Welcome to our monthly trawl for developmental biology (and related) preprints. 

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Another month, another net full of exciting science. Look out for WNT vampires, regenerating lampreys, polarising ctenophores, plus investigations into niche architecture, tissue mechanics and the dynamics of developmental signalling.

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

 

Developmental biology

| Patterning & signalling

| Morphogenesis & mechanics

| Genes & genomes

| Stem cells, regeneration & disease modelling

Evo-devo & evo

Cell biology

Modelling

Tools & resources

Research practice & education

Why not…

 

 

Developmental biology

| Patterning & signalling

 

Heterogeneity of Sonic Hedgehog Response Dynamics and Fate Specification in Single Neural Progenitors
Fengzhu Xiong, Andrea R Tentner, Tom W Hiscock, Peng Huang, Sean Megason

 

The Ciliopathy Gene Ftm/Rpgrip1l Controls Mouse Forebrain Patterning Via Region-Specific Modulation Of Hedgehog/Gli Signaling.
Abraham Andreu-Cervera, Isabelle Anselme, Alice Karam, Martin Catala, Sylvie Schneider-Maunoury

 

GPR17 is an Essential Component of the Negative Feedback Loop of the Sonic Hedgehog Signalling Pathway in Neural Tube Development
Atsuki Yatsuzuka, Akiko Hori, Minori Kadoya, Mami Matsuo-Takasaki, Toru Kondo, Noriaki Sasai

 

 

Gata4 drives Hh-signaling for second heart field migration and outflow tract development
Jielin Liu, Henghui Cheng, Menglan Xiang, Lun Zhou, Ke Zhang, Ivan P. Moskowitz, Linglin Xie

 

Endothelial cells form transient Notch-dependent NO-containing cystic structures during zebrafish cerebrovascular development
Elisabeth Kugler, Karishma Chhabria, Stephan Daetwyler, Jan Huisken, Karen Plant, Aaron Savage, Robert Neil Wilkinson, Paul Armitage, Timothy James Chico

 

 

Notch signalling maintains Hedgehog responsiveness via a Gli-dependent mechanism during spinal cord patterning in zebrafish
Craig T Jacobs, Peng Huang

 

 

 

Vegfa expression is activated through positive and negative transcriptional regulatory networks controlled by the ETS factor Etv6 in vivo
Lei Li, Rossella Rispoli, Roger Patient, Aldo Ciau-Uitz, Catherine Porcher

 

foxc1a and foxc1b differentially regulate angiogenesis from arteries and veins by modulating Vascular Endothelial Growth Factor signalling
Zhen Jiang, Teri Forey, Aaron M Savage, Matthew W Loose, Timothy JA Chico, Fredericus JM van Eeden, Robert N Wilkinson

 

COMPASS Family Histone Methyltransferase ASH2L Mediates Corticogenesis via Transcriptional Regulation of Wnt Signalling
Liang Li, Xiangbin Ruan, Chang Wen, Pan Chen, Wei Liu, Liyuan Zhu, Pan Xiang, Xiaoling Zhang, Qunfang Wei, Lin Hou, Bin Yin, Jiangang Yuan, Boqin Qiang, Pengcheng Shu, Xiaozhong Peng

 

 

Spatial and temporal inhibition of FGFR2b ligands reveals continuous requirements and novel targets in mouse inner ear morphogenesis
Lisa D Urness, Xiaofen Wang, Huy Doan, Nathan Shumway, C Albert Noyes, Edgar Gutierrez-Magana, Ree Lu, Suzanne L Mansour

 

Cell competition corrects noisy Wnt morphogen gradients to achieve robust patterning
Yuki Akieda, Shohei Ogamino, Hironobu Furuie, Shizuka Ishitani, Ryutaro Akiyoshi, Jumpei Nogami, Takamasa Masuda, Nobuyuki Shimizu, Yasuyuki Ohkawa, Tohru Ishitani

 

Synergy with TGFβ ligands switches WNT pathway dynamics from transient to sustained during human pluripotent cell differentiation
Joseph Massey, Yida Liu, Omar Alvarenga, Teresa Saez, Matthew Schmerer, Aryeh Warmflash

 

wnt4a Promotes Female Development and Reproductive Duct Elongation in Zebrafish
Bruce W Draper, Michelle E Kossack, Samantha K High, Rachel E Hopton, Yi-lin Yan, John H Postlethwait

 

 

SIX1 cooperates with RUNX1 and SMAD4 in cell fate commitment of Müllerian duct epithelium
jumpei Terakawa, Vanida A Serna, Devi Nair, Shigeru Sato, Kiyoshi Kawakami, Sally Radovick, Pascal Maire, Takeshi Kurita

 

YAP activity is necessary and sufficient for basal progenitor abundance and proliferation in the developing neocortex
Milos Kostic, Judith T.M.L. Paridaen, Katherine R. Long, Nereo Kalebic, Barbara Langen, Pauline Wimberger, Hiroshi Kawasaki, Takashi Namba, Wieland B. Huttner

 

Onecut factors and Pou2f2 regulate diversification and migration of V2 interneurons in the mouse developing spinal cord
Audrey Harris, Gauhar Masgutova, Amandine Collin, Mathilde Toch, Maria Hidalgo-Figueroa, Benvenuto Jacob, Lynn M Corcoran, Cedric Francius, Frederic Clotman

 

Synaptic proteins expressed by oligodendrocytes mediate CNS myelination
Alexandria N. Hughes, Bruce Appel

 

PADI2-mediated citrullination is required for efficient oligodendrocyte differentiation and myelination
Ana Mendanha Falcao, Mandy Meijer, Antonella Scaglione, Puneet Rinwa, Eneritz Agirre, Jialiang Liang, Sara C. Larsen, Abeer Heskol, Rebecca Frawley, Michael Klingener, Manuel Varas-Godoy, Alexandre A.S.F. Raposo, Patrik Ernfors, Diogo S. Castro, Michael L. Nielsen, Patrizia Casaccia, Goncalo Castelo-Branco

 

Identification of a Sulf2-dependant astrocyte subtype that stands out through the expression of Olig2 in the ventral spinal cord
David Ohayon, Nathalie Escalas, Philippe Cochard, Bruno Glise, Cathy Danesin, Cathy Soula

 

Deciphering defective subventricular adult neurogenesis in cyclin D2-deficient mice
Rafał Płatek, Leszek Kaczmarek, Artur Czupryn

 

 

Reverse genetic screen reveals that Il34 facilitates yolk sac macrophage distribution and seeding of the brain
Laura E Kuil, Nynke Oosterhof, Samuel N Geurts, Herma C van der Linde, Erik Meijering, Tjakko J van Ham

 

Maternal inflammation significantly impacts cortical interneuron development in a subtype-specific manner
Navneet A Vasistha, Maria Pardo-Navarro, Janina Gasthaus, Dilys Weijers, Michaela K Mueller, Ulrich Pfisterer, Jakob von Engelhardt, Karin S Hougaard, Konstantin Khodosevich

 

Fate Before Function: Specification of the Hair Follicle Niche Occurs Prior to its Formation and Is Progenitor Dependent
Ka Wai Mok, Nivedita Saxena, Nicholas Heitman, Laura Grisanti, Devika Srivastava, Mauro Muraro, Tina Jacob, Rachel Sennett, Zichen Wang, Yutao Su, Lu Yang, Avi Ma’ayan, David Ornitz, Maria Kasper, Michael Rendl

 

Induction of Sertoli cells from human fibroblasts by NR5A1 and GATA4
Jianlin Liang, Nan Wang, Jing He, Jian Du, Yahui Guo, Lin Li, Kehkooi Kee

 

Functional importance of JMY expression by Sertoli cells in mediating mouse spermatogenesis
Yue Liu, Jiaying Fan, Yan Yan, Xuening Dang, Ran Zhao, Yimei Xu, Zhide Ding

 

Miro-dependent mitochondrial pool of CENP-F and its farnesylated C-terminal domain are dispensable for normal development in mice
Martin Peterka, Benoît Kornmann

 

Bovine blastocyst development depends on threonine catabolism
Vahid Najafzadeh, Harold Henderson, Ryan Martinus, Bjorn Oback

