the community site for and by
developmental and stem cell biologists

April in preprints

Posted by , on 9 May 2017

Our latest monthly trawl for developmental biology (and other cool) preprints. See June’s introductory post for background, and let us know if we missed anything


 

At the end of April, life science preprinting received a boost with the news that the Chan Zuckerberg Initiative will provide funding for the main preprint server, bioRxiv, which had the week before celebrated hosting its 10,000th article.

 

 

And a good month for bioRxiv was also a good month for developmental biology (and related) preprints. This month we found 115 preprints covering coral regeneration, spider development, a root-on-a-chip, a lot of discussion about publishing in our ‘Research Practise’ section, and a range of stem cell and cell biology, hosted on bioRxiv, F1000Research, 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

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

 

 

Developmental biology

| Patterning & signalling

An Embryonic System To Assess Wnt Transcriptional Targets. Jahnavi Suresh, Nathan Harmston, Ka Keat Lim, Prameet Kaur, Helen Jingshu Jin, Jay B. Lusk, Enrico Petretto, Nicholas S. Tolwinski

 

C. elegans Flavin Monooxygenases Regulate C. elegans Axon Guidance and Growth Cone Protrusion with UNC-6/Netrin signaling and Rac GTPases. Mahekta R. Gujar, Aubrie M. Stricker, Erik A. Lundquist

 

TGF(beta) Mediated Structural Remodeling Facilitates Optic Fissure Fusion And The Necessity Of BMP Antagonism In This Process. Max D. Knickmeyer, Juan L. Mateo, Priska Eckert, Eleni Roussa, Belal Rahhal, Aimee Zuniga, Kerstin Krieglstein, Joachim Wittbrodt, Stephan Heermann

 

Alternative cleavage of a bone morphogenetic protein (BMP) produces ligands with distinct developmental functions and receptor preference. Edward N Anderson, Kristi A Wharton

 

MCAM controls cell autonomous polarity in myogenic and chondrogenic differentiation. Artal Moreno-Fortuny, Laricia Bragg, Giulio Cossu, Urmas Roostalu

 

Cardiomyocyte cell shape and heart morphology in ncx1 mutants, from Chen, et al’s preprint.

 

The Calcineurin-FoxO-MuRF1 Signaling Pathway Regulates Myofibril Integrity in Cardiomyocytes. Jau-Nian Chen, Hirohito Shimizu, Adam D Langenbacher, Jie Huang, Kevin Wang, Georg Otto, Robert Geisler, Yibin Wang

 

Secretogranin-II Plays A Critical Role In Zebrafish Neurovascular Modeling. Binbin Tao, Hongling Hu, Kimberly Mitchell, Ji Chen, Haibo Jia, Zuoyan Zhu, Vance Trudeau, Wei Hu

 

Sympathetic Nerve Activity Promotes Cardiomyocyte Cell-Cycle Arrest And Binucleation. Li Chen, Alexander Y Payumo, Kentaro Hirose, Rachel B. Bigley, Jonathan Lovas, Rejji Kuruvilla, Guo N. Huang

 

| Morphogenesis & mechanics

Par3/Baz levels control epithelial folding at actomyosin-enriched compartmental boundaries. Jose M Urbano, Huw W Naylor, Elena Scarpa, Leila Muresan, Bénédicte Sanson

 

Diagramming forces and tissue movements in Xenopus morphogenesis, from Shook, et al’s preprint

 

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

 

Cells From The Same Lineage Switch From Reduction To Enhancement Of Size Variability In Arabidopsis Sepals. Satoru Tsugawa, Nathan Hervieux, Daniel Kierzkowski, Anne-Lise Routier-Kierzkowska, Aleksandra Sapala, Olivier Hamant, Richard S. Smith, Adrienne H. K. Roeder, Arezki Boudaoud, Chun-Biu Li

 

Auxin depletion and gene expression, from Caggiano, et al’s preprint

 

Cell type boundaries organize plant development. Monica Pia Caggiano, Xiulian Yu, Neha Bhatia, André Larsson, Hasthi Ram, Carolyn K Ohno, Pia Sappl, Elliot M Meyerowitz, Henrik Jönsson, Marcus G Heisler

 

Microtubule structures in tubulin mutant worms from Zheng, et al’s manuscript

 

