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

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On February 20^th, The Company of Biologists launched preLights, a community-led preprint highlighting service. A panel of early career researchers (the ‘preLighters’) select and comment on recent preprints that caught their eye, and encourage preprint authors to answer any questions about the work that they had. So far it looks great, and the developmental biology content has been especially good (see the dedicated subject category). We’d love to know what you think: you can contact the team via the site or the Twitter feed.

 

 

The idea behind the site was influenced in part by this list – as it got longer and longer (reflecting increased preprint usage), we were wondering how else we could encourage and promote the discussion of preprints, and the preLights idea took form. Rest assured that this list will live on, at least until the point at which it gets impossibly long!

And here’s the list – all the developmental biology I could find, plus relevant and cool other preprints thrown in for good measure.

The preprints were hosted on bioRxiv, PeerJ, and arXiv. Use these links to get to the section you want:

 

Developmental biology

| Patterning & signalling

| Morphogenesis & mechanics

| Genes & genomes

| Stem cells, regeneration & disease modelling

Evo-devo & evo

Cell biology

Modelling

Tools & resources

| Imaging etc.

| Genome tools

Research practice & education

Why not…

 

Developmental biology

| Patterning & signalling

 

Human axial progenitors generate trunk neural crest cells. Thomas J.R. Frith, Ilaria Granata, Erin Stout, Matthew Wind, Oliver Thompson, Katrin Neumann, Dylan Stavish, Paul R Heath, James O.S. Hackland, Konstantinos Anastassiadis, Mina Gouti, James Briscoe, Valerie Wilson, Mario R Guarracino, Peter W Andrews, Anestis Tsakiridis

 

Lineage tracing axial progenitors using Nkx1.2CreERT2 mice defines their trunk and tail contributions. Aida Rodrigo Albors, Pamela A Halley, Kate G Storey

 

 

A conserved regulatory program drives emergence of the lateral plate mesoderm. Christopher Hess, Karin Dorien Prummel, Susan Nieuwenhuize, Hugo Parker, Katherine W. Rogers, Iryna Kozmikova, Claudia Racioppi, Sibylle Burger, Eline C. Brombacher, Alexa Burger, Anastasia Felker, Elena Chiavacci, Gopi Shah, Jan Huisken, Zbynek Kozmik, Lionel Christiaen, Patrick Mueller, Marianne Bronner, Robb Krumlauf, Christian Mosimann

 

Hedgehog signaling controls progenitor differentiation timing during heart development. Megan Rowton, Andrew D. Hoffmann, Jeffrey D. Steimle, Xinan Holly Yang, Alexander Guzzetta, Sonja Lazarevic, Chul Kim, Nikita Deng, Emery Lu, Jessica Jacobs-Li, Shuhan Yu, Erika Hanson, Carlos Perez-Cervantes, Sunny Sun-Kin Chan, Kohta Ikegami, Daniel J. Garry, Michael Kyba, Ivan P. Moskowitz

 

SOX2 Regulation by Hedgehog Signaling Controls Adult Lingual Epithelium Homeostasis. David Castillo-Azofeifa, Kerstin Seidel, Lauren Gross, Belkis Jacquez, Ophir D Klein, Linda A. Barlow

 

Extracellular Pax6 regulates tangential Cajal-Retzius cell migration. Hadhemi Kaddour, Eva Coppola, Ariel Di Nardo, Andrea Wizenmann, Michel Volovitch, Alain Prochiantz, Alessandra Pierani

 

Axon Guidance Signaling Modulates Epithelial to Mesenchymal Transition in Stem Cell-Derived Retinal Pigment Epithelium. Srinivas R. Sripathi, Melissa M. Liu, Ming-Wen Hu, Jun Wan, Jie Cheng, Yukan Duan, Joseph Mertz, Karl Wahlin, Julien Maruotti, Cynthia A Berlinicke, Jiang Qian, Donald J. Zack

 

Neuroligins mediate presynaptic maturation through brain-derived neurotrophic factor signaling. Andoniya Petkova, Nina Goedecke, Martin Korte, Thomas Dresbach

 

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

 

Osteoclasts control sensory neurons axonal growth through epidermal growth factor receptor signaling. Estrela Neto, Daniela Sousa, Francisco Conceição, Luís Leitão, Cecília Juliana Alves, Inês Alencastre, Jonathan West, Richard O. C. Oreffo, Meriem Lamghari

 

FGF activity asymmetrically regulates the timing of habenular neurogenesis in a Nodal-dependent manner. Benjamin J Dean, Joshua T Gamse, Shu-Yu Wu

 

The transcription factor Tfap2e/AP-2ε plays a pivotal role in maintaining the identity of basal vomeronasal sensory neurons. Jennifer M Lin, Ed Zandro M Taroc, Jesus A Frias, Aparna Prasad, Allison N Catizone, Morgan A Sammons, Paolo E. Forni

 

Tdrd6a regulates the aggregation of Buc into functional subcellular compartments that drive germ cell specification. Elke F Roovers, Lucas JT Kaaij, Stefan Redl, Alfred W Bronkhorst, Kay Wiebrands, Antonio Miguel de Jesus Domingues, Hsin-Yi Huang, Chung-Ting Han, Willi Salvenmoser, Dominic Gruen, Falk Butter, Alexander van Oudenaarden, Rene F Ketting

 

 

Blimp-1 mediates the temporal control of embryonic tube maturation. Arzu Ozturk-Colak, Camille Stephan-Otto Attolini, Jordi Casanova, Sofia J. Araujo

 

The integrated stress response regulates BMP signaling through effects on translation. Elke Malzer, Caia S Dominicus, Joseph E Chambers, Souradip Mookerjee, Stefan J Marciniak

 

Dietary lipids modulate Notch signaling and influence adult intestinal development and metabolism in Drosophila. Rebecca Obniski, Matthew Sieber, Allan C Spradling

 

 

Spatio-temporal relays control layer specificity of motion-direction sensitive neurons in Drosophila. Holger Apitz, Iris Salecker

 

Torso-like is a component of the hemolymph and regulates the insulin signalling pathway in Drosophila. Michelle A Henstridge, Lucinda Aulsebrook, Takashi Koyama, Travis K Johnson, James C Whisstock, Tony Tiganis, Christen K Mirth, Coral G Warr

 

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

 

The Atypical Rho GTPase CHW-1 Works With SAX-3/Robo to Mediate Axon Guidance in Caenorhabditis elegans. Jamie Alan, Sara Robinson, Katie Magsig, Rafael Demarco, Erik A. Lundquist

 

 

Phospho-regulation of Atoh1 is required for plasticity of secretory progenitors and tissue regeneration. Goran Tomic, Edward Morrissey, Sarah Kozar, Shani Ben-Moshe, Alice Hoyle, Roberta Azzarelli, Richard Kemp, Chandra Sekhar Reddy Chilamakuri, Shalev Itzkovitz, Anna Philpott, Douglas Winton

 