 

The role of BMP6 in the proliferation and differentiation of chicken cartilage cells
Fei Ye, Hengyong Xu, Huadong Yin, Xiaoling Zhao, Diyan Li, Qing Zhu, Yan Wang

 

Nested oscillatory dynamics in cortical organoids model early human brain network development
Cleber A. Trujillo, Richard Gao, Priscilla D. Negraes, Isaac A. Chaim, Alain Domissy, Matthieu Vandenberghe, Anna Devor, Gene W. Yeo, Bradley Voytek, Alysson R. Muotri

 

A non-canonical JAGGED1 signal to JAK2 mediates osteoblast commitment in cranial neural crest cells
Archana Kamalakar, Melissa S Oh, Yvonne C Stephenson, Samir A Ballestas-Naissir, Michael E Davis, Nick J Willett, Hicham M Drissi, Steven L Goudy

 

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

 

Mapping the complex paracrine response to hormones in the human breast at single-cell resolution
Lyndsay M Murrow, Robert J Weber, Joseph Caruso, Christopher S McGinnis, Alexander D Borowsky, Tejal A Desai, Matthew Thomson, Thea D Tlsty, Zev Jordan Gartner

 

Planar cell polarity pathway and development of the human visual cortex
Jean Shin, Shaojie Ma, Edith Hofer, Yash Patel, Gennady Roshchupkin, Andre M Sousa, Xueqiu Jian, Rebecca Gottesmann, Thomas H Mosley, Myriam Fornage, Yasaman Saba, Lukas Pirpamer, Reinhold Schmidt, Helena Schmidt, Bernard Mazoyer, Amaia Carrion-Castillo, Joshua Bis, Shuo Li, Qiong Yang, Michelle Luciano, Sherif Karama, Lindsay Lewis, Mark Bastin, Matthew A Harris, Ian Deary, Joanna M Wardlaw, Markus Scholz, Markus Loeffler, Veronica Witte, Frauke Beyer, Arno Villringer, Hieab HHH Adams, M Arfan Ikrum, William S Kremen, Nathan A Gillespie, the ENIGMA Consortium, Nenad Sestan, Zdenka Pausova, Sudha Seshadri, Tomas Paus, the neuroCHARGE Working Group

 

Master regulators of signaling pathways coordinate key processes of embryonic development in breast cancer
Enrique Hernandez-Lemus, Diana Tapia-Carrillo, Hugo Tovar, Tadeo Enrique Velázquez-Caldelas

 

Timing mechanism of sexually dimorphic nervous system differentiation
Laura Pereira, Florian Aeschimann, Chen Wang, Hannah Lawson, Esther Serrano-Saiz, Douglas S Portman, Helge Grosshans, Oliver Hobert

 

Protein Disulfide Isomerases Control the Secretion of Wnt proteins
Nanna Torpe, Sandeep Gopal, Oguzhan Balatci, Lorenzo Rella, Ava Handley, Henrik C Korswagen, Roger Pocock

 

Towards identifying subnetworks from FBF binding landscapes in Caenorhabditis spermatogenic or oogenic germlines
Douglas Frank Porter, Aman Prasad, Brian H Carrick, Peggy Kroll-Connor, Marvin Wickens, Judith Kimble

 

 

The C. elegans SMOC-1 protein acts cell non-autonomously to promote bone morphogenetic protein signaling
Melisa S DeGroot, Herong Shi, Alice Eastman, Alexandra N McKillop, Jun Liu

 

Variability in the timing of a β-catenin pulse biases a stochastic cell fate decision in C. elegans
Jason R Kroll, Jasonas Tsiaxiras, Jeroen S van Zon

 

The Emergent Connectome in Caenorhabditis elegans Embryogenesis
DevoWorm Group, Bradly J. Alicea

 

Inhibition of cell fate repressors secures the differentiation of the touch receptor neurons of Caenorhabditis elegans
Chaogu Zheng, Felix Qiaochu Jin, Brian Loeber Trippe, Ji Wu, Martin Chalfie

 

Evidence of functional long-range Wnt/Wg in the developing Drosophila wing epithelium
Varun Chaudhary, Michael Boutros

 

Dynamic 3D tissue architecture directs BMP morphogen signaling during Drosophila wing morphogenesis
Jinghua Gui, Yunxian Huang, Martin Kracklauer, Daniel Toddie-Moore, Kenji Kikushima, Stephanie Nix, Yukitaka Ishimoto, Osamu Shimmi

 

The Dlg-module and clathrin-mediated endocytosis regulate EGFR signaling and cyst cell-germline coordination in the Drosophila testis
Fani Papagiannouli, Cameron Wynn Berry, Margaret T. (MINX) Fuller

 

 

An ATF4-mediated transcriptional adaptation of electron transport chain disturbance primes progenitor cells for proliferation in vivo
Sebastian Sorge, Jonas Theelke, Christian Altburger, Ingrid Lohmann

 

Drosophila insulin-like peptide 1 (DILP1) promotes organismal growth during non-feeding stages
Sifang Liao, Stephanie Post, Jan A Veenstra, Marc Tatar, Dick R Nassel

 

Anthranilic acid regulates subcellular localization of auxin transporters during root gravitropism
Siamsa M Doyle, Adeline Rigal, Peter Grones, Michal Karady, Deepak K Barange, Mateusz Majda, Michael Karampelias, Marta Zwiewka, Aleš Pěnčik, Fredrik Almqvist, Karin Ljung, Ondřej Novák, Stéphanie Robert

 

 

| Morphogenesis & mechanics

 

 

Nodal and Eph signalling relay drives the transition between apical constriction and apico-basal shortening during ascidian endoderm invagination
Ulla-Maj Fiuza, Takefumi Negishi, Alice Rouan, Hitoyoshi Yasuo, Patrick Lemaire

 

 

Transcriptional initiation and mechanically driven self-propagation of a tissue contractile wave during axis elongation
Anais Bailles, Claudio Collinet, Jean-Marc Philippe, Pierre-François Lenne, Edwin Munro, Thomas Lecuit

 

Distinct contributions of tensile and shear stress on E-cadherin levels during morphogenesis
Girish R Kale, Xingbo Yang, Jean-Marc Philippe, Madhav Mani, Pierre-Francois Lenne, Thomas Lecuit

 

Evolutionary rate covariation analysis of E-cadherin identifies Raskol as regulator of cell adhesion and actin dynamics in Drosophila
Qanber Raza, Jae Young Choi, Yang Li, Roisin M O’Dowd, Simon C Watkins, Yang Hong, Nathan L Clark, Adam V Kwiatkowski

 

 

Differential expression and homotypic enrichment of a classic Cadherin directs tissue-level contractile asymmetry during neural tube closure
Hidehiko Hashimoto, Edwin M Munro

 

 

Cdh2 coordinates Myosin-II dependent internalisation of the zebrafish neural plate
Claudio Araya, Hanna-Maria Hakkinen, Luis Carcamo, Mauricio Cerda, Thierry Savy, Nadine Peyrieras, Christopher Rookyard, Jonathan Clarke

 

 

Mechanical Coupling Coordinates the Co-elongation of Axial and Paraxial Tissues in Avian Embryos
Fengzhu Xiong, Wenzhe Ma, Bertrand Benazeraf, L Mahadevan, Olivier Pourquie

 

Quantitative study of the somitogenetic wavefront in zebrafish
Weiting Zhang, Bertrand Ducos, Marine Delagrange, Sophie Vriz, David Bensimon

 

A tensile ring drives tissue flows to shape the gastrulating amniote embryo
Mehdi Saadaoui, Francis Corson, Didier Rocancourt, Julian Roussel, Jerome Gros

 

Strain maps characterize the symmetry of convergence and extension patterns during Zebrafish gastrulation
Dipanjan Bhattacharya, Jun Zhong, Sahar Tavakoli, Alexandre Kabla, Paul Matsudaira

 

 

Three-dimensional tissue stiffness mapping in the mouse embryo supports durotaxis during early limb bud morphogenesis
Min Zhu, Hirotaka Tao, Mohammad Samani, Mengxi Luo, Xian Wang, Sevan Hopyan, Yu Sun