Distinct effects of tubulin isotype mutations on neurite growth in Caenorhabditis elegans. Chaogu Zheng, Margarete Diaz-Cuadros, Susan Laura Jao, Ken Nguyen, David H Hall, Martin Chalfie

 

Myomerger Induces Fusion Of Non-Fusogenic Cells And Is Required For Myoblast Fusion. Malgorzata Quinn, Qingnian Goh, Mitsutoshi Kurosaka, Dilani Gamage, Michael Petrany, Vikram Prasad, Douglas Millay

 

| Genes & genomes

Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos. Shai Joseph, Mate Palfy, Lennart Hilbert, Mukesh Kumar, Jens Karschau, Vasily Zaburdaev, Andrej Shevchenko, Nadine Vastenhouw

 

Comprehensive Characterization Of The Complex Lola Locus Reveals A Novel Role In The Octopaminergic Pathway Via Tyramine Beta-Hydroxylase Activation. Nadja Dinges, Violeta Morin, Nastasja Kreim, Tony Southall, Jean-Yves Roignant

 

Genomic and chromatin features shaping meiotic double-strand break formation and repair in mice. Shintaro Yamada, Seoyoung Kim, Sam E Tischfield, Julian Lange, Maria Jasin, Scott Keeney

 

Wild type and mutant Drosophila testes from Yamashita and Lu’s preprint

 

Germ cell connectivity enhances cell death in response to DNA damage in Drosophila testis. Yukiko M Yamashita, Kevin L Lu

 

The G-box transcriptional regulatory code in Arabidopsis. Daphne Ezer, Samuel JK Shepherd, Anna Brestovitsky, Patrick Dickinson, Sandra Cortijo, Varodom Charoensawan, Mathew S Box, Surojit Biswas, Philip Wigge

 

Cross-talk between active DNA demethylation, resetting of cellular metabolism and shoot apical growth in poplar bud break. Daniel Conde, Mariano Perales, Anne-Laure Le Gac, Christopher Dervinis, Matias Kirst, Stephane Maury, Pablo Gonzalez-Melendi, Isabel Allona

 

The ‘Hawaiian Skirt’ Arabidopsis mutant, from Lang, et al’s preprint

 

A Role For The F-Box Protein HAWAIIAN SKIRT In Plant miRNA Function. Patricia Lang, Michael Christie, Ezgi Dogan, Rebecca Schwab, Joerg Hagmann, Anna-Lena Van de Weyer, Detlef Weigel

 

Sequence Features Of MADS-Domain Proteins That Act As Hubs In The Protein-Protein Interaction Network Controlling Flower Development. Florian Ruempler, Guenter Theissen, Rainer Melzer

 

Ubx in the Drosophila embryo, from Crocker, et al’s preprint

 

Nuclear Microenvironments Modulate Transcription From Low-Affinity Enhancers. Justin Crocker, Albert Tsai, Anand K Muthusamy, Luke D Lavis, Robert H Singer, David L Stern

 

Genetical genomics reveals Ras/MAPK modifier loci. Mark G. Sterken, Linda Van Bemmelen van der Plaat, Joost A.G. Riksen, Miriam Rodriguez, Tobias Schmid, Alex Hajnal, Jan E. Kammenga, Basten L. Snoek

 

5-Hydroxymethylcytosine Is Highly Dynamic Across Human Fetal Brain Development. Helen Spiers, Eilis Hannon, Leonard Schalkwyk, Nicholas Bray, Jonathan Mill

 

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

 

Transcription Activation Of Early Human Development Suggests DUX4 As An Embryonic Regulator. Virpi Töhönen, Shintaro Katayama, Liselotte Vesterlund, Mona Sheikhi, Liselotte Antonsson, Giuditta Filippini-Cattaneo, Marisa Jaconi, Anna Johnsson, Sten Linnarsson, Outi Hovatta, Juha Kere

 

Extensive alternative splicing transitions during postnatal skeletal muscle development are required for Ca2+ handling. Tom Cooper

 

| Stem cells, regeneration & disease modelling

Morphogen And Community Effects Determine Cell Fates In Response To BMP4 Signaling In Human Embryonic Stem Cells. Anastasiia Nemashkalo, Albert Ruzo, Idse Heemskerk, Aryeh Warmflash

 

