July in preprints

Our latest monthly trawl for preprints. See June’s post for background, and let us know if we missed anything

This month we found preprints on various themes in developmental biology, as well as a lot of work that we hope will be of general interest to the community.

One of July’s most talked-about preprints tackled a subject felt keenly by most scientists, let alone developmental biologists: the journal impact factor. Vincent Lariviere, Stephen Curry and colleagues from Springer, AAAS, PloS, The Royal Society, eLife and EMBO presented an alternative method to generate citation distributions. July’s tranche also features zebrafish lamination and echinoderm regeneration, a hefty dose of evo-devo,  plenty of techniques and resources, and expanded genomes for humans, flies and mice.

The preprints listed below are hosted on biorxiv, arxiv and F1000Research.

Happy preprinting!

Developmental Biology & Related

• Precision of readout at the hunchback gene. Jonathan Desponds, Huy Tran, Teresa Ferraro, Tanguy Lucas, Carmina Perez Romero, Aurelien Guillou, Cecile Fradin, Mathieu Coppey, Nathalie Dostatni, Aleksandra M Walczak
•  Nkx2.1 regulates the proliferation and cell fate of telencephalic astrocytes during embryonic development. Shilpi Minocha, Delphine Valloton, Yvan Arsenijevic,  Jean-Rene Cardinaux, Raffaella Dreier Guidi,  Jean-Pierre Hornung, Cecile Lebrand
• Independent modes of ganglion cell translocation ensure correct lamination of the zebrafish retina. Jaroslav Icha, Christiane Grunert, Mauricio Rocha-Martins, Caren Norden
• Foxc1 Controls Cell Fate Decisions During Transforming Growth Factor β Induced Epithelial to Mesenchymal Transition Through the Regulation of Fibroblast Growth Factor Receptor 1 Expression. Alexander Hopkins, Mackenzie L Coatham, Fred B Berry
• R-spondin1 regulates muscle progenitor cell fusion through control of antagonist Wnt signaling pathways. Floriane Lacour, Elsa Vezin, Florian Bentzinger, Marie-Claude Sincennes, Michael A Rudnicki, Robert D Mitchell, Ketan Patel, Marie-Christine Chaboissier, Anne-Amandine Chassot,  Fabien Le Grand
• Inhibition of cell proliferation does not slow down echinoderm neural regeneration. Vladimir Mashanov, Olga Zueva, Jose Garcia-Arraras
• Single Cell Pluripotency Regulatory Networks. Patrick S Stumpf, Rob Ewing, Ben D MacArthur
• A conceptual view at microtubule plus end dynamics in neuronal axons. André Voelzmann, Ines Hahn, Simon Pearce, Natalia P Sánchez-Soriano, Andreas Prokop
• The mitotic spindle in the one-cell C. elegans embryo is positioned with high precision and stability. Jacques Pecreaux, Stephanie Redemann, Zahraa Alayan, Benjamin Mercat, Sylvain Pastezeur, Carlos Garzon Coral, Anthony A Hyman, Jonathon Howard 
• A Dynamic Mode of Mitotic Bookmarking by Transcription Factors. Sheila S Teves, Luye An, Anders S Hansen, Liangqi Xie, Xavier Darzacq, Robert Tjian
• The genome of the crustacean Parhyale hawaiensis: a model for animal development, regeneration, immunity and lignocellulose digestion. Damian Kao, Alvina G Lai, Evangelia Stamataki, Silvana Rosic, Nikolaos Konstantinides, Erin Jarvis, Alessia Di Donfrancesco, Natalia Pouchkina-Stantcheva, Marie Semon, Marco Grillo, Heather Bruce, Suyash Kumar, Igor Siwanowicz, Andy Le, Andrew Lemire, Cassandra Extavour, William Browne, Carsten Wolff, Michalis Averof, Nipam H Patel, Peter Sarkies, Anastasios Pavlopoulos, Aziz Aboobaker
• Transition from environmental to partial genetic sex determination in Daphnia through the evolution of a female-determining incipient W-chromosome. Celine M. O. Reisser, Dominique Fasel, Evelin Hurlimann, Marinela Dukic, Cathy Haag-Liautard, Virginie Thuillier, Yan Galimov, Christoph R Haag
• Deep, Staged Transcriptomic Resources for the Novel Coleopteran Models Atrachya menetriesi and Callosobruchus maculatus. Matthew Alan Benton, Nathan James Kenny, Kai Hans Conrads, Siegfried Roth, Jeremy A Lynch
• The evolutionary origin of bilaterian smooth and striated myocytes. Thibaut Brunet, Antje H. L. Fischer, Patrick R. H. Steinmetz, Antonella Lauri, Paola Bertucci, Detlev Arendt

