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developmental and stem cell biologists

December in preprints

Posted by , on 3 January 2019

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

December’s haul includes a succession of preprints on Drosophila patterning (embryos, wings, brains and intestines), single cell investigations into the neural crest, hair cells, spinal cord and retina, a comparison of  primate brain organoids, and plant development covered from root to shoot.

The preprints were hosted on bioRxivPeerJ, 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

Plant development

Evo-devo & evo
Cell biology
Tools & resources
Research practice & education
Why not…



Developmental biology

| Patterning & signalling


Fly embryo cell divisions Mercator-style in Rahimi, et al.’s preprint


Dynamics of Spaetzle morphogen shuttling in the Drosophila embryo shapes pattern
Neta Rahimi, Inna Averbukh, Shari Carmon, Eyal D Schejter, Naama Barkai, Ben-Zion Shilo


Speeding up anterior-posterior patterning of insects by differential initialization of the gap gene cascade
Heike Rudolf, Christine Zellner, Ezzat El-Sherif


Precise spatial scaling in the early fly embryo
Victoria Antonetti, William Bialek, Thomas Gregor, Gentian Muhaxheri, Mariela Petkova, Martin Scheeler


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


Fly egg chambers and eggs from Dold, et al.’s preprint


Rab converter DMon1 constitutes a novel node in the brain-gonad axis essential for female germline maturation
Neena Dhiman, Girish Deshpande, Girish S Ratnaparkhi, Anuradha Ratnaparkhi


Makorin1 controls embryonic patterning by alleviating Bruno-mediated repression of oskar translation
Annabelle Dold, Hong Han, Niankun Liu, Andrea Hildebrandt, Mirko Brüggemann, Cornelia Rücklé, Anke Busch, Petra Beli, Kathi Zarnack, Julian König, Jean-Yves Roignant, Paul Lasko


Serial synapse formation through filopodial competition for synaptic seeding factors
Mehmet Neset Ozel, Abhishek Kulkarni, Amr Hasan, Josephine Brummer, Marian Moldenhauer, Ilsa-Maria Daumann, Heike Wolfenberg, Vincent Dercksen, Ferdi Ridvan Kiral, Martin Weiser, Steffen Prohaska, Max von Kleist, Peter Robin Hiesinger


The Tenets of Teneurin: Conserved Mechanisms Regulate Diverse Developmental Processes in the Drosophila Nervous System
Alison T DePew, Michael A Aimino, Timothy J Mosca


A refutation to ‘A new A-P compartment boundary and organizer in holometabolous insect wings.’
Peter A. Lawrence, Jose Casal, Jose F. de Celis, Gines Morata


The Notch and EGFR signaling regulate caspase inhibitor Diap1 to match supply with intestinal demand
Tobias Reiff, Zeus A Antonello, Esther Ballesta-Illan, Laura Mira, Salvador Sala, Maria Navarro, Luis M Martinez, Maria Dominguez


Tracking gene expression in the fly embryo, from  Falo-Sanjuan, et al.’s preprint


Enhancer priming enables fast and sustained transcriptional responses to Notch signaling
Julia Falo-Sanjuan, Nicholas C Lammers, Hernan G Garcia, Sarah Bray


Dynamics of Notch-dependent transcriptional bursting in its native context
ChangHwan Lee, Heaji Shin, Judith Kimble


The Caenorhabditis elegans HAM-1 protein modifies G protein signaling and membrane extension to reverse the polarity of asymmetric cell division
Jerome Teuliere, Gian Garriga


Symmetry breaking in the embryonic skin triggers a directional and sequential front of competence during plumage patterning
Richard Bailleul, Carole Desmarquet-Trin Dinh, Magdalena Hidalgo, Camille Curantz, Jonathan Touboul, Marie Manceau


Scale invariance of BMP signaling gradients in zebrafish
Yan Huang, David Umulis


Embryo geometry drives formation of robust signaling gradients through receptor localization
Zhechun Zhang, Steven Zwick, Ethan Loew, Joshua S Grimley, Sharad Ramanathan


Mouse in situs in Carthy, et al.’s preprint


Arkadia degrades SNON to activate level-specific NODAL responses
Jonathon M Carthy, Marilia Ioannou, Vasso Episkopou


Wnt/β-catenin signaling is required for the development of multiple nephron segments
Patrick Deacon, Charles W Concodora, Eunah Chung, Joo-Seop Park


Spinal cord vasculature in Garcia-Diaz, et al.’s preprint


Blood vessels guide Schwann cell migration in the adult demyelinated CNS through Eph/ephrin signaling
Beatriz Garcia-Diaz, Corinne Bachelin, Fanny Coulpier, Gaspard Gerschenfeld, Cyrille Deboux, Violetta Zujovic, Patrick Charnay, Piotr Topilko, Anne Baron-Van Evercooren


CDX4 regulates the progression of neural maturation in the spinal cord
Piyush Joshi, Andrew J. Darr, Isaac Skromne


Posterior axis formation requires Dlx5/Dlx6 expression at the neural plate border
Nicolas Narboux-Neme, Marc Ekker, Giovanni Levi, Eglantine Heude


Loss of YAP/TAZ impaired the proliferation and differentiation ability of neural progenitor cells
Shanshan Kong, Xinwei Cao


Cortical areas in Gomez, e tal.’s preprint


Human visual cortex is organized along two genetically opposed hierarchical gradients with unique developmental and evolutionary origins
Jesse Gomez, Zonglei Zhen, Kevin Weiner


Longitudinal dissection in brain organoids at single cell resolution uncovers the developmental role of GSK3 in human corticogenesis
Alejandro Lopez Tobon, Carlo Emanuele Villa, Cristina Cheroni, Sebastiano Trattaro, Nicolo Caporale, Paola Conforti, Raffaele Iennaco, Maria Lachgar, Marco Tullio Rigoli, Berta Marco de la Cruz, Pietro Lo Riso, Erika Tenderini, Flavia Troglio, Marco de Simone, Isabel Liste, Stefano Piccolo, Giuseppe Macino, Massimigliano Pagani, Elena Cattaneo, Giuseppe Testa


Gene expression in t-SNE plot and tissue, from Guo and Li’s preprint


Defining developmental diversification of diencephalon neurons through single-cell gene expression profiling
Qiuxia Guo, James Y.H. Li


Prediction and control of symmetry breaking in embryoid bodies by environment and signal integration
Naor Sagy, Shaked Slovin, Maya Allalouf, Maayan Pour, Gaya Savyon, Jonathan Boxman, Iftach Nachman


Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids.
Sapna Chhabra, Lizhong Liu, Ryan Goh, Aryeh Warmflash


RLIM enhances BMP signalling mediated fetal lung development in mice
Molka Kammoun, Elke Maas, Nathan Criem, Joost Gribnau, An Zwijsen, Joris Robert Vermeesch


Mouse follicles in Machado, et al.’s preprint


Mitofusin 1 is required for the oocyte-granulosa cell communication that regulates oogenesis
Thiago S Machado, Karen F. Carvalho, Bruna M. Garcia, Amanda F. Zangirolamo, Carolina H. Macabelli, Fabricia H. C. Sugiyama, Mateus P. Grejo, Jose Djaci Augusto Neto, Fernanda K. S. Ribeiro, Fabiana D. Sarapiao, Flavio V. Meirelles, Francisco E. G. Guimaraes, Lena Pernas, Marcelo M. Seneda, Marcos R. Chiaratti


Fetal and trophoblast PI3Kp110α have distinct roles in regulating resource supply to the growing fetus
Jorge Lopez-Tello, Vicente Perez-Garcia, Jaspreet Khaira, Laura C Kusinski, Wendy N Cooper, Adam Andrani, Imogen Grant, Edurne Fernandez de Liger, Myriam Hemberger, Ionel Sandovici, Miguel Constancia, Amanda N Sferruzzi-Perri