Knocking down 21 phosphatases and assaying the effects on keratinocyte colony growth, from Mishra, et al’s preprint

 

A protein phosphatase network controls temporal and spatial dynamics of differentiation commitment in human epidermis. Ajay Mishra, Angela Oliveira Pisco, Benedicte Oules, Tony Ly, Kifayathullah Liakath-Ali, Gernot Walko, Priyalakshmi Viswanathan, Jagdeesh Nijjher, Sara-Jane Dunn, Angus I Lamond, Fiona M Watt

 

The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during trophectoderm and inner cell mass specification. Daosheng Huang, Xiaoping Han, Ping Yuan, Amy Ralston, Lingang Sun, Mikael Huss, Tapan Mistri, Luca Pinello, Huck Hui Ng, Guocheng Yuan, Junfeng Ji, Janet Rossant, Paul Robson, Guoji Guo

 

A lncRNA/Lin28/Let7 Axis Coupled To DNA Methylation Fine Tunes The Dynamics Of A Cell State Transition. Meng Amy Li, Paulo P. Amaral, Priscilla Cheung, Jan H. Bergmann, Masaki Kinoshita, Tuzer Kalkan, Meryem Ralser, Sam Robson, Ferdinand von Meyenn, Maike Paramor, Fengtang Yang, Caifu Chen, Jennifer Nichols, David L. Spector, Tony Kouzarides, Lin He, Austin Smith

 

Getting to the same destination but taking a different journey, from Briggs, et al’s preprint

 

Mouse embryonic stem cells can differentiate via multiple paths to the same state. James Alexander Briggs, Victor C Li, Seungkyu Lee, Clifford J Woolf, Allon Klein, Marc W Kirschner

 

Pervasive Discordance Between mRNA And Protein Expression During Embryonic Stem Cell Differentiation. Patrick van den Berg, Bogdan Budnik, Nikolai Slavov, Stefan Semrau

 

Establishment In Culture Of Expanded Potential Stem Cells. Jian Yang, David Ryan, Wei Wang, Cheuk-Ho J Tsang, Guocheng Lan, Xuefei Gao, Liliana Antunes, Adam Clifford Wilkinson, Yong Yu, Aleksandra Kolodziejczyk, Lia Campos, Juexuan Wang, Fengtang Yang, Yosuke Tanaka, Melanie Eckersley-Maslin, Michael Woods, James Bussell, Ramiro Ramirez-Solis, Wolf Reik, Bertie Gottgens, Xiangang Zou, Liming Lu, Cui Wang, Hideki Masaki, Jacqui White, Hiro Nakauchi, Zheng Zhong, Sarah Teichmann, Beiyuan Fu, Zhexin Zhu, Pentao Liu

 

Fused dorsal-ventral cerebral organoids model human cortical interneuron migration. Joshua A Bagley, Daniel Reumann, Shan Bian, Juergen A. Knoblich

 

Transcription Factors Orchestrate Dynamic Interplay Between Genome Topology And Gene Regulation During Cell Reprogramming. Ralph Stadhouders, Enrique Vidal, François Serra, Bruno Di Stefano, François Le Dily, Javier Quilez, Antonio Gomez, Samuel Collombet, Clara Berenguer, Yasmina Cuartero, Jochen Hecht, Guillaume Filion, Miguel Beato, Marc A. Marti-Renom, Thomas Graf

 

Direct Conversion Of Human Fibroblasts Into Osteoblasts And Osteocytes With Small Molecules And A Single Factor, Runx2. Yanjiao Li, YaoLong Wang, Juehua Yu, Zhaoxia Ma, Qiong Bai, Xingfei Wu, Pengfei Bao, Lirong Li, Daiping Ma, Jingxue Liu, Change Liu, Fangyun Chen, Min Hu

 

 

Zebrafish skeletal preps from Bennett, et al’s preprint

 

RNA helicase, DDX27 regulates proliferation and myogenic commitment of muscle stem cells. Alexis Bennett, Marie Francoise O’Donohue, Stacey Gundry, Aye Chan, Jeffery Widrick, Isabelle Draper, Anirban Chakraborty, Yi Zhou, Leonard Zon, Pierre-Emmanuel Gleizes, Alan Beggs, Vandana Gupta

 