 

Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish
Thomas R Whitesell, Paul Chrystal, Jae-Ryeon Ryu, Nicole Munsie, Ann Grosse, Curtis French, Matthew L Workentine, Rui Li, Lihua Julie Zhu, Andrew Waskiewicz, Ordan J Lehmann, Nathan D Lawson, Sarah J Childs

 

 

Dynamin binding protein is required for Xenopus laevis kidney development
Bridget D DeLay, Tanya A Baldwin, Rachel K Miller

 

 

Integrin-mediated attachment of the blastoderm to the vitelline envelope impacts gastrulation of insects
Stefan Munster, Akanksha Jain, Alexander Mietke, Anastasios Pavlopoulos, Stephan Wolfgang Grill, Pavel Tomancak

 

Integrin alpha11 is an Osteolectin receptor and is required for the maintenance of adult skeletal bone mass
Bo Shen, Kristy Vardy, Payton Hughes, Alpaslan Tasdogan, Zhiyu Zhao, Genevieve Crane, Sean J Morrison

 

Draxin alters laminin expression during basement membrane reorganization to control cranial neural crest EMT
Erica J Hutchins, Marianne E. Bronner

 

Endoglycan plays a role in axon guidance and neuronal migration by negatively regulating cell-cell adhesion
Esther T Stoeckli, Thomas Baeriswyl, Georgia Tsapara, Vera Niederkofler, Jeannine A. Frei, Nicole H. Wilson, Matthias Gesemann

 

A specific Ret receptor isoform is required for pioneer axon outgrowth and growth cone dynamics
Adam M Tuttle, Catherine M Drerup, Molly H Marra, Alex V Nechiporuk

 

 

Transsynaptic interactions between IgSF proteins DIP-α and Dpr10 are required for motor neuron targeting specificity in Drosophila
James Ashley, Violet Sorrentino, Sonal Nagarkar-Jaiswal, Liming Tan, Shuwa Xu, Qi Xiao, Kai Zinn, Robert A Carrillo

 

 

A conserved morphogenetic mechanism for epidermal ensheathment of nociceptive sensory neurites
Nan Jiang, Jeffrey P Rasmussen, Joshua A Clanton, Marci Rosenberg, Kory P Luedke, Mark R Cronan, Edward Parker, Hyeon-Jin Kim, Joshua C Vaughan, Alvaro Sagasti, Jay Parrish

 

Dystroglycan is a scaffold for extracellular axon guidance decisions
L. Bailey Lindenmaier, Nicolas Parmentier, Caying Guo, Fadel Tissir, Kevin Wright

 

Endothelial Cells Filopodia Participation In The Anastomosis Of CNS Capillaries
Miguel Marin-Padilla Sr., Louisa Howard

 

Extracellular matrix stiffness regulates force transmission pathways in multicellular ensembles of human airway smooth muscle cells.
Samuel R Polio, Suzanne Stasiak, Ramaswamy Krishnan, Harikrishnan Parameswaran

 

Zebrafish Otolith Biomineralization Requires Polyketide Synthase
Kevin D Thiessen, Steven J Grzegorski, Lisa Higuchi, Jordan A Shavit, Kenneth L Kramer

 

Actomyosin controls planarity and folding of epithelia in response to compression
Tom P.J. Wyatt, Jonathan Fouchard, Ana Lisica, Nargess Khalilgharibi, Buzz Baum, Pierre Recho, Alexandre J. Kabla, Guillaume T. Charras

 

Arabidopsis class I formin FH1 relocates between membrane compartments during root cell ontogeny and associates with plasmodesmata
Denisa Oulehlová, Eva Kollárová, Petra Cifrová, Přemysl Pejchar, Viktor Žárský, Fatima Cvrčková

 

 

| Genes & genomes

A cell atlas of the adult Drosophila midgut
Ruei-Jiun Hung, Yanhui Hu, Rory Kirchner, Fangge Li, Chiwei Xu, Aram Comjean, Sudhir Gopal Tattikota, Wei Roc Song, Shannon Ho Sui, Norbert Perrimon

 

 

Nuclear transcriptomes of the seven neuronal cell types that constitute the Drosophila mushroom bodies.
Meng-Fu Maxwell Shih, Fred Pejman Davis, Gilbert Lee Henry, Josh Dubnau

 

 

Boundaries support specific long-distance interactions between enhancers and promoters in Drosophila Bithorax complex
Pavel Georgiev, Nikolay Postika, Mario Metzler, Markus Affolter, Martin Müller, Paul Schedl, Olga Kyrchanova

 

Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity
Jeehae Park, Javier Estrada, Gemma Johnson, Chiara Ricci-Tam, Meghan Bragdon, Yekaterina Shulgina, Anna Cha, Jeremy Gunawardena, Angela H DePace

 

Precision in a rush: trade-offs between reproducibility and steepness of the hunchback expression pattern
Huy Tran, Jonathan Desponds, Carmina Angelica Perez Romero, Mathieu Coppey, Cecile Fradin, Nathalie Dostatni, Aleksandra M Walczak

 

Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs
Jeremy Dufourt, Antonio Trullo, Jennifer Hunter, Carola Fernandez, Jorge Lazaro, Matthieu Dejean, Lucas Morales, Katharine N Schulz, Melissa M Harrison, Ovidiu Radulescu, Cyril Favard, Mounia Lagha

 

Ratio-based sensing of two transcription factors regulates the transit to differentiation
Sebastian M. Bernasek, Jean-François Boisclair Lachance, Nicolás Peláez, Rachael Bakker, Heliodoro Tejedor Navarro, Luis A. N. Amaral, Neda Bagheri, Ilaria Rebay, Richard W. Carthew

 

The eukaryotic Initiation Factor 6 (eIF6) regulates ecdysone biosynthesis by modulating translation in Drosophila
Arianna Russo, Guido Gatti, Roberta Alfieri, Elisa Pesce, Kelly Soanes, Sara Ricciardi, Marilena Mancino, Cristina Cheroni, Thomas Vaccari, Stefano Biffo, Piera Calamita

 

Caenorhabditis elegans germline development requires brap-2

Dayana R D’Amora, Queenie Hu, Monica Pizzardi, Terrance Kubiseski

 

DOT1L suppresses nuclear RNAi originating from enhancer elements in Caenorhabditis elegans
Ruben Esse, Ekaterina Gushchanskaia, Avery Lord, Alla Grishok

 

The interplay between small RNA pathways shapes chromatin landscape in C. elegans
Ekaterina Gushchanskaia, Ruben Esse, Qicheng Ma, Nelson Lau, Alla Grishok

 

MET-2, a SETDB1 family methyltransferase, coordinates embryo events through distinct histone H3 methylation states
Beste Mutlu, Huei-Mei Mei Chen, David H. Hall, Susan E. Mango

 

Mutual transcriptional repression between Gli3 and Hox13 genes determines the anterior-posterior asymmetry of the autopod
Maria Felix Bastida, Rocio Perez-Gomez, Anna Trofka, Rushikesh Sheth, H. Scott Stadler, Susan Mackem, Marian A Ros

 

 

The Lineage-Specific Transcription Factor CDX2 Navigates Dynamic Chromatin to Control Distinct Stages of Intestine Development
Namit Kumar, Yu-Hwai Tsai, Lei Chen, Anbo Zhou, Kushal J Banerjee, Madhurima Saxena, Sha Huang, Jinchuan Xing, Ramesh A Shivdasani, Jason R Spence, Michael Verzi

 

Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics
Roser Vento-Tormo, Mirjana Efremova, Rachel A. Botting, Margherita Y. Turco, Miquel Vento-Tormo, Kerstin B. Meyer, Jongeun Park, Emily Stephenson, Krzysztof Polański, Rebecca P. Payne, Angela Goncalves, Angela Zou, Johan Henriksson, Laura Wood, Steve Lisgo, Andrew Filby, Gavin J. Wright, Michael J. Stubbington, Muzlifah Haniffa, Ashley Moffett, Sarah A. Teichmann

 

Fine-tuned adaptation of embryo-endometrium pairs at implantation revealed by gene regulatory networks
Fernando Biase, Isabelle Hue, Sarah Dickinson, Florence Jaffrezic, Denis Laloe, Harris Lewin, Olivier Sandra

