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

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This month features a series of preprints on stem cell mechanics and tools to help you make organoids, some nectins and some nestins, plenty of auxin in our plant section, and some phantom crustaceans and macabre French genomics in our ‘Why Not’ section.

They 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

| Plant development

Evo-devo & evo

Cell biology

Modelling

Tools & resources

Research practice & education

Why not…

 

 

Developmental biology

| Patterning & signalling

Pegasus, a small extracellular peptide regulating the short-range diffusion of Wingless
Emile G Magny, Jose I Pueyo, Sarah A Bishop, Daniel Aguilar-Hidalgo, Juan Pablo Couso

 

A dynamic cell recruitment process drives growth of the Drosophila wing by overscaling the Vestigial expression pattern
Luis Manuel Muñoz-Nava, Hugo Ariel Alvarez, Marycruz Flores-Flores, Osvaldo Chara, Marcos Nahmad

 

 

Muscle-derived Myoglianin regulates Drosophila melanogaster imaginal disc growth
Ambuj Upadhyay, Aidan J. Peterson, Michael B. O’Connor

 

 

Egg activation triggers clearance of maternally deposited RNA binding proteins
Michael Zavortink, Lauren N. Rutt, Svetlana Dzitoyeva, Chloe Barrington, Danielle Y. Bilodeau, Miranda Wang, Xiao Xiao Lily Chen, Olivia S. Rissland

 

Selective disruption of synaptic BMP signaling by a Smad mutation adjacent to the highly conserved H2 helix
Tho Huu Nguyen, Tae Hee Han, Stuart Newfeld, Mihaela Serpe

 

Neto-α controls synapse organization and homeostasis at the Drosophila neuromuscular junction
Tae Hee Han, Rosario Vicidomini, Cathy I Ramos, Qi Wang, Peter Nguyen, Michal Jarnik, Moyi Li, Michal Stawarski, Roberto Hernandez, Gregory Macleod, Mihaela Serpe

 

Salt Inducible Kinases as Novel Notch Interactors in the Developing Drosophila Retina
H. Bahar Şahin, Sercan Sayın, Kuyaş Buğra, Arzu Çelik

 

 

A functional analysis of the Drosophila gene hindsight: evidence for positive regulation of EGFR signaling
Minhee Kim, Olivia Y. Du, Rachael J. Whitney, Ronit Wilk, Jack Hu, Henry Krause, Joshua Kavaler, Bruce H. Reed

 

Interplay between axonal Wnt5-Vang and dendritic Wnt5-Drl/Ryk signaling controls glomerular patterning in the Drosophila antennal lobe
Huey Hing, Jennifer Snyder, Noah Reger, Lee G. Fradkin

 

Optogenetic rescue of a developmental patterning mutant
Heath E. Johnson, Stanislav Y. Shvartsman, Jared E. Toettcher

 

speck, first identified in Drosophila melanogaster in 1910, is encoded by the Arylalkalamine N-acetyltransferase (AANAT1) gene
Eric P. Spana, Amanda B. Abrams, Katharine T. Ellis, Jason C. Klein, Brandon T. Ruderman, Alvin H. Shi, Daniel Zhu, Andrea Stewart, Susan May

 

Temporal regulation of nicotinic acetylcholine receptor subunits supports central cholinergic synapse development
Justin S. Rosenthal, Jun Yin, Caixia Long, Emma Spillman, Chengyu Sheng, Quan Yuan

 

Dis3L2 regulates cellular proliferation through a PI3-Kinase dependent signalling pathway
Benjamin P Towler, Amy L Pashler, Hope J Haime, Katarzyna M Przybyl, Sandra C Viegas, Rute G Matos, Simon J Morley, Cecilia M. Arraiano, Sarah F Newbury

 

Paralytic, the Drosophila voltage-gated sodium channel, regulates proliferation of neural progenitors
Beverly J. Piggott, Christian J. Peters, Ye He, Xi Huang, Susan Younger, Lily Yeh Jan, Yuh Nung Jan

 

Wnt signaling activates gene expression in the absence of the C. elegans DREAM repressor complex in somatic cells
Jerrin R. Cherian, Lisa N. Petrella

 

 

Stress-induced dendritic branching in C. elegans requires both common arborization effectors and stress-responsive molecular pathways
Rebecca J. Androwski, Nadeem Asad, Janet G. Wood, Allison Hofer, Steven Locke, Cassandra M. Smith, Becky Rose, Nathan E. Schroeder

 

Altered germline cyst and oocyte differentiation in Tex14 mutant mice reveal a new mechanism underlying female reproductive life-span
Nafisa Nuzhat, Kanako Ikami, Haley Abbott, Heather Tanner, Allan C Spradling, Lei Lei

 

p38-mitogen activated kinases mediate a developmental regulatory response to amino acid depletion and associated oxidative stress in mouse blastocyst embryos
Pablo Bora, Vasanth Thamodaran, Andrej Šušor, Alexander W. Bruce

 

 

Nanog safeguards early embryogenesis against global activation of maternal β-catenin activity by interfering with TCF factors
Mudan He, Ru Zhang, Fenghua Zhang, Shengbo Jiao, Ding Ye, Houpeng Wang, Yonghua Sun

 

Glucose metabolism distinguishes TE from ICM fate during mammalian embryogenesis
Fangtao Chi, Mark S. Sharpley, Raghavendra Nagaraj, Shubhendu Sen Roy, Utpal Banerjee

 

Generation and Trapping of a Mesoderm Biased State of Human Pluripotency
Dylan Stavish, Charlotta Böiers, Christopher Price, Thomas J R Frith, Jason Halliwell, Ivana Barbaric, John Brown, Jonathon Carr, Chela James, Peter W Andrews, Tariq Enver

 

A Highly Conserved Shh Enhancer Coordinates Hypothalamic and Craniofacial Development
Zoe Crane-Smith, Jeffrey Schoenebeck, Katy A Graham, Paul S Devenney, Lorraine Rose, Mark Ditzell, Natasha Klenin, Deborah M Kurrasch, Laura A Lettice, Robert E Hill

 

Radial Glial from mammalian developing neocortex can perform symmetric proliferative divisions in vitro
Mario Ledesma-Terrón, Nuria Peralta-Cañadas, David G. Míguez

 

A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells
José M. Dias, Zhanna Alekseenko, Ashwini Jeggari, Marcelo Boareto, Jannik Vollmer, Mariya Kozhevnikova, Hui Wang, Michael P. Matise, Andrey Alexeyenko, Dagmar Iber, Johan Ericson

 

Shh induces symmetry breaking in the presomitic mesoderm by inducing tissue shear and orientated cell rearrangements
J. Yin, T. E. Saunders

 

 

TGF-β signaling is critical for maintenance of the tendon cell fate
Guak-Kim Tan, Brian A. Pryce, Anna Stabio, John V. Brigande, ChaoJie Wang, Zheng Xia, Sara F. Tufa, Douglas R. Keene, Ronen Schweitzer

 

A signaling axis involving CNOT3, Aurora B and ERK promotes mesendodermal differentiation of ES cells in response to FGF2 and BMP4
Moumita Sarkar, Matteo Martufi, Monica Roman-Trufero, Yi-Fang Wang, Chad Whilding, Dirk Dormann, Pierangela Sabbattini, Niall Dillon

 

LRP2 controls sonic hedgehog-dependent differentiation of cardiac progenitor cells during outflow tract formation
Annabel Christ, Thomas E. Willnow

 

Interaction of YAP with the Myb-MuvB (MMB) complex defines a transcriptional program to promote the proliferation of cardiomyocytes
Marco Gründl, Susanne Walz, Laura Hauf, Melissa Schwab, Kerstin Marcela Werner, Susanne Spahr, Carsten P. Ade, Stefan Gaubatz

 

Foxi1 inactivation rescues loss of principal cell fate selection in Hes1-deficient kidneys but does not ensure maintenance of principal cell gene expression
Malini Mukherjee, Jennifer DeRiso, Madhusudhana Janga, Eric Fogarty, Kameswaran Surendran

 

Thyroid hormone receptor beta mutations alter photoreceptor development and function in Danio rerio (zebrafish)
Ciana Deveau, Xiaodong Jiao, Sachihiro Suzuki, Asha Krishnakumar, Takeshi Yoshimatsu, J Fielding Hejtmancik, Ralph F. Nelson

 

BMP signaling regulates Id1 mediated neural stem cell quiescence in the adult zebrafish brain via a phylogenetically conserved enhancer module
Gaoqun Zhang, Marco Ferg, Luisa Lübke, Tanja Beil, Victor Gourain, Nicolas Diotel, Uwe Strähle, Sepand Rastegar

 

 

Retinoic acid organizes the vagus motor topographic map via spatiotemporal regulation of Hgf/Met signaling
Adam J. Isabella, Gabrielle R. Barsh, Jason A. Stonick, Cecilia B. Moens

 

