April in preprints
Posted by the Node, 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.
bioRxiv just passed 10,000 papers! :-)
Huge thanks to all involved https://t.co/xfNeiSBk3v pic.twitter.com/BQhIohafNX— Richard Sever (@cshperspectives) April 21, 2017
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
| 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
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
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
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
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
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
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
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
| 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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