 

Single-cell RNA-seq analysis maps the development of human fetal retina
Yufeng Lu, Wenyang Yi, Qian Wu, Suijuan Zhong, Zhentao Zuo, Fangqi Zhao, Mei Zhang, Nicole Tsai, Yan Zhuo, Sheng He, Jun Zhang, Xin Duan, Xiaoqun Wang, Tian Xue

 

Single-cell transcriptional dynamics and origins of neuronal diversity in the developing mouse neocortex
Ludovic Telley, Gulistan Agirman, Julien Prados, Sabine Fievre, Polina Oberst, Ilaria Vitali, Laurent Nguyen, Alexandre Dayer, Denis Jabaudon

 

Single-cell transcriptomics of the mouse gonadal soma reveals the establishment of sexual dimorphism in distinct cell lineages
Isabelle Stevant, Francoise Kuhne, Andy Greenfield, Marie-Christine Chaboissier, Emmanouil T Dermitzakis, Serge Nef

 

Regulation of Cell-Type-Specific Transcriptomes by miRNA Networks During Human Brain Development
Tomasz J Nowakowski, Neha Rani, Mahdi Golkaram, Hongjun R Zhou, Beatriz Alvarado, Kylie Huch, Jay West, Anne Leyrat, Alex A Pollen, Arnold R Kriegstein, Linda R Petzold, Kenneth S Kosik

 

Divergent neuronal DNA methylation patterns across human cortical development: Critical periods and a unique role of CpH methylation
Amanda J. Price, Leonardo Collado-Torres, Nikolay A. Ivanov, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E Jaffe

 

Dazl regulates germ cell survival through a network of polyA proximal mRNA interactions
Leah L Zagore, Thomas J Sweet, Molly M Hannigan, Sebastien M Weyn-Vanhentenryck, Raul Jobava, Maria Hatzoglou, Chaolin Zhang, Donny D Licatalosi

 

Gene-specific transcriptional memory in mammalian cell lineages
Nicholas E Phillips, Aleksandra Mandic, Saeed Omidi, Felix Naef, David M Suter

 

 

 

Live-Cell Imaging Reveals Enhancer-dependent Sox2 Transcription in the Absence of Enhancer Proximity
Jeffrey M Alexander, Juan Guan, Bo Huang, Stavros Lomvardas, Orion D Weiner

 

Conserved mechanism of nucleoporin regulation of the Kcnq1ot1 imprinted domain with divergence in embryonic and trophoblast stem cells
Saqib Sachani, William MacDonald, Ashley Foulkrod, Carlee White, Liyue Zhang, Mellissa Mann

 

SWI/SNF coordinates transcriptional activation through Rpd3-mediated histone hypoacetylation during quiescence entry
Marla M Spain, Keean C.A. Braceros, Toshio Tsukiyama

 

GIGANTEA promotes sorghum flowering by stimulating floral activator gene expression
Frank G Harmon, Junping Chen, Zhanguo Xin

 

CrRLK1L receptor-like kinases HERK1 and ANJEA are female determinants of pollen tube reception
Sergio Galindo-Trigo, Noel Blanco-Tourinan, Thomas A DeFalco, Cyril Zipfel, Julie E Gray, Lisa M Smith

 

Characterization of the role of several COPI complex isoforms during the early acceptance of compatible pollen grains in Arabidopsis thaliana.
Daniel A Cabada Gomez, Maria Isabella Chavez, Emily Indriolo

 

Epigenetic signatures associated with imprinted paternally-expressed genes in the Arabidopsis endosperm
Claudia Köhler, Jordi Moreno-Romero, Gerardo Del Toro De León, Vikash Kumar Yadav, Juan Santos-González

 

 

| Stem cells, regeneration & disease modelling

Stage-specific transcriptomes and DNA methylomes indicate an early and transient loss of transposon control in Arabidopsis shoot stem cells
Ortrun Mittelsten Scheid, Ruben Gutzat, Klaus Rembart, Thomas Nussbaumer, Rahul Pisupati, Falko Hofmann, Gabriele Bradamante, Nina Daubel, Angelika Gaidora, Nicole Lettner, Mattia Dona, Magnus Nordborg, Michael Nodine

 

Mi-2/NuRD complex protects stem cell progeny from mitogenic Notch signalling
Evanthia Zacharioudaki, Julia Falo Sanjuan, Sarah Bray

 

Stem cell mitotic drive ensures asymmetric epigenetic inheritance
Rajesh Ranjan, Jonathan Snedeker, Xin Chen

 

 

Niche maintenance of germline stem cells in C. elegans males
Sarah L Crittenden, ChangHwan Lee, Ipsita Mohanty, Sindhu Battula, Judith Kimble

 

Stem cell receptor degradation by niche cells restricts signaling
Sophia Ladyzhets, Mayu Inaba

 

The RNA-Binding Protein DND1 Acts Sequentially as a Negative Regulator of Pluripotency and a Positive Regulator of Epigenetic Modifiers Required for Germ Cell Reprogramming
Victor A Ruthig, Matthew B Friedersdorf, Jason A Garness, Steve C Munger, Corey Bunce, Jack D Keene, Blanche Capel

 

Multi-Omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency
Pengyi Yang, Sean J Humphrey, Senthilkumar Cinghu, Rajneesh Pathania, Andrew J Oldfield, Dhirendra Kumar, Dinuka Perera, Jean Y.H. Yang, David E James, Matthias Mann, Raja Jothi

 

Notch2 signaling regulates Id4 and cell cycle genes to maintain neural stem cell quiescence in the adult hippocampus
Runrui Zhang, Marcelo Boareto, Anna Engler, Angeliki Louvi, Claudio Giachino, Dagmar Iber, Verdon Taylor

 

 

Retinoblastoma binding protein 4 maintains cycling neural stem cells and prevents DNA damage and Tp53-dependent apoptosis in rb1 mutant neural progenitors
Laura E. Schultz-Rogers, Maira P. Almeida, Wesley A. Wierson, Marcel Kool, Maura McGrail

 

 

Id4 eliminates the pro-activation factor Ascl1 to maintain quiescence of adult hippocampal stem cells
Isabelle Maria Blomfield, Brenda Rocamonde, Maria Del Mar Masdeu, Eskeatnaf Mulugeta, Stefania Vaga, Debbie L. C. van den Berg, Emmanuelle Huillard, Francois Guillemot, Noelia Urban

 

Mutational impact of culturing human pluripotent and adult stem cells
Ewart Kuijk, Myrthe Jager, Bastiaan van der Roest, Mauro Locati, Arne van Hoeck, Jerome Korzelius, Roel Janssen, Nicolle Besselink, Sander Boymans, Ruben van Boxtel, Edwin Cuppen

 

Discovery and characterization of variance QTLs in human induced pluripotent stem cells
Abhishek K Sarkar, Po-Yuan Tung, John D. Blischak, Jonathan E. Burnett, Yang I. Li, Matthew Stephens, Yoav Gilad

 

Partial reprogramming induces a steady decline in epigenetic age before loss of somatic identity
Nelly Olova, Daniel J Simpson, Riccardo Marioni, Tamir Chandra

 

Wdr5, Brca1 and Bard1 link the DNA damage response to the mesenchymal-to-epithelial transition during early reprogramming.
Georgina Penalosa-Ruiz, Vicky Vicky Bousgouni, Jan P Gerlach, Susan Waarlo, Joris V van de Ven, Tim E Veenstra, Jose C.R Silva, Simon J van Heeringen, Chris Bakal, Klaas W Mulder, Gert Jan C Veenstra

 

 

Astrocytes Regulate the Development and Maturation of Retinal Ganglion Cells Derived from Human Pluripotent Stem Cells
Kirstin B Langer, Ridhima Vij, Sarah K Ohlemacher, Akshayalakshmi Sridhar, Clarisse M Fligor, Elyse M Feder, Michael C Edler, Anthony J Baucum, Theodore M Cummins, Jason S Meyer

 