Retinoic acid accelerates the specification of enteric neural progenitors from in vitro-derived neural crest
Thomas J.R Frith, Antigoni Gogolou, James O.S Hackland, Ivana Barbaric, Nikhil Thapar, Alan J. Burns, Peter W Andrews, Anestis Tsakiridis, Conor J. McCann

 

CIC is a Critical Regulator of Neuronal Differentiation
Inah Hwang, Heng Pan, Jun Yao, Olivier Elemento, Hongwu Zheng, Jihye Paik

 

Terminal neuron localization to the upper cortical plate is controlled by the transcription factor NEUROD2
Gizem Guzelsoy, Cansu Akkaya, Dila Atak, Cory David Dunn, Alkan Kabakcioglu, Nurhan Ozlu, Gulayse Ince-Dunn

 

Activin receptor ALK4 coordinates extracellular signals and intrinsic transcriptional programs to regulate development of cortical somatostatin interneurons
Christina Gongrich, Favio Krapacher, Hermany Munguba, Diana Fernandez-Suarez, Annika Andersson, Jens Hjerling-Leffler, Carlos F. Ibanez

 

FICD activity and AMPylation remodelling modulate human neurogenesis
Pavel Kielkowski, Isabel Y. Buchsbaum, Volker C. Kirsch, Nina C. Bach, Micha Drukker, Silvia Cappello, Stephan A. Sieber

 

Physical interactions between Gsx2 and Ascl1 regulate the balance between progenitor expansion and neurogenesis in the mouse lateral ganglionic eminence
Kaushik Roychoudhury, Joseph Salomone, Shenyue Qin, Masato Nakafuku, Brian Gebelein, Kenneth Campbell

 

Effects of mutations in pigeon Mc1r implicate an expanded plumage color patterning regulatory network
Shreyas Krishnan, Richard L. Cryberg

 

A Synthetic Biology Approach to Sequential Stripe Patterning and Somitogenesis
Fuqing Wu, Changhan He, Xin Fang, Javier Baez, Thai Ohnmacht, Qi Zhang, Xingwen Chen, Kyle R. Allison, Yang Kuang, Xiao Wang

 

 

 

| Morphogenesis & mechanics

 

 

A fibronectin mechanotransduction pathway translates segmentation clock oscillations into periodic somite formation
Patrícia Gomes de Almeida, Pedro Rifes, Ana Patrícia Martins-Jesus, Gonçalo G. Pinheiro, Raquel P. Andrade, Sólveig Thorsteinsdóttir

 

ER transmembrane protein TMTC3 contributes to O-mannosylation of E-cadherin, Cellular Adherence and Embryonic Gastrulation
Jill B. Graham, Johan C. Sunryd, Ketan Mathavan, Emma Weir, Ida Signe Bohse Larsen, Adnan Halim, Henrik Clausen, Hélène Cousin, Dominque Alfandari, Daniel N. Hebert

 

An adhesion code ensures robust pattern formation during tissue morphogenesis
Tony Y.-C. Tsai, Mateusz Sikora, Peng Xia, Tugba Colak-Champollion, Holger Knaut, Carl-Philipp Heisenberg, Sean G. Megason

 

The perinuclear ER scales nuclear size independently of cell size in early embryos
Richik Nilay Mukherjee, Jérémy Sallé, Serge Dmitrieff, Katherine Nelson, John Oakey, Nicolas Minc, Daniel L. Levy

 

Embryonic organoids recapitulate early heart organogenesis
Giuliana Rossi, Andrea Boni, Romain Guiet, Mehmet Girgin, Robert G. Kelly, Matthias P. Lutolf

 

High resolution, dynamic imaging of early mouse and human liver bud morphogenesis in three dimensions
Tala Mon, Ogechi Ogoke, Claire Shamul, Shatoni Ross, Saroja Rao, Natesh Parashurama

 

A sheath of motile cells supports collective migration in of the Zebrafish posterior lateral line primordium under the skin
Damian Dalle Nogare, Naveen Natesh, Ajay Chitnis

 

Dynamically Evolving Cell Sizes During Early Development Enable Normal Gastrulation Movements In Zebrafish Embryos
Triveni Menon, Asfa Sabrin Borbora, Rahul Kumar, Sreelaja Nair

 

Amyloid precursor protein-b facilitates cell adhesion during early development in zebrafish
Rakesh Kumar Banote, Jasmine Chebli, Tuğçe Munise Şatır, Gaurav K. Varshney, Rafael Camacho, Johan Ledin, Shawn M. Burgess, Alexandra Abramsson, Henrik Zetterberg

 

longfin causes cis-ectopic expression of the kcnh2a ether-a-go-go K+ channel to autonomously prolong fin outgrowth
Scott Stewart, Heather K. Le Bleu, Gabriel A. Yette, Astra L. Henner, Joshua A. Braunstein, Kryn Stankunas

 

Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation
Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky

 

Matrix mechanotransduction mediated by thrombospondin-1/integrin/YAP signaling pathway in the remodeling of blood vessels
Yoshito Yamashiro, Bui Quoc Thang, Karina Ramirez, Seung Jae Shin, Tomohiro Kohata, Shigeaki Ohata, Tram Anh Vu Nguyen, Sumio Ohtsuki, Kazuaki Nagayama, Hiromi Yanagisawa

 

Capillary morphogenesis gene 2 mediates multiple pathways of growth factor-induced angiogenesis by regulating endothelial cell chemotaxis
Lorna Cryan, Tsz-Ming Tsang, Jessica Stiles, Lauren Bazinet, Sai-Lun Lee, Samuel Garrard, Cody Roberts, Jessie Payne, P Christine Ackroyd, Kenneth A Christensen, Michael Rogers

 

Nervous System and Tissue Polarity Dynamically Adapt to New Morphologies in Planaria
Johanna Bischof, Margot E. Day, Kelsie A. Miller, Joshua LaPalme, Michael Levin

 

 

Interplay between cortical actin and E-cadherin dynamics regulates cell shape in the Drosophila embryonic epidermis
Joshua Greig, Natalia A. Bulgakova

 

Oriented basement membrane fibrils provide a memory for F-actin planar polarization via the Dystrophin-Dystroglycan complex during tissue elongation
Fabiana Cerqueira Campos, Cynthia Dennis, Hervé Alégot, Cornelia Fritsch, Adam Isabella, Pierre Pouchin, Olivier Bardot, Sally Horne-Badovinac, Vincent Mirouse

 

Cofilin loss in Drosophila contributes to myopathy through defective sarcomerogenesis and aggregate formation during muscle growth
Mridula Balakrishnan, Shannon F. Yu, Samantha M. Chin, David B. Soffar, Stefanie E. Windner, Bruce L. Goode, Mary K. Baylies

 

Prostaglandins regulate invasive, collective border cell migration
Emily F. Fox, Maureen C. Lamb, Samuel Q. Mellentine, Tina L. Tootle

 

The Arp2/3 complex and the formin, Diaphanous, are both required to regulate the size of germline ring canals in the developing egg chamber
Josephine Thestrup, Marina Tipold, Alexandra Kindred, Kara Stark, Travis Curry, Lindsay Lewellyn

 

Mechanosensitive recruitment of BAF to the nuclear membrane inhibits nuclear E2F1 and Yap levels
C.P. Unnikannan, Adriana Reuveny, Devora Tamar Grunberg, Talila Volk

 

 

The C. elegans homolog of the Evi1 proto-oncogene, egl-43, coordinates G1 cell cycle arrest with pro-invasive gene expression during anchor cell invasion
Ting Deng, Michael Daube, Alex Hajnal, Evelyn Lattmann

 

Dendrites with specialized glial attachments develop by retrograde extension using SAX-7 and GRDN-1
Elizabeth R. Cebul, Ian G. McLachlan, Maxwell G. Heiman

 

Establishment of morphological atlas of Caenorhabditis elegans embryo with cellular resolution using deep-learning-based 4D segmentation
Jianfeng Cao, Guoye Guan, Ming-Kin Wong, Lu-Yan Chan, Chao Tang, Zhongying Zhao, Hong Yan

 

Plexin-B2 is a key regulator of cell mechanics during multicellular organization
Chrystian Junqueira Alves, Rafael Dariolli, Theodore Hannah, Robert J. Wiener, Nicolas Daviaud, Rut Tejero, G. Luca Gusella, Nadejda M. Tsankova, Rodrigo Alves Dias, José Paulo R. Furtado de Mendonça, Evren U. Azeloglu, Roland H. Friedel, Hongyan Zou

 

Curling of epithelial monolayers reveals coupling between active bending and tissue tension
Jonathan Fouchard, Tom P.J Wyatt, Amsha Proag, Ana Lisica, Nargess Khalilgharibi, Pierre Recho, Magali Suzanne, Alexandre Kabla, Guillaume Charras

 

Cortical contraction drives the 3D patterning of epithelial cell surfaces
Aaron P. van Loon, Ivan S. Erofeev, Ivan V. Maryshev, Andrew B. Goryachev, Alvaro Sagasti

 

