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May in preprints

Posted by , on 5 June 2017

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


This month featured a host of preprints on plants, stem cells, connectomics and modelling. Plus the first preprint from Nobel laureate and recent Development interviewee Eric Wieschaus, an introduction to the concept of the Human Cell Atlas, and a plea from Science Editor-in-Chief Marcia McNutt and colleagues for transparency in author contributions. The preprints were 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

Plant development

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

 

Developmental biology

| Patterning & signalling

Concentration Dependent Chromatin States Induced by the Bicoid Morphogen Gradient. Colleen E Hannon, Shelby A Blythe, Eric F Wieschaus

 

Dense Bicoid Hubs Accentuate Binding along the Morphogen Gradient. Mustafa Mir, Armando Reimer, Jenna E. Haines, Xiao-Yong Li, Michael Stadler, Hernan Garcia, Michael B. Eisen, Xavier Darzacq

 

Copb2 Is Essential For Embryogenesis And Hypomorphic Mutations Cause Human Microcephaly. Andrew DiStasio, Ashley Driver, Kristen Sund, Milene Donlin, Shabnam Pooya, Beth Kline-Fath, Kenneth Kaufman, Cynthia Prows, Elizabeth Schorry, Biplab DasGupta, Rolf Stottmann

 

Hydrozoans used in Takeda, et al.’s preprint

 

Jellyfish Oocyte Maturation Inducing Hormone And Neuroendocrine Regulation Of Reproduction. Noriyo Takeda, Yota Kon, Gonzalo Quiroga Artigas, Pascal Lapébie, Carine Barreau, Osamu Koizumi, Takeo Kishimoto, Kazunori Tachibana, Evelyn Houliston, Ryusaku Deguchi

 

CRISPR/Cas9 Mutation Of A Gonad-Expressed Opsin Prevents Jellyfish Light-Induced SpawningGonzalo Quiroga Artigas, Pascal Lapébie, Lucas Leclère, Noriyo Takeda, Ryusaku Deguchi, Gáspár Jékely, Tsuyoshi Momose, Evelyn Houliston

 

Intestinal cell kinase regulates chondrocyte proliferation and maturation during skeletal development. Mengmeng Ding, Li Jin, Lin Xie, So Hyun Park, Yixin Tong, Di Wu, Zheng Fu, Xudong Li

 

Post-Transcriptional Control Of EMT Is Coordinated Through Combinatorial Targeting By Multiple microRNAs. Joseph Cursons, Katherine A. Pillman, Kaitlin Scheer,Philip A. Gregory, Momeneh Foroutan, Soroor Hediyeh Zadeh, John Toubia, Edmund J. Crampin, Gregory J. Goodall, Cameron P. Bracken, Melissa J. Davis

 

A Novel Reporter Allele For Monitoring Dll4 Expression Within The Embryonic And Adult Mouse. Alexander M. Herman, Alexander M. Rhyner, W. Patrick Devine, Sean P. Marrelli, Benoit G. Bruneau, Joshua D. Wythe

 

Human intestinal organoid from Hill, et al.’s preprint

 

Bacterial Colonization Stimulates A Complex Physiological Response In The Immature Human Intestinal Epithelium. David R. Hill, Sha Huang, Courtney Fields, Dishari Mukherjee, Brooke Bons, Shrikar Thodla, Priya H. Dedhia, Alana M. Chin, Yu-Hwai Tsai, Melinda S. Nagy, Thomas Schmidt, Seth Walk, Vincent B. Young, Jason R. Spence

 

Conserved Neural Circuit Structure Across Drosophila Larva Development Revealed By Comparative Connectomics. Stephan Gerhard, Ingrid Andrade, Richard D. Fetter, Albert Cardona, Casey M. Schneider-Mizell

 

Organization Of The Drosophila Larval Visual Circuit. Ivan Larderet, Pauline Fritsch, Nanae Gendre, Larisa Maier, Rick D. Fetter, Casey Schneider-Mizell, James Truman, Marta Zlatic, Albert Cardona, Simon Sprecher

 

Kenyon cells from a first instar fly larvae in Eichler, et al.’s preprint

 

The Complete Connectome Of A Learning And Memory Center In An Insect Brain. Katharina Eichler, Ashok Litwin-Kumar, Feng Li, Youngser Park, Ingrid Andrade, Casey M. Schneider-Mizell, Timo Saumweber, Annina Huser, Claire Eschbach, Bertram Gerber, Richard D. Fetter, James W. Truman, Carey E. Priebe, L. F. Abbott, Andreas S. Thum, Marta Zlatic, Albert Cardona