The TMEM16A Channel Mediates the fast polyspermy block in Xenopus Laevis. Katherine L Wozniak, Wesley A Phelps, Maiwase Tembo, Miler T Lee, Anne E Carlson

 

Early lethality of embryos derived from transgenic Xenopus females is associated with reduced ovarian grem1 expression. Caroline W Beck, Joanna Ward, Lisa Troise, Catherine Brochard

 

Genetic inactivation of alpha-synuclein affects embryonic development of dopaminergic neurons of the substantia nigra but not the ventral tegmental area in mouse brain. Tatyana V Tarasova, Olga A Lytkina, Valeria V Goloborshcheva, Larisa N Skuratovskaya, Alexandr I Antohin, Ruslan K Ovchinnikov, Michail S Kukharsky​

 

 

Single-cell analysis of progenitor cell dynamics and lineage specification of the human fetal kidney. Rajasree Menon, Edgar A. Otto, Austin Kokoruda, Jian Zhou, Zidong Zhang, Euisik Yoon, Yu-Chih Chen, Olga Troyanscaya, Jason Spence, Matthias Kretzler, Cristina Cebrian

 

A hypomorphic Stip1 allele reveals the requirement for chaperone networks in mouse development and aging. Rachel Lackie, Marilene H Lopes, Sali M.K. Farhan, Abdul Razzaq, Gilli Moshitzky, Mariana B Prado, Flavio H Beraldo, Andrzej Maciejewski, Robert Gros, Jue Fan, Wing-Yiu Choy, David Greenberg, Vilma R Martins, Martin Duennwald, Hermona Soreq, Vania F Prado, Marco A. M. Prado

 

Bioelectric-calcineurin signaling module regulates allometric growth and size of the zebrafish fin. Jacob Daane, Jennifer Lanni, Ina Rothenberg, Guiscard Seebohm, Charles Higdon, Stephen Johnson, Matthew Harris

 

GEMC1 and CCNO are required for efferent duct development and male fertility. Berta Terre, Michael Lewis, Gabriel Gil-Gomez, Travis H Stracker

 

| Morphogenesis & mechanics

Characterization of convergent thickening, a major convergence force producing morphogenic movement in amphibians. David R Shook, Jason Wen, Ana Rolo, Brian Francica, Destiny Dobins, Paul Skoglund, Douglas DeSimone, Rudolf Winklbauer, Ray Keller

 

 

Large, long range tensile forces drive convergence during Xenopus blastopore closure and body axis elongation. David R Shook, Ray Keller, Lance Davidson, Eric M. Kasprowicz

 

Contact-dependent cell communications drive morphological invariance during ascidian embryogenesis. Leo Guignard, Ulla-Maj Fiuza, Bruno Leggio, Emmanuel Faure, Julien Laussu, Lars Hufnagel, Gregoire Malandain, Christophe Godin, Patrick Lemaire

 

 

 

Tbx1 regulates extracellular matrix- and cell-cell interactions in the second heart field. Antonio Baldini, Daniela Alfano, Alessandra Altomonte, Marchesa Bilio

 

An unconventional myosin, myosin 1d regulates Kupffer’s vesicle morphogenesis and laterality. Manush Saydmohammed, Hisato Yagi, Michael Calderon, Madeline J Clark, Timothy Feinstein, Ming Sun, Donna B Stolz, Simon C Watkins, Jeffrey Amack, Cecilia Lo, Michael Tsang

 

Myosin1D is an evolutionarily conserved determinant of animal Left/Right asymmetry. Thomas Juan, Charles Géminard, Jean-Baptiste Coutelis, Delphine Cerezo, Sophie Polès, Stéphane Noselli, Maximilian Fürthauer

 

 

Integrin signaling downregulates filopodia in muscle-tendon attachment. Benjamin Richier, Yoshiko Inoue, Ulrich Dobramysl, Jonathan Friedlander, Nicholas H. Brown, Jennifer Louise Gallop

 

Long-range Notch-mediated tissue patterning requires actomyosin contractility. Ginger Hunter, Li He, Norbert Perrimon, Guillaume Charras, Edward Giniger, Buzz Baum

 

 

Atf3 links loss of epithelial polarity to defects in cell differentiation and cytoarchitecture. Colin D. Donohoe, Gabor Csordas, Andreia Correia, Marek Jindra, Corinna Klein, Bianca Habermann, Mirka Uhlirova

 

Myosin Heavy Chain-embryonic is a crucial regulator of skeletal muscle development and differentiation. Akashi Sharma, Megha Agarwal, Amit Kumar, Pankaj Kumar, Masum Saini, Gabrielle Kardon, Sam Mathew

 

The C. elegans heterochronic gene lin-28 coordinates the timing of hypodermal and somatic gonadal programs for hermaphrodite reproductive system morphogenesis. Sungwook Choi, Victor Ambros

 

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

 

A microtubule-based mechanism predicts cell division orientation in plant embryogenesis. Bandan Chakrabortty, Viola Willemsen, Thijs de Zeeuw, Che-Yang Liao, Dolf Weijers, Bela Mulder, Ben Scheres

 

 

Feeling the force: how pollen tubes deal with obstacles. Jan T Burri, Hannes Vogler, Nino F Läubli, Chengzhi Hu, Ueli Grossniklaus, Bradley J Nelson

 

 

Microtubule-associated protein IQ67 DOMAIN5 regulates interdigitation of leaf pavement cells in Arabidopsis thaliana. Dipannita Mitra, Pratibha Kumari, Jakob Quegwer, Sandra Klemm, Birgit Moeller, Yvonne Poeschl, Paul Pflug, Gina Stamm, Steffen Abel, Katharina Bürstenbinder

 

Cell death in cells overlying lateral root primordia contributes to organ growth in Arabidopsis. Sacha Escamez, Benjamin Bollhoner, Hardy Hall, Domenique Andre, Beatrice Berthet, Ute Voss, Amnon Lers, Alexis Maizel, Malcolm Bennett, Hannele Tuominen

 

FERONIA’s sensing of cell wall pectin activates ROP GTPase signaling in Arabidopsis. Wenwei Lin, Wenxin Tang, Charles Anderson, Zhenbiao Yang

 

Adaptive diversification of growth allometry in the plant Arabidopsis thaliana. Francois Vasseur, Moises Exposito-Alonso, Oscar Javier Ayala-Garay, George Wang, Brian J Enquist, Denis Vile, Cyrille Violle, Detlef Weigel

 

A mechanism for the proliferative control of tissue mechanics in the absence of growth. Min Wu, Madhav Mani

 

 

Endothelia extrude apoptotic cells to maintain a constant barrier. Tara Mleynek, Dean Li, Jody Rosenblatt, Michael Jarman Redd, Aubrey Chan, Yapeng Gu

 

Cellular Migration May Exhibit Intrinsic Left-Right Asymmetries: A meta-analysis. Kelly G. Sullivan, Laura N. Vandenberg, Michael Levin

 

Increased prenatal brain growth in a transgenic mouse model decreases cranial development: An expensive tissue hypothesis for the skull. Elisabeth K N López​, Matthew J Ravosa

 

In vivo optochemical control of cell contractility at single cell resolution by Ca2+ induced myosin activation. Deqing Kong, Fred Wolf, Joerg Grosshans.