Glycogen Synthase Kinase 3 induces multilineage maturation of human pluripotent stem cell-derived lung progenitors in 3D culture.
Hans-Willem Snoeck, Ana Luisa Rodrigues Toste de Carvalho, Alexandros Strikoudis, Tiago Dantas, Ya-Wen Chen, Hsiao-Yun Liu, Richard B Vallee, Jorge Correia-Pinto

 

HSCs contribute actively to native multilineage hematopoiesis but with reduced differentiation capacity upon aging
Petter Säwen, Mohamed Eldeeb, Eva Erlandsson, Trine A Kristiansen, Cecilia Laterza, Zaal Kokaia, Göran Karlsson, Joan Yuan, Shamit Soneji, Pankaj K Mandal, Derrick Rossi, David Bryder

 

Checkpoint kinase 1 is essential for fetal haematopoiesis and hematopoietic stem cell survival
Andreas Villunger, Fabian Schuler, Sehar Afreen, Claudia Manzl, Georg Haecker, Miriam Erlacher

 

Interactome comparison of human embryonic stem cell lines with the inner cell mass and trophectoderm
Adam Stevens, Helen Smith, Terence Garner, Ben Minogue, Sharon Sneddon, Lisa Shaw, Rachel Oldershaw, Nicola Bates, Daniel Brison, Susan Kimber

 

Capicua regulates neural stem cell proliferation and lineage specification through control of Ets factors
Sheikh Tanveer Ahmad, Alexandra D Rogers, Myra J Chen, Rajiv Dixit, Lata Adnani, Luke Frankiw, Samuel O Lawn, Michael D Blough, Mana Alshehri, Wei Wu, Stephen M Robbins, Gregory Cairncross, Carol Schuurmans, Jennifer Chan

 

Rat bone marrow derived mesenchymal stem cells differentiate to germ cell like cells
Kuldeep Kumar, Kinsuk Das, Madhusoodan AP, Ajay Kumar, Purnima Singh, Tanmay Mondal, Sadhan Bag

 

Linking YAP to Müller glia quiescence exit in the degenerative retina
Hanaïg Hamon, Divya Ail, Diana García-García, Juliette Bitard, Deniz Dalkara, Morgane Locker, Jérôme Roger, Muriel Perron

 

Oct1/Pou2f1 is selectively required for gut regeneration and regulates gut malignancy
Karina Vázquez-Arreguín, Claire Bensard, John C Schell, Eric Swanson, Xinjian Chen, Jared Rutter, Dean Tantin

 

FGF1 Promotes Xenopus laevis Lens Regeneration
Lisa Moore, Kimberly J Perry, Cindy Sun, Jonathan J Henry

 

 

Drug Combinations targeting multiple cellular mechanisms enable axonal regeneration from crushed optic nerve into the brain
Mustafa M. Siddiq, Yana Zorina, Arjun Yadaw, Jens Hansen, Vera Rabinovich, Sarah M. Gregorich, Yuguang Xiong, Rosa E Tolentino, Sari S Hannila, Ehud Kaplan, Robert D. Blitzer, Marie T. Filbin, Christopher L. Passaglia, Ravi Iyengar

 

 

Regenerative capacity in the lamprey spinal cord is not altered after a repeated transection
Kendra L. Hanslik, Scott R. Allen, Tessa L. Harkenrider, Stephanie M. Fogerson, Eduardo Guadarrama, Jennifer Morgan

 

Microglia limit lesion expansion and promote functional recovery after spinal cord injury in mice
Faith H. Brennan, Jodie C.E. Hall, Zhen Guan, Phillip G. Popovich

 

Damage-induced reactive oxygen species enable zebrafish tail regeneration by repositioning of Hedgehog expressing cells.
Henry Roehl, Montserrat Garcia Romero, Gareth McCathie, Philip Jankun

 

The influence of cyclic tensile strain on multi-compartment collagen-GAG scaffolds for tendon-bone junction regeneration
William K. Grier, Raul A. Sun Han Chang, Matthew D. Ramsey, Brendan A.C. Harley

 

Effects of BMP-2 dose and delivery of microvascular fragments on healing of bone defects with concomitant volumetric muscle loss
Marissa Ruehle, Laxminarayanan Krishnan, Casey E Vantucci, Yuyan Wang, Hazel Y Stevens, Krishnendu Roy, Robert E Guldberg, Nick J Willett

 

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

 

 

Active WNT vampirization by glioblastoma network leads to brain tumor growth and neurodegeneration
Marta Portela Esteban, Varun Venkataramani, Natasha Fahey-Lozano, Esther Seco, Maria Losada-Perez, Frank Winkler, Sergio Casas-Tinto

 

Loss of zebrafish ctnnd2b results in disorganised forebrain neuron clusters
Wolfgang Hofmeister, Raquel Vaz, Steven Edwards, Alfredo Duanas Rey, Anna Lindstrand

 

Early postnatal development of the cellular and circuit properties of striatal D1 and D2 spiny projection neurons
Rohan N Krajeski, Anežka Macey-Dare, Fran van Heusden, Farid Ebrahimjee, Tommas J Ellender

 

Haploinsufficiency of the schizophrenia risk gene Cyfip1 causes abnormal postnatal hippocampal neurogenesis through a novel microglia dependent mechanism
Niels Haan, Jenny Carter, Laura J Westacott, Michael J Owen, William P Gray, Jeremy Hall, Lawrence S Wilkinson

 

Myh10 deficiency leads to defective extracellular matrix remodeling and pulmonary disease
Hyun-Taek Kim, Wenguang Yin, Young-June Jin, Paolo Panza, Felix Gunawan, Beate Grohmann, Carmen Buettner, Anna M. Sokol, Jens Preussner, Stefan Guenther, Sawa Kostin, Clemens Ruppert, Aditya M. Bhagwat, Xuefei Ma, Johannes Graumann, Mario Looso, Andreas Guenther, Robert S. Adelstein, Stefan Offermanns, Didier Y.R. Stainier

 

Gpr63 is a novel modifier of microcephaly in Ttc21b mouse mutants.
John Snedeker, William J Gibbons Jr., Daniel R Prows, Rolf Stottmann

 

The zebrafish orthologue of familial Alzheimer’s disease gene PRESENILIN 2 is required for normal adult melanotic skin pigmentation.
Haowei Jiang, Morgan Newman, Michael Lardelli

 

 

 

A CRISPR/Cas9-generated zebrafish mutant implicates PPP2R3B loss in idiopathic scoliosis pathogenesis in Turner syndrome.
Dagan Jenkins, Marian Seda, Berta Crespo Lopez, Michelangelo Corcelli

 

Integrative analysis of Paneth cell proteomic data from intestinal organoids reveals functional processes affected in Crohn’s disease due to autophagy impairment
Emily Jones, Zoe Matthews, Lejla Gul, Padhmanand Sudhakar, Devina Divekar, Jasmine Buck, Matthew Jefferson, Stuart Armstrong, Alastair Watson, Simon Carding, Ulrike Mayer, Penny Powell, Isabelle Hautefort, Tom Wileman, Tamas Korcsmaros

 

The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders
Cheen Euong Ang, Qing Ma, Orly Wapinski, ShengHua Fan, Ryan A Flynn, Bradley Coe, Masahiro Onoguchi, Victor H Olmos, Brian T Do, Lynn Dukes-Rimsky, Jin Xu, Qian Yi Lee, Koji Tanabe, LiangJiang Wang, Ulrich Elling, Josef Penninger, Kun Qu, Evan E Eichler, Anand Srivastava, Marius Wernig, Howard Chang

 

Systematic functional characterization of the intellectual disability-associated SWI/SNF complex reveals distinct roles for the BAP and PBAP complexes in post-mitotic memory forming neurons of the Drosophila mushroom body
Melissa C Chubak, Max H Stone, Nicholas Raun, Shelby L Rice, Mohammed Sarikahya, Spencer G Jones, Taylor A Lyons, Taryn E Jakub, Roslyn LM Mainland, Maria J Knip, Tara N Edwards, Jamie Kramer

 

Long-term phenotypic effects following vitrified-thawed embryo transfer in a rabbit model
Francisco Marco-Jiménez, Joaquín Cañizares, David Sanchez Peñaranda, Ximo Garcia-Dominguez, José Salvador Vicente, Guillem Estruch, José Miguel Blanca, Victor García-Carpintero