Cell based strain stiffening of a non-fibrous matrix as organizing principle for morphogenesis
Daniel Rüdiger, Kerstin Kick, Andriy Goychuk, Angelika M. Vollmar, Erwin Frey, Stefan Zahler

 

 

| Genes & genomes

Loss of Competence in early development is mediated by loss of chromatin accessibility
Melody Esmaeili, Shelby A. Blythe, John W. Tobias, Kai Zhang, Jing Yang, Peter S. Klein

 

A Chromatin Accessibility Atlas of the Developing Human Telencephalon
Eirene Markenscoff-Papadimitriou, Sean Whalen, Pawel Przytycki, Reuben Thomas, Fadya Binyameen, Tomasz J. Nowakowski, Stephan J. Sanders, Matthew W. State, Katherine S. Pollard, John L. Rubenstein

 

 

Minimal in vivo requirements for developmentally regulated cardiac long intergenic non-coding RNAs
Matthew R. George, Qiming Duan, Abigail Nagle, Irfan S. Kathiriya, Yu Huang, Kavitha Rao, Saptarsi M. Haldar, Benoit G. Bruneau

 

Characterization of splice isoform switching during human kidney development
Yishay Wineberg, Itamar Kanter, Nissim Ben-Haim, Naomi Pode-Shakked, Efrat Bucris, Tali Hana Bar-Lev, Sarit Oriel, Yishai Yehuda, Rotem Gershon, Rachel Shukrun, Dekel Dov Bar-Lev, Achia Urbach, Benjamin Dekel, Tomer Kalisky

 

Genomic features of BRDT binding sites in gene units suggest transcriptional partners and specific epigenetic landscapes to regulate transcriptional activity during spermatogenesis
Li Wang, Iouri Chepelev, Yoon Ra Her, Marcia Manterola, Binyamin Berkovits, Kairong Cui, Keji Zhao, Debra J. Wolgemuth

 

Regulation of FXR1 by alternative splicing is required for muscle development and controls liquid-like condensates in muscle cells
Jean A. Smith, Ennessa G. Curry, R. Eric Blue, Christine Roden, Samantha E. R. Dundon, Anthony Rodríguez-Vargas, Danielle C. Jordan, Xiaomin Chen, Shawn M. Lyons, John Crutchley, Paul Anderson, Marko E. Horb, Amy S. Gladfelter, Jimena Giudice

 

HOX13-dependent chromatin accessibility modulates the target repertoires of the HOX factors
Ines Desanlis, Yacine Kherdjemil, Alexandre Mayran, Yasser Bouklouch, Claudia Gentile, Rushikesh Sheth, Rolf Zeller, Jacques Drouin, Marie Kmita

 

 

A Complex Regulatory Landscape Involved In The Development Of External Genitals
Ana Rita Amândio, Lucille Lopez-Delisle, Christopher Chase Bolt, Bénédicte Mascrez, Denis Duboule

 

The role of atoh1 genes in the development of the lower rhombic lip during zebrafish hindbrain morphogenesis
Ivan Belzunce, Cristina Pujades

 

Transgene-mediated skeletal phenotypic variation in zebrafish
Charles B. Kimmel, Alexander L. Wind, Whitney Oliva, Samuel D. Ahlquist, Charline Walker, John Dowd, Bernardo Blanco-Sánchez, Tom A. Titus, Peter Batzel, John H. Postlethwait, James T. Nichols

 

Genetic interaction of mammalian IFT-A paralogs regulates cilia disassembly, ciliary protein trafficking, Hedgehog signaling and embryogenesis
Wei Wang, Bailey A. Allard, Tana S. Pottorf, Jay L. Vivian, Pamela V. Tran

 

In vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation
Nathan J. VanDusen, Julianna Y. Lee, Weiliang Gu, Isha Sethi, Yanjiang Zheng, Justin S. King, Ping-Zhu Zhou, Shengbao Suo, Yuxuan Guo, Qing Ma, Guo-Cheng Yuan, William T. Pu

 

ISX-9 manipulates endocrine progenitor fate revealing conserved intestinal lineages in mouse and human
Anastasia Tsakmaki, Patricia Fonseca Pedro, Polychronis Pavlidis, Bu’Hussain Hayee, Gavin A Bewick

 

Significant improvement of reprogramming efficiency by transient overexpression of ZGA inducer Dux but not Dppa2/4
Lei Yang, Xuefei Liu, Lishuang Song, Anqi Di, Guanghua Su, Chunling Bai, Zhuying Wei, Guangpeng Li

 

The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues
Francesc Muyas, Luis Zapata, Roderic Guigó, Stephan Ossowski

 

Integrating healthcare and research genetic data empowers the discovery of 49 novel developmental disorders
Joanna Kaplanis, Kaitlin E Samocha, Laurens Wiel, Zhancheng Zhang, Kevin Arvai, Ruth Eberhardt, Giuseppe Gallone, Stefan H Lelieveld, Hilary Martin, Jeremy McRae, Patrick Short, Rebecca Torene, Elke de Boer, Petr Danecek, Eugene James Gardner, Ni Huang, Jenny Lord, Inigo Martincorena, Rolph Pfundt, Margot Reijnders, Alison Yeung, Helger Yntema, DDD study, Lisenka Vissers, Jane Juusola, Caroline Wright, Han Brunner, Helen V Firth, David R Fitzpatrick, Jeffrey C Barrett, Matthew E Hurles, Christian Gilissen, Kyle Retterer

 

Defining epidermal basal cell states during skin homeostasis and wound healing using single-cell transcriptomics
Daniel Haensel, Suoqin Jin, Rachel Cinco, Peng Sun, Quy Nguyen, Zixuan Cang, Morgan Dragan, Yanwen Gong, Adam L MacLean, Kai Kessenbrock, Enrico Gratton, Qing Nie, Xing Dai

 

Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex
Kira A. Perzel Mandell, Amanda J. Price, Richard Wilton, Leonardo Collado-Torres, Ran Tao, Nicholas J. Eagles, Alexander S. Szalay, Thomas M. Hyde, Daniel R. Weinberger, Joel E. Kleinman, Andrew E. Jaffe

 

Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development
Maya Sen, Dylan Mooijman, Jean-Charles Boisset, Alex Chialastri, Mina Popovic, Björn Heindryckx, Susana M. Chuva de Sousa Lopes, Siddharth S. Dey, Alexander van Oudenaarden

 

Single-cell analysis of human retina identifies evolutionarily conserved and species-specific mechanisms controlling development
Yufeng Lu, Fion Shiau, Wenyang Yi, Suying Lu, Qian Wu, Joel D. Pearson, Alyssa Kallman, Suijuan Zhong, Thanh Hoang, Zhentao Zuo, Fangqi Zhao, Mei Zhang, Nicole Tsai, Yan Zhuo, Sheng He, Jun Zhang, Genevieve L. Stein-O’Brien, Thomas D. Sherman, Xin Duan, Elana J. Fertig, Loyal A. Goff, Donald J. Zack, James T. Handa, Tian Xue, Rod Bremner, Seth Blackshaw, Xiaoqun Wang, Brian S. Clark

 

Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos
Yang Wang, Peng Yuan, Zhiqiang Yan, Ming Yang, Ying Huo, Yanli Nie, Xiaohui Zhu, Liying Yan, Jie Qiao

 

 

Dissecting the initiation of female meiosis in the mouse at single-cell resolution
Wei Ge, Jun-Jie Wang, Rui-Qian Zhang, Shao-Jing Tan, Fa-Li Zhang, Wen-Xiang Liu, Lan Li, Xiao-Feng Sun, Shun-Feng Cheng, Paul W. Dyce, Massimo De Felici, Wei Shen

 

Transcriptome Landscape Reveals Underlying Mechanisms of Ovarian Cell Fate Differentiation and Primordial Follicle Assembly
Jun-Jie Wang, Wei Ge, Qiu-Yue Zhai, Jing-Cai Liu, Xiao-Wen Sun, Wen-Xiang Liu, Lan Li, Chu-Zhao Lei, Paul W. Dyce, Massimo De Felici, Wei Shen

 

A single-cell transcriptional atlas identifies extensive heterogeneity in the cellular composition of tendons
Jacob B Swanson, Andrea J De Micheli, Nathaniel P Disser, Leandro M Martinez, Nicholas R Walker, Benjamin D Cosgrove, Christopher L Mendias

 

The transcriptional landscape of the murine middle ear epithelium in vitro
Apoorva Mulay, Md Miraj K Chowdhury, Cameron James, Lynne Bingle, Colin D Bingle

 

Single-cell RNA sequencing of adult Drosophila ovary identifies transcriptional programs governing oogenesis
Allison Jevitt, Deeptiman Chatterjee, Gengqiang Xie, Xian-Feng Wang, Taylor Otwell, Yi-Chun Huang, Wu-Min Deng

 