 

A quantitative study of blood circulation in the developing adult ascidian tunicate Ciona savignyi (Cionidae). Michael W Konrad

 

Tissue-specific activities of the Fat1 cadherin cooperate to control neuromuscular morphogenesis. Francoise Helmbacher

 

 

Zebrafish sp7 mutants show tooth cycling independent of attachment, eruption and poor differentiation of teeth. Erika Kague, Paul Eckhard Witten, Mieke Soenens, Camila Lovaglio Campos, Tiago Lubiana, Shannon Fisher, Chrissy Hammond, Kate Robson Brown, Maria Rita Passos Bueno, Ann Huysseune

 

| Genes & genomes

Disruption in A-to-I editing levels affects C. elegans development more than a complete lack of editing. Nabeel S. Ganem, Noa Ben-Asher, Aidan C. Manning, Sarah N. Deffit, Michael C. Washburn, Emily C. Wheeler, Gene W Yeo, Orna Ben-Naim Zgayer, Einav Mantsur, Heather A. Hundley, Ayelet T Lamm

 

ADAR1 A-to-I RNA editing alters codon usage. Pavla Brachova, Nehemiah S Alvarez, Xiaoman Hong, Kailey A. Vincent, Keith E. Latham, Lane K. Christenson

 

Identification of piRNA binding sites reveals the Argonaute regulatory landscape of the C. elegans germline. En-Zhi Shen, Hao Chen, Ahmet R. Ozturk, Shikui Tu, Masaki Shirayama, Wen Tang, Yue-He Ding, Si-Yuan Dai, Zhiping Weng, Craig C. Mello

 

 

H3K9 methylation maintains female identity in Drosophila germ cells through repression of the spermatogenesis program. Anne Smolko, Laura Shapiro-Kulnane, Helen Salz

 

Fanconi Anemia FANCM/FNCM-1 and FANCD2/FCD-2 are required for maintaining histone methylation levels and interact with the histone demethylase LSD1/SPR-5 in C. elegans. Hyun-Min Kim, Sara E Beese-Sims, Monica P. Colaiácovo

 

 

GTSF-1 is required for the formation of a functional RNA-dependent RNA Polymerase complex in C. elegans. Miguel V. Almeida, Sabrina Dietz, Stefan Redl, Emil Karaulanov, Andrea Hildebrandt, Christian Renz, Helle D. Ulrich, Julian König, Falk Butter, René F. Ketting

 

Dissection of the microProtein miP1 floral repressor complex in Arabidopsis. Vandasue L. Rodrigues, Ulla Dolde, Daniel Straub, Tenai Eguen, Esther Botterweg-Paredes, Bin Sun, Shinyoung Hong, Moritz Graeff, Man-Wah Li, Joshua Gendron, Stephan Wenkel

 

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

 

Incomplete reprogramming of cell-specific epigenetic marks during asexual reproduction leads to heritable phenotypic variation in plants. Anjar Wibowo, Claude Becker, Julius Durr, Jonathan Price, Stijn Staepen, Sally Hilton, Hadi Putra, Ranjith Papareddy, Quentin Saintain, Sarah Harvey, Gary D Bending, Paul Schulze-Lefert, Detlef Weigel, Jose Gutierrez-Marcos

 

Epigenomic plasticity of Arabidopsis msh1 mutants under prolonged cold stress. Sunil Kumar Kenchanmane Raju, Mon-Ray Shao, Yashitola Wamboldt, Sally Mackenzie

 

A Lotus japonicus E3 ligase interacts with the Nod factor receptor 5 and positively regulates nodulation. Daniela Tsikou, Estrella E. Ramirez, Ioanna S Psarrakou, Jaslyn E Wong, Dorthe B Jensen, Erika Isono, Simona Radutoiu, Kalliope K Papadopoulou

 

 

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

 

Enhancer RNAs are necessary and sufficient for activity-dependent neuronal gene transcription. Nancy V.N. Gallus, Rhiana A. Simon, Aaron J Salisbury, Jasmin S. Revanna, Kendra D. Bunner, Katherine E. Savell, Faraz A. Sultan, Charles A. Gersbach, Jeremy J. Day

 

Mef-2 and p300 interact to regulate expression of the homeostatic regulator Pumilio in Drosophila. Wei-Hsiang Lin, Richard Baines

 

APC/C-Vihar regulates centrosome activity and stability in the Drosophila germline. Alexis L. Braun, Francesco Meghini, Gema Villa-Fombuena, Elisa M. Fernandez, Morgane Guermont, David M Glover, Maria D. Martin-Bermudo, Acaimo Gonzalez-Reyes, Yuu Kimata

 

A Genetic Program Mediates Cold-warming Response and Promotes Stress-induced Phenoptosis in C. elegans. Wei Jiang, Yuehua Wei, Yong Long, Arthur Owen, Bingying Wang, Xuebing Wu, Shuo Luo, Yongjun Dang, Dengke K. Ma

 

DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory organ of Corti. Ofer Yizhar-Barnea, Cristina Valensisi, Kamal Kishore, Naresh Doni Jayavelu, Colin Andrus, Tal Koffler-Brill, Kathy Ushakov, Kobi Perl, Yael Noy, Yoni Bhonker, Mattia Pelizzola, R. David Hawkins, Karen B. Avraham

 

Aggregation recovers developmental plasticity in mouse polyploid embryos. Hiroyuki Imai, Wataru Fujii, Ken Takeshi Kusakabe, Yasuo Kiso, Kiyoshi Kano

 

Capturing the onset of PRC2-mediated repressive domain formation. Ozgur Oksuz, Varun Narendra, Chul-Hwan Lee, Nicolas Descostes, Gary LeRoy, Ramya Raviram, Lili Blumenberg, Kelly Karch, Pedro R. Rocha, Benjamin A. Garcia, Jane A. Skok, Danny Reinberg

 

Cell type-dependent control of p53 transcription and enhancer activity by p63. Gizem Karsli Uzunbas, Faraz Ahmed, Morgan A Sammons

 

 

Genome-wide enhancer – gene regulatory maps in two vertebrate genomes. Yves Clément, Patrick Torbey, Pascale Gilardi-Hebenstreit, Hugues Roest Crollius

 

KLF6 and STAT3 co-occupy regulatory DNA and functionally synergize to promote axon growth in CNS neurons. Zimei Wang, Ishwariya Venkatesh, Vatsal Mehra, Matthew Simpson, Brian Maunze, Erik Eastwood, Lyndsey Holan, Murray Blackmore

 

Germline DNA replication timing shapes mammalian genome composition. Yishai Yehida, Britny Blumenfeld, Nina Mayorek, Kirill Makedonski, Oriya Vardi, Yousef Mansour, Hagit Masika, Marganit Farago, Shulamit Baror-Sebban, Yosef Buganim, Amnon Koren, Itamar Simon