 

Lovastatin, not simvastatin, corrects core phenotypes in the fragile X mouse model
Melania Muscas, Susana R Louros, Emily K Osterweil

 

Comprehensive modeling of Spinal Muscular Atrophy in Drosophila melanogaster
Ashlyn M. Spring, Amanda C. Raimer, Christine D. Hamilton, Michela J. Schillinger, A. Gregory Matera

 

A human embryonic stem cell model of Aβ–dependent chronic progressive neurodegeneration
Teresa Ubina, Martha Magallanes, Saumya Srivastava, Charles Warden, Jiing-Kuan Yee, Paul M. Salvaterra

 

 

Evo-devo & evo

 

 

Par-Cteno-Genesis or Cteno Par-Genesis
Miguel Salinas-Saavedra, Mark Q. Martindale

 

 

Redundant and cryptic enhancer activities of the Drosophila yellow gene
Gizem Kalay, Jennifer Lachowiec, Ulises Rosas, Mackenzie R. Dome, Patricia J Wittkopp

 

Thyroid hormone modulation during zebrafish development recapitulates evolved diversity in danionin jaw protrusion mechanics
Demi Galindo, Elly Sweet, Zoey DeLeon, Mitchel Wagner, Adrian DeLeon, Casey Carter, Sarah McMenamin, W. James Cooper III

 

 

 

Evolution of gastrulation in cavefish: heterochronic cell movements and maternal factors
Jorge Torres-Paz, Julien Leclercq, Sylvie Retaux

 

 

millepattes micropeptides are an ancient developmental switch required for embryonic patterning
Suparna Ray, Miriam I Rosenberg, Hélène Chanut-Delalande, Amelie Decaras, Barbara Schwertner, William Toubiana, Tzach Auman, Irene Schnellhammer, Matthias Teuscher, Abderrahman Khila, Martin Klingler, François Payre

 

Dnmt1 has an essential function despite the absence of CpG DNA methylation in the red flour beetle Tribolium castaneum
Nora Kristin Elisa Schulz, Clara Isabel Wagner, Julia Ebeling, Günter Raddatz, Maike Folina Diddens-de Buhr, Frank Lyko, Joachim Kurtz

 

Transgenerational developmental effects of immune priming in the red flour beetle Tribolium castaneum
Nora Kristin Elisa Schulz, Marie Pauline Sell, Kevin Ferro, Nico Kleinhölting, Joachim Kurtz

 

Hox genes limit germ cell formation in the short germ insect Gryllus bimaculatus.
Austen A. Barnett, Taro Nakamura, Cassandra G. Extavour

 

A female alternative life-history strategy arose via novel recruitment of homeobox gene, BarH-1
Alyssa Woronik, Kalle Tunstrom, Michael W Perry, Ramprasad Neethiraj, Constanti Stefanescu, Maria de la Paz Celorio-Mancera, Oskar Brattstrom, Jason Hill, Philipp Lehmann, Reijo Kakela, Christopher W Wheat

 

Comparative evidence for the independent evolution of hair and sweat gland traits in primates
Yana G Kamberov, Samantha M Guhan, Alessandra DeMarchis, Judy Jiang, Sara Sherwood Wright, Bruce A Morgan, Pardis C Sabeti, Clifford J Tabin, Daniel E Lieberman

 

Evolution of embryo implantation was enabled by the origin of decidual cells in eutherian mammals
Arun R. Chavan, Oliver W. Griffith, Daniel Stadtmauer, Jamie Maziarz, Mihaela Pavlicev, Ruth Fishman, Lee Koren, Roberto Romero, Gunter P. Wagner

 

Coalescent-based phylogenetic inference from genes with unequivocal historical signal suggests a polytomy at the root of the placental mammal tree of life
Filipe R. R. Moreira, Carlos E. G. Schrago

 

 

Electroporation of short hairpin RNAs for rapid and efficient gene knockdown in the starlet sea anemone, Nematostella vectensis
Ahmet C Karabulut, Shuonan He, Cheng-Yi Chen, Sean A McKinney, Matthew C Gibson

 

Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group
Danang Crysnanto, Darren Obbard

 

A large close relative of C. elegans is slow-developing but not long-lived
Gavin C. Woodruff, Erik Johnson, Patrick Phillips

 

De novo assembly and annotation of the larval transcriptome of two spadefoot toads widely divergent in developmental rate
H. Christoph Liedtke, Jessica Gomez Garrido, Anna Esteve-Codina, Marta Gut, Tyler Alioto, Ivan Gomez-Mestre

 

A unified, mechanistic framework for developmental and evolutionary change
Enrico Borriello, Sara I. Walker, Manfred D. Laubichler

 

Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks.
Jukka-Pekka Verta, Felicity Jones

 

A phylogenomic resolution of the sea urchin tree of life
Nicolas Mongiardino Koch, Simon E Coppard, Harilaos A Lessios, Derek EG Briggs, Rich Mooi, Greg W Rouse

 

 

A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology
Masatoshi Matsunami, Miyuki Suzuki, Yoshikazu Haramoto, Akimasa Fukui, Takeshi Inoue, Katsushi Yamaguchi, Ikuo Uchiyama, Kazuki Mori, Kosuke Tashiro, Yuzuru Ito, Takashi Takeuchi, Ken-ichi T Suzuki, Kiyokazu Agata, Shuji Shigenobu, Toshinori Hayashi

 

Very few sites can reshape a phylogenetic tree
Warren R Francis, Don E Canfield

 

Meta-population structure and the evolutionary transition to multicellularity
Caroline J Rose, Katrin Hammerschmidt, Paul B Rainey

 

The Invariant Nature of a Morphological Character and Character State: Insights from Gene Regulatory Networks
Sergei Tarasov

 

 

Germline-Restricted Chromosome (GRC) is Widespread among Songbirds
Anna A Torgasheva, Lyubov P Malinovskaya, Kira S Zadesenets, Tatyana V Karamysheva, Elena A Kizilova, Inna E Pristyazhnyuk, Elena P Shnaider, Valeria A Volodkina, Alsu F Saifutdinova, Svetlana A Galkina, Denis M Larkin, Nikolay B Rubtsov, Pavel M Borodin

 

 

Cell biology

 

Tissue self-organization based on collective cell migration by contact activation of locomotion and chemotaxis
Taihei Fujimori, Akihiko Nakajima, Nao Shimada, Satoshi Sawai

 

 

The telomere bouquet is a hub where meiotic double-strand breaks, synapsis, and stable homolog juxtaposition are coordinated in the zebrafish, Danio rerio
Yana P. Blokhina, An D. Nguyen, Bruce W. Draper, Sean M. Burgess

 

Fascetto Interacting Protein (FIP) Regulates Fascetto (PRC1) to Ensure Proper Cytokinesis and Ploidy
Zachary T Swider, Rachel K Ng, Ramya Varadarajan, Carey J Fagerstrom, Nasser M Rusan

 

The GATOR complex regulates an essential response to meiotic double-stranded breaks in Drosophila
Youheng Wei, Lucia Bettedi, Kuikwon Kim, Chun-Yuan Ting, Mary Lilly

 

Decoupling the roles of cell shape and mechanical stress in orienting and cueing epithelial mitosis
Alexander Nestor-Bergmann, Georgina A Stooke-Vaughan, Georgina K Goddard, Tobias Starborg, Oliver E Jensen, Sarah Woolner

 

Efa6 regulates axon growth, branching and maintenance by eliminating off-track microtubules at the cortex
Yue Qu, Ines Hahn, Meredith Lees, Jill Parkin, Andre Voelzmann, Karel Dorey, Alex Rathbone, Claire Friel, Victoria Allan, Pilar Okenve-Ramos, Natalia Sanchez-Soriano, Andreas Prokop

 

WNT4 and WNT3A activate cell autonomous Wnt signaling independent of secretion
Deviyani M Rao, Rebecca L Ferguson, Tomomi M Yamamoto, Benjamin G Bitler, Matthew J Sikora

 