Predicting cellular position in the Drosophila embryo from Single-Cell Transcriptomics data
Jovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, Ke Xu, Xiaoyu Liang, Ying Hu, Hoang V.V. Pham, Li Xiaomei, Thuc D. Le, Adi L. Tarca, Gaurav Bhatti, Roberto Romero, Nestoras Karathanasis, Phillipe Loher, Yang Chen, Zhengqing Ouyang, Disheng Mao, Yuping Zhang, Maryam Zand, Jianhua Ruan, Christoph Hafemeister, Peng Qiu, Duc Tran, Tin Nguyen, Attila Gabor, Thomas Yu, Enrico Glaab, Roland Krause, Peter Banda, DREAM SCTC Consortium, Gustavo Stolovitzky, Nikolaus Rajewsky, Julio Saez-Rodriguez, Pablo Meyer

 

A Single-Cell Atlas and Lineage Analysis of the Adult Drosophila Ovary
Katja Rust, Lauren Byrnes, Kevin Shengyang Yu, Jason S. Park, Julie B. Sneddon, Aaron D. Tward, Todd G. Nystul

 

A single-cell transcriptome atlas of the adult muscle precursors uncovers early events in fiber-type divergence in Drosophila
Maria Paula Zappia, Lucia de Castro, Majd M. Ariss, Abul B.M.M.K. Islam, Maxim V Frolov

 

Developmental regulation of Canonical and small ORF translation from mRNA
Pedro Patraquim, M. Ali Mumtaz, Jose Pueyo, Julie Aspden, Juan Pablo Couso

 

Compensatory replacement of the BigH1 variant histone by canonical H1 supports normal embryonic development in Drosophila
Kaili K. Li, Dongsheng Han, Fang Chen, Ruihao Li, Bing-Rui Zhou, Yawen Bai, Kai Yuan, Yikang S. Rong

 

Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs
René M. Arvola, Chung-Te Chang, Joseph P. Buytendorp, Yevgen Levdansky, Eugene Valkov, Peter L. Freddolino, Aaron C. Goldstrohm

 

Establishment of chromatin accessibility by the conserved transcription factor Grainy head is developmentally regulated
Markus Nevil, Tyler J. Gibson, Constantine Bartolutti, Anusha Iyengar, Melissa M Harrison

 

A developmental gene regulatory network for invasive differentiation of the C. elegans anchor cell
Taylor N. Medwig-Kinney, Jayson J. Smith, Nicholas J. Palmisano, Sujata Tank, Wan Zhang, David Q. Matus

 

C. elegans LIN-28 controls temporal cell-fate progression by regulating LIN-46 expression via the 5’UTR of lin-46 mRNA
Orkan Ilbay, Charles Nelson, Victor Ambros

 

Persistent chromatin states, pervasive transcription, and shared cis-regulatory sequences have shaped the C. elegans genome
James M. Bellush, Iestyn Whitehouse

 

Transcription-independent TFIIIC-bound sites cluster near heterochromatin boundaries within lamina-associated domains in C. elegans
Alexis Stutzman, April Liang, Vera Beilinson, Kohta Ikegami

 

 

| Stem cells, regeneration & disease modelling

Competence to epithelialise coincides with competence to differentiate in pluripotent cells
Chia-Yi Lin, Tulin Tatar, Guillaume Blin, Mattias Malaguti, Rosa Portero Migueles, Hongyu Shao, Naiming Chen, Ian Chambers, Sally Lowell

 

 

Hippocampal neural stem cells facilitate access from circulation via apical cytoplasmic processes
Tamar Licht, Eli Keshet

 

Cell surface mechanics gate stem cell differentiation
Martin Bergert, Sergio Lembo, Danica Milovanović, Mandy Börmel, Pierre Neveu, Alba Diz-Muñoz

 

Membrane tension mediated mechanotransduction drives fate choice in embryonic stem cells
Henry De Belly, Philip H. Jones, Ewa K. Paluch, Kevin J. Chalut

 

Abscission couples cell division to embryonic stem cell fate
Agathe Chaigne, Celine Labouesse, Meghan Agnew, Edouard Hannezo, Kevin J Chalut, Ewa K Paluch

 

Mad dephosphorylation at the nuclear envelope is essential for asymmetric stem cell division
Justin Sardi, Muhammed Burak Bener, Taylor Simao, Abigail E Descoteaux, Boris M Slepchenko, Mayu Inaba

 

Cell cycle-balanced expression of pluripotency regulators via cyclin-dependent kinase 1
Sergo Kasvandik, Reelika Schilf, Merilin Saarma, Mart Loog, Kersti Jääger

 

Guiding T lymphopoiesis from pluripotent stem cells by defined transcription factors
Rongqun Guo, Fangxiao Hu, Qitong Weng, Cui Lv, Hongling Wu, Lijuan Liu, Zongcheng Li, Yang Zeng, Zhijie Bai, Mengyun Zhang, Yuting Liu, Xiaofei Liu, Chengxiang Xia, Tongjie Wang, Peiqing Zhou, Kaitao Wang, Yong Dong, Yuxuan Luo, Xiangzhong Zhang, Yuxian Guan, Yang Geng, Juan Du, Yangqiu Li, Yu Lan, Jiekai Chen, Bing Liu, Jinyong Wang

 

Map3k2-Regulated Intestinal Stromal Cells (MRISC) Define a Distinct Sub-cryptic Stem Cell Niche for Damage Induced Wnt Agonist R-spondin1 Production
Ningbo Wu, Hongxiang Sun, Xiaoyun Zhao, Lei Chen, Yuanyuan Qi, Yuheng Han, Xianan Liu, Caixia Gao, Qun Wang, Lingjuan He, Xiaoyin Niu, Zhiduo Liu, Hua-Bing Li, Yi Arial Zeng, Manolis Roulis, Dou Liu, Zhengfeng Yang, Bin Zhou, Richard A. Flavell, Bing Su

 

Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches
A Treveil, P Sudhakar, Z J Matthews, T Wrzesinski, E J Jones, J Brooks, M Olbei, I Hautefort, L J Hall, S R Carding, U Mayer, P P Powell, T Wileman, F Di Palma, W Haerty, T Korcsmáros

 

Encapsulation boosts islet-cell signature in differentiating human induced pluripotent stem cells via integrin signalling
Heidrun Vethe, Thomas Aga Legøy, Shadab Abadpour, Berit L. Strand, Hanne Scholz, Joao A. Paulo, Helge Ræder, Luiza Ghila, Simona Chera

 

A wave of hematopoietic stem cell-derived T/ILC-restricted progenitors initiates thymopoiesis and shapes the embryonic thymus architecture
Ramy Elsaid, Sylvain Meunier, Odile Burlen-Defranoux, Francisca Soares-da-Silva, Thibaut Perchet, Lorea Iturri, Laina Freyer, Paulo Vieira, Pablo Pereira, Rachel Golub, Antonio Bandeira, Elisa Gomez Perdiguero, Ana Cumano

 

A Versatile Polypharmacology Platform Promotes Cytoprotection and Viability of Human Pluripotent and Differentiated Cells
Yu Chen, Carlos A. Tristan, Lu Chen, Vukasin Jovanovic, Claire Malley, Pei-Hsuan Chu, Seungmi Ryu, Tao Deng, Pinar Ormanoglu, Dingyin Tao, Yuhong Fang, Jaroslav Slamecka, Christopher A. LeClair, Sam Michael, Christopher P. Austin, Anton Simeonov, Ilyas Singec

 

 

An abundant quiescent stem cell population in Drosophila Malpighian tubules protects principal cells from kidney stones
Chenhui Wang, Allan C. Spradling

 

PUF family proteins FBF-1 and FBF-2 regulate germline stem and progenitor cell proliferation and differentiation in C. elegans
Xiaobo Wang, Mary Ellenbecker, Benjamin Hickey, Nicholas J. Day, Ekaterina Voronina

 

GLP-1 Notch – LAG-1 CSL control of the germline stem cell fate is mediated by transcriptional targets lst-1 and sygl-1
Jian Chen, Ariz Mohammad, Nanette Pazdernik, Huiyan Huang, Beth Bowman, Eric Tycksen, Tim Schedl

 

Bone morphogenetic protein 15 induces differentiation of mesenchymal stem cell derived from human follicular fluid to oocyte like cell
Mahin Taheri Moghadam, Ali Reza Eftekhari Moghadam​, Ghasem Saki, Roshan Nikbakht

 

The roles of hox 13 genes in newt limb development and regeneration
Takashi Takeuchi, Fumina Minamitani, Kazuki Koriyama, Yukio Satoh, Ken-ichi Suzuki, Shuji Shigenobu, Takeshi Inoue, Kiyokazu Agata, Toshinori Hayashi

 

 

Regenerative capacity in Drosophila imaginal discs is controlled by damage-responsive, maturity-silenced enhancers
Robin E. Harris, Michael J. Stinchfield, Spencer L. Nystrom, Daniel J. McKay, Iswar K. Hariharan

 

Heterogeneity of satellite cells implicates DELTA1/NOTCH2 signaling in self-renewal
Valeria Yartseva, Leonard D. Goldstein, Julia Rodman, Lance Kates, Mark Z. Chen, Ying-Jiun J. Chen, Oded Foreman, Christopher W. Siebel, Zora Modrusan, Andrew S. Peterson, Ana Jovičić