 

A Complete Electron Microscopy Volume Of The Brain Of Adult Drosophila melanogaster. Zhihao Zheng, J. Scott Lauritzen, Eric Perlman, Camenzind G. Robinson, Matthew Nichols, Daniel Milkie, Omar Torrens, John Price, Corey B. Fisher, Nadiya Sharifi, Steven A. Calle-Schuler, Lucia Kmecova, Iqbal J. Ali, Bill Karsh, Eric T. Trautman, John Bogovic, Philipp Hanslovsky, Gregory S. X. E. Jefferis, Michael Kazhdan, Khaled Khairy, Stephan Saalfeld, Richard D. Fetter, Davi D. Bock

 

Whole-Brain Serial-Section Electron Microscopy In Larval Zebrafish. David Grant Colburn Hildebrand, Marcelo Cicconet, Russel Miguel Torres, Woohyuk Choi, Tran Minh Quan, Jungmin Moon, Arthur Willis Wetzel, Andrew Scott Champion, Brett Jesse Graham, Owen Randlett, George Scott Plummer, Ruben Portugues, Isaac Henry Bianco, Stephan Saalfeld, Alex David Baden, Kunal Lillaney, Randal Burns, Joshua Tzvi Vogelstein, Alexander Franz Schier, Wei-Chung Allen Lee, Won-Ki Jeong, Jeff William Lichtman, Florian Engert

 

Skeletal Cell YAP And TAZ Redundantly Promote Bone Development By Regulation Of Collagen I Expression And Organization. Christopher D. Kegelman, Devon E. Mason, James H. Dawahare, Genevieve D. Vigil, Scott S. Howard, Teresita M. Bellido, Alexander G. Robling, Joel Boerckel

 

Neurotrophin Receptor Ntrk2b Function In The Maintenance Of Dopamine And Serotonin Neurons In Zebrafish. Madhusmita Priyadarshini Sahu, Ceren Pajanoja, Stanislav Rozov, Pertti Panula, Eero Castren

 

 

| Morphogenesis & mechanics

Cell Dynamics Underlying Oriented Growth Of The Drosophila Imaginal Wing Disc. Natalie A. Dye, Marko Popovic, Stephanie Spannl, Raphael Etournay, Dagmar Kainmueller, Eugene W. Myers, Frank Julicher, Suzanne Eaton

 

The nuclear rim and the chromatin within, from Penfield, et al.’s preprint

 

Dynein Pulling Forces On Ruptured Nuclei Counteract Lamin-Mediated Nuclear Envelope Repair Mechanisms In Vivo. Lauren Penfield, Brian Wysolmerski, Reza Farhadifar, Michael Martinez, Ronald Biggs, Hai-Yin Wu, Michael Mauro, Curtis Broberg, Daniel Needleman, Shirin Bahmanyar

 

Forces driving cell sorting in Hydra. Olivier Cochet-Escartin, Tiffany Tian Locke, Winnie H Shi, Robert E Steele, Eva-Maria S Collins

 

Endolymphatic sac inflation and deflation, from Swinburne, et al’s preprint

 

Lamellar Junctions In The Endolymphatic Sac Act As A Relief Valve To Regulate Inner Ear Pressure. Ian A. Swinburne, Kishore R. Mosaliganti, Srigokul Upadhyayula, Tsung-Li Liu, David Grant Colburn Hildebrand, Tony Tsai, Anzhi Chen, Ebaa Al-Obeidi, Anna Fass, Samir Malhotra, Florian Engert, View ORCID ProfileJeff W. Lichtman, Tom Kirchhausen, Eric Betzig, Sean G. Megason

 

Mechanics of epithelial tissue formation in early insect embryos. Tania Vazquez-Faci, Ruben van Drongelen, Maurijn van der Zee, Timon Idema

 

Optic Fissure Margin Morphogenesis Sets The Stage For Consecutive Optic Fissure Fusion, Pioneered By A Distinct Subset Of Margin Cells Using A Hyaloid Vessel As Scaffold. Priska Eckert, Lucas Schuetz, Joachim Wittbrodt, Stephan Heermann

 

Activity-Dependent Control Of Inhibitory Interneuron Number In The Mammalian Cortex. Myrto Denaxa, Guilherme Neves, Adam Rabinowitz, Sarah Kemlo, Petros Liodis, Juan Burrone, Vassilis Pachnis

 