Constitutive Immune Activity Promotes Tumorigenesis in Drosophila Intestinal Progenitor Cells. Kristina Petkau, Silvia Guntermann, Edan Foley

 

Conservation of EMT transcription factor function in controlling pluripotent adult stem cell migration in vivo in planarians. Prasad Abnave, Ellen Aboukhatwa, Nobuyoshi Kosaka, James Thompson, Mark Hill, Aziz Aboobaker

 

Regenerating planarians from Mihaylova, et al’s preprint

 

MLL3/4 Prevents Stem Cell Hyperplasia And Controls Differentiation Programs In A Planarian Cancer Stem Cell Model. Yuliana Mihaylova, Damian Kao, Samantha Hughes, Alvina Lai, Farah Jaber-Hijazi, Nobuyoshi Kosaka, Prasad Abnave, Aziz Aboobaker

 

PHRED-1 Is A Divergent Neurexin-1 Homolog That Organizes Muscle Fibers And Patterns Organs During Regeneration. Carolyn E. Adler, Alejandro Sanchez Alvarado

 

Post-transcriptional regulation of adult CNS axonal regeneration by Cpeb1. Wilson Pak-Kin Lou, Alvaros Mateos, Marta Koch, Stefan Klussmann, Chao Yang, Na Lu, Stefanie Limpert, Manuel Göpferich, Marlen Zschaetzsch, Carlos Maillo, Elena Senis, Dirk Grimm, Raúl Méndez, Kai Liu, Bassem A Hassan, Ana Martin-Villalba

 

Some stressed out coral from Boness, et al’s preprint

 

Exposure to elevated sea-surface temperatures below the bleaching threshold impairs coral recovery and regeneration following injury. Joshua Louis Boness, William Leggat, Tracy Danielle Ainsworth

 

Necroptosis promotes the Aging of the Male Reproductive System in Mice. Xiaodong Wang, Dianrong Li, Lingjun Meng, Tao Xu, Yaning Su, Xiao Liu, Zhiyuan Zhang

 

Tissue-specific downregulation of EDTP removes polyglutamine protein aggregates and extends lifespan in Drosophila. Chengfeng Xiao, Shuang Qiu, R Meldrum Robertson, Laurent Seroude

 

Reversal of cardiac and skeletal manifestations of Duchenne muscular dystrophy by cardiosphere-derived cells and their exosomes in mdx dystrophic mice and in human Duchenne cardiomyocytes. Mark A Aminzadeh, Russell G Rogers, Kenneth Gouin, Mario Fournier, Rachel E Tobin, Xuan Guan, Martin K Childers, Allen M Andres, David J Taylor, Ahmed Ibrahim, Xiang-ming Ding, Angelo Torrente, Joshua I Goldhaber, Ronald A Victor, Roberta A Gottlieb, Michael Lewis, Eduardo Marban

 

PERTURBATION OF PTEN-PI3K/AKT SIGNALLING IMPAIRED AUTOPHAGY MODULATION IN DYSTROPHIN-DEFICIENT MYOBLASTS. Muhammad Dain Yazid, Janet Smith

 

Modeling Zika Virus Congenital Eye Disease: Differential Susceptibility of Fetal Retinal Progenitor Cells and iPSC-Derived Retinal Stem Cells to Zika Virus Infection. Deisy Contreras, Melissa Jones, Laura E Martinez, Vineela Gangalapudi, Jie Tang, Ying Wu, Jiagang J. Zhao, Zhaohui Chen, Shaomei Wang, Vaithilingaraja Arumugaswami

 

Cell biology

Astral microtubule dynamics regulate anaphase oscillation onset and set a robust final position for the Caenorhabditis elegans zygote spindle. Helene Bouvrais, Laurent Chesneau, Sylvain Pastezeur, Marie Delattre, Jacques Pecreaux

 

Depletion of ANI-2 and cell division in c elegans, from Goupil, et al’s preprint

 

Anillin proteins stabilize the cytoplasmic bridge between the two primordial germ cells during C. elegans embryogenesis. Eugenie Goupil, Rana Amini, Jean-Claude Labbe

 

Local Nucleation Of Microtubule Bundles Through Tubulin Concentration Into A Condensed Tau Phase. Amayra Hernández-Vega, Marcus Braun, Lara Scharrel, Marcus Jahnel, Susanne Wegmann, Bradley T. Hyman, Simon Alberti, Stefan Diez, Anthony A. Hyman