Novel cytokine interactions identified during perturbed hematopoiesis
Madison Ski Krieger, Joshua M Moreau, Haiyu Zhang, May Chien, James L Zehnder, Martin A. Nowak, Morgan Craig


Fibroblast growth factor receptors function redundantly during zebrafish embryonic development
Dena M Leerberg, Rachel E Hopton, Bruce W Draper


Differential physiological role of BIN1 isoforms in skeletal muscle development, function and regeneration
Ivana Prokic, Belinda Simone Cowling, Candice Kutchukian, Christine Kretz, Hichem Tasfaout, Josiane Hergueux, Olivia Wendling, Arnaud Ferry, Anne Toussaint, Christos Gavriilidis, Vasugi Nattarayan, Catherine Koch, Jeanne Lainné, Roy Combe, Laurent Tiret, Vincent Jacquemond, Fanny Pilot-Storck, Jocelyn Laporte


| Morphogenesis & mechanics

Shaping the zebrafish myotome by differential friction and active stress
Sham Tlili, Jianmin Yin, Jean-Francois Rupprecht, Gauthier Weissbart, Jacques Prost, Timothy E Saunders


Cell size heterogeneity early in development is required for collective cell migration during gastrulation in zebrafish
Triveni Menon, Rahul Kumar, Sreelaja Nair


The zebrafish notocord in Bevilacqua, et al.’s preprint


Imaging mechanical properties of sub-micron ECM in live zebrafish using Brillouin microscopy
Carlo Bevilacqua, Héctor Sánchez Iranzo, Dmitry Richter, Alba Diz-Muñoz, Robert Prevedel


Geometry of epithelial cells provides a robust method for image based inference of stress within tissues
Nicholas Noll, Sebastian J. Streichan, Boris I. Shraiman


Netrin/UNC-6 triggers actin assembly and non-muscle myosin activity to drive dendrite retraction in the self-avoidance response.
Lakshmi Sundararajan, Cody Smith, Joseph Watson, Bryan Millis, Matthew Tyska, David Miller


Measurement of junctional tension in epithelial cells at the onset of primitive streak formation in the chick embryo via non-destructive optical manipulation
Valentina Ferro, Manli Chuai, David McGloin, Cornelis Weijer


Tonotopy of the mammalian cochlea is associated with stiffness and tension gradients of the hair cell’s tip-link complex.
Mélanie Tobin, Vincent Michel, Nicolas Michalski, Pascal Martin


Liquid-crystal organization of liver tissue
Hernan Morales-Navarrete, Hidenori Nonaka, Andre Scholich, Fabian Segovia-Miranda, Walter de Back, Kirstin Meyer, Roman L Bogorad, Victor Koteliansky, Lutz Brusch, Yannis Kalaidzidis, Frank Julicher, Benjamin M. Friedrich, Marino Zerial


Confinement-induced transition between wave-like collective cell migration modes
Vanni Petrolli, Magali Le Goff, Monika Tadrous, Kirsten Martens, Cédric Allier, Ondrej Mandula, Lionel Hervé, Silke Henkes, Rastko Sknepnek, Thomas Boudou, Giovanni Cappello, Martial Balland


Sustained oscillations of epithelial cell sheets
Gregoire Peyret, Romain Mueller, Joseph d’Alessandro, Simon Begnaud, Philippe Marcq, Rene-Marc Mege, Julia Yeomans, Amin Doostmohammadi, Benoit Ladoux


Extracellular Matrix acts as pressure detector in biological tissues
Monika E Dolega, Benjamin Brunel, Magali Le Goff, Magdalena Greda, Claude Verdier, Jean-Francois Joanny, Pierre Recho, Giovanni Cappello


Force inference predicts local and tissue-scale stress patterns in epithelia
Weiyuan Kong, Olivier Loison, Pruthvi Chavadimane Shivakumar, Claudio Collinet, Pierre-François Lenne, Raphaël Clément


YAP/TAZ-TEAD Activity Links Mechanical Cues To Cell Progenitor Behavior During Hindbrain Segmentation
Adria Voltes, Covadonga F Hevia, Chaitanya Dingare, Simone Calzolari, Javier Terriente, Caren Norden, Virginie Lecaudey, Cristina Pujades


The Caspase-3 homolog DrICE regulates endocytic trafficking during Drosophila tracheal morphogenesis
Saoirse McSharry, Greg J Beitel


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


| Genes & genomes


Assaying chick enhancers in Williams, et al.’s preprint


Reconstruction of the global neural crest gene regulatory network in vivo
Ruth M Williams, Ivan Candido-Ferreira, Emmanouela Repapi, Daria Gavriouchkina, Upeka Senanayake, Jelena Telenius, Stephen Taylor, Jim Hughes, Tatjana Sauka-Spengler


Lineage tracing on transcriptional landscapes links state to fate during differentiation
Caleb Weinreb, Alejo E Rodriguez-Fraticelli, Fernando D Camargo, Allon M Klein


Zebrafish neuromasts in Lush, et al.’s preprint


Single cell RNA-Seq reveals distinct stem cell populations that drive sensory hair cell regeneration in response to loss of Fgf and Notch signaling
Mark E. Lush, Daniel C. Diaz, Nina Koenecke, Sungmin Baek, Helena Boldt, Madeleine K. St. Peter, Tatiana Gaitan-Escudero, Andres Romero-Carvajal, Elisabeth Busch-Nentwich, Anoja Perera, Kate Hall, Allison Peak, Jeffrey S. Haug, Tatjana Piotrowski


Transverse sections of the mouse spinal cord, from Delile, et al.’s preprint


Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord
Julien Delile, Teresa Rayon, Manuela Melchionda, Ameila Edwards, James Briscoe, Andreas Sagner


Transcriptional logic of cell fate specification and axon guidance in early born retinal neurons revealed by single-cell mRNA profiling
Quentin Lo Giudice, Marion Leleu, Pierre J. Fabre


An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo
Steffen Israel, Mathias Ernst, Olympia Psathaki, Hannes C. A. Drexler, Ellen Casser, Yutaka Suzuki, Wojciech Makalowski, Michele Boiani, Georg Fuellen, Leila Taher


Genetic approaches in mice demonstrate that neuro-mesodermal progenitors express T/Brachyury but not Sox2
Dorothee Mugele, Dale Moulding, Dawn Savery, Matteo Mole, Nicholas Greene, Juan Pedro Martinez-Barbera, Andrew Copp


Xenopus embryos from Gentsch, et al.’s preprint


The Spatio-Temporal Control of Zygotic Genome Activation
George Gentsch, Nick D. L. Owens, James C. Smith


Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development
Elo Madissoon, Anastasios Damdimopoulos, Shintaro Katayama, Kaarel Krjutskov, Elisabet Einarsdottir, Katariina Mamia, Bert De Groef, Outi Hovatta, Juha Kere, Pauliina Damdimopoulou


Ezh2-dependent epigenetic reprogramming controls a developmental switch between modes of gastric neuromuscular regulation
Sabriya Syed, Yujiro Hayashi, Jeong-Heon Lee, Huihuang Yan, Andrea Lorincz, Peter R Strege, Gabriella B Gajdos, Srdjan Milosavljevic, Jinfu Nie, Juri J Rumessen, Simon J Gibbons, Viktor J Horvath, Michael R Bardsley, Doug D Redelman, Sabine Klein, Dieter Saur, Gianrico Farrugia, Zhiguo Zhang, Raul Urrutia, Tamas Ordog


Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells
Christopher D Todd, Ozgen Deniz, Miguel R Branco


PTBP2-dependent alternative splicing regulates protein transport and mitochondria morphology in post-meiotic germ cells.
Molly M Hannigan, Hisashi Fujioka, Adina Brett-Morris, Jason A Mears, Donny D Licatalosi


Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination
Hequan Sun, Beth A Rowan, Pádraic J Flood, Ronny Brandt, Janina Fuss, Angela M Hancock, Richard W Michelmore, Bruno Huettel, Korbinian Schneeberger


Mouse gonads from Garcia-Moreno, et al.’s preprint


CBX2 is required during male sex determination to repress female fate at bivalent loci
Sara Alexandra Garcia-Moreno, Yi-Tzu Lin, Christopher Futtner, Isabella Salamone, Danielle Maatouk, Blanche Capel


Exploring the role of Polycomb recruitment in Xist-mediated silencing of the X chromosome in ES cells
Aurelie Bousard, Ana Claudia Raposo, Jan Jakub Zylicz, Christel Picard, Vanessa Borges Pires, Yanyan Qi, Laurene Syx, Howard Y. Chang, Edith Heard, Simao Teixeira da Rocha


3D Chromatin Architecture Remodeling during Human Cardiomyocyte Differentiation Reveals A Novel Role of HERV-H In Demarcating Chromatin Domains
Yanxiao Zhang, Ting Li, Sebastian Preissl, Jonathan Grinstein, Elie Farah, Eugin Destici, Ah Young Lee, Sora Chee, Yunjiang Qiu, Kaiyue Ma, Zhen Ye, Quan Zhu, Hui Huang, Rong Hu, Rongxin Fang, Sylvia Evans, Neil Chi, Bing Ren


Human sperm chromatin forms spatially restricted nucleosome domains consistent with programmed nucleosome positioning
Wei-Hong Huang, Mei-Zi Zhang, Xiao-Min Cao, Feng-Qin Xu, Xiao-Wei Liang, Long-Long Fu, Fang-Zhen Sun, Xiu-Ying Huang


Mouse spermatocytes at
different stages of meiotic prophase I, from Chuong, et al.’s preprint


Heterochromatin Interactions Maintain Homologous Centromere Associations in Mouse Spermatocyte Meiosis
Hoa H Chuong, Craig Eyster, Chih-Ying Lee, Roberto Pezza, Dean Dawson


Time-resolved succession of epigenetic regulation during early mammalian development
Hebing Chen, Hao Li, Shuai Jiang, Xin Huang, Wanying Li, Ruijiang Li, Zhuo Zhang, Hao Hong, Chenghui Zhao, Xiaochen Bo


The WT1-BASP1 complex is required to maintain the differentiated state of taste receptor cells
Yankun Gao, Debarghya Dutta Banik, Stefan Roberts, Kathryn Medler


LEDGF and HDGF2 relieve the nucleosome-induced barrier to transcription
Gary LeRoy, Ozgur Oksuz, Nicolas Descostes, Yuki Aoi, Rais Ganai, Havva Ortabozkoyun, Jia-Ray Yu, Chul-Hwan Lee, James Stafford, Ali Shilatifard, Danny Reinberg


PLZF limits enhancer activity during hematopoietic progenitor aging
Mathilde Poplineau, Julien Vernerey, Nadine Platet, Lia Nguyen, Leonard Herault, Michela Esposito, Andrew Saurin, Christel Guilouf, Atsushi Iwama, Estelle Duprez


Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis
Satish K Nandakumar, Sean K McFarland, Laura Marlene Mateyka, Caleb A Lareau, Jacob C Ulirsch, Leif S Ludwig, Gaurav Agarwal, Jesse M Engreitz, Bartlomiej Przychodzen, Marie McConkey, Glenn S Cowley, John G Doench, Jaroslaw Maciejewski, Benjamin L Ebert, David E Root, Vijay G. Sankaran


Mutations in the zebrafish hmgcs1 gene reveal a novel function for isoprenoids during red blood cell development.
Jose A Hernandez, Victoria L Castro, Nayel Reyes-Nava, Laura P Montes, Anita M Quintana


Basal Role for Nrf2-transgne on transcriptional (mRNA/miRNA) regulation in the mouse myocardium
Arun Jyothidasan, Gobinath Shanmugam, John Zhang, Brain Dally, David Crossman, Rajasekaran Namakkal Soorappan


Dynamics Of Cardiomyocyte Transcriptome And Chromatin Landscape Demarcates Key Events Of Heart Development
Michal Pawlak, Katarzyna Z Kedzierska, Maciej Migdal, Karim Abu Nahia, Jordan A Ramilowski, Lukasz Bugajski, Kosuke Hashimoto, Aleksandra Marconi, Katarzyna Piwocka, Piero Carninci, Cecilia L Winata


miRNAs, target genes expression and morphological analysis on the heart in gestational protein-restricted offspring
José A.R. Gontijo, Heloisa Balan Assalin, Patrícia Aline Boer


Dynamics of microRNA expression during mouse prenatal development
Rabi Murad, Sorena Rahmanian, Alessandra Breschi, Weihua Zeng, Brian A Williams, Mark Mackiewicz, Brian Roberts, Sarah Meadows, Dianne Moore, Carrie Davis, Diane Trout, Chris Zaleski, Alexander Dobin, Lei-Hoon Sei, Jorg Drenkow, Alex Scavelli, Thomas R Gingeras, Barbara Wold, Richard M. Myers, Roderic Guigo, Ali Mortazavi


The landscape of DNA methylation associated with the transcriptomic network in laying hens and broilers gets insight into embryonic muscle development in chicken
Zihao Liu, Xiaoxu Shen, Shunshun Han, Yan Wang, Qing Zhu, Can Cui, Haorong He, Jing Zhao, Yuqi Chen, Yao Zhang, Lin Ye, Zhichao Zhang, Diyan Liu, Xiaoling Zhao, Huadong Yin


Expression of matrix metalloproteinases to induce the expression of genes associated with apoptosis during corpus luteum development in bovine

Sang Hwan Kim, Ji Hye Lee, Jong Taek Yoon


Neuroblast-specific chromatin landscapes allow integration of spatial and temporal cues to generate neuronal diversity in Drosophila
Chris Q Doe, Sonia Sen, Sachin Chanchani, Tony Southall


Fly testes and chromosome spreads from them, in Watase & Yamashita’s preprint


Ribosomal DNA and the rDNA-binding protein Indra mediate non-random sister chromatid segregation in Drosophila male germline stem cells
George Watase, Yukiko Yamashita


Discovery of Alstrom syndrome gene as a regulator of centrosome duplication in asymmetrically dividing stem cells in Drosophila.
Cuie Chen, Yukiko Yamashita


Separate Polycomb Response Elements control chromatin state and activation of the vestigial gene
Kami Ahmad, Amy E Spens


The coordination of terminal differentiation and cell cycle exit is mediated through the regulation of chromatin accessibility
Yiqin Ma, Daniel J McKay, Laura Buttitta


A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.
Alexandra L McCorkindale, Philipp Wahle, Sascha Werner, Irwin Jungreis, Peter Menzel, Chinmay J Shukla, Ruben Lopes Pereira Abreu, Rafael Irizarry, Irmtraud Meyer, Manolis Kellis, Robert P Zinzen


Age-dependent changes in transcription factor FOXO targeting in Drosophila melanogaster
Allison Birnbaum, Xiaofen Wu, Marc Tatar, Nan Liu, Hua Bai


Female genetic contributions to sperm competition in Drosophila melanogaster
Dawn S. Chen, Sofie Y.N. Delbare, Simone L. White, Jessica L. Sitnik, Martik Chatterjee, Elizabeth L. DoBell, Orli D. Weiss, Andrew G. Clark, Mariana F. Wolfner


A Regulatory Loop between the Retinoid-Related Orphan Nuclear Receptor NHR-23 and let-7 family microRNAs Modulates the C. elegans Molting Cycle
Ruhi Patel, Alison R Frand