 

 

| Stem cells, regeneration & disease modelling

Tracing the Transitions from Pluripotency to Germ Cell Fate with CRISPR Screening. Jamie A Hackett, Yun Huang, Ufuk Gunesdogan, Kristjan Holm-Gretarsson, Toshihiro Kobayashi, Azim M Surani

 

Neutralizing Gatad2a-Chd4-Mbd3 Axis within the NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency. Nofar Mor, Yoach Rais, Shani Peles, Daoud Sheban, Alejandro Aguilera-Castrejon, Asaf Zviran, Dalia Elinger, Sergey Viukov, Shay Geula, Vladislav Krupalnik, Mirie Zerbib, Elad Chomsky, Lior Lasman, Tom Shani, Jonathan Bayerl, Ohad Gafni, Suhair Hanna, Jason Buenrostro, Tzachi Hagai, Hagit Masika, Yehudit Bergman, William J. Greenleaf, Miguel A. Esteban, Yishai Levin, Rada Massarwa, Yifat Merbl, Noa Novershtern, Jacob H. Hanna

 

Delayed activation of the DNA replication licensing system in Lgr5(+) intestinal stem cells. Thomas Carroll, Ian Newton, Yu Chen, Julian J. Blow, Inke Nathke

 

Efficient differentiation of vascular endothelial cells from dermal-derived mesenchymal stem cells induced by endothelial cell lines conditioned medium. Ling Zhou, Xuping Niu, Jiannan Liang, Junqin Li, Jiao Li, Yueai Cheng, Yanfeng Meng, Qiang Wang, Xiaoli Yang, Gang Wang, Yu Shi, Erle Dang, Kaiming Zhang

 

Clonal Level Lineage Commitment Pathways of Hematopoietic Stem Cells In Vivo. Rong Lu, Agnieszka Czechowicz, Jun Seita, Du Jiang, Irving L Weissman

 

Hematopoietic Stem And Progenitor Cells Use Podosomes To Transcellularly Home To The Bone Marrow. Timo Rademakers, Marieke Goedhart, Mark Hoogenboezem, Alexander García Ponce, Jos van Rijssel, Maryna Samus, Michael Schnoor, Stefan Butz, Stephan Huveneers, Dietmar Vestweber, Martijn A Nolte, Carlijn Voermans, Jaap D van Buul

 

Epigenetic aging of human hematopoietic cells is not accelerated upon transplantation into mice. Joana Frobel, Susann Rahmig, Julia Franzen, Claudia Waskow, Wolfgang Wagner

 

 

Emergence of the erythroid lineage from multipotent hematopoiesis. Betsabeh Khoramian Tusi, Samuel L Wolock, Caleb Weinreb, Yung Hwang, Daniel Hidalgo, Rapolas Zilionis, Ari Waisman, Jun Huh, Allon M Klein, Merav Socolovsky

 

An immortalised mesenchymal stem cell line maintains mechano-responsive behaviour and can be used as a reporter of substrate stiffness. Asier Galarza Torre, Joshua E Shaw, Amber Wood, Hamish T J Gilbert, Oana Dobre, Paul Genever, Keith Brennan, Stephen M Richardson, Joe Swift

 

Heat shock induces the depletion of Oct4 in mouse blastocysts and stem cells. Mo-bin Cheng, Xue Wang, Yue Huang, Ye Zhang

 

Single-cell transcriptome of antler stem cells from antlerogenic periosteum. Hengxing Ba, Datao Wang, Weiyao Wu, Hongmei Sun, Chunyi Li

 

Xist Intron 1 Repression by TALE Transcriptional Factor Improves Somatic Cell Reprogamming in Mice. Jindun Zhang, Xuefei Gao, Jian Yang, Xiaoying Fan, Wei Wang, Yanfeng Liang, Lihong Fan, Hongmei Han, Xiaorong Xu, Fuchou Tang, Siqin Bao, Pentao Liu, Xihe Li

 

 

Tectal stem cells display diverse regenerative capacities. Benjamin W Lindsey, Georgia E Aitken, Jean K Tang, Mitra Khabooshan, Celia Vandestadt, Jan Kaslin

 

Developmental chromatin restriction of pro-growth gene networks acts as an epigenetic barrier to axon regeneration in cortical neurons. Ishwariya Venkatesh, Vatsal Mehra, Zimei Wang, Ben Califf, Murray Blackmore

 

Neuregulin-1 exerts molecular control over axolotl lung regeneration through ErbB family receptors. Tyler B Jensen, Peter Giunta, Natalie Grace Schulz, Yaa Kyeremateng, Hilary Wong, Adeleso Adesina, James R Monaghan

 

Targeting TrkB with a brain-derived neurotrophic factor mimetic promotes myelin repair in the brain. Jessica Louise Fletcher, Rhiannon J Wood, Jacqueline Nguyen, Eleanor ML Normon, Christine MK Jun, Alexa R Prawdiuk, Melissa Biemond, Huynh TH Nguyen, Susan E Northfield, Richard A Hughes, David G Gonsalvez, Junhua Xiao, Simon S Murray

 

Age-dependent dormant resident progenitors are stimulated by injury to regenerate Purkinje neurons. Nermin Sumru Bayin, Alexandre Wojcinski, Aurelien Mourton, Hiromitsu Saito, Noboru Suzuki, Alexandra L Joyner

 

Reversing Glial Scar Back To Neural Tissue Through NeuroD1-Mediated Astrocyte-To-Neuron Conversion. Lei Zhang, Zhuofan Lei, Ziyuan Guo, Zifei Pei, Yuchen Chen, Fengyu Zhang, Alice Cai, Yung Kin Mok, Grace Lee, Vishal Swaminathan, Fan Wang, Yuting Bai, Gong Chen

 

Loss of embryonic neural crest cardiomyocytes causes adult hypertrophic cardiomyopathy. Sarah Abdul-Wajid, Bradley Demarest, H. Joseph Yost

 

p53 deletion rescues apoptosis and microcephaly in a Kif20b mouse mutant. Jessica Neville Little, Noelle D. Dwyer

 

Altered neocortical gene expression, brain overgrowth and functional over-connectivity in Chd8 haploinsufficient mice. Philipp Suetterlin, Shaun Hurley, Conor Mohan, Kimberley L. H. Riegman, Marco Pagani, Angela Caruso, Jacob Ellegood, Alberto Galbusera, Ivan Crespo-Enriquez, Caterina Michetti, Yohan Yee, Robert Ellingford, Olivier Brock, Alessio Delogu, Philippa Francis-West, Jason P. Lerch, Maria Luisa Scattoni, Alessandro Gozzi, Cathy Fernandes, Albert Basson

 

 

Survey of human chromosome 21 gene expression effects on early development in Danio rerio. Sarah Edie, Norann A Zaghloul, Carmen C Leitch, Donna K Klinedinst, Janette Lebron, Joey F Thole, Andrew S. McCallion, Nicholas Katsanis, Roger H. Reeves