 

An Arf6- And Caveolae-Dependent Pathway Links Hemidesmosome Remodeling And Mechanoresponse. Naël Osmani, Julien Pontabry, Jordi Comelles, Nina Fekonja, Jacky G Goetz, Daniel Riveline, Elisabeth Georges-Labouesse, Michel Labouesse

 

Cell size sensing in animal cells coordinates growth rates and cell cycle progression to maintain cell size uniformity. Miriam Bracha Ginzberg, Nancy Chang, Ran Kafri, Marc W Kirschner

 

Scc2-Mediated Loading Of Cohesin Onto Chromosomes In G1 Yeast Cells Is Insufficient To Build Cohesion During S Phase. Kim Nasmyth

 

Gradients Of Rac1 Nanoclusters Support Spatial Patterns Of Rac1 Signaling. Amanda Remorino, Simon De Beco, Fanny Cayrac, Fahima Di Federico, Gaetan Cornilleau, Alexis Gautreau, Maria Carla Parrini, Jean-Baptiste Masson, Maxime Dahan, Mathieu Coppey

 

Chytrid zoospores from Fritz-Laylin, et al’s preprint

 

WASP and SCAR are evolutionarily conserved in actin-filled pseudopod-based motility. Lillian K. Fritz-Laylin, Samuel J. Lord, R. Dyche Mullins

 

Optogenetic Control of RhoA Reveals Zyxin-mediated Elasticity of Stress Fibers. Patrick W Oakes, Elizabeth Wagner, Christoph A Brand, Dimitri Probst, Marco Linke, Ulrich S Schwarz, Michael Glotzer, Margaret L Gardel

 

MDCK cell acini from Fessenden, et al’s preprint

 

Formin-Dependent Adhesions Are Required For Invasion By Epithelial Tissues. Tim B Fessenden, Yvonne Beckham, Mathew Perez-Neut, Aparajita H Chourasia, Kay F Macleod, Patrick W Oakes, Margaret L Gardel

 

Fast Activation Cycles Of Rac1 At The Lamellipodium Tip Trigger Membrane Protrusion. Amine Mehidi, Olivier Rossier, Anael Chazeau, Fabien Biname, Amanda Remorino, Mathieu Coppey, Zeynep Karatas, Jean-Baptiste Sibarita, Violaine Moreau, Gregory Giannone

 

Combinatorial Regulation Of The Balance Between Dynein Microtubule End Accumulation And Initiation Of Directed Motility. Rupam Jha, Johanna Roostalu, Martina Trokter, Thomas Surrey

 

The Ndc80 complex targets Bod1 to human mitotic kinetochores. Katharina Schleicher, Sara ten Have, Iain M Porter, Jason R Swedlow

 

Dynactin Binding To Tyrosinated Microtubules Promotes Centrosome Centration In C. Elegans By Enhancing Dynein-Mediated Organelle Transport. Daniel J. Barbosa, Joana Duro, Dhanya K. Cheerambathur, Bram Prevo, Ana X. Carvalho, Reto Gassmann

 

Long-Term Memory In The Migration Movements Of Enucleated Amoeba proteus. Carlos Bringas, Iker Malaina, Alberto Perez-Samartin, Maria Dolores Boyano, Maria Fedetz, Gorka Perez-Yarza, Jesus Cortes, Ildefonso Martinez de la Fuente

 

Do gametes woo? Evidence for non-random unions at fertilization. Joseph H Nadeau

 

 

Modelling

Pairwise hybrid incompatibilities dominate allopatric speciation for a simple biophysical model of development. Bhavin S Khatri, Richard Goldstein

 

A model for autonomous and non-autonomous effects of the Hippo pathway in Drosophila. Jia Gou, Lin Lin, Hans G Othmer

 

Single-Cell Genome Dynamics in Early Embryo Development: A Statistical Thermodynamics Approach. Alessandro Giuliani, Masa Tsuchiya, Kenichi Yoshikawa

 

On The Principles Of Cell Decision-Making: Intracellular Coupling Improves Cell Responses Fidelity Of Noisy Signals. Andreas Reppas, Eduard Jorswieck, Haralampos Hatzikirou