LIN-15B promotes enrichment of H3K9me2 on the promoters of a subset of germline genes that are repressed in somatic cells in C. elegans
Andreas Rechtsteiner, Meghan E. Costello, Thea A. Egelhofer, Jacob M. Garrigues, Susan Strome, Lisa Petrella


| Stem cells, regeneration & disease modelling

Geometry alone influences stem cell differentiation in a precision 3D printed stem cell niche
Elisabetta Prina, Laura Sidney, Maximilian Tromayer, Jonathan Moore, Robert Liska, Marina Bertolin, Stefano Ferrari, Andrew Hopkinson, Harminder Dua, Jing Yang, Ricky Wildman, Felicity RAJ Rose


Lgr5+ stem/progenitor cells reside at the apex of the embryonic hepatoblast pool
Nicole Prior, Christopher J Hindley, Fabian Rost, Elena Melendez Esteban, Winnie W. Y. Lau, Berthold Gottgens, Steffen Rulands, Benjamin D Simons, Meritxell Huch


Homeostatic and tumourigenic activity of SOX2+ pituitary stem cells is controlled by the LATS/YAP/TAZ cascade
Emily J Lodge, Alice Santambrogio, John P Russell, Paraskevi Xekouki, Thomas Jacques, Randy Johnson, Selvam Thavaraj, Stefan R Bornstein, Cynthia Lilian Andoniadou


Mouse stem cells in Evano, et al.’s preprint


Differential cell fates of muscle stem cells are accompanied by symmetric segregation of canonical H3 histones in vivo
Brendan Evano, Gilles Le Carrou, Genevieve Almouzni, Shahragim Tajbakhsh


Bioprinted kidney organoids from Higgins, et al.’s preprint


Bioprinted pluripotent stem cell-derived kidney organoids provide opportunities for high content screening.
J. William Higgins, Alison Chambon, Kristina Bishard, Anke Hartung, Derek Arndt, Jamie Brugnano, Pei Xuan Er, Kynan T Lawlor, Jessica M Vanslambrouck, Sean Wilson, Alexander N Combes, Sara E Howden, Ker Sin Tan, Santhosh V Kumar, Lorna J Hale, Benjamin Shepherd, Stephen Pentoney, Sharon C Presnell, Alice E Chen, Melissa H Little


Cell division history determines hematopoietic stem cell potency
Fumio Arai, Patrick S Stumpf, Yoshiko M Ikushima, Kentaro Hosokawa, Aline Roch, Matthias P Lutolf, Toshio Suda, Ben D MacArthur


Maintenance of active chromatin states by Hmgn1 and Hmgn2 is required for stem cell identity
Sylvia Garza-Manero, Abdulmajeed A. A. Sindi, Gokula Mohan, Ohoud Rehbini, Valentine H. M. Jeantet, Mariarca Bailo, Faeezah Abdul Latif, Maureen West, Ross Gurden, Lauren Finlayson, Silvija Svambaryte, Adam G. West, Katherine West


MicroRNA-deficient embryonic stem cells acquire a functional Interferon response
Jeroen Witteveldt, Lisanne Iris Knol, Sara Macias


Comparative RNAi Screens in Isogenic Human Stem Cells Reveal SMARCA4 as a Differential Regulator
Ceren Güneş, Maciej Paszkowski-Rogacz, Susann Rahmig, Shahryar Khattak, Martin Wermke, Andreas Dahl, Martin Bornhäuser, Claudia Waskow, Frank Buchholz


An acute immune response underlies the benefit of cardiac adult stem cell therapy
Ronald Vagnozzi, Marjorie Maillet, Michelle Sargent, Hadi Khalil, Anne Katrine Johansen, Jennifer Schwanekamp, Allen J York, Vincent Huang, Matthias Nahrendorf, Sakthivel Sadayappan, Jeffery D Molkentin


Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in muscle stem cells
Irene Hernando-Herraez, Brendan Evano, Thomas Stubbs, Pierre-Henri Commere, Stephen Clark, Simon Andrews, Shahragim Tajbakhsh, Wolf Reik


Loss of muscle stem cells in aged mice is replenished by muscle-secreted niche factor G-CSF
Hu Li, Qian Chen, Changyin Li, Ran Zhong, Yixia Zhao, Dahai Zhu, Yong Zhang


Environmental Optimization Enables Maintenance of Quiescent Hematopoietic Stem Cells Ex Vivo
Hiroshi Kobayashi, Takayuki Morikawa, Ayumi Okinaga, Fumie Hamano, Tomomi Hashidate-Yoshida, Shintaro Watanuki, Daisuke Hishikawa, Hideo Shindou, Fumio Arai, Yasuaki Kabe, Makoto Suematsu, Takao Shimizu, Keiyo Takubo


Mechanobiological Conditioning of Mesenchymal Stem Cells Enhances Therapeutic Angiogenesis by Inducing a Hybrid Pericyte-Endothelial Phenotype
Jason Lee, Kayla Henderson, Miguel Armenta-Ochoa, Austin Veith, Pablo Maceda, Eun Yoon, Lara Samarneh, Mitchell Wong, Andrew Dunn, Aaron Baker


Hierarchical stem cell topography splits growth and homeostatic functions in the fish gill
Julian Stolper, Elizabeth Mayela Ambrosio, Diana-Patricia Danciu, David Elliott, Kiyoshi Naruse, Anna Marciniak-Czochra, Lazaro Centanin


Tapeworm heads in Rozario, et al.’s preprint


Region-specific regulation of stem cell-driven regeneration in tapeworms
Tania Rozario, Edward B Quinn, Jianbin Wang, Richard A Davis, Phillip A Newmark


General characterization of regeneration in Aeolosoma viride
Chiao-Ping Chen, Sheridan Ke-Wing Fok, Yu-Wen Hsieh, Cheng-Yi Chen, Fei-Man Hsu, Jiun-Hong Chen


UNC-16/JIP3 inhibits the function of the regeneration promoting isoform of DLK-1
Sucheta S Kulkarni, Seema Sheoran, Kunihiro Matsumoto, Naoki Hisamoto, Sandhya P Koushika


A metabolic switch from OXPHOS to glycolysis is essential for cardiomyocyte proliferation in the regenerating heart
Hessel Honkoop, Dennis de Bakker, Alla Aharonov, Fabian Kruse, Avraham Shakked, Phong Nguyen, Cecilia de Heus, Laurence Garric, Mauro Muraro, Adam Shoffner, Federico Tessadori, Joshua Peterson, Wendy Noort, George Posthuma, Dominic Grun, Willem van der Laarse, Judith Klumperman, Richard Jaspers, Kenneth Poss, Alexander van Oudenaarden, Eldad Tzahor, Jeroen Bakkers


Tissue repair in the mouse liver following acute carbon tetrachloride depends on injury-induced Wnt/β-catenin signaling
Ludan Zhao, Yinhua Jin, Katie Donahue, Margaret Tsui, Matt Fish, Catriona Logan, Bruce Wang, Roel Nusse


In vivo epigenetic editing of sema6a promoter reverses impaired transcallosal connectivity caused by C11orf46/ARL14EP neurodevelopmental risk gene
Cyril J. Peter, Atsushi Saito, Yuto Hasegawa, Yuya Tanaka, Gabriel Perez, Emily Alway, Sergio Espesio-gil, Tariq Fayyad, Chana Ratner, Aslihan Dincer, Achla Gupta, Lakshmi Devi, John G. Pappas, François M. Lalonde, John A. Butman, Joan C. Han, Schahram Akbarian, Atsushi Kamiya


Zebrafish cephalic vasculature in de los Angeles Serrano, et al.’s preprint


Inhibition of Notch signaling rescues cardiovascular development in Kabuki Syndrome
Maria de los Angeles Serrano, Bradley L. Demarest, Tarlynn Tone-Pah-Hote, Martin Tristani, H. Joseph Yost