 

Regulation of midgut cell proliferation impacts Aedes aegypti susceptibility to dengue virus. Mabel L. Taracena, Vanessa Bottino-Rojas, Octavio A.C. Talyuli, Ana Beatriz Walter-Nuno, Jose Henrique M. Oliveira, Yesseinia I. Anglero-Rodriguez, Michael B. Wells, George Dimopoulos, Pedro L. Oliveira, Gabriela O. Paiva-Silva

 

Ablation of Ezh2 in neural crest cells leads to Hirschsprung’s disease-like phenotype in mice. Joomyeong Kim, Hana Kim, Ingeborg M. Langohr, Mohammad Faisal, Margaret McNulty, Caitlin Thorn

 

Building a schizophrenia genetic network: Transcription Factor 4 regulates genes involved in neuronal development and schizophrenia risk. Hanzhang Xia, Fay M Jahr, Nak-Kyeong Kim, Linying Xie, Andrey A Shabalin, Julien Bryois, Douglas H Sweet, Mohamad M Kronfol, Preetha Palasuberniam, MaryPeace McRae, Brien P Riley, Patrick F Sullivan, Edwin J van den Oord, Joseph McClay

 

Pervasive epistasis modulates neurodevelopmental defects of the autism-associated 16p11.2 deletion. Janani Iyer, Mayanglambam Dhruba Singh, Matthew Jensen, Payal Patel, Lucilla Pizzo, Emily Huber, Haley Koerselman, Alexis T. Weiner, Paola Lepanto, Komal Vadodaria, Alexis Kubina, Qingyu Wang, Abigail Talbert, Sneha Yennawar, Jose Badano, J. Robert Manak, Melissa M. Rolls, Arjun Krishnan, Santhosh Girirajan

 

The critical role of ASD-related gene CNTNAP3 in regulating synaptic development and social behavior in mice. Dali Tong, Ruiguo Chen, Yulan Lu, Weike Li, Yuefang Zhang, Junkai Lin, Lingjie He, Ting Dang, Shifang Shan, Xiaohong Xu, Yi Zhang, Chen Zhang, Yasong Du, Wen-Hao Zhou, Xiaoqun Wang, Zilong Qiu

 

Haploinsufficiency of autism candidate gene NUAK1 impairs cortical development and behavior. Virginie Courchet, Amanda J Roberts, Peggy Del Carmine, Tommy L Lewis Jr., Franck Polleux, Julien Courchet

 

The dyslexia susceptibility KIAA0319 gene shows a highly specific expression pattern during zebrafish development supporting a role beyond neuronal migration. Monika Gostic, Angela Martinelli, Carl Tucker, Zhengyi Yang, Federico Gasparoli, Kishan Dholakia, Keith Sillar, Javier Tello, Silvia Paracchini

 

Accelerated brain aging towards transcriptional inversion in a zebrafish model of familial Alzheimer’s disease. Nhi Hin, Morgan Newman, Jan Kaslin, Alon M. Douek, Amanda Lumsden, Xin-Fu Zhou, Noralyn B. Mañucat-Tan, Alastair Ludington, David L. Adelson, Stephen Pederson, Michael Lardelli

 

Ratiometric assays of autophagic flux in zebrafish for analysis of familial Alzheimer’s disease-like mutations. Haowei Jiang, Morgan Newman, Dhanushika Ratnayake, Michael Lardelli

 

Increased autophagy in ephrinB2 deficient osteocytes is associated with hypermineralized, brittle bones. Christina Vrahnas, Toby A Dite, Niloufar Ansari, Blessing Crimeen-Irwin, Huynh Nguyen, Mark R Forwood, Yifang Hu, Mika Ikegame, Keith R Bambery, Cyril Petibois, Mark J Tobin, Gordon K Smyth, Jonathan S Oakhill, T John Martin, Natalie A Sims

 

Evo-devo & evo

 

 

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

 

 

Endoderm Morphogenesis Reveals Integration of Distinct Processes in the Development and Evolution of Pharyngeal Arches. Shinji Takada, Kazunori Okada, Hiroshi Wada

 

 

Developmental Mechanisms Linking Form and Function During Jaw Evolution. Katherine C Woronowicz, Stephanie E Gline, Safa T Herfat, Aaron J Fields, Richard A Schneider

 

An evolutionary-conserved Wnt3/β-catenin/Sp5 feedback loop restricts head organizer activity in Hydra. Matthias Christian Vogg, Leonardo Beccari, Laura Iglesias Olle, Christine Rampon, Sophie Vriz, Chrystelle Perruchoud, Yvan Wenger, Brigitte Galliot

 

 

tarsal-less is expressed as a gap gene but has no gap gene phenotype in the moth midge Clogmia albipunctata. eva jimenez-guri, Karl Wotton, Johannes Jaeger

 

Evidence of adhesion and signaling roles for β-catenin in the sponge Ephydatia muelleri. Klaske J. Schippers, Scott A. Nichols

 

From spiral cleavage to bilateral symmetry: The developmental cell lineage of the annelid brain. Pavel Vopalensky, Maria Antonietta Tosches, Kaia Achim, Mette Handberg-Thorsager, Detlev Arendt

 

 

Elongation during segmentation shows axial variability, low mitotic rates, and synchronized cell cycle domains in the crustacean, Thamnocephalus platyurus. Savvas J Constantinou, Nicole Duan, Ariel D. Chipman, Lisa M. Nagy, Terri A. Williams

 

Changes in the neuropeptide complement correlate with nervous system architectures in xenacoelomorphs. Daniel Thiel, Mirita Franz-Wachtel, Felipe Aguilera, Andreas Hejnol

 

Intergenerational epigenetic inheritance in reef-building corals. Yi Jin Liew, Emily J. Howells, Xin Wang, Craig T. Michell, John A. Burt, Youssef Idaghdour, Manuel Aranda

 

Expanding the genetic toolkit of Tribolium castaneum. Johnathan C Rylee, Dylan J Siniard, Kaitlin Doucette, Gabriel E Zentner, Andrew Zelhof

 

Convergent evolution of gene expression in two high-toothed stickleback populations. James C Hart, Nicholas A Ellis, Michael B Eisen, Craig T Miller

 

Identification of general patterns of sex-biased expression in Daphnia, a genus with environmental sex determination. Cécile Molinier, Céline Reisser, Peter Fields, Adeline Segard, Yan Galimov, Christoph R. Haag

 

Genomic imprinting mediates dosage compensation in a young plant XY system. Aline Muyle, Niklaus Zemp, Cecile Fruchard, Radim Cegan, Jan Vrana, Clothilde Deschamps, Raquel Tavares, Franck Picard, Roman Hobza, Alex Widmer, Gabriel Marais

 

Delegating sex: differential gene expression in stolonizing syllids uncovers the hormonal control of reproduction in Annelida. Patricia Alvarez-Campos, Nathan Kenny, Aida Verdes, Rosa Maria Fernandez, Marta Novo, Gonzalo Giribet, Ana Riesgo