 

Correlating Cell Shape and Cellular Stress in Motile Confluent Tissues. Xingbo Yang, Dapeng Bi, Michael Czajkowski, Matthias Merkel, M. Lisa Manning, M. Cristina Marchetti

 

 

Evo-devo & evo

apterous A Specifies Dorsal Wing Patterns And Sexual Traits In Butterflies. Anupama Prakash, Antonia Monteiro

 

Butterfly wings from Bhardwaj, et al’s preprint

 

Sex Differences In 20-Hydroxyecdysone Hormone Levels Control Sexual Dimorphism In Bicyclus anynana Butterfly Wing Patterns. Shivam Bhardwaj, Kathleen L Prudic, Ashley Bear, Mainak Das Gupta, Bethany R Wasik, Xiaoling Tong, Wei Fun Cheong, Markus R Wenk, Antonia Monteiro

 

A practical guide to CRISPR/Cas9 genome editing in Lepidoptera. Linlin Zhang, Robert Reed

 

Tracking BMP activity in spider embryos, from Pechmann, et al’s preprint

 

A novel role for Ets4 in axis specification and cell migration in the spider Parasteatoda tepidariorum. Matthias Pechmann, Matthew Alan Benton, Nathan James Kenny, Nico Posnien, Siegfried Roth

 

Evolution And Multiple Roles Of The Pancrustacea Specific Transcription Factor zelda In Insects. Lupis Ribeiro, Vitoria Tobias-Santos, Danielle Santos, Felipe Antunes, Georgia Feltran, Jackson de Souza Menezes, L Aravind, Thiago M Venancio, Rodrigo Nunes da Fonseca

 

Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Alex S Flynt, Alexandra Panzarino, Md Mosharrof Hossain Mondal, Adam Siepel, Jaaved Mohammed, Eric Lai

 

Tools & resources

Single Molecule Fluorescence In Situ Hybridisation For Quantitating Post-Transcriptional Regulation In Drosophila Brains. Lu Yang, Josh Titlow, Darragh Ennis, Carlas Smith, Jessica Mitchell, Florence L. Young, Scott Waddell, David Ish-Horowicz, Ilan Davis

 

A Versatile Compressed Sensing Scheme For Faster And Less Phototoxic 3D Fluorescence Microscopy. Maxime Woringer, Xavier Darzacq, Christophe Zimmer, Mustafa Mir

 

Three-Dimensional Two-Photon Optogenetics And Imaging Of Neural Circuits In Vivo. Weijian Yang, Luis Carrillo-Reid, Yuki Bando, Darcy S. Peterka, Rafael Yuste

 

SpyTagging, from Pessino, et al’s preprint

 

Covalent Protein Labeling By SpyTag-SpyCatcher In Fixed Cells For Super-Resolution Microscopy. Veronica Pessino, Y. Rose Citron, Siyu Feng, Bo Huang

 

Photoacoustic molecular rulers based on DNA nanostructures. James Joseph, Philipp Koehler, Tim J. Zuehlsdorff, Daniel J Cole, Kevin N. Baumann, Judith Weber, Sarah E. Bohndiek, Silvia Hernandez-Ainsa

 

Tracking the brain of the fish as it eats, from Cong, et al’s preprint

 

Rapid Whole Brain Imaging Of Neural Activities In Freely Behaving Larval Zebrafish. Lin Cong, Zeguan Wang, Yuming Chai, Wei Hang, Chunfeng Shang, Wenbin Yang, Lu Bai, Jiulin Du, Kai Wang, Quan Wen

 

A general method to fine-tune fluorophores for live-cell and in vivo imaging. Jonathan B. Grimm, Anand K. Muthusamy, Yajie Liang, Timothy A. Brown, William C. Lemon, Ronak Patel, Rongwen Lu, John J. Macklin, Phillip J. Keller, Na Ji,Luke D. Lavis

 

Real-Time Observation Of Light-Controlled Transcription In Living Cells. Anne Rademacher, Fabian Erdel, Jorge Trojanowski, Karsten Rippe

 

FiloQuant reveals increased filopodia density during DCIS progression. Guillaume Jacquemet, Ilkka Paatero, Alexandre Carisey, Artur Padzik, Jordan Orange, Hellyeh Hamidi, Johanna Ivaska