Transcriptional suppression from KMT2D loss disrupts cell cycle and hypoxic responses in neurodevelopmental models of Kabuki syndrome
Giovanni A Carosso, Leandros Boukas, Jonathan J Augustin, Ha Nam Nguyen, Briana L Winer, Gabrielle H Cannon, Johanna D Robertson, Li Zhang, Kasper D Hansen, Loyal A Goff, Hans T Bjornsson


Tracking dynamic changes in Alzheimer’s disease brain proteome reveals ageing-independent damage in Drosophila
Harry M Scholes, Adam Cryar, Fiona Kerr, David Sutherland, Lee A Gethings, Johannes P C Vissers, Jonathan G Lees, Christine A Orengo, Linda Partridge, Konstantinos Thalassinos


Microglial activation in an amyotrophic lateral sclerosis-like model caused by Ranbp2 loss and nucleocytoplasmic transport impairment in retinal ganglion neurons
Kyoung-in Cho, Dosuk Yoon, Minzhong Yu, Neal S Peachey, Paulo A Ferreira


Fly neuromuscular junctions in Held, et al.’s preprint


Circuit dysfunction in SOD1-ALS model first detected in sensory feedback prior to motor neuron degeneration is alleviated by BMP signaling
Aaron Held, Paxton Major, Asli Sahin, Robert Reenan, Diane Lipscombe, Kristi Wharton


Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis
Manoj K Bandaru, Anastasia Emmanouilidou, Petter Ranefall, Benedikt von der Heyde, Eugenia Mazzaferro, Tiffany Klingstroem, Mauro Masiero, Olga Dethlefsen, Johan Ledin, Anders Larsson, Hannah L Brooke, Carolina Wahlby, Erik Ingelsson, Marcel den Hoed


Inner hair cell and neuron degeneration contribute to hearing loss in a DFNA2-like mouse model
Camila Carignano, Esteban P Barila, Ezequiel I Rias, Leonardo Dionisio, Eugenio Aztiria, Guillermo Spitzmaul


Developmental Dieldrin Exposure Alters DNA Methylation at Genes Related to Dopaminergic Neuron Development and Parkinson’s Disease in Mouse Midbrain
Joseph Kochmanski, Sarah E. VanOeveren, Alison I. Bernstein


Gene augmentation and read-through rescue channelopathy in an iPSC-RPE model of congenital blindness
Pawan K Shahi, Dalton Hermans, Divya Sinha, Simran Brar, Hannah Moulton, Sabrina Stulo, Katarzyna D Borys, Elizabeth Capowski, De-Ann M Pillers, David M Gamm, Bikash R Pattnaik



| Plant development


Arabidopsis inflorescences in Denay, et al.’s preprint


Control of stem-cell niche establishment in Arabidopsis flowers by REVOLUTA and the LEAFY-RAX1 module
Gregoire Denay, Gabrielle Tichtinsky, Marie Le Masson, Hicham Chahtane, Sylvie Huguet, Irene Lopez-Vidriero, Christian Wenzl, Jose-Manuel Franco-Zorrilla, Ruediger Simon, Jan U. Lohmann, Francois Parcy


Genetic and physical interactions between the organellar mechanosensitive ion channel homologs MSL1, MSL2, and MSL3 reveal a role for inter-organellar communication in plant development
Josephine Lee, Margaret Wilson, Ryan Richardson, Elizabeth Haswell


Excess light priming in Arabidopsis thaliana with altered DNA methylomes
Diep R Ganguly, Bethany AB Stone, Steven R Eichten, Barry J Pogson


Light remote control of alternative splicing in roots through TOR kinase
Stefan Riegler, Lucas Servi, Armin Fuchs, Micaela A. Godoy Herz, Maria Guillermina Kubaczka, Peter Venhuizen, Alois Schweighofer, Craig Simpson, John W.S. Brown, Christian Meyer, Maria Kalyna, Andrea Barta, Ezequiel Petrillo


Pheophorbide a, a chlorophyll catabolite may regulate jasmonate signalling during dark-induced senescence in Arabidopsis
Sylvain Aubry, Niklaus Fankhauser, Serguei Ovinnikov, Krzysztof Zienkiewicz, Ivo Feussner, Stefan Hortensteiner


N. benthamiana leaf epidermis cells in Hazak, et al.’s preprint


The Ca2+ sensor protein CMI1 fine tunes root development, auxin distribution and responses
Ora Hazak, Elad Mamon, Meirav Lavy, Hasana Sternberg, Smrutisanjita Behera, Ina Schmitz-Thom, Daria Bloch, Olga Dementiev, Itay Gutman, Tomer Danziger, Netanel Schwarz, Anas Abuzeineh, Keithanne Mockaitis, Mark Estelle, Joel Hirsch, Jörg Kudla, Shaul Yalovsky


Origin of gibberellin-dependent transcriptional regulation by molecular exploitation of a transactivation domain in DELLA proteins
Jorge Hernandez-Garcia, Asier Briones-Moreno, Renaud Dumas, Miguel A Blazquez


Anchorene is an endogenous diapocarotenoid required for anchor root formation in Arabidopsis
Kunpeng Jia, Alexandra J. Dickinson, Jianing Mi, Guoxin Cui, Najeh M. Kharbatia, Xiujie Guo, Erli Sugiono, Manuel Aranda, Magnus Rueping, Philip N. Benfey, Salim Al-Babili


An interaction map of transcription factors controlling gynoecium development in Arabidopsis
Humberto Herrera-Ubaldo, Sergio E. Campos, Valentin Luna Garcia, Victor M. Zuniga-Mayo, Gerardo Armas-Caballero, Alexander DeLuna, Nayelli Marsch-Martinez, Stefan de Folter


Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth.
Qianqian Guo, PeiQin Ng, Shanshan Shi, Diwen Fan, Jun Li, Hua Wang, Trung Do, Rakesh David, Parul Mittal, Ralph Bock, Ming Zhao, Wenbin Zhou, Iain R Searle


Functional characterization of Arabidopsis ARGONAUTE 3 in reproductive tissue
Pauline E Jullien, Stefan Grob, Antonin Marchais, Nathan Pumplin, Clement Chevalier, Caroline Otto, Gregory Schott, Olivier Voinnet


Arabidopsis Myosins XI Are Involved in Exocytosis of Cellulose Synthase Complexes
Weiwei Zhang, Chao Cai, Christopher J Staiger


Arabidopsis pollen grains from Cheng, et al.’s preprint


βVPE is involved in tapetal degradation and pollen development by activating proprotease maturation in Arabidopsis thaliana
Ziyi Cheng, Bin Yin, Jiaxue Zhang, Yadi Liu, Bing Wang, Hui Li, Hai Lu


A novel role for Cyclic Nucleotide-Gated Ion Channel 2 (DND1) in auxin signaling
Sonhita Chakraborty, Masatsugu Toyota, Wolfgang Moeder, Kimberley Chin, Alex Fortuna, Marc Champigny, Steffen Vanneste, Simon Gilroy, Tom Beeckman, Keiko Yoshioka


A regulatory module controlling stress-induced cell cycle arrest in Arabidopsis
Naoki Takahashi, Nobuo Ogita, Tomonobu Takahashi, Shoji Taniguchi, Maho Tanaka, Motoaki Seki, Masaaki Umeda


Effects of FLOWERING LOCUS T on FD during the transition to flowering at the shoot apical meristem of Arabidopsis thaliana
Silvio Collani, Manuela Neumann, Levi Yant, Markus Schmid


Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize
Chong Teng, Han Zhang, Reza Hammond, Kun Huang, Blake Meyers, Virginia Walbot