 

Rapidly cycling stem cells regenerate the intestine independent of Lgr5high cells
Xiaole Sheng, Ziguang Lin, Cong Lv, Chunlei Shao, Xueyun Bi, Min Deng, Jiuzhi Xu, Christian F. Guerrero-Juarez, Mengzhen Li, Xi Wu, Ran Zhao, Xiaowei Liu, Qingyu Wang, Qing Nie, Wei Cui, Shan Gao, Hongquan Zhang, Zhihua Liu, Yingzi Cong, Maksim V. Plikus, Christopher J. Lengner, Bogi Andersen, Fazheng Ren, Zhengquan Yu

 

Regenerating axons and blood vessels in tissue engineered scaffolds have defined spatial relationships after spinal cord injury
Ahad M. Siddiqui, Priska Summer, David Oswald, Domnhall Kelly, Jeffrey Hakim, Bingkun Chen, Michael J. Yaszemski, Anthony J. Windebank, Nicolas N. Madigan

 

Skeletal geometry and niche transitions restore organ size and shape during zebrafish fin regeneration
Scott Stewart, Gabriel A. Yette, Heather K. Le Bleu, Astra L. Henner, Joshua A. Braunstein, Jad W. Chehab, Michael J. Harms, Kryn Stankunas

 

DNA demethylation is a driver for chick retina regeneration
Agustín Luz-Madrigal, Erika Grajales-Esquivel, Jared Tangeman, Sarah Kosse, Lin Liu, Kai Wang, Andrew Fausey, Chun Liang, Panagiotis A. Tsonis, Katia Del Rio-Tsonis

 

 

Runx1 promotes scar deposition and inhibits myocardial proliferation and survival during zebrafish heart regeneration
Jana Koth, Xiaonan Wang, Abigail C. Killen, William T. Stockdale, Helen G. Potts, Andrew Jefferson, Florian Bonkhofer, Paul R. Riley, Roger Patient, Berthold Göttgens, Mathilda T.M. Mommersteeg

 

Transient Reprogramming of Neonatal Cardiomyocytes to a Proliferative Dedifferentiated State
Thomas Kisby, Irene de Lázaro, Maria Stylianou, Giulio Cossu, Kostas Kostarelos

 

Patterned Neuronal Activities Dictate Cell Type-specific Axon Regeneration
Kendra Takle Ruppell, Fei Wang, Feng Li, Ye Shang, Jiaxin Gong, Pavi Guttipatti, Yuanquan Song, Yang Xiang

 

Molecular and histologic outcomes following spinal cord injury in spiny mice, Acomys cahirinus
K.A. Streeter, M.D. Sunshine, J.O. Brant, M. A.G.W. Sandoval, M. Maden, D.D. Fuller

 

Integrin-alpha-6+ Stem Cells (ISCs) are responsible for whole body regeneration in a basal chordate
Susannah H. Kassmer, Adam Langenbacher, Anthony W. De Tomaso

 

 

Retinal ganglion cells harboring the OPTN(E50K) mutation exhibit neurodegenerative phenotypes when derived from hPSC-derived three dimensional retinal organoids
KB VanderWall, KC Huang, Y Pan, SS Lavekar, CM Fligor, A Allsop, K Lentsch, P Dang, C Zhang, HC Tseng, TR Cummins, JS Meyer

 

Single-Cell RNA-Seq Reveals Endocardial Defect in Hypoplastic Left Heart Syndrome
Yifei Miao, Lei Tian, Marcy Martin, Sharon L. Paige, Francisco X. Galdos, Jibiao Li, Alyssa Guttman, Yuning Wei, Jan-Renier Moonen, Hao Zhang, Ning Ma, Bing Zhang, Paul Grossfeld, Seema Mital, David Chitayat, Joseph C. Wu, Marlene Rabinovitch, Timothy J. Nelson, Shuyi Nie, Sean M. Wu, Mingxia Gu

 

Human glial progenitor cells effectively remyelinate the demyelinated adult brain
Martha Windrem, Steven Schanz, Lisa Zou, Devin Chandler-Militello, Nicholas J. Kuypers, John N. Mariani, Steven A. Goldman

 

Loss of Dnmt3a dependent methylation in inhibitory neurons impairs neural function through a mechanism that impacts Rett syndrome
Laura A Lavery, Kerstin Ure, Ying-Wooi Wan, Chongyuan Luo, Alexander J Trostle, Wei Wang, Joanna Lopez, Jacinta Lucero, Mark A Durham, Rosa Castanon, Joseph R Nery, Zhandong Liu, Margaret A Goodell, Joseph R Ecker, M. Margarita Behrens, Huda Zoghbi

 

Suppressor mutations in Mecp2-null mice reveal that the DNA damage response is key to Rett syndrome pathology
Adebola Enikanolaiye, Julie Ruston, Rong Zeng, Christine Taylor, Marijke Shrock, Christie M. Buchovecky, Jay Shendure, Elif Acar, Monica J. Justice

 

 

Loss of Nance-Horan Syndrome b (nhsb) prevents expansion growth of retinal progenitor cells by selective up-regulation of Δ113p53
Paul J. Vorster, John Ojumu, Amanda J. G. Dickinson, Gregory S. Walsh

 

 

Parkinson’s disease phenotypes in patient specific brain organoids are improved by HP-β-CD treatment
Kyriaki Barmpa, Isabel Rosety, Lisa M. Smits, Jonathan Arias-Fuenzalida, Jonas Walter, Gemma Gomez-Giro, Anna S Monzel, Xiaobing Qing, Gerald Cruciani, Ibrahim Boussaad, Christian Jaeger, Aleksandar Rakovic, Emanuel Berger, Paul Antony, Christine Klein, Rejko Krüger, Philip Seibler, Javier Jarazo, Jens C. Schwamborn, Silvia Bolognin

 

Promoter proximal pausing limits Yki-induced tumorous growth in Drosophila
Sanket Nagarkar, Ruchi Wasnik, Pravallika Govada, Stephen M Cohen, LS S SHASHIDHARA

 

Atypical neurogenesis in induced pluripotent stem cell (iPSC) from autistic individuals
Dwaipayan Adhya, Vivek Swarup, Roland Nagy, Lucia Dutan Polit, Carole Shum, Kamila Jozwik, Paulina Nowosiad, Irene Lee, David Skuse, Eva Loth, Deirdre Howley, Frances A Flinter, Grainne McAlonan, Maria Andreina Mendez, Jamie Horder, Declan Murphy, Daniel H. Geschwind, Jack Price, Jason Carroll, Deepak P. Srivastava, Simon Baron-Cohen

 

Prenatal alcohol exposure disrupts Shh pathway and primary cilia genes in the mouse neural tube
Karen E Boschen, Eric W. Fish, Scott E. Parnell

 

NCBP2 modulates neurodevelopmental defects of the 3q29 deletion in Drosophila and X. laevis models
Mayanglambam Dhruba Singh, Matthew Jensen, Micaela Lasser, Emily Huber, Tanzeen Yusuff, Lucilla Pizzo, Brian Lifschutz, Inshya Desai, Alexis Kubina, Sneha Yennawar, Sydney Kim, Janani Iyer, Diego E. Rincon-Limas, Laura Anne Lowery, Santhosh Girirajan

 

RRP7A links primary microcephaly to radial glial cells and dysfunction of ribosomal biogenesis, neurogenesis and ciliary resorption
Muhammad Farooq, Louise Lindbæk, Nicolai Krogh, Canan Doganli, Cecilie Keller, Maren Mönnich, Srinivasan Sakthivel, Yuan Mang, Ambrin Fatima, Vivi Søgaard Andersen, Muhammad. S. Hussain, Hans Eiberg, Lars Hansen, Klaus Wilbrandt Kjaer, Jay Gopalakrishnan, Lotte Bang Pedersen, Kjeld Møllgård, Henrik Nielsen, Shahid. M. Baig, Niels Tommerup, Søren Tvorup Christensen, Lars Allan Larsen

 

Human iPSC modeling elucidates mutation-specific responses to gene therapy in a genotypically diverse dominant maculopathy
Divya Sinha, Benjamin Steyer, Pawan K. Shahi, Katherine Mueller, Rasa Valiauga, Kimberly L. Edwards, Cole Bacig, Stephanie S. Steltzer, Sandhya Srinivasan, Amr Abdeen, Evan Cory, Viswesh Periyasamy, Alireza Fotuhi Siahpirani, Sushmita Roy, Bikash R. Pattnaik, Krishanu Saha, David M. Gamm

 

Overexpression of CD47 is associated with brain overgrowth in 16p11.2 deletion syndrome
Jingling Li, Thomas Brickler, Allison Banuelos, Kristopher Marjon, Jing Bian, Cyndhavi Narayanan, Irving L. Weissman, Sundari Chetty

 

 

