marie Hoeger, Sarah K. Nyquist, Valeriya Korchina, Kelcie Pletch, Joseph P. Flanagan, Ania Tomaszewicz, Denise McAloose, Cynthia Pérez Estrada, Ben J. Novak, Arina D. Omer, Erez Lieberman Aiden

 

5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design. Ji Hun Kim, Katelyn Titus, Wanfeng Gong, Jonathan Beagan, Zhendong Cao, Jennifer E Phillips-Cremins

 

Multiplex Chromatin Interaction Analysis with Single-Molecule Precision. Meizhen Zheng, Simon Zhongyuan Tian, Rahul Maurya, Byoungkoo Lee, Minji Kim, Daniel Capurso, Emaly Piecuch, Liang Gong, Jacqueline Jufen Zhu, Chee Hong Wong, Chew Yee Ngan, Ping Wang, Xiaoan Ruan, Chia-Lin Wei, Yijun Ruan

 

TET-mediated epimutagenesis of the Arabidopsis thaliana methylome. Lexiang Ji, William T. Jordan, Xiuling Shi, Lulu Hu, Chuan He, Robert J. Schmitz

 

Homology-directed repair of a defective glabrous gene in Arabidopsis with Cas9-based gene targeting. Florian Hahn, Marion Eisenhut, Otho Mantegazza, Andreas P M Weber

 

Targeted epigenomic changes to the maize methylome resulting from tissue culture. Zhaoxue Han, Peter A Crisp, Scott Stelpflug, Shawn Kaeppler, Qing Li, Nathan M Springer

 

A Comprehensive Tool Set for Inducible, Cell Type-Specific Gene Expression in Arabidopsis. Ann-Kathrin Schuerholz, Vadir Lopez-Salmeron, Zhenni Li, Joachim Forner, Christian Wenzl, Christophe Gaillochet, Sebastian Augustin, Amaya Vilches Barro, Michael Fuchs, Michael Gebert, Joop E.M. Vermeer, Jan U. Lohmann, Thomas Greb, Sebastian Wolf

 

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Stephen J. Clark, Ricard Argelaguet, Chantriolnt-Andreas Kapourani, Thomas M. Stubbs, Heather J. Lee, Celia Alda-Catalinas, Felix Krueger, Guido Sanguinetti, Gavin Kelsey, John C. Marioni, Oliver Stegle, Wolf Reik

 

Equivalent high-resolution identification of neuronal cell types with single-nucleus and single-cell RNA-sequencing. Trygve E Bakken, Rebecca D Hodge, Jeremy M Miller, Zizhen Yao, Thuc N Nguyen, Brian Aevermann, Eliza Barkan, Darren Bertagnolli, Tamara Casper, Nick Dee, Emma Garren, Jeff Goldy, Lucas T Gray, Matthew Kroll, Roger S Lasken, Kanan Lathia, Sheana Parry, Christine Rimorin, Richard H Scheuermann, Nicholas J Schork, Soraya I Shehata, Michael Tieu, John W Phillips, Amy Bernard, Kimberly A Smith, Hongkui Zeng, Ed S Lein, Bosiljka Tasic

 

A robust method for RNA extraction and purification from a single adult mouse tendon. Mor Grinstein, Heather L Dingwall, Rishita R Shah, Terence D Capellini, Jenna L Galloway

 

Evaluating Cell Identity from Transcription Profiles. Nancy Mah, Katerina Taškova, Khadija El Amrani, Krithika Hariharan, Andreas Kurtz, Miguel A. Andrade-Navarro

 

Mapping nonapoptotic caspase activity with a transgenic reporter in mice. Peter Nicholls, Thomas Pack, Nikhil Urs, Sunil Kumar, Gabor Turu, Evan Calabrese, Wendy Roberts, Ping Fan, Valeriy Ostapchenko, Monica Guzman, Flavio Beraldo, Vania Prado, Marco Prado, Ivan Spasojevic, Joshua Snyder, Kafui Dzirasa, G. Allan Johnson, Marc Caron

 

High Aspect Ratio Nanomaterials Enable Biomolecule Delivery and Transgene Expression or Silencing in Mature Plants. Gozde S. Demirer, Huan Zhang, Juliana Matos, Roger Chang, Linda Chio, Brian Staskawicz, Markita P. Landry