Maize meiocytes in Ronceret, et al.’s preprint


The dynamic association of SPO11-1 with conformational changes of meiotic axial elements in maize
Arnaud Ronceret, Inna Golubovskaya, Jia-Chi Ku, Ding Hua Lee, Ljudmilla Timofejeva, Ana Karen Gomez Angoa, Yu-Hsin Kao, Karl Kremling, Rosalind Williams-Carrier, Robert Meeley, Alice Barkan, W. Zacheus Cande, Chung-Ju Rachel Wang


A wheat/rye polymorphism affects seminal root length and is associated with drought and waterlogging tolerance
Tyson Howell, Jorge I. Moriconi, Xueqiang Zhao, Joshua Hegarty, Tzion Fahima, Guillermo Santa-Maria, Jorge Dubcovsky


Isolation and characterisation of mutants with altered seminal root numbers in hexaploid wheat
Oluwaseyi Shorinola, Ryan Kaye, Guy Golan, Zvi Peleg, Stefan Kepinski, Cristobal Uauy


Clonal seeds in hybrid rice using CRISPR/Cas9
Chun Wang, Qing Liu, Yi Shen, Yufeng Hua, Junjie Wang, Jianrong Lin, Mingguo Wu, Tingting Sun, Zhukuan Cheng, Raphael Mercier, Kejian Wang


Barley yield formation under abiotic stress depends on the interplay between flowering time genes and environmental cues
Mathias Wiegmann, Andreas Maurer, Anh Pham, Timothy March, Ayed Al-Abdallat, William Thomas, Hazel Bull, Mohammed Shahid, Jason Eglinton, Michael Baum, Andrew Flavell, Mark Tester, Klaus Pillen


Evo-devo & evo

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
Alex A Pollen, Aparna Bhaduri, Madeline G Andrews, Tomasz J Nowakowski, Olivia S Meyerson, Mohammed A Mostajo-Radji, Elizabeth Di Lullo, Beatriz Alvarado, Melanie Bedolli, Max L Dougherty, Ian T Fiddes, Zev N Kronenberg, Joe Shuga, Anne A Leyrat, Jay A West, Marina Bershteyn, Craig B Lowe, Bryan J Pavolvic, Sofie R Salama, David Haussler, Evan Eichler, Arnold A Kriegstein


The mayfly embryonic nervous system, from Almudi, et al.’s preprint


Establishment of the mayfly Cloeon dipterum as a new model system to investigate insect evolution
Isabel Almudi, Carlos Martin-Blanco, Isabel Maria Garcia-Fernandez, Adrian Lopez-Catalina, Kristofer Davie, Stein Aerts, Fernando Casares


Deep evolutionary origin of limb and fin regeneration
Sylvain Darnet, Aline Cutrim Dragalzew, Danielson Baia Amaral, Andrew W Thompson, Amanda N Cass, Jamily Lorena, Josane F Sousa, Carinne M Costa, Marcos P Sousa, Nadia B Froebisch, Patricia N Schneider, Marcus C Davis, Ingo Braasch, Igor Schneider


Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings
Thomas A Stewart, Cong Liang, Justin Cotney, James P Noonan, Thomas Sanger, Gunter Wagner


Ascidian embryos from Irvine, et al.’s preprint


High temperature limits on developmental canalization in the ascidian Ciona intestinalis
Steven Q Irvine, Katherine B McNulty, Evelyn M Siler, Rose E Jacobson


Sea anemone embryos from Pukhlyakova, et al.’s preprint


Cadherin switch marks germ layer formation in the diploblastic sea anemone Nematostella vectensis
Ekaterina Pukhlyakova, Anastasia Kirillova, Yulia Kraus, Ulrich Technau


The genetic basis of hindwing eyespot number variation in Bicyclus anynana butterflies
Angel G Rivera-Colón, Erica Westerman, Steven van Belleghem, Antonia Monteiro, Riccardo Papa


Fly wing interference patterns in Hawkes, et al.’s preprint


Sexual selection drives the evolution of wing interference patterns.
MF Hawkes, Eoin Duffy, Richa Joag, Alison Skeats, Jacek Radwan, Nina Wedell, Manmohan Sharma, DJ Hosken, Jollyon Troscianko


Silent crickets reveal the genomic footprint of recent adaptive trait loss
Sonia Pascoal, Judith E. Risse, Xiao Zhang, Mark Blaxter, Timothee Cezard, Richard J. Challis, Karim Gharbi, John Hunt, Sujai Kumar, Emma Langan, Xuan Liu, Jack G. Rayner, Michael G. Ritchie, Basten L. Snoek, Urmi Trivedi, Nathan Bailey


Bat ankles from Stanchak, et al.’s preprint


Anatomical diversification of a skeletal novelty in bat feet
Kathryn E Stanchak, Jessica H Arbour, Sharlene E Santana


Opsin gene evolution in amphibious and terrestrial combtooth blennies (Blenniidae)
Fabio Cortesi, Karen M Cheney, Georgina M Cooke, Terry Ord


FISHed mouse chromosomes in Skinner, et al.’s preprint


Automated nuclear cartography reveals conserved sperm chromosome territory localization across 2 million years of mouse evolution
Benjamin Matthew Skinner, Joanne Bacon, Claudia Cattoni Rathje, Erica Lee Larson, Emily Emiko Konishi Kopania, Jeffrey Martin Good, Nabeel Ahmed Affara, Peter James Ivor Ellis


Genome wide screen reveals a specific interaction between autosome and X that is essential for hybrid male sterility
Zhongying Zhao, Yu Bi, Xiaoliang Ren, Runsheng Li, Qiutao Ding, Dongying Xie


Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila
Doris Bachtrog, Chris Ellison


Recurrent gene amplification on Drosophila Y chromosomes suggests cryptic sex chromosome drive is common on young sex chromosomes
Doris Bachtrog, Chris Ellison


Parallel patterns of development between independent cases of hybrid seed inviability in Mimulus
Jenn M. Coughlan, John H. Willis


Adaptation to developmental diet influences the response to selection on age at reproduction in the fruit fly
Tina May, Joost van den Heuvel, Agnieszka Doroszuk, Katja Hoedjes, Thomas Flatt, Bas Zwaan


Evolution of sperm competition: Natural variation and genetic determinants of Caenorhabditis elegans sperm size
Clotilde Gimond, Anne Vielle, Nuno Silva Soares, Stefan Zdraljevic, Patrick McGrath, Erik Andersen, Christian Braendle


Sex chromosome evolution via two genes
Alex Harkess, Kun Huang, Ron van der Hulst, Bart Tissen, Jeffrey L Caplan, Aakash Koppula, Mona Batish, Blake C Meyers, Jim Leebens-Mack


Pretty passerines in Leroy, et al.’s preprint


A bird’s white-eye shot: looking down on a new avian sex chromosome evolution
Thibault Leroy, Yoann Anselmetti, Marie-Ka Tilak, Severine Berard, Laura Csukonyi, Maeva Gabrielli, Celine Scornavacca, Borja Mila, Christophe Thebaud, Benoit Nabholz


Programmed DNA elimination of germline development genes in songbirds
Cormac M. Kinsella, Francisco J. Ruiz-Ruano, Anne-Marie Dion-Côté, Alexander J. Charles, Toni I. Gossmann, Josefa Cabrero, Dennis Kappei, Nicola Hemmings, Mirre J. P. Simons, Juan P. M. Camacho, Wolfgang Forstmeier, Alexander Suh


The loci of behavioral evolution: Fas2 and tilB underlie differences in pupation site choice behavior between Drosophila melanogaster and D. simulans
Alison Pischedda, Michael P Shahandeh, Thomas L Turner


Recombination in a natural population of the bdelloid rotifer Adineta vaga
Olga A. Vakhrusheva, Elena A. Mnatsakanova, Yan R. Galimov, Tatiana V. Neretina, Evgeny S. Gerasimov, Svetlana G. Ozerova, Arthur O. Zalevsky, Irina A. Yushenova, Irina R. Arkhipova, Aleksey A. Penin, Maria D. Logacheva, Georgii A. Bazykin, Alexey S. Kondrashov