 

| Plant development

Cellular heterogeneity in pressure and growth emerges from tissue topology and geometry
Yuchen Long, Ibrahim Cheddadi, Vincent Mirabet, Gabriella Mosca, Mathilde Dumond, Jan Traas, Christophe Godin, Arezki Boudaoud

 

A two-way molecular dialogue between embryo and endosperm required for seed development
N. M. Doll, S. Royek, S. Fujita, S. Okuda, A. Stintzi, T. Widiez, M. Hothorn, A. Schaller, N. Geldner, G. Ingram

 

Local auxin biosynthesis promotes stem cell differentiation and organogenesis in Arabidopsis shoot apex
Shalini Yadav, Harish Kumar, Ram Kishor Yadav

 

Tissue-wide integration of mechanical cues promotes efficient auxin patterning
João R. D. Ramos, Alexis Maizel, Karen Alim

 

Auxin-dependent xyloglucan remodelling defines differential tissue expansion in Arabidopsis thaliana
Silvia Melina Velasquez, Marçal Gallemi, Bibek Aryal, Peter Venhuizen, Elke Barbez, Kai Dünser, Maria Kalyna, Grégory Mouille, Eva Benkova, Rishikesh Bhalerao, Jürgen Kleine-Vehn

 

Auxin export from proximal fruits drives arrest in competent inflorescence meristems
Alexander Ware, Catriona H. Walker, Jan Šimura, Karin Ljung, Anthony Bishopp, Zoe Wilson, Tom Bennett

 

IBA endogenous auxin regulates Arabidopsis root system development in a glutathione-dependent way and is important for adaptation to phosphate deprivation
José A. Trujillo-Hernandez, Laetitia Bariat, Lucia C. Strader, Jean-Philippe Reichheld, Christophe Belin

 

PLETHORA and WOX5 interaction and subnuclear localisation regulates Arabidopsis root stem cell maintenance
Rebecca C. Burkart, Vivien I. Strotmann, Gwendolyn K. Kirschner, Abdullah Akinci, Laura Czempik, Alexis Maizel, Stefanie Weidtkamp-Peters, Yvonne Stahl

 

GPI-anchored SKU5/SKS are maternally required for integument development in Arabidopsis
Ke Zhou

 

A specific exocytic pathway is essential for polarization of PIN proteins in the establishment and maintenance of auxin gradients
Xiaoyan Gu, Kumari Fonseka, Stuart A. Casson, Andrei Smertenko, Guangqin Guo, Jennifer F. Topping, Patrick J. Hussey, Keith Lindsey

 

Network analyses implicate a role for PHYTOCHROME-mediated light signaling in the regulation of cuticle development in plant leaves
Pengfei Qiao, Richard Bourgault, Marc Mohammadi, Laurie G Smith, Michael A Gore, Isabel Molina, Michael J Scanlon

 

A mechanism coordinating root elongation, endodermal differentiation, redox homeostasis and response
Jing Fu, Jia-Ming Liu, Xudong Gao, Xinglin Zhang, Juan Bai, Yueling Hao, Hongchang Cui

 

A cell surface O-glycosylated peptide, AGP21, acts on the brassinosteroid pathway and modulates root hair cell fate
Cecilia Borassi, Javier Gloazzo Dorosz, Martiniano M. Ricardi, Laercio Pol Fachin, Mariana Carignani Sardoy, Eliana Marzol, Silvina Mangano, Diana Rosa Rodríguez Garcia, Javier Martínez Pacheco, Yossmayer del Carmen Rondón Guerrero, Silvia M. Velasquez, Bianca Villavicencio, Marina Ciancia, Georg Seifert, Hugo Verli, José M. Estevez

 

Mechanical properties of the stigmatic cell wall mediate pollen tube path in Arabidopsis
Lucie Riglet, Frédérique Rozier, Chie Kodera, Isabelle Fobis-Loisy, Thierry Gaude

 

Stem Cell Activity And Regeneration In Roots Require Non-Cell Autonomous Regulation From The Ground Tissue
Alvaro Sanchez-Corrionero, Pablo Perez-Garcia, Javier Cabrera, Javier Silva-Navas, Juan Perianez-Rodriguez, Inmaculada Gude, Juan Carlos del Pozo, Miguel Angel Moreno-Risueno

 

GAL4/GFP enhancer-trap lines for identification and manipulation of cells and tissues in developing Arabidopsis leaves
Brindhi Amalraj, Priyanka Govindaraju, Anmol Krishna, Dhruv Lavania, Nguyen Manh Linh, Sree Janani Ravichandran, Enrico Scarpella

 

Live imaging-assisted domain-specific CRISPR genome editing at single cell resolution in plants
Ting Li, An Yan, Elliot M. Meyerowitz

 

Global transcriptome profiling uncovers footprints of root and shoot development in crop models barley and tomato
Ali Ahmad Naz, Michael Schneider, Lucia Vedder, Bobby Mathew, Heiko Schoof, Jens Léon

 

 

Highly expressed maize pollen genes display coordinated expression with neighboring transposable elements and contribute to pollen fitness
Cedar Warman, Kaushik Panda, Zuzana Vejlupkova, Sam Hokin, Erica Unger-Wallace, Rex A Cole, Antony M Chettoor, Duo Jiang, Erik Vollbrecht, Matthew MS Evans, R Keith Slotkin, John E Fowler

 

Transcriptomics at maize embryo/endosperm interfaces identify a novel transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum (EAS)
Nicolas M. Doll, Jeremy Just, Véronique Brunaud, José Caïus, Aurélie Grimault, Nathalie Depège-Fargeix, Eddi Esteban, Asher Pasha, Nicholas J. Provart, Gwyneth C. Ingram, Peter M. Rogowsky, Thomas Widiez

 

Interaction between induced and natural variation at oil yellow1 delays reproductive maturity in maize
Rajdeep S. Khangura, Bala P. Venkata, Sandeep R. Marla, Michael V. Mickelbart, Singha Dhungana, David M. Braun, Brian P. Dilkes, Gurmukh S. Johal

 

 

The maize heterotrimeric G-protein β subunit controls shoot meristem development and immune responses
Qingyu Wu, Fang Xu, Lei Liu, Si Nian Char, Yezhang Ding, Eric Schmelz, Bing Yang, David Jackson

 

From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy
Noémie Vimont, Mathieu Fouché, José Antonio Campoy, Meixuezi Tong, Mustapha Arkoun, Jean-Claude Yvin, Philip A. Wigge, Elisabeth Dirlewanger, Sandra Cortijo, Bénédicte Wenden

 

Potential function of CbuSPL and gene encoding its interacting protein during flowering in Catalpa bungei
Zhi Wang, Tianqing Zhu, Erqin Fan, Nan Lu, Fangqun Ouyang, Nan Wang, Guijuan Yang, Lisheng Kong, Guanzheng Qu, Shougong Zhang, Wenjun Ma, Junhui Wang

 

Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis
Federica Brunoni, Silvio Collani, Rubén Casanova-Saéz, Jan Šimura, Michal Karady, Markus Schmid, Karin Ljung, Catherine Bellini

 

Plants with self-sustained luminescence
Tatiana Mitiouchkina, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, Kseniia A. Palkina, Ekaterina S. Shakhova, Liliia I. Fakhranurova, Sofia V. Chekova, Aleksandra S. Tsarkova, Yaroslav V. Golubev, Vadim V. Negrebetsky, Sergey A. Dolgushin, Pavel V. Shalaev, Olesya A. Melnik, Victoria O. Shipunova, Sergey M. Deyev, Andrey I. Bubyrev, Alexander S. Pushin, Vladimir V. Choob, Sergey V. Dolgov, Fyodor A. Kondrashov, Ilia V. Yampolsky, Karen S. Sarkisyan

 

Building customizable auto-luminescent luciferase-based reporters in plants
Arjun Khakhar, Colby Starker, James Chamness, Nayoung Lee, Sydney Stokke, Cecily Wang, Ryan Swanson, Furva Rizvi, Takato Imaizumi, Dan Voytas

 

 

Evo-devo & evo

Developmental variability drives mouse molar evolution along an evolutionary line of least resistance
Luke Hayden, Katerina Lochovska, Marie Sémon, Sabrina Renaud, Marie-Laure Delignette-Muller, Maurine Vilcot, Renata Peterkova, Maria Hovorakova, Sophie Pantalacci

 

Hox genes are essential for the development of novel serial homologous eyespots on the wings of Bicyclus anynana butterflies
Yuji Matsuoka, Antonia Monteiro

 

nkx3.2 mutant zebrafish accommodate jaw joint loss through a phenocopy of the head shapes of Paleozoic jawless fish
Tetsuto Miyashita, Pranidhi Baddam, Joanna Smeeton, Adam Phillip Oel, Natasha Natarajan, Brogan Gordon, A. Richard Palmer, Gage Crump, Daniel Graf, W. Ted Allison

 