 

Concurrent duplication of the Cid and Cenp-C genes in the Drosophila subgenus with signatures of subfunctionalization and male germline-biased expression. Jose R. Teixeira, Guilherme B. Dias, Marta Svartman, Alfredo Ruiz, Gustavo C. S. Kuhn

 

Convergent regulatory evolution and the origin of flightlessness in palaeognathous birds. Timothy B. Sackton, Phil Grayson, Alison Cloutier, Zhirui Hu, Jun S. Liu, Nicole E. Wheeler, Paul P. Gardner, Julia A. Clarke, Allan J. Baker, Michele Clamp, Scott V. Edwards

 

 

Genotyping-by-sequencing supports a genetic basis for alpine wing-reduction in a New Zealand stonefly. Andrew J. Veale, Brodie J. Foster, Peter K. Dearden, Jon M. Waters

 

Transposable elements generate regulatory novelty in a tissue specific fashion. Marco Trizzino, Aurelie Kapusta, Christopher Brown

 

The effects of haploid selection on Y chromosome evolution in a dioecious plant. George Sandler, Felix E.G. Beaudry, Spencer C.H. Barrett, Stephen I. Wright

 

Adaptive Reduction of Male Gamete Number in a Selfing Species. Takashi Tsuchimatsu, Hiroyuki Kakui, Misako Yamazaki, Cindy Marona, Hiroki Tsutsui, Afif Hedhly, Dazhe Meng, Yutaka Sato, Thomas Stadler, Ueli Grossniklaus, Masahiro M. Kanaoka, Michael Lenhard, Magnus Nordborg, Kentaro K. Shimizu

 

Firefly genomes illuminate parallel origins of bioluminescence in beetles. Timothy R Fallon, Sarah E Lower, Ching-Ho Chang, Manabu Bessho-Uehara, Gavin J Martin, Adam J Bewick, Megan Behringer, Humberto J Debat, Isaac Wong, John C Day, Anton Suvorov, Christian J Silva, Kathrin F Stanger-Hall, David W Hall, Robert J. Schmitz, David R Nelson, Sara Lewis, Shuji Shigenobu, Seth M Bybee, Amanda M Larracuente, Yuichi Oba, Jing-Ke Weng

 

 

The Aquilegia genome: adaptive radiation and an extraordinarily polymorphic chromosome with a unique history. Daniele Filiault, Evangeline Ballerini, Terezie Mandakova, Gokce Akoz, Nathan Derieg, Jeremy Schmutz, Jerry Jenkins, Jane Grimwood, Shengqiang Shu, Richard Hayes, Uffe Hellsten, Kerrie Barry, Juyiang Yan, Sirma Mihaltcheva, Miroslava Karafiatova, Viktoria Nizhynska, Martin Lysak, Scott Hodges, Magnus Nordborg

 

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

 

Cell biology

F-actin patches nucleated on chromosomes coordinate capture by microtubules in oocyte meiosis. Mariia Burdyniuk, Andrea Callegari, Masashi Mori, Francois Nedelec, Peter Lenart

 

Rab-mediated trafficking in the secondary cells of Drosophila male accessory glands and its role in fecundity. Elodie Prince, Marko Brankatschk, Benjamin Kroeger, Clive Wilson, Dragan Gligorov, Suzanne Eaton, Francois Karch, Robert K Maeda

 

Persistent cell motility requires transcriptional feedback of cytoskeletal – focal adhesion equilibrium by YAP/TAZ. Devon E Mason, James H Dawahare, Trung Dung Nguyen, Yang Lin, Sherry L. Voytik-Harbin, Pinar Zorlutuna, Mervin E Yoder, Joel D Boerckel

 

 

Absence of the Spindle Assembly Checkpoint restores mitotic fidelity upon loss of sister chromatid cohesion. Rui D Silva, Mihailo Mirkovic, Leonardo G Guilgur, Om S. Rathore, Rui Gonçalo Martinho, Raquel A Oliveira

 

 

Focal adhesion kinase regulates early steps of myofibrillogenesis in cardiomyocytes. Nilay Taneja, Abigail C Neininger, Matthew R Bersi, W David Merryman, Dylan T Burnette

 

Recruitment of Two Dyneins to an mRNA-Dependent Bicaudal D Transport Complex. Thomas E. Sladewski, Neil Billington, M. Yusuf Ali, Carol S. Bookwalter, Hailong Lu, Elena B. Krementsova, Trina A. Schroer, Kathleen M. Trybus

 

RNA-directed activation of cytoplasmic dynein-1 in reconstituted transport RNPs. Mark A McClintock, Carly I Dix, Christopher M Johnson, Stephen H McLaughlin, Rory J Maizels, Ha Thi Hoang, Simon L Bullock

 

Dynein-2 intermediate chains play crucial but distinct roles in primary cilia formation and function. Laura Vuolo, Nicola L Stevenson, Kate Heesom, David J Stephens

 

Regulator of calcineurin-2 is a centriolar protein with a role in cilia length control. Nicola Stevenson, Dylan Bergen, Amadeus Xu, Emily Wyatt, Freya Henry, Janine McCaughey, Laura Vuolo, Chrissy Hammond, David Stephens

 

Actin and Src-family kinases regulate nuclear YAP1 and its export. Nil Ege, Anna M Dowbaj, Ming Jiang, Michael Howell, Robert P Jenkins, Erik Sahai

 

Rotational 3D mechanogenomic Turing patterns of human colon Caco-2 cells during differentiation. Gen Zheng, Alexandr A. Kalinin, Ivo D. Dinov, Walter Meixner, Shengtao Zhu, John W. Wile

 

Collagen stiffness modulates MDA-MB231 cell metabolism through adhesion-mediated contractility. Emma J. Mah, Gabrielle E. McGahey, Albert F. Yee, Michelle A. Digman

 

Tunable molecular tension sensors reveal extension-based control of vinculin loading. Andrew S LaCroix, Andrew D Lynch, Matthew E Berginski, Brenton D Hoffman

 

CLIC4 is regulated by RhoA-mDia2 signaling through Profilin-1 binding to modulate filopodia length. Elisabetta Argenzio, Katarzyna M Kedziora, Leila Nahidiazar, Tadamoto Isogai, Anastassis Perrakis, Kees Jalink, Wouter H Moolenaar, Metello Innocenti

 

 

Shugoshin is essential for meiotic prophase checkpoints in C. elegans. Tisha Bohr, Christian R. Nelson, Stefani Giacopazzi, Piero Lamelza, Needhi Bhalla

 

Shugoshin protects centromere pairing and promotes segregation of non-exchange partner chromosomes in meiosis. Luciana Previato, Emily L Kurdzo, Craig A Eyster, Mara N Gladstone, Hoa H Chuong, Elena Llano, Alberto M Pendas, Roberto J Pezza, Dean S Dawson

 