 

 

The root-on-a-chip set up from Stanley, et al’s preprint

 

An organ-on-a-chip approach for investigating root-environment interactions in heterogeneous conditions. Claire E. Stanley, Jagriti Shrivastava, Rik Brugman, Dirk van Swaay, Guido Grossmann

 

Disabling Cas9 by an anti-CRISPR DNA mimic. Jiyung Shing, Fuguo Jiang, Jun-Jie Liu, Nicholas L Bray, Benjamin J Rauch, Seung Hyun Baik, Eva Nogales, Joseph Bondy-Denomy, Jacob E Corn, Jennifer A Doudna

 

Modulation of Genome Editing Outcomes by Cell Cycle Control of Cas9 Expression. Yuping Huang, Caitlin McCann, Andrey Samsonov, Dmitry Malkov, Greg D Davis, Qingzhou Ji

 

The WPRE Improves Genetic Engineering With Site-Specific Nucleases. Jessica M. Ong, Christopher R Brown, Matthew C. Mendel, Gregory J Cost

 

A Versatile Genetic Tool For Post-Translational Control Of Gene Expression With A Small Molecule In Drosophila melanogaster. Sachin Sethi, Jing W. Wang

 

Rapid DNA Re-Identification for Cell Line Authentication and Forensics. Sophie Zaaijer, Yaniv Erlich, Daniel Speyer, Robert Piccone, Assaf Gordon

 

Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing. Andrew M Smith, Miten Jain, Logan Mulroney, Daniel R Garalde, Mark Akeson

 

Single-cell analysis of clonal dynamics in direct lineage reprogramming: a combinatorial indexing method for lineage tracing. Brent A Biddy, Sarah E Waye, Tao Sun, Samantha A Morris

 

Nanopore sequencing and assembly of a human genome with ultra-long reads. Miten Jain, Sergey Koren, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes, Sunir Malla, Hannah Marriott, Karen H Miga, Tom Nieto, Justin O’Grady, Hugh E Olsen, Brent S Pedersen, Arang Rhie, Hollian Richardson, Aaron Quinlan, Terrance P Snutch, Louise Tee, Benedict Paten, Adam M. Phillippy, Jared T Simpson, Nicholas James Loman, Matthew Loose

 

Beyond The Linear Genome: Comprehensive Determination Of The Endogenous Circular Elements In C. elegans And Human Genomes Via An Unbiased Genomic-Biophysical Method. Massa Shoura, Idan Gabdank, Loren Hansen, Jason Merker, Jason Gotlib, Stephen Levene, Andrew Fire

 

Expression of short hairpin RNAs using the compact architecture of retroviral microRNA genes. James M Burke, Rodney P. Kincaid, Francesca Aloisio, Nicole Welch, Christopher S. Sullivan

 

Improved maize reference genome with single molecule technologies. Yinping Jiao, Paul Peluso, Jinghua Shi, Tiffany Liang, Michelle C Stitzer, Bo Wang, Michael Campbell, Joshua C Stein, Xuehong Wei, Chen-Shan Chin, Katherine Guill, Michael Regulski, Sunita Kumari, Andrew Olson, Jonathan Gent, Kevin L Schneider, Thomas K Wolfgruber, Michael R May, Nathan M Springer, Eric Antoniou, Richard McCombie, Gernot G Presting, Michael McMullen, Jeffrey Ross-Ibarra, R. Kelly Dawe, Alex Hastie, David R Rank, Doreen Ware

 

The Drosophila ventral nervous system from Court, et al’s preprint

 

A Systematic Nomenclature for the Drosophila Ventral Nervous System. Robert Christopher Court, James Douglas Armstrong, Jana Borner, Gwyneth Card, Marta Costa, Michael Dickinson, Carsten Duch, Wyatt Korff, Richard Mann, David Merritt, Rod Murphey, Shigehiro Namiki, Andrew Seeds, David Shepherd, Troy Shirangi, Julie Simpson, James Truman, John Tuthill, Darren Williams

 

MAPseq: Improved Speed, Accuracy And Consistency In Ribosomal RNA Sequence Analysis. Joao F Matias Rodrigues, Thomas SB Schmidt, Janko Tackmann, Christian von Mering

 