Membrane capacitance recordings resolve dynamics and complexity of receptor-mediated endocytosis in Wnt signalling
Vera Bandmann, Ann Schirin Mirsanaye, Johanna Schaefer, Gerhard Thiel, Thomas W. Holstein, Melanie Mikosch-Wersching

 

Molecular organization of integrin-based adhesion complexes in mouse Embryonic Stem Cells
Shumin Xia, Evelyn K.F. Yim, Pakorn Kanchanawong

 

The Desmosome is a Mesoscale Lipid Raft-Like Membrane Domain
Joshua D Lewis, Amber L Caldara, Stephanie E Zimmer, Anna Seybold, Nicole L Strong, Sara N Stahley, Achilleas S Frangakis, Ilya Levental, James K Wahl III, Alexa L Mattheyses, Takashi Sasaki, Kazuhiko Nakabayashi, Kenichiro Hata, Yoichi Matsubara, Akemi Ishida-Yamamoto, Masayuki Amagai, Akiharu Kubo, Andrew P Kowalczyk

 

Vimentin filaments interact with the mitotic cortex allowing normal cell division
Sofia Duarte, Álvaro Viedma-Poyatos, Elena Navarro-Carrasco, Alma E Martínez, María A Pajares, Dolores Pérez-Sala

 

Superresolution architecture of pluripotency guarding adhesions
Aki Stubb, Camilo Guzmán, Elisa Närvä, Jesse Aaron, Teng-Leong Chew, Markku Saari, Mitro Miihkinen, Guillaume Jacquemet, Johanna Ivaska

 

 

Modelling

 

 

Modularity, criticality and evolvability of a developmental gene regulatory network
Berta Verd, Nicholas AM Monk, Johannes Jaeger

 

The statistics of noisy growth with mechanical feedback in elastic tissues
Ojan Khatib Damavandi, David K. Lubensky

 

Noise-driven cell differentiation and the emergence of spatiotemporal patterns
Hadiseh Safdari, Ata Kalirad, Cristian Picioreanu, Rouzbeh Tusserkani, Bahram Goliaei, Mehdi Sadeghi

 

Modulation of tissue growth heterogeneity by responses to mechanical stress
Antoine Fruleux, Arezki Boudaoud

 

Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis

Bradly J Alicea​, Richard Gordon

 

Multicellular actomyosin cables in epithelia under external anisotropic stress
Meryl A Spencer, Jesus Lopez-Gay, Hayden Nunley, Yohanns Bellaïche, David K Lubensky

 

Statistical and mathematical modeling of spatiotemporal dynamics of stem cells
Walter de Back, Thomas Zerjatke, Ingo Roeder

 

Hematopoietic Stem Cell Dynamics are Regulated by Progenitor Demand: Lessons from a Quantitative Modeling Approach
Markus Klose, Maria Carolina Florian, Hartmut Geiger, Ingmar Glauche

 

Unjamming and nematic flocks in endothelial monolayers during angiogenesis : theoretical and experimental analysis
Horacio Lopez-Menendez, Joseph D’Alessandro

 

 

A coupled bulk-surface model for cell polarisation
Davide Cusseddu, Leah Edelstein-Keshet, John A. Mackenzie, Stéphanie Portet, Anotida Madzvamuse

 

Modelling cell-cell collision and adhesion with the Filament Based Lamellipodium Model
Nikolaos Sfakianakis, Diane Peurichard, Aaron Brunk, Christian Schmeiser

 

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

 

Comprehensive computational modelling of the development of mammalian cortical connectivity underlying an architectonic type principle
Sarah F. Beul, Alexandros Goulas, Claus C. Hilgetag

 

Chromatin compaction states, nuclear shape fluctuations and auxeticity: A biophysical interpretation of the epigenetic landscape of stem cells
Kamal Tripathi, Gautam I Menon

 

 

Tools & resources

Label free 3D analysis of organelles in living cells by refractive index shows pre-mitotic organelle spinning in mammalian stem cells
Patrick A Sandoz, Christopher Tremblay, Sebastien Equis, Sorin Pop, Lisa Pollaro, Yann Cotte, Gisou F van der Goot, Mathieu Frechin

 

NATF (Native And Tissue-specific Fluorescence): A strategy for bright, tissue-specific GFP labeling of native proteins.
Siwei He, Andrea Cuentas-Condori, David M Miller III

 

Bleaching-independent, whole-cell, 3D and multi-color STED imaging with exchangeable fluorophores
Christoph Spahn, Jonathan B Grimm, Luke D Lavis, Marko Lampe, Mike Heilemann

 

 

Enhanced in vivo-imaging in fish by optimized anaesthesia, fluorescent protein selection and removal of pigmentation
Colin Q. Lischik, Leonie Adelmann, Joachim Wittbrodt

 

 

Polyacrylamide Bead Sensors for in vivo Quantification of Cell-Scale Stress in Zebrafish Development
Nicole Traeber, Klemens Uhlmann, Salvatore Girardo, Gokul Kesavan, Katrin Wagner, Jens Friedrichs, Ruchi Goswami, Keliya Bai, Michael Brand, Carsten Werner, Daniel Balzani, Jochen Guck

 

Automated High-Throughput Light-Sheet Fluorescence Microscopy of Larval Zebrafish
Savannah L Logan, Christopher Dudley, Ryan P Baker, Michael J Taormina, Edouard A Hay, Raghuveer Parthasarathy

 

Microinjection into the Caenorhabditis elegans embryo using an uncoated glass needle enables cell lineage visualization and reveals cell-non-autonomous adhesion control
Yohei Kikuchi, Akatsuki Kimura

 

Liposome-based transfection enhances RNAi and CRISPR-mediated mutagenesis in non-model nematode systems
Sally Adams, Prachi Pathak, Hongguang Shao, James B. Lok, Andre Pires da Silva

 

Efficient generation of endogenous fluorescent reporters by Nested CRISPR in Caenorhabditis elegans
Jeremy Vicencio, Carmen Martinez-Fernandez, Xenia Serrat, Julian Ceron

 

 

Studying 3D cell cultures in a microfluidic droplet array under multiple time-resolved conditions
Raphael Tomasi, Sebastien Sart, Tiphaine Champetier, Charles Baroud

 

Organoid culture media containing growth factors of defined cellular activity
Manuela Urbischek, Helena Rannickmae, Thomas Foets, Katharina Ravn, Marko Hyvonen, Marc Andrew de la Roche

 

Re-Evaluating One-step Generation of Mice Carrying Conditional Alleles by CRISPR-Cas9-Mediated Genome Editing Technology
Channabasavaiah Gurumurthy, Rolen Quadros, John Adams Jr., Pilar Alcaide, Shinya Ayabe, Johnathan Ballard, Surinder K Batra, Marie-Claude Beauchamp, Kathleen A Becker, Guillaume Bernas, David Brough, Francisco Carrillo-Salinas, Ruby Dawson, Victoria DeMambro, Jinke D’Hont, Katharine Dibb, James D Eudy, Lin Gan, Jing Gao, Amy Gonzales, Anyonya Guntur, Huiping Guo, Donald W Harms, Anne Harrington, Kathryn E Hentges, Neil Humphreys, Shiho Imai, Hideshi Ishii, Mizuho Iwama, Eric Jonasch, Michelle Karolak, Bernard Keavney, Nay-Chi Khin, Masamitsu Konno, Yuko Kotani, Yayoi Kunihiro, Imayavaramban Lakshmanan, Catherine Larochelle, Catherine B Lawrence, Lin Li, Volkhard Lindner, Xian-De Liu, Gloria Lopez-Castejon, Andrew Loudon, Jenna Lowe, Loydie Jerome-Majeweska, Taiji Matsusaka, Hiromi Miura, Yoshiki Miyasaka, Benjamin Morpurgo, Katherine Motyl, Yo-ichi Nabeshima, Koji Nakade, Toshiaki Nakashiba, Kenichi Nakashima, Yuichi Obata, Sanae Ogiwara, Mariette Ouellet, Leif Oxburgh, Sandra Piltz, Ilka Pinz, Moorthy P Ponnusamy, David Ray, Ronald J Redder, Clifford J Rosen, Nikki Ross, Mark T Ruhe, Larisa Ryzhova, Ane M Salvador, Radislav Sedlacek, Karan Sharma, Chad Smith, Katrien Staes, Lora Starrs, Fumihiro Sugiyama, Satoru Takahashi, Tomohiro Tanaka, Andrew Trafford, Yoshihiro Uno, Leen Vanhoutte, Frederique Vanrockeghem, Brandon J Willis, Christian S Wright, Yuko Yamauchi, Xin Yi, Kazuto Yoshimi, Xuesong Zhang, Yu Zhang, Masato Ohtsuka, Satyabrata Das, Daniel J Garry, Tino Hochepied, Paul Thomas, Jan Parker-Thornburg, Antony D Adamson, Atsushi Yoshiki, Jean-Francois Schmouth, Andrei Golovko, William R Thompson, KC. Kent Lloyd, Joshua A Wood, Mitra Cowan, Tomoji Mashimo, Seiya Mizuno, Hao Zhu, Petr Kasparek, Lucy Liaw, Joseph M Miano, Gaetan Burgio