Techniques

• Massively multiplex single-cell Hi-C. Vijay Ramani, Xinxian Deng, Kevin L Gunderson, Frank J Steemers,Christine M Disteche, William S Noble, Zhijun Duan, Jay Shendure
• Construction of thousands of single cell genome sequencing libraries using combinatorial indexing. Sarah A Vitak, Kristof A Torkenczy, Jimi L Rosenkrantz, Andrew J Fields, Lena Christiansen, Melissa H Wong, Lucia Carbone, Frank J Steemers, Andrew Adey
• Massively parallel digital transcriptional profiling of single cells. Grace X.Y. Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W. Bent, Ryan Wilson, Solongo B. Ziraldo, Tobias D. Wheeler, Geoff P. McDermott, Junjie Zhu, Mark T. Gregory, Joe Shuga, Luz Montesclaros, Donald A Masquelier, Stefanie Y. Nishimura, Michael Schnall-Levin, Paul W Wyatt, Christopher M. Hindson, Rajiv Bharadwaj, Alexander Wong, Kevin D. Ness, Lan W. Beppu, Joachim Deeg, Christopher McFarland, Keith R. Loeb, William J. Valente, Nolan G. Ericson, Emily A. Stevens, Jerald P. Radich, Tarjei S. Mikkelsen, Benjamin J. Hindson, Jason H Bielas
• Rapidly evolving homing CRISPR barcodes. Reza Kalhor, Prashant Mali, George M Church
• Genome Editing With Targeted Deaminases. Luhan Yang, Adrian Briggs, Wei Leong Chew, Prashant Mali, Marc Guell, John Aach, Daniel Goodman, David Cox, Yinan Kan, Emal Lesha, Venkataramanan Soundararajan, Feng Zhang, George Church
• Bright photoactivatable fluorophores for single-molecule imaging. Luke D Lavis, Jonathan B Grimm, Brian P English, Heejun Choi, Anand K Muthusamy, Brian P Mehl, Peng Dong, Timothy A Brown, Jennifer Lippincott-Schwartz, Zhe Liu, Timothée Lionnet
• In vivo mapping of tissue- and subcellular-specific proteomes in Caenorhabditis elegans. Aaron W Reinke, Raymond Mak, Emily R Troemel, Eric J Bennett
• iDamIDseq and iDEAR: An improved method and a computational pipeline to profile chromatin-binding proteins of developing organisms. Jose Arturo Gutierrez-Triana, Juan Mateo, David Ibberson, Joachim Wittbrodt
• RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods. Aliaksei Z Holik, Charity W Law, Ruijie Liu, Zeya Wang, Wenyi Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, Gordon K Smyth, Matthew E Ritchie
• Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies. Lilah Toker, Min Feng, Paul Pavlidis
• Ingested double-stranded RNA and their mobile RNA derivatives have different requirements for gene silencing in C. elegans. Pravrutha Raman, Soriayah Zaghab, Edward Traver, Antony Jose

In Silico Modelling/Tools/Stats

• Hydrodynamic theory of tissue shear flow. Marko Popović, Amitabha Nandi, Matthias Merkel, Raphaël Etournay, Suzanne Eaton, Frank Jülicher, Guillaume Salbreux
• Triangles bridge the scales: how cellular processes cause tissue deformation. Matthias Merkel, Raphaël Etournay, Marko Popović, Guillaume Salbreux, Suzanne Eaton, Frank Jülicher
• Chaotic propagation of spatial cytoskeletal instability modulates integrity of podocyte foot processes. Cibele V Falkenberg, Evren U Azeloglu, Mark Stothers, Thomas J Deerinck, Yibang Chen, John C He, Mark H. Ellisman, James C. Hone, Ravi Iyengar, Leslie M. Loew
•  Information Isometry Technique Reveals Organizational Features in Developmental Cell Lineages. Bradly John Alicea, Thomas E. Portegys, Richard Gordon
• Stem Cell Networks. Eric Werner
• Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks. Tanja Muetze, Ivan H. Goenawan, Heather L. Wiencko, Manuel Bernal-Llinares, Kenneth Bryan, David J. Lynn
• AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. Mike Kucera, Ruth Isserlin, Arkady Arkhangorodsky, Gary D. Bader
• A statistical definition for reproducibility and replicability. Prasad Patil, Roger D. Peng, Jeffrey Leek

Genomics

• Deep Sequencing of 10,000 Human Genomes. Amalio Telenti, Levi T Pierce, William H Biggs, Julia di Iulio, Emily H.M. Wong, Martin M Fabani, Ewen F Kirkness, Ahmed Moustafa, Naisha Shah, Chao Xie, Suzanne C Brewerton, Nadeem Bulsara, Chad Garner, Gary Metzker, Efren Sandoval, Brad A Perkins, Franz J Och, Yaron Turpaz, J. Craig Venter
• Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation, and homozygous truncating mutations. Thomas Keane, Anthony Doran, David Adams, Kent Hunter,Jonathan Flint, Kim Wong
• A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus. Justin B Lack, Jeremy D Lange, Alison B Tang, Russell B Corbett-Detig, John E Pool
• Stable C. elegans chromatin domains separate broadly expressed and developmentally regulated genes. Kenneth J Evans, Ni Huang, Przemyslaw Stempor, Michael A Chesney, Thomas A Down,  Julie Ahringer
• Functional and non-functional classes of peptides produced by long non-coding RNAs. Jorge Ruiz-Orera, Pol Verdaguer-Grau, José Luis Villanueva-Cañas, Xavier Messeguer, M Mar Albà

Publishing

• A simple proposal for the publication of journal citation distributions. Vincent Lariviere,  Veronique Kiermer,  Catriona J MacCallum,  Marcia McNutt,  Mark Patterson,  Bernd Pulverer,  Sowmya Swaminathan,  Stuart Taylor, Stephen Curry

(4 votes)

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