Genomic features of asexual animals
Kamil S. Jaron, Jens Bast, T. Rhyker Ranallo-Benavidez, Marc Robinson-Rechavi, Tanja Schwander


The quagga mussel genome and the evolution of freshwater tolerance
Andrew D Calcino, Andre Luiz de Oliveira, Oleg Simakov, Thomas Schwaha, Elisabeth Zieger, Tim Wollesen, Andreas Wanninger


The draft genome of an octocoral, Dendronephthya gigantea
Yeonsu Jeon, Seung Gu Park, Nayun Lee, Jessica A. Weber, Hui-Su Kim, Sung-Jin Hwang, Seonock Woo, Hak-min Kim, Youngjune Bhak, Sungwon Jeon, Nayoung Lee, Yejin Jo, Asta Blazyte, Taewoo Ryu, Yun Sung Cho, Hyunho Kim, Jung-Hyun Lee, Hyung-Soon Yim, Jong Bhak, Seungshic Yum


Cell biology

Cytoplasmic self-organization established by internal lipid membranes in the interplay with either actin or microtubules
Sindy Tang, Malte Renz, Tom Shemesh, Meghan Driscoll, Jennifer Lippincott-Schwartz


Myosin driven Actin Filament Sliding is Responsible for Endoplasmic Reticulum and Golgi Movement
Joseph F McKenna, Stephen E D Webb, Verena Kriechbaumer, Chris Hawes


Transcription factor TAp73 and microRNA-449 complement each other to support multiciliogenesis
Merit Wildung, Tilman Uli Esser, Katie Baker Grausam, Cornelia Wiedwald, Larisa Volceanov-Hahn, Dietmar Riedel, Sabine Beuermann, Li Li, Jessica Lynn Simcox Zylla, Ann-Kathrin Guenther, Magdalena Wienken, Evrim Ercetin, Zhiyuan Han, Felix Bremmer, Orr Shomroni, Stefan Andreas, Haotian Zhao, Muriel Lizé


Xenopus axons from Shigeoka, et al.’s preprint


On-site ribosome remodeling by locally synthesized ribosomal proteins in axons
Toshiaki Shigeoka, Max Koppers, Hovy Ho-Wai Wong, Julie Qiaojin Lin, Asha Dwivedy, Janaina de Freitas Nascimento, Roberta Cagnetta, Francesca van Tartwijk, Florian Strohl, Jean-Michel Cioni, Mark Carrington, Clemens F. Kaminski, William A. Harris, Hosung Jung, Christine E. Holt


Actomyosin-II facilitates long-range retrograde transport of large cargoes by controlling axonal radial contractility
Tong Wang, Wei Li, Sally Martin, Andreas Papadopulos, Golnoosh Shamsollahi, Vanessa Lanoue, Pranesh Padmanabhan, He Huang, Xiaojun Yu, Victor Anggono, Frederic Meunier



Mouse bones from Barnea, et al.’s preprint


R51Q SNX10 induces osteopetrosis by promoting uncontrolled fusion of monocytes to form giant, non-functional osteoclasts
Maayan Barnea, Merle Stein, Sabina Winograd-Katz, Moran Shalev, Esther Arman, Ori Brenner, Fadi Thalji, Moien Kanaan, Hila Elinav, Polina Stepensky, Benjamin Geiger, Jan Tuckermann, Ari Elson


Dynamics of centriole amplification in centrosome-depleted brain multiciliated progenitors
Olivier MERCEY, Adel Al Jord, Philippe Rostaing, Alexia Mahuzier, Aurelien Fortoul, Amelie-Rose Boudjema, Marion Faucourt, Nathalie Spassky, Alice Meunier


Regulation of Cilia Abundance in Multiciliated Cells
Rashmi Nanjundappa, Dong Kong, Kyuhwan Shim, Tim Stearns, Steven Brody, Jadranka Loncarek, Moe Mahjoub


SGK regulates pH increase and cyclin B-Cdk1 activation to resume meiosis in starfish ovarian oocytes
Enako Hosoda, Daisaku Hiraoka, Noritaka Hirohashi, Saki Omi, Takeo Kishimoto, Kazuyoshi Chiba


Aberrant chromatin resolution in G2/M leads to chromosome instability
Lora Boteva, Ryu-Suke Nozawa, Catherine Naughton, Kumiko Samejima, William Earnshaw, Nick Gilbert


Rescue of DNA damage in cells after constricted migration reveals bimodal mechano-regulation of cell cycle
Yuntao Xia, Charlotte R Pfeifer, Kuangzheng Zhu, Jerome Irianto, Dazhen Liu, Kalia Pannell, Emily J Chen, Lawrence J Dooling, Roger A Greenberg, Dennis E Discher


Mitochondrial cristae biogenesis coordinates with ETC complex IV assembly during Drosophila maturation
Yi-fan Jiang, Hsiang-ling Lin, Li-jie Wang, Tian Hsu, Chiyu Fu


Rapid Whole Cell Imaging Reveals An APPL1-Dynein Nexus That Regulates Stimulated EGFR Trafficking
Harrison York, Amandeep Kaur, Abhishek Patil, Aditi Bhowmik, Ullhas K Moorthi, Geoffrey J Hyde, Hetvi Gandhi, Katharina Gaus, Senthil Arumugam


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




The fly embryo in silico, from McCleery et al.’s preprint


Elongated cells drive morphogenesis in a surface-wrapped finite element model of germband retraction
W. Tyler McCleery, Jim H Veldhuis, G. Wayne Brodland, Monica E Bennett, M. Shane Hutson


Theory of mechano-chemical patterning in biphasic biological tissues
Pierre Recho, Adrien Hallou, Edouard Hannezo


An individual-based mechanical model of cell movement in heterogeneous tissues and its coarse-grained approximation
Ryan Murphy, Pascal Buenzli, ruth E Baker, Matthew J Simpson


Cross-talk between Hippo and Wnt signalling pathways in intestinal crypts: insights from an agent-based model
Daniel Ward, Alexander G. Fletcher, Martin Homer, Lucia Marucci


Cell-based model of the generation and maintenance of the shape and structure of the multi-layered shoot apical meristem of Arabidopsis thaliana
Mikahl Banwarth-Kuhn, Ali Nematbakhsh, Kevin W. Rodriguez, Stephen Snipes, Carolyn G. Rasmussen, G. Venugopala Reddy, Mark Alber


Spatiotemporal Integration in Plant Tropisms
Yasmine Meroz, Renaud Bastien, L Mahadevan


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


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


Tools & resources

Single-copy Knock-In Loci for Defined Gene Expression in C. elegans
Carlos G Silva-Garcia, Caroline Heintz, Sneha Dutta, Nicole M Clark, Anne Lanjuin, William B Mair


Endogenous CRISPR arrays for scalable whole organism lineage tracing
James Cotterell, James Sharpe


Strong gene activation with genome-wide specificity using a new orthogonal CRISPR/Cas9-based Programmable Transcriptional Activator.
Sara Selma, Joan Bernabe-Orts, Marta Vazquez-Vilar, Borja Diego, Maria Ajenjo, Victor Garcia-Carpintero, Antonio Granell, Diego Orzaez


Direct capture of CRISPR guides enables scalable, multiplexed, and multi-omic Perturb-seq
Joseph M Replogle, Albert Xu, Thomas M Norman, Elliott J Meer, Jessica M Terry, Daniel Riordan, Niranjan Srinivas, Tarjei S Mikkelsen, Jonathan S Weissman, Britt Adamson


A benchmark of computational CRISPR-Cas9 guide design methods
Jake Bradford, Dimitri Perrin