 

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

 

Heat-shock inducible CRISPR/Cas9 system generates heritable mutations in rice
Soumen Nandy, Bhuvan Pathak, Shan Zhao, Vibha Srivastava

 

Optimization of T-DNA architecture for Cas9-mediated mutagenesis in Arabidopsis
Baptiste Castel, Laurence Tomlinson, Federica Locci, Ying Yang, Jonathan D. G. Jones

 

Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants: An expanded toolkit for precision genome engineering
Oleg Raitskin, Christian Schudoma, Anthony West, Nicola J Patron

 

CRISPRpic: Fast and precise analysis for CRISPR-induced mutations via prefixed index counting
Seung Woo Cho, HoJoon Lee, Howard Y Chang, Hanlee P Ji

 

 

Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks
Adam J Rubin, Kevin R Parker, Ansuman T Satpathy, Yanyan Qi, Beijing Wu, Alvin J Ong, Maxwell R Mumbach, Andrew L Ji, Daniel S Kim, Sueng Woo Cho, Brian J Zarnegar, William J Greenleaf, Howard Y Chang, Paul A Khavari

 

CRISPR Artificial Splicing Factors
Nathaniel Jillette, Albert W Cheng

 

Reversible disruption of specific transcription factor-DNA interactions using CRISPR/Cas9
Ali Shariati, Antonia Dominguez, Marius Wernig, Stanley Qi, Jan Skotheim

 

pheno-seq – linking morphological features to gene expression in 3D cell culture systems
Stephan M. Tirier, Jeongbin Park, Friedrich Preusser, Lisa Amrhein, Zuguang Gu, Simon Steiger, Jan-Philipp Mallm, Marcel Waschow, Bjoern Eismann, Marta Gut, Ivo G. Gut, Karsten Rippe, Matthias Schlesner, Fabian Theis, Christiane Fuchs, Claudia R. Ball, Hanno Glimm, Roland Eils, Christian Conrad

 

High-Throughput ChIPmentation: freely scalable, single day ChIPseq data generation from very low cell-numbers
Charlotte Gustafsson, Ayla De Paepe, Christian Schmidl, Robert Mansson

 

Comparative analysis of droplet-based ultra-high-throughput single-cell RNA-seq systems
Xiannian Zhang, Tianqi Li, Feng Liu, Yaqi Chen, Jiacheng Yao, Zeyao Li, Yanyi Huang, Jianbin Wang

 

A tunable dual-input system for ‘on-demand’ dynamic gene expression regulation.
Elisa Pedone, Dan Lazzarini Rocca, Lorena Postiglione, Francesco Aulicino, Sandra Montes-Olivas, Diego di Bernardo, Maria Pia Cosma, Lucia Marucci

 

SuperCT: A supervised-learning-framework to enhance the characterization of single-cell transcriptomic profiles
Peng Xie, Mingxuan Gao, Chunming Wang, Pawan Noel, Chaoyong Yang, Daniel Von Hoff, Haiyong Han, Michael Zhang, Wei Lin

 

cellHarmony: Cell-level matching and comparison of single-cell transcriptomes
Erica AK DePasquale, Kyle Ferchen, Stuart Hay, David E Muench, H. Leighton Grimes, Nathan Salomonis

 

SMARTer single cell total RNA sequencing
Karen Verboom, Celine Everaert, Nathalie Bolduc, Kenneth J Livak, Nurten Yigit, Dries Rombaut, Jasper Anckaert, Morten T Veno, Jorgen Kjems, Frank Speleman, Pieter Mestdagh, Jo Vandesompele

 

 

Research practice & education

Data organization in spreadsheets

Karl W Broman​, Kara H. Woo

 

 

PlotsOfData – a web app for visualizing data together with its summaries
Marten Postma, Joachim Goedhart

 

Pixel: a digital lab assistant to integrate biological data in multi-omics projects
Thomas Denecker, William Durand, Julien Maupetit, Charles Hebert, Jean-Michel Camadro, Pierre Poulain, Gaelle Lelandais

 

Gelbox – An Interactive Simulation Tool for Gel Electrophoresis
Chaim Gingold, Shawn M Douglas

 

The PCR Simulator: an on-line application for teaching Design of Experiments and the polymerase chain reaction
Harold Fellermann, Ben Shirt-Ediss, Jerzy W Kozyra, Matthew Linsley, Dennis Lendrem, Thomas Howard

 

A data-driven approach to reduce gender disparity in invited speaker programs at scientific meetings
Ann-Maree Vallence, Mark Hinder, Hakeui Fujiyama

 

FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies
Susanna-Assunta Sansone, Peter McQuilton, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Massimiliano Izzo, Allyson Lister, Milo Thurston, Dominique Batista, Ramon Granell, Melanie Adekale, Delphine Dauga, Emma Ganley, Simon Hodson, Rebecca Lawrence, Varsha Khodiyar, Jessica Tenenbaum, J. Myles Axton, Michael Ball, Sebastien Besson, Theodora Bloom, Vivien Bonazzi, Rafael Jimenez, David Carr, Wei Mun Chan, Caty Chung, Geraldine Clement-Stoneham, Helena Cousijn, Saravanan Dayalan, Michel Dumontier, Esther Dzale Yeumo, Scott Edmunds, Nicholas Everitt, Dom Fripp, Carole Goble, Martin Golebiewski, Neil Hall, Robert Hanisch, Michael Hucka, Michael Huerta, Amye Kenall, Robert Kiley, Juergen Klenk, Dimitrios Koureas, Jennie Larkin, Thomas Lemberger, Nick Lynch, Lynn Schriml, Avi Ma’ayan, Catriona MacCallum, Barend Mons, Josh Moore, Wolfgang Muller, Hollydawn Murray, Tomoe Nobusada, Daniel Noesgaard, Jennifer Paxton-Boyd, Sandra Orchard, Gabriella Rustici, Stephan Schurer, Kathryn Sharples, Marina Soares e Silva, Natalie J Stanford, Inmaculada Subirats-Coll, Jason Swedlow, Weida Tong, Mark Wilkinson, John Wise, Pelin Yilmaz

 

Seven simple suggestions to be a better teacher sooner: experiences of a nearly new lecturer

Thomas R Etherington

 

Time to Stop Telling Biophysics Students that Light is Primarily a Wave
Philip C. Nelson

 

 

Why not…

Life Inside A Dinosaur Bone: A Thriving Microbiome
Evan Thomas Saitta, Renxing Liang, Chui Y Lau, Caleb M Brown, Nicholas R Longrich, Thomas G Kaye, Ben J Novak, Steven Salzberg, Paul Donohoe, Marc Dickinson, Jakob Vinther, Ian D Bull, Richard A Brooker, Peter Martin, Geoffrey D Abbott, Timothy DJ Knowles, Kirsty Penkman, Tullis C Onstott

 

Tibetan antelope rests like a Puppet
Yunchao Luo, Lin Wang, Le Yang, Ming Tan, Yiqian Wu, Yuhang Li, Zhongqiu Li

 

Continuous and discrete quantity discrimination in tortoises
Andrea Gazzola, Giorgio Vallortigara, Daniele Pellitteri-Rosa

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