Ancestral Regulatory Mechanisms Specify Conserved Midbrain Circuitry in Arthropods and Vertebrates
Jessika C. Bridi, Zoe N. Ludlow, Benjamin Kottler, Beate Hartmann, Lies Vanden Broeck, Jonah Dearlove, Markus Göker, Nicholas J. Strausfeld, Patrick Callaerts, Frank Hirth

 

Molecular and Morphological Signatures of Chordate Development: Two Distinct Pathways, One Tunicate
Mark Kowarsky, Chiara Anselmi, Kohji Hotta, Paolo Burighel, Giovanna Zaniolo, Federico Caicci, Benyamin Rosental, Norma F Neff, Katherine J Ishizuka, Karla J Palmeri, Jennifer Okamoto, Tal Gordon, Irving L Weissman, Stephen R Quake, Lucia Manni, Ayelet Voskoboynik

 

Heterochronically expressed midline netrin was recruited to guide mesoderm migration in epibolic gastrulation of the leech
Jun-Ru Lee, Dian-Han Kuo

 

Conserved nuclear receptors controlling a novel trait target fast-evolving genes expressed in a single cell
Bogdan Sieriebriennikov, Shuai Sun, James W. Lightfoot, Hanh Witte, Eduardo Moreno, Christian Rödelsperger, Ralf J. Sommer

 

 

A G-protein-coupled receptor mediates neuropeptide-induced oocyte maturation in the jellyfish Clytia
Gonzalo Quiroga Artigas, Pascal Lapébie, Lucas Leclère, Philip Bauknecht, Julie Uveira, Sandra Chevalier, Gáspár Jékely, Tsuyoshi Momose, Evelyn Houliston

 

 

Hox gene expression during the development of the phoronid Phoronopsis harmeri
Ludwik Gąsiorowski, Andreas Hejnol

 

Genetic architecture underlying changes in carotenoid accumulation during the evolution of the Blind Mexican cavefish, Astyanax mexicanus
Misty R. Riddle, Ariel Aspiras, Fleur Damen, John N. Hutchinson, Daniel Chinnapen, Clifford J. Tabin

 

A Hypomorphic Cystathionine β-Synthase Gene Contributes to Cavefish Eye Loss by Disrupting Optic Vasculature
Li Ma, Aniket V Gore, Daniel Castranova, Janet Shi, Mandy Ng, Kelly A Tomins, Corine M. van der Weele, Brant M Weinstein, William R. Jeffery

 

Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices
Claudia Racioppi, Keira A Wiechecki, Lionel Christiaen

 

Ecology, phylogeny, and the evolution of developmental duration in birds
Christopher R. Cooney, Catherine Sheard, Andrew D. Clark, Susan D. Healy, András Liker, Sally E. Street, Camille A. Troisi, Gavin H. Thomas, Tamás Székely, Nicola Hemmings, Alison E. Wright

 

The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations
Mosè Manni, Felipe A. Simao, Hugh M. Robertson, Marco A. Gabaglio, Robert M. Waterhouse, Bernhard Misof, Oliver Niehuis, Nikolaus U. Szucsich, Evgeny M. Zdobnov

 

Evolution of CDK1 paralog specializations in a lineage with fast developing planktonic embryos
Xiaofei Ma, Jan Inge Øvrebø, Eric M Thompson

 

Characterization of the genetic architecture underlying eye size variation within Drosophila melanogaster and Drosophila simulans
Pedro Gaspar, Saad Arif, Lauren Sumner-Rooney, Maike Kittelmann, Andrew J. Bodey, David L. Stern, Maria D. S. Nunes, Alistair P. McGregor

 

Pleiotropy of Bcl-2 family proteins is an ancient trait in the metazoan evolution
Nikolay Popgeorgiev, Lea Jabbour, Trang Thi Minh Nguyen, Nikola Ralchev, Rudy Gadet, Stéphen Manon, Hans-Jürgen Osigus, Bernd Schierwater, Ruth Rimokh, Germain Gillet

 

Insights into the origin of metazoan multicellularity from predatory unicellular relatives of animals
Denis V. Tikhonenkov, Elisabeth Hehenberger, Anton S. Esaulov, Olga I. Belyakova, Yuri A. Mazei, Alexander P. Mylnikov, Patrick J. Keeling

 

Modern human changes in regulatory regions implicated in cortical development
Juan Moriano, Cedric Boeckx

 

The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence
Richard P Meisel, Pablo J Delclos, Judith R Wexler

 

Novelty and emergent patterns in sperm: morphological diversity and evolution of spermatozoa and sperm conjugation in ground beetles (Coleoptera: Carabidae)
R. Antonio Gomez, David R. Maddison

 

Sex-specific transgenerational plasticity in threespined sticklebacks
Jennifer K Hellmann, Syed Abbas Bukhari, Jack Deno, Alison M Bell

 

A tale of winglets: evolution of flight morphology in stick insects
Yu Zeng, Conner O’Malley, Sonal Singhal, Faszly Rahim, Sehoon Park, Xin Chen, Robert Dudley

 

 

 

Cell biology

Mechanistic insight into crossing over during mouse meiosis
Shaun E. Peterson, Scott Keeney, Maria Jasin

 

Nectins rather than E-cadherin anchor the actin belts at cell-cell junctions of epithelia
Pierre Mangeol, Dominique Massey-Harroche, André Le Bivic, Pierre-François Lenne

 

Nestin selectively facilitates the phosphorylation of the Lissencephaly-linked protein doublecortin (DCX) by cdk5/p35 to regulate growth cone morphology and Sema3a sensitivity in developing neurons
Christopher J. Bott, Jason M. Keil, Lloyd P. McMahon, Chan Choo Yap, Kenneth Y. Kwan, Bettina Winckler

 

Cleavage-furrow formation without F-actin in Chlamydomonas
Masayuki Onishi, James G. Umen, Frederick R. Cross, John R. Pringle

 

 

Prophase removal of chromosome-associated RNAs facilitates anaphase chromosome segregation
Judith A. Sharp, Wei Wang, Michael D. Blower

 

A weak link with actin organizes tight junctions to control epithelial permeability
Brian Belardi, Tiama Hamkins-Indik, Andrew R Harris, Daniel A Fletcher

 

The SMYD3 methyltransferase promotes myogenesis by activating the myogenin regulatory network
Roberta Codato, Martine Perichon, Arnaud Divol, Ella Fung, Athanassia Sotiropoulos, Anne Bigot, Jonathan B Weitzman, Souhila Medjkane

 

Cell division Rate Controls Cell Shape Remodeling in Epithelia
John Devany, Daniel M. Sussman, M. Lisa Manning, Margaret L. Gardel

 

Biophysical properties of intermediate states of EMT outperform both epithelial and mesenchymal states
Yoran Margaron, Tomoaki Nagai, Laurent Guyon, Laetitia Kurzawa, Anne-Pierre Morel, Alice Pinheiro, Laurent Blanchoin, Fabien Reyal, Alain Puisieux, Manuel Théry

 

A proximity biotinylation map of a human cell
Christopher D. Go, James D.R. Knight, Archita Rajasekharan, Bhavisha Rathod, Geoffrey G. Hesketh, Kento T. Abe, Ji-Young Youn, Payman Samavarchi-Tehrani, Hui Zhang, Lucie Y. Zhu, Evelyn Popiel, Jean-Philippe Lambert, Étienne Coyaud, Sally W.T. Cheung, Dushyandi Rajendran, Cassandra J. Wong, Hana Antonicka, Laurence Pelletier, Brian Raught, Alexander F. Palazzo, Eric A. Shoubridge, Anne-Claude Gingras

 

Collective MAPK Signaling Dynamics Coordinates Epithelial Homeostasis
Timothy J. Aikin, Amy F. Peterson, Michael J. Pokrass, Helen R. Clark, Sergi Regot

 

 

Modelling

 

Discovery of the prickle patterning on the stem of rose and the mathematical model of the pattern
Kazuaki Amikura, Hiroshi Ito

 

A Mechanical Model of Early Somite Segmentation
Priyom Adhyapok, Agnieszka M Piatkowska, Sherry G Clendenon, Claudio D Stern, James A Glazier, Julio M Belmonte

 

Tissue evolution: Mechanical interplay of adhesion, pressure, and heterogeneity
Tobias Büscher, Nirmalendu Ganai, Gerhard Gompper, Jens Elgeti

 

Modeling a gene regulatory network of EMT hybrid states for mouse embryonic skin cells
Dan Ramirez, Vivek Kohar, Ataur Katebi, Mingyang Lu

 

A least microenvironmental uncertainty principle (LEUP) as a generative model of collective cell migration mechanisms
Arnab Barua, Josue M. Nava-Sedeño, Haralampos Hatzikirou

 

Effective physical properties of cell–cell interaction explain basic structural units of three-dimensional morphogenesis
Hiroshi Koyama, Hisashi Okumura, Atsushi M. Ito, Tetsuhisa Otani, Kazuyuki Nakamura, Kagayaki Kato, Toshihiko Fujimori

 