High Accuracy Base Calls in Nanopore Sequencing. Philippe Christophe Faucon, Robert Trevino, Parithi Balachandran, Kylie Standage-Beier, Xiao Wang

 

BasePlayer: Versatile Analysis Software For Large-Scale Genomic Variant Discovery. Riku Katainen, Iikki Donner, Tatiana Cajuso, Eevi Kaasinen, Kimmo Palin, Veli Mäkinen, Lauri A Aaltonen, Esa Pitkänen

 

CiliaCarta: An Integrated And Validated Compendium Of Ciliary Genes. Teunis J. P. van Dam, Julie Kennedy, Robin van der Lee, Erik de Vrieze, Kirsten A. Wunderlich, Suzanne Rix, Gerard W. Dougherty, Nils J. Lambacher, Chunmei Li, Victor L. Jensen, Michael R. Leroux, Rim Hjeij, Nicola Horn, Yves Texier, Yasmin Wissinger, Jeroen van Reeuwijk, Gabrielle Wheway, Barbara Knapp, Jan F. Scheel, Brunella Franco, Dorus A. Mans, Erwin van Wijk, François Képès, Gisela G. Slaats, Grischa Toedt, Hannie Kremer, Heymut Omran, Katarzyna Szymanska, Konstantinos Koutroumpas, Marius Ueffing, Thanh-Minh T. Nguyen, Stef J. F. Letteboer, Machteld M. Oud, Sylvia E. C. van Beersum, Miriam Schmidts, Philip L. Beales, Qianhao Lu, Rachel H. Giles, Radek Szklarczyk, Robert B. Russell, Toby J. Gibson, Colin A. Johnson, Oliver E. Blacque, Uwe Wolfrum, Karsten Boldt, Ronald Roepman, Victor Hernandez-Hernandez, Martijn A. Huynen

 

 

Research practice

Looking Into Pandora’s Box: The Content Of Sci-Hub And Its Usage. Bastian Greshake

 

Anticipated effects of an open access policy at a private foundation. Eesha Khare, Carly Strasser

 

Gender disparity in computational biology research publications. Kevin S. Bonham, Melanie I. Stefan

 

Why Do Scientists Fabricate And Falsify Data? A Matched-Control Analysis Of Papers Containing Problematic Image Duplications. Daniele Fanelli, Rodrigo Costas, Ferric C Fang, Arturo Casadevall, Elisabeth M Bik

 

Addressing the digital divide in contemporary biology: Lessons from teaching UNIX. Serghei Mangul, Lana Martin, Alexander Hoffmann, Matteo Pellegrini, Eleazar Eskin

 

The appropriation of GitHub for curation. Yu Wu​, Na Wang, Jessica Kropczynski, John M Carroll

 

The earth is flat (p>0.05): Significance thresholds and the crisis of unreplicable research. Valentin Amrhein​, Fränzi Korner-Nievergelt, Tobias Roth

 

What is open peer review? A systematic review. Tony Ross-Hellauer

 

Standardising and harmonising research data policy in scholarly publishing. Iain Hrynaszkiewicz,Aliaksandr Birukou, Mathias Astell, Sowmya Swaminathan, Amye Kenall, Varsha Khodiyar

 

TOWARDS COORDINATED INTERNATIONAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES. Warwick Anderson, Rolf Apweiler, Alex Bateman, Guntram A Bauer, Helen Berman, Judith A Blake, Niklas Blomberg, Stephen K Burley, Guy Cochrane, Valentina Di Francesco, Tim Donohue, Christine Durinx, Alfred Game, Eric Green, Takashi Gojobori, Peter Goodhand, Ada Hamosh, Henning Hermjakob, Minoru Kanehisa, Robert Kiley, Johanna McEntyre, Rowan McKibbin, Satoru Miyano, Barbara Pauly, Norbert Perrimon, Mark A Ragan, Geoffrey Richards, Yik-Ying Teo, Monte Westerfield, Eric Westhof, Paul F Lasko

 

Why not…

Caterpillars lack a resident gut microbiome. Tobin J Hammer, Daniel H Janzen, Winnifred Hallwachs, Samuel L Jaffe, Noah Fierer

 

Estimating The Extinction Date Of The Thylacine Accounting For Unconfirmed Sightings. Colin J Carlson, Alexander L Bond, Kevin R Burgio

 

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