A positive feedback-based mechanism for constriction rate acceleration during cytokinesis in C. elegans. Renat Khaliullin, Rebecca Green, Linda Shi, Michael Berns, J. Sebastian Gomez-Cavazos, Arshad Desai, Karen Oegema

 

Cell-matrix adhesion controls Golgi organization and function by regulating Arf1 activation in anchorage-dependent cells. Vibha Singh, Chaitanya Erady, Nagaraj Balasubramanian

 

Modelling

Spatial dynamics of flower organ formation. Yuriria Cortes Poza, Pablo Padilla Longoria, Elena Alvarez Buylla

 

Mathematical modelling of cortical neurogenesis reveals that the founder population does not necessarily scale with neuronal output. Noemi Picco, Fernando Garcia-Moreno, Thomas Woolley, Philip Maini, Zoltan Molnar

 

From jamming to collective cell migration through a boundary induced transition. Oleksandr Chepizhko, Maria Chiara Lionetti, Chiara Malinverno, Giorgio Scita, Stefano Zapperi, Caterina A. M. La Porta

 

 

Stochastic simulation of pattern formation in growing tissue: a multilevel approach. Stefan Engblom

 

Self-organization principles of intracellular pattern formation. Jacob Halatek, Fridtjof Brauns, Erwin Frey

 

Modeling cell-substrate de-adhesion dynamics under fluid shear. Renu Maan, Gautam I Menon, Pramod A Pullarkat

 

Theory of Morphogenesis. Andrey Minarsky, Nadya Morozova, Robert Penner, Christophe Soule

 

A mathematical model of the metabolism of a cell. Self-organization and chaos. V.I. Grytsay, I.V. Musatenko

 

 

Transition State Characteristics During Cell Differentiation. Rowan Brackston, Eszter Lakatos, Michael P.H. Stumpf

 

Riding the Cell Jamming Boundary: Geometry, Topology, and Phase of Human Corneal Endothelium. Nigel H Brookes

 

Stochasticity of cellular growth: sources, propagation and consequences. Philipp Thomas, Guillaume Terradot, Vincent Danos, Andrea Weisse

 

Statistical Inference in Cell Lineage Trees. Damien G Hicks, Terence P Speed, Mohammed Yassin, Sarah M Russell

 

Generative adversarial networks uncover epidermal regulators and predict single cell perturbations. Arsham Ghahramani, Fiona M Watt, Nicholas M Luscombe

 

Information Isometry Technique Reveals Organizational Features in Developmental Cell Lineages. Bradly John Alicea, Thomas E. Portegys, Richard Gordon

 

In silico mechanobiochemical modeling of morphogenesis in cell monolayers. Bahador Marzban, Xiao Ma, Xiaoliang Qing, Hongyan Yuan

 

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

 

Tools & resources

| Imaging etc.

 

 

Long-term live imaging of the Drosophila adult midgut reveals real-time dynamics of cell division, differentiation, and loss. Judy Martin, Erin Nicole Sanders, Paola Moreno-Roman, Shruthi Balachandra, XinXin Du, Leslie Ann Jaramillo Koyama, Lucy Erin O’Brien

 

 

Application of the Mesolens for sub-cellular resolution imaging of intact larval and whole adult Drosophila. Gail McConnell, William B. Amos

 

Brain Development: Machine Learning Analysis Of Individual Stem Cells In Live 3D Tissue. Martin Hailstone, Lu Yang, Dominic Waithe, Tamsin J. Samuels, Yoav Arava, Tomasz Dobrzycki, Richard M. Parton, Ilan Davis

 

Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging. Adam K Glaser, Ye Chen, Chengbo Yin, Linpeng Wei, Lindsey Barner, Nicholas Reder, Jonathan Liu

 

Forget Pixels: Adaptive Particle Representation of Fluorescence Microscopy Images. Bevan L. Cheeseman, Ulrik Günther, Mateusz Susik, Krzysztof Gonciarz, Ivo F. Sbalzarini

 

Image-based methods for phenotyping growth dynamics and fitness in Arabidopsis thaliana. Francois Vasseur, George Wang, Justine Bresson, Rebecca Schwab, Detlef Weigel

 

Mid-infrared optoacoustic microscopy with label-free chemical contrast in living cells and tissues. Miguel A. Pleitez, Asrar Ali Khan, Josefine Reber, Andriy Chmyrov, Markus Seeger, Marcel Scheideler, Stephan Herzig, Vasilis Ntziachristos

 

High Numerical Aperture Epi-illumination Selective Plane Illumination Microscopy. Bin Yang, Yina Wang, Siyu Feng, Veronica Pessino, Nico Stuurman, Bo Huang

 

Imaging the Developing Heart: Synchronized Timelapse Microscopy During Developmental Changes. Carl J. Nelson, Charlotte Buckley, John J. Mullins, Martin A. Denvir, Jonathan Taylor

 

4D blood flow mapping using SPIM-microPIV in the developing zebrafish heart. Vytautas Zickus, Jonathan M. Taylor

 

Quantitative mapping of fluorescently tagged cellular proteins using FCS-calibrated four dimensional imaging. Antonio Z Politi, Yin Cai, Nike Walther, M. Julius Hossain, Birgit Koch, Malte Wachsmuth, Jan Ellenberg

 

ChromoTrace: Reconstruction of 3D Chromosome Configurations by Super-Resolution Microscopy. Carl Barton, Sandro Morganella, Oeyvind Oedegaard, Stephanie Alexander, Jonas Ries, Tomas Fitzgerald, Jan Ellenberg, Ewan Birney

 

Estimating numbers of fluorescent molecules in single cells by analysing fluctuations in photobleaching. Elco Bakker, Peter S. Swain

 

Using Deep Learning for Segmentation and Counting within Microscopy Data. Carlos X. Hernández, Mohammad M. Sultan, Vijay S. Pande

 

 

High-quality ultrastructural preservation using cryofixation for 3D electron microscopy of genetically labeled tissues. Tin Ki Tsang, Eric A Bushong, Daniela Boassa, Junru Hu, Benedetto Romoli, Sebastien Phan, Davide Dulcis, Chih-Ying Su, Mark H Ellisman

 

| Genome tools

In vivo CRISPR-Cas gene editing with no detectable genome-wide off-target mutations. Pinar Akcakaya, Maggie L. Bobbin, Jimmy A. Guo, Jose Malagon Lopez, M. Kendell Clement, Sara P. Garcia, Mick D. Fellows, Michelle J. Porritt, Mike A. Firth, Alba Carreras, Tania Baccega, Frank Seeliger, Mikael Bjursell, Shengdar Q. Tsai, Nhu T. Nguyen, Roberto Nitsch, Lorenz Mayr, Luca Pinello, Mohammad Bohlooly-Y, Martin J. Aryee, Marcello Maresca, J. Keith Joung

 

No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice. Vivek Iyer, Katharina Boroviak, Mark Thomas, Brendan Doe, Edward Ryder, David Adams

 

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

 

 