 

Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers. Yu Fu, Pei-Hsuan Wu, Timothy Beane, Phillip D. Zamore, Zhiping Weng

 

Unsupervised embedding of single-cell Hi-C data. Jie Liu, Dejun Lin, Gurkan Yardimci, William Noble

 

Intron-mediated enhancement boosts Rtn4 circRNA expression: A robust method for exploring circRNA function. Dingding Mo, Xinping Li

 

QTLseqr: An R package for bulk segregant analysis with next-generation sequencing. Ben N. Mansfeld, Rebecca Grumet

 

LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies. Meyer Verena Hannah, Francesco Paolo Casale, Oliver Stegle, Ewan Birney

 

Detection and removal of barcode swapping in single-cell RNA-seq data. Jonathan A. Griffiths, Arianne C. Richard, Karsten Bach, Aaron T.L. Lun, John C. Marioni

 

An atlas of silencer elements for the human and mouse genomes. Naresh Doni Jayavelu, Ajay Jajodia, Arpit Mishra, R. David Hawkins

 

Topographer Reveals Stochastic Dynamics of Cell Fate Decisions from Single-Cell RNA-Seq Data. Jiajun Zhang, Tianshou Zhou

 

Sharq, a versatile preprocessing and QC pipeline for Single Cell RNA-seq. Tito Candelli, Philip Lijnzaad, Mauro J Muraro, Alexander van Oudenaarden, Thanasis Margaritis, Frank Holstege

 

Research practice & education

How the US can best support the careers of promising young biomedical scientists. Bruce Alberts, Tony Hyman, Chris Pickett​, Shirley Tilghman, Harold Varmus

 

Public archives for biological image data. Jan Ellenberg, Jason R Swedlow, Mary Barlow, Charles E Cook, Ardan Patwardhan, Alvis Brazma, Ewan Birney

 

Centralized “big science” communities more likely generate non-replicable results. Valentin Danchev, Andrey Rzhetsky, James A. Evans

 

Ethical Shades of Gray: Questionable Research Practices in Health Professions Education. Anthony R Artino Jr., Erik A Driessen, Lauren A Maggio

 

A survey on information sources used by academic researchers to evaluate scientific instruments. Carsten Bergenholtz, Samuel C MacAulay, Christos Kolympiris, Inge Seim

 

Open access policies of high impact medical journals: a cross-sectional study. Tim Ellison, Tim Koder, Laura Schmidt, Amy Williams, Christopher Winchester

 

Open access levels: a quantitative exploration using Web of Science and oaDOI data. Jeroen Bosman​​, Bianca Kramer

 

Harmonizing semantic annotations for computational models in biology. Maxwell L Neal, Matthias König, David Nickerson, Goksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba, Samuel H Friedman, Alan Garny, John H Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick Juty, Nicolas Le Novère, Chris Myers, Brett G Olivier, Herbert M Sauro, Martin Scharm, Jacky L Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath

 

Female grant applicants are equally successful when peer reviewers assess the science, but not when they assess the scientist. Holly O Witteman, Michael Hendricks, Sharon Straus, Cara Tannenbaum

 

Opportunities And Obstacles For Deep Learning In Biology And Medicine. Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M Hoffman, Wei Xie, Gail L. Rosen, Benjamin J. Lengerich, Johnny Israeli, Jack Lanchantin, Stephen Woloszynek, Anne E. Carpenter, Avanti Shrikumar, Jinbo Xu, Evan M. Cofer, Christopher A Lavender, Srinivas C Turaga, Amr M Alexandari, Zhiyong Lu, David J. Harris, Dave DeCaprio, Yanjun Qi, Anshul Kundaje, Yifan Peng, Laura K. Wiley, Marwin H. S. Segler, Simina M Boca, S. Joshua Swamidass, Austin Huang, Anthony Gitter, Casey S. Greene

 

FAIRsharing: working with and for the community to describe and link data standards, repositories and policies. Susanna-Assunta Sansone, Peter McQuilton, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Massimiliano Izzo, Allyson Lister, Milo Thurston, FAIRsharing Community

 

“As-you-go” instead of “after-the-fact”: A network approach to scholarly communication and evaluation. Chris HJ Hartgerink, Marino van Zelst

 

Why not…

Soft song: help thine enemy! Szabolcs Szamado

 

To jump or not to jump: The Bereitschaftspotential required to jump into 192-meter abyss. Marius Nann, Leonardo G. Cohen, Lüder Deecke, Surjo R. Soekadar

 

 

(No Ratings Yet)
Loading...