Robustness of bidirectional microtubule network self-organization
Aleksandra Z. Płochocka, Alexander M. Davie, Natalia. A. Bulgakova, Lyubov Chumakova

 

Simulations of particle tracking in the oligociliated mouse node and implications for left-right symmetry breaking mechanics
Meurig T. Gallagher, Thomas D. Montenegro-Johnson, David J. Smith

 

 

Tools & resources

Profiling the endothelial translatome in vivo using ‘AngioTag’ zebrafish
Mayumi Miller, Derek E. Gildea, Kathryn Monzo, Lisa Wiliams-Simons, Van N. Pham, Natalie Aloi, Andreas D. Baxevanis, Brant M. Weinstein

 

A photostable monomeric superfolder GFP
Fernando Valbuena, Ivy Fizgerald, Rita L. Strack, Neal Andruska, Luke Smith, Benjamin S. Glick

 

An engineered CRISPR/Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells
Sarah Bowling, Duluxan Sritharan, Fernando G. Osorio, Maximilian Nguyen, Priscilla Cheung, Alejo Rodriguez-Fraticelli, Sachin Patel, Yuko Fujiwara, Bin E. Li, Stuart H. Orkin, Sahand Hormoz, Fernando D. Camargo

 

Niche-inspired synthetic matrices for epithelial organoid culture
Victor Hernandez-Gordillo, Timothy Kassis, Arinola Lampejo, GiHun Choi, Mario E Gamboa, Juan S Gnecco, David Breault, Rebecca Carrier, Linda G Griffith

 

The potentials and pitfalls of a human cervical organoid model including Langerhans cells
Robert Jackson, Jordan D Lukacs, Ingeborg Zehbe

 

Mechano-modulatory synthetic niches for liver organoid derivation
Giovanni Sorrentino, Saba Rezakhani, Ece Yildiz, Sandro Nuciforo, Markus H. Heim, Matthias P. Lutolf, Kristina Schoonjans

 

High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue
Yang Liu, Mingyu Yang, Yanxiang Deng, Graham Su, Cindy C. Guo, Di Zhang, Dongjoo Kim, Zhiliang Bai, Yang Xiao, Rong Fan

 

A method to estimate the frequency of chromosomal rearrangements induced by CRISPR/Cas9 multiplexing in Drosophila.
William A. Ng, Bruce H. Reed

 

New Additions to the CRISPR Toolbox: CRISPR-CLONInG and CRISPR-CLIP for Donor Construction in Genome Editing
Dorjee T.N. Shola, Chingwen Yang, Vhy-Shelta Kewaldar, Pradip Kar, Victor Bustos

 

CRISPR-Cas12a-assisted PCR tagging of mammalian genes
Julia Fueller, Konrad Herbst, Matthias Meurer, Krisztina Gubicza, Bahtiyar Kurtulmus, Julia D. Knopf, Daniel Kirrmaier, Benjamin C. Buchmuller, Gislene Pereira, Marius K. Lemberg, Michael Knop

 

Coolpup.py: versatile pile-up analysis of Hi-C data
Ilya M. Flyamer, Robert S. Illingworth, Wendy A. Bickmore

 

GranatumX: A community engaging and flexible software environment for single-cell analysis
Xun Zhu, Breck Yunits, Thomas Wolfgruber, Yu Liu, Qianhu Huang, Olivier Poirion, Cedric Arisdakessian, Tianying Zhao, David Garmire, Lana Garmire

 

Chi.Bio: An open-source automated experimental platform for biological science research
Harrison Steel, Robert Habgood, Ciarán Kelly, Antonis Papachristodoulou

 

 

Accelerated clearing and molecular labeling of large tissue samples using magnetohydrodynamic force
Joseph Dwyer, M. Desmond Ramirez, Paul S. Katz, Rolf O. Karlstrom, Joseph Bergan

 

3D super-resolution deep-tissue imaging in living mice
Mary Grace M. Velasco, Mengyang Zhang, Jacopo Antonello, Peng Yuan, Edward S. Allgeyer, Dennis May, Ons M’Saad, Phylicia Kidd, Andrew E. S. Barentine, Valentina Greco, Jaime Grutzendler, Martin J. Booth, Joerg Bewersdorf

 

A versatile twin-microscope system for light-sheet imaging
Kevin Keomanee-Dizon, Scott E. Fraser, Thai V. Truong

 

Towards Automatic Embryo Staging in 3D+T Microscopy Images using Convolutional Neural Networks and PointNets
Manuel Traub, Johannes Stegmaier

 

Minutes-timescale 3D isotropic imaging of entire organs at subcellular resolution by content-aware compressed-sensing light-sheet microscopy
Chunyu Fang, Tingting Chu, Tingting Yu, Yujie Huang, Yusha Li, Peng Wan, Dan Wang, Xuechun Wang, Wei Mei, Dan Zhu, Peng Fei

 

Two simple criteria to estimate an objective’s performance when imaging in non design tissue clearing solutions
Sabrina Asteriti, Valeria Ricci, Lorenzo Cangiano

 

DeepImageJ: A user-friendly plugin to run deep learning models in ImageJ
Estibaliz Gómez-de-Mariscal, Carlos García-López-de-Haro, Laurène Donati, Michael Unser, Arrate Muñoz-Barrutia, Daniel Sage

 

 

Research practice & education

Releasing a preprint is associated with more attention and citations for the peer-reviewed article
Darwin Y. Fu, Jacob J. Hughey

 

Insights from a survey-based analysis of the academic job market
Jason D. Fernandes, Sarvenaz Sarabipour, Christopher T. Smith, Natalie M. Niemi, Nafisa M. Jadavji, Ariangela J. Kozik, Alex S. Holehouse, Vikas Pejaver, Orsolya Symmons, Alexandre W. Bisson Filho, Amanda Haage

 

Longitudinal study of persistence in professional development outcomes of early career biology faculty
Nathan C Emery, Jessica Middlemis Maher, Diane Ebert-May

 

The Future of OA: A large-scale analysis projecting Open Access publication and readership
Heather Piwowar, Jason Priem, Richard Orr

 

Data Reuse and the Social Capital of Open Science
Bradly Alicea

 

Women in Science and Technology: An Indian scenario
Akanksha Swarup, Tuli Dey

 

Community Standards for Open Cell Migration Data
Alejandra N. Gonzalez-Beltran, Paola Masuzzo, Christophe Ampe, Gert-Jan Bakker, Sébastien Besson, Robert H. Eibl, Peter Friedl, Matthias Gunzer, Mark Kittisopikul, Sylvia E. Le Dévédec, Simone Leo, Josh Moore, Yael Paran, Jaime Prilusky, Philippe Rocca-Serra, Philippe Roudot, Marc Schuster, Gwendolien Sergeant, Staffan Strömblad, Jason R. Swedlow, Merijn van Erp, Marleen Van Troys, Assaf Zaritsky, Susanna-Assunta Sansone, Lennart Martens

 

Scientific societies advancing STEM workforce diversity: Lessons and Outcomes from the Minorities Affairs Committee of the American Society for Cell Biology
Verónica A Segarra, Sydella Blatch, Michael Boyce, Franklin Carrero-Martinez, Renato J Aguilera, Michael J Leibowitz, MariaElena Zavala, Latanya Hammonds-Odie, Ashanti Edwards

 

Wikidata as a FAIR knowledge graph for the life sciences
Andra Waagmeester, Gregory Stupp, Sebastian Burgstaller-Muehlbacher, Benjamin M. Good, Malachi Griffith, Obi Griffith, Kristina Hanspers, Henning Hermjakob, Kevin Hybiske, Sarah M. Keating, Magnus Manske, Michael Mayers, Elvira Mitraka, Alexander R. Pico, Timothy Putman, Anders Riutta, Núria Queralt-Rosinach, Lynn M. Schriml, Denise Slenter, Ginger Tsueng, Roger Tu, Egon Willighagen, Chunlei Wu, Andrew I. Su

 

Guidelines for reporting single-cell RNA-Seq experiments
Anja Füllgrabe, Nancy George, Matthew Green, Parisa Nejad, Bruce Aronow, Laura Clarke, Silvie Korena Fexova, Clay Fischer, Mallory Ann Freeberg, Laura Huerta, Norman Morrison, Richard H. Scheuermann, Deanne Taylor, Nicole Vasilevsky, Nils Gehlenborg, John Marioni, Sarah Teichmann, Alvis Brazma, Irene Papatheodorou

 

 

Why not…

MinION sequencing of seafood in Singapore reveals creatively labelled flatfishes, confused roe, pig DNA in squid balls, and phantom crustaceans
Jonathan K. I. Ho, Jayanthi Puniamoorthy, Amrita Srivathsan, Rudolf Meier

 

Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793)
Toni de-Dios, Lucy van Dorp, Philippe Charlier, Sofia Morfopoulou, Esther Lizano, Celine Bon, Corinne Le Bitouzé, Marina Álvarez-Estapé, Tomas Marquès-Bonet, François Balloux, Carles Lalueza-Fox

 

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