Highly efficient CRISPR/Cas9-mediated tissue specific mutagenesis in Drosophila. Amy R Poe, Bei Wang, Maria L Sapar, Hui Ji, Kailyn Li, Tireniolu Onabajo, Rushaniya Fazliyeva, Mary Gibbs, Yue Qiu, Yuzhao Hu, Chun Han

 

Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence repair outcome. Eirini M Kallimasioti-Pazi, Keerthi Thelakkad Chathoth, Gillian C Taylor, Alison Meynert, Tracy Ballinger, Martijn J Kelder, Sebastien Lalevee, Ildem Sanli, Robert Feil, Andrew J Wood

 

Machine learning of stem cell identities from single-cell expression data via regulatory network archetypes. Patrick S. Stumpf, Ben D. MacArthur

 

Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing. Edwin A. Solares, Mahul Chakraborty, Danny E. Miller, Shannon Kalsow, Kate E. Hall, Anoja G. Perera, J.J. Emerson, R. Scott Hawley

 

High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing. Danny E. Miller, Cynthia Staber, Julia Zeitlinger, R. Scott Hawley

 

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci. Jingtao Lilue, Anthony G Doran, Ian T Fiddes, Monica Abrudan, Joel Armstrong, Ruth Bennett, William Chow, Joanna Collins, Anne Czechanski, Petr Danecek, Mark Diekhans, Dirk-Dominic Dolle, Matt Dunn, Richard Durbin, Dent Earl, Anne Ferguson-Smith, Paul Flicek, Jonathan Flint, Adam Frankish, Beiyuan Fu, Mark Gerstein, James Gilbert, Leo Goodstadt, Jennifer Harrow, Kerstin Howe, Mikhail Kolmogorov, Stefanie Koenig, Chris Lelliott, Jane Loveland, Richard Mott, Paul Muir, Fabio Navarro, Duncan Odom, Naomi Park, Sarah Pelan, Son K Phan, Michael Quail, Laura Reinholdt, Lars Romoth, Lesley Shirley, Cristina Sisu, Marcela Sjoberg-Herrera, Mario Stanke, Charles Steward, Mark Thomas, Glen Threadgold, David Thybert, James Torrance, Kim Wong, Jonathan Wood, Fengtang Yang, David J Adams, Benedict Paten, Thomas M Keane

 

Programmable single and multiplex base-editing in Bombyx mori using RNA-guided cytidine deaminases. Qingyou Xia, Yufeng Li, Sanyuan Ma, Le Sun, Tong Zhang, Jiasong Chang, Wei Lu, Xiaoxu Chen, Yue Liu, Xiaogang Wang, Run Shi, Ping Zhao

 

A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. Christian Pflueger, Dennis Tan, Tessa Swain, Trung Viet Nguyen, Jahnvi Pflueger, Christian Nefzger, Jose M Polo, Ethan Ford, Ryan Lister

 

Addressing the looming identity crisis in single cell RNA-seq. Megan Crow, Anirban Paul, Sara Ballouz, Z. Josh Huang, Jesse Gillis

 

Enhancing resolution of natural methylome reprogramming behavior in plants. Robersy Sanchez, Xiaodong Yang, Hardik Kundariya, Jose Raul Barreras, Yashitola Wamboldt, Sally Mackenzie

 

Verified the effectiveness of AsCpf1 system in a variety of vertebrate species. Zhuo Li, Zhaoying Shi, Nana Fan, Yongqiang Chen, Jing Guo, Jingchun Wu, Hong Song, Shilong Chu, Kunlun Mo, Bentian Zhao, Zhen Ouyang, Dandan Tian, Shaoyang Zhao, Jieying Zhu, Jiekai Chen, Yonglong Chen, Liangxue Lai, Duanqing Pei

 

CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity. Houxiang Zhu, Chun Liang

 

CONSTRUCTION OF WHOLE GENOMES FROM SCAFFOLDS USING SINGLE CELL STRAND-SEQ DATA. Mark Hills, Ester Falconer, Kieran O’Neil, Ashley Sanders, Kerstin Howe, Victor Guryev, Peter M Lansdorp

 

Cas-CLIP: a method for customizing pooled CRISPR libraries. Jiyeon Kweon, Da-eun Kim, An-Hee Jang, Yongsub Kim

 

TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses. Christine Tranchant-Dubreuil, Sebastien Ravel, Cecile Monat, Gautier Sarah, Abdoulaye Diallo, Laura Helou, Alexis Dereeper, Ndomassi Tando, Julie Orjuela-Bouniol, Francois Sabot

 

An Interpretable Framework for Clustering Single-Cell RNA-Seq Datasets. Jesse M Zhang, Jue Fan, H. Christina Fan, David Rosenfeld, David N. Tse

 

Research practice & education

Gender balance in time-keeping at life science conferences. Petra Edlund, Erin M Tranfield, Vera van Noort, Karen Siu Ting, Sofia Tapani, Johanna Hoog

 

Building a local community of practice in scientific programming for Life Scientists. Sarah L.R. Stevens, Mateusz Kuzak, Carlos Martinez, Aurelia Moser, Petra M. Bleeker, Marc Galland

 

The impact on authors and editors of introducing Data Availability Statements at Nature journals. Rebecca Grant, Iain Hrynaszkiewicz

 

Intellectual Synthesis in Mentorship Determines Success in Academic Careers. Jean F Lienard, Titipat Achakulwisut, Daniel E Acuna, Stephen V David

 

Reproducible big data science: A case study in continuous FAIRness. Ravi K Madduri, Kyle Chard, Mike D’Arcy, Segun C Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric W Deutsch, Cory Funk, Ben Heavner, Matthew Richards, Paul Shannon, Ivo Dinov, Gustavo Glusman, Nathan Price, John D Van Horn, Carl Kesselman, Arthur W Toga, Ian Foster

 

Twenty steps towards an adequate inferential interpretation of p-values. Norbert Hirschauer​, Sven Grüner​, Oliver Mußhoff, Claudia Becker

 

Sci-Hub provides access to nearly all scholarly literature. Daniel S Himmelstein, Ariel R Romero, Jacob G Levernier, Thomas A Munro, Stephen R McLaughlin, Bastian Greshake Tzovaras, Casey S Greene

 

Sharing is not erring: Pseudo-reciprocity in collective search. Imen Bouhlel, eCharley M. Wu, Nobuyuki Hanaki, Robert L. Goldstone

 

Why not…

FGF21, a liver hormone that inhibits alcohol intake in mice, increases in human circulation after acute alcohol ingestion and sustained binge drinking at Oktoberfest. Susanna Soeberg, Emilie S. Andersen, Niels B. Dalgaard, Ida Jarlhelt, Nina L. Hansen, Nina Hoffmann, Tina Vilsboell, Anne Chenchar, Michal Jensen, Trisha J. Grevengoed, Sam A.J. Trammell, Filip K. Knop, Matthew P. Gillum

 

Biomechanics of the peafowl’s crest: a potential mechanosensory role for feathers during social display. Suzanne Amador Kane, Daniel Van Beveren, Roslyn Dakin

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