Towards best-practice approaches for CRISPR/Cas9 gene engineering
Claude Van Campenhout, Pauline Cabochette, Anne-Clemence Veillard, Miklos Laczik, Agnieszka Zelisko-Schmidt, Celine Sabatel, Maxime Dhainaut, Benoit Vanhollebeke, Cyril Gueydan, Veronique Kruys


Main constraints for RNAi induced by expressed long dsRNA in mouse cells
Tomas Demeter, Michaela Vaskovicova, Radek Malik, Filip Horvat, Josef Pasulka, Eliska Svobodova, Matyas Flemr, Petr Svoboda


Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Aaron Lun, Samantha Riesenfeld, Tallulah Andrews, The Phuong Dao, Tomas Gomes, participants in the 1st Human Cell Atlas Jamboree, John Marioni


Snapshot: clustering and visualizing epigenetic history during cell differentiation
Guanjue Xiang, Belinda Giardine, Lin An, Chen Sun, Cheryl Keller, Elisabeth Heuston, David Bodine, Ross Hardison, Yu Zhang


An approach for accelerated isolation of genetically manipulated cell clones with reduced clonal variability
Natania Casden, Oded Behar


Cell type purification by single-cell transcriptome-trained sorting
Chloe S Baron, Aditya Barve, Mauro J Muraro, Gitanjali Dharmadhikari, Reinier van der Linden, Anna Lyubimova, Eelco JP de Koning, Alexander van Oudenaarden


SingleCellNet: a computational tool to classify single cell RNA-Seq data across platforms and across species
Yuqi Tan, Patrick Cahan


scAlign: a tool for alignment, integration and rare cell identification from scRNA-seq data
Nelson Johansen, Gerald Quon


Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing
Isac Lee, Roham Razaghi, Timothy Gilpatrick, Norah Sadowski, Fritz Sedlazeck, Winston Timp


Fragmentation Through Polymerization (FTP): A New Method to Fragment DNA for Next-Generation Sequencing
Konstantin B. Ignatov, Konstantin A. Blagodatskikh, Dmitry S. Shcherbo, Tatiana Kramarova, Yulia A. Monakhova, Vladimir M. Kramarov


High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® Axiom® array
Clément Mabire, Jorge Duarte, Aude Darracq, Ali Pirani, Hélène Rimbert, Delphine Madur, Valérie Combes, Clémentine Vitte, Sébastien Praud, Nathalie Riviere, Johann Joets, Jean-Philippe Pichon, Stéphane D Nicolas


Single-cell multi-omic profiling of chromatin conformation and DNA methylome
Dong-Sung Lee, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R Nery, Conor Fitzpatrick, Carolyn O’Connor, Jesse R Dixon, Joseph R. Ecker


ASCOT identifies key regulators of neuronal subtype-specific splicing
Jonathan P. Ling, Christopher Wilks, Rone Charles, Devlina Ghosh, Lizhi Jiang, Clayton P. Santiago, Bo Pang, Anand Venkataraman, Brian S. Clark, Abhinav Nellore, Ben Langmead, Seth Blackshaw


frenchFISH: Poisson models for quantifying DNA copy-number from fluorescence in situ hybridisation of tissue sections
Geoff Macintyre, Anna M Piskorz, Edith Ross, David B Morse, Ke Yuan, Darren Ennis, Jeremy A Pike, Teodora Goranova, Iain McNeish, James D Brenton, Florian Markowetz


Multiplexed detection of RNA using MERFISH and branched DNA amplification
Chenglong Xia, Hazen P Babcock, Jeffrey R Moffitt, Xiaowei Zhuang


DeepCell 2.0: Automated cloud deployment of deep learning models for large-scale cellular image analysis
Dylan Bannon, Erick Moen, Enrico Borba, Andrew Ho, Isabella Camplisson, Brian Chang, Eric Osterman, William Graf, David Van Valen


Transgenic Mice and Pluripotent Stem Cells Express EGFP under the Control of miR-302 Promoter
Karim Rahimi, Sara Parsa, Mehrnoush Nikzaban, Seyed Javad Mowla, Fardin Fathi


A fluorescent reporter enables instantaneous measurement of cell cycle speed in live cells
Anna E Eastman, Xinyue Chen, Xiao Hu, Amaleah A Hartman, Aria M Pearlman Morales, Cindy Yang, Jun Lu, Hao Yuan Kueh, Shangqin Guo


Surrogate R-spondin agonists for tissue-specific potentiation of Wnt signaling
Vincent C Luca, Yi Miao, Xingnan Li, Michael J Hollander, Calvin J Kuo, K. Christopher Garcia


A larval zebrafish brain from Greer & Holy’s preprint


Fast Objective Coupled Planar Illumination Microscopy
Cody J Greer, Timothy E Holy


Segmenting cells in Czech, et al.’s preprint


Cytokit: A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging
Eric Czech, Bulent Arman Aksoy, Pinar Aksoy, Jeffrey Hammerbacher


The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images
Jianxu Chen, Liya Ding, Matheus P. Viana, Melissa C. Hendershott, Ruian Yang, Irina A. Mueller, Susanne M. Rafelski


FishNET: An automated relational database for zebrafish colony management.
Abiud Cantu Gutierrez, Manuel Cantu Gutierrez, Alexander M. Rhyner, Oscar Ruiz, George T. Eisenhoffer, Joshua D Wythe


Adult zebrafish euthanasia: efficacy of anaesthesia overdose versus rapid cooling
Jorge M Ferreira, I Anna S Olsson, Ana M Valentim​


Dissection of intestines from larval zebrafish for molecular analysis
Bilge San, Marco Aben, Gert Flik, Leonie Kamminga


Science Family skills: An Alexa Assistant Tailored for Laboratory Routine
Tiago Lubiana Alves, Andre A.N.A. Goncalves, Helder I Nakaya


Research practice & education

Talent Identification at the limits of Peer Review: an analysis of the EMBO Postdoctoral Fellowships Selection Process
Bernd Klaus, David del Alamo


Non-academic employability of life science PhDs: the importance of training beyond the bench
Sohyoung Her, Mathieu Jacob, Sharon Wang, Songyi Xu, David Sealey


Roles matter: Graduate student perceptions of active learning in the STEM courses they take and those they teach
Everett W. Wischusen, Lorelei Patrick, Leigh Anne Howell


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


On the value of preprints: an early career researcher perspective
Sarvenaz Sarabipour, Humberto J Debat, Edward Emmott, Steven Burgess, Benjamin Schwessinger, Zach Hensel​


The Case For and Against Double-blind Reviews
Amelia R Cox, Robert Montgomerie


Academic publishing empires need to go
Joona Lehtomäki​, Johanna Eklund, Tuuli Toivonen


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


Introduction to Genomic Analysis Workshop: A catalyst for engaging life-science researchers in high throughput analysis
Phillip Andrew Richmond, Wyeth W Wasserman


Using bioinformatics training to boost research capacities in resource-limited regions
Serghei Mangul​​, Lana Martin​, Ben Langmead, Javier Sanchez Galan, Ian Toma, Pavel Pevzner, Eleazar Eskin


A comment on computational biology and connecting the dots.
Christopher J Lortie


Why not…

Where does time go when you blink?
Shany Grossman, Chen Guata, Slav Pesin, Rafael Malach, Ayelet N Landau


Stone Age “chewing gum” yields 5,700 year-old human genome and oral microbiome
Theis ZT Jensen, Jonas Niemann, Katrine Hoejholt Iversen, Anna K Fotakis, Shyam Gopalakrishnan, Mikkel HS Sinding, Martin R Ellegaard, Morten E Allentoft, Liam T Lanigan, Alberto J Taurozzi, Sofie Holtsmark Nielsen, Michael W Dee, Martin N Mortensen, Mads C Christensen, Soeren A Soerensen, Matthew J Collins, Tom Gilbert, Martin Sikora, Simon Rasmussen, Hannes Schroeder

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