Recently, Nature published my correspondence “Dispense with redundant P values”. It highlights my concern that p-values are often calculated because “everybody does it”. This reminded me of the mechanical repetition that parrots are well-known for (footnote 1). Parroting of p-value reporting should stop and I suggest to only present a p-value in a figure if it is necessary for interpretation.

During the editing process of my contribution a specific example of a redundant p-value was removed. The reasoning was that it seemed unfair to single out only one paper. I agreed and I would like to stress that parroting of p-value reporting is not restricted to a specific paper, a specific issue of Nature or to some specific journal. It’s just that I found it very ironic that in the same issue of Nature that proposes  “Five ways to fix statistics” (Leek et al., 2017) there are several clear examples of figures (in different papers) with meaningless p-values.

Since I am convinced that an example will clarify my point, I have extracted the data (see footnote 2) from one of the papers in the aforementioned issue (without disclosing the nature of the paper). I performed a t-test (two-tailed, unequal variances) as described in the paper and reproduced the p-value (footnote 3). The resulting figure is shown below on the left and closely mimics the figure of the original paper.

 

Clearly, there is a large difference between the ’Control’ and ‘Treated’ condition, reflecting a large effect of the treatment. To reach that conclusion, there is no need for a p-value. Moreover, the p-value does not convey any relevant information for interpretation of the figure. As such, the p-value qualifies as chartjunk (E.R. Tufte, 1983) and should be omitted. This will generate a cleaner figure (shown above on the right) that emphasizes the data.

The problems with p-values are larger than their meaningless use in figures whenever the effects are large. The way that p-values are defined has some confusing backward logic (footnote 4). Consequently, p-values are often misinterpreted (Greenland et al., 2016, Lakens, 2017) or misused as a ‘measure of credibility’ (Goodman, 2016). The misconception that p-values represent the strength of evidence is reinforced by catogerizing p-values, e.g. by using increasing number of asterisks (e.g. * P < 0.05; ** P < 0.01; *** P < 0.001). P-values cannot be used as a rating system (Wasserstein and Lazar, 2016) and categories should be avoided at all times.

To avoid the unnecessary, and at times misleading, use of p-values, the mechanical repetition of current practices should stop. Whether p-values are important for the interpretation of the figure should be a central question. Before that question can be answered, the correct definition of a p-value needs to be thoroughly understood. In addition, the correct interpretation and common misconceptions (Greenland et al., 2016) of p-values should be considered. I hope that careful reflection on the meaning of p-values will decrease their use and improve figures.

 

Acknowledgments: I am indebted to Marten Postma for the many discussions about statistical concepts and applied statistics, that have increased my understanding of the topic.

 

Footnotes

Footnote 1: The original title of my correspondence was “Prevent p-value parroting”. This title was changed to “Dispense with redundant P values” by Nature after I returned the proofs and without consulting me.

Footnote 2: The raw data that I extracted is listed below in csv format:

Condition,Value
Control,305
Control,318
Control,355
Control,364
Treated,160
Treated,125
Treated,120
Treated,127

 

Footnote 3: This is an example of yet another questionable practice, i.e. calculating a p-value for a dataset with only a couple of datapoints per condition. Ironically, several examples can be found in the aforementioned issue while this matter has also been addressed previously by David Vaux (2012) in Nature (and by many others as well).

Footnote 4: The p-value is the probability of the observed data (or more extreme values), assuming that the null-hypothesis (there is zero difference between the two conditions) is true.

 

(19 votes)
Loading...

Hi!

Do you play bass? Guitar? Keys? Sax? Brass? We’re putting together an SDB all-star jazz combo to play at the SDB meeting in Portland, and we’re looking for a couple more players! Feel free to reach out to me at david.matus@stonybrook.edu if you’re interested!

(No Ratings Yet)
Loading...