On growth and form of the distal air exchange surfaces within the lung. David Warburton, Clarence Wigfall, Harvey Pollack, David Koos, Denise Al Alam, Gianluca Turcatel, Wei Shi, Scott E Fraser, Rex Moats

 

Cell-Accurate Optical Mapping Across The Entire Developing Heart. Michael Weber, Nico Scherf, Peter Kohl, Jan Huisken

 

 

| Genes & genomes

High Resolution Epigenomic Atlas of Early Human Craniofacial Development. Andrea Wilderman, Jeffrey Kron, Jennifer VanOudenhove, James P. Noonan, Justin Cotney

 

Limbs and pelvic bones from Sarro, et al.’s preprint

 

Disrupting Pitx1 Regulatory Topology Results In Overtly Normal Limb Development. Richard Sarro, Deena Emera, Severin Uebbing, Emily V. Dutrow, Scott D. Weatherbee, Timothy Nottoli, James P. Noonan

 

The Core Transcriptome Of Mammalian Placentas And The Divergence Of Expression With Placental Shape. Don Leigh Armstrong II, Michael R. McGowen, Amy Weckle, Priyadarshini Pantham, Jason Caravas, Dalen Agnew, Kurt Benirschke, Sue Savage-Rumbaugh, Eviatar Nevo, Chong J. Kim, Günter P. Wagner, Roberto Romero, Derek E. Wildman

 

Static And Dynamic DNA Loops Form AP-1 Bound Activation Hubs During Macrophage Development. Douglas H. Phanstiel, Kevin Van Bortle, Damek V. Spacek, Gaelen T. Hess, Muhammad Saad Shamim, Ido Machol, Michael I. Love, Erez Lieberman Aiden, Michael C. Bassik, Michael P. Snyder

 

Creation of distal enhancers defines human-specific features of interphase chromatin architecture in embryonic stem cells. Gennadi Glinsky

 

Transcription Factors Recognize DNA Shape Without Nucleotide Recognition. Md. Abul Hassan Samee, Benoit Bruneau, Katherine Pollard

 

An imaginal disc from Chandler, et al.’s preprint

 

How Well Do You Know Your Mutation? Complex Effects Of Genetic Background On Expressivity, Complementation, And Ordering Of Allelic Effects. Christopher H. Chandler, Sudarshan Chari, Alycia Kowalski, Lin Choi, David Tack, Michael DeNieu, William R. Pitchers, Anne Sonnenschein, Leslie Marvin, Kristen Hummel, Christian Marier, Andrew Victory, Cody Porter, Anna Mammel, Julie Holms, Gayatri Sivaratnam, Ian Dworkin

 

Cohesin Loss Eliminates All Loop Domains, Leading To Links Among Superenhancers And Downregulation Of Nearby Genes. Suhas Rao, Su-Chen Huang, Brian Glenn St. Hilaire, Jesse M. Engreitz, Elizabeth M. Perez, Kyong-Rim Kieffer-Kwon, Adrian L. Sanborn, Sarah E. Johnstone, Ivan D. Bochkov, Xingfan Huang, Muhammad S. Shamim, Arina D. Omer, Bradley E. Bernstein, Rafael Casellas, Eric S. Lander, Erez Lieberman Aiden

 

Using Large-Scale Mutagenesis To Guide Single Amino Acid Scanning Experiments. Vanessa E. Gray, Ronald J. Hause, Douglas M. Fowler

 

Contribution Of Genetic Variation And Developmental Stage To Methylome Dynamics In Myeloid Differentiation. Xiang Chen, Yiping Fan, Jinjun Cheng, Beisi Xu, Yong-Dong Wang, Donald Yergeau, John Easton, James R. Downing, JInghui Zhang

 

 

| Stem cells, regeneration & disease modelling

TDG Regulates Cell Cycle Progression In Human Neural Progenitors. Igal Germanguz, Jenny Park, Jessica Cinkornpumin, Areyh Soloman, Minori Ohashi, William E. Lowry

 

Satellite cells from Chal, et al.’s preprint

 

Recapitulating Early Development Of Mouse Musculoskeletal Precursors Of The Paraxial Mesoderm In Vitro. Jerome Chal, Ziad Al Tanoury, Masayuki Oginuma, Philippe Moncuquet, Benedicte Gobert, Ayako Miyanari, Olivier Tassy, Getzabel Guevara, Agata Bera, Olga Sumara, Jean-Marie Garnier, Leif Kennedy, Marie Knockaert, Barbara Gayraud-Morel, Shahragim Tajbakhsh, Olivier Pourquie

 

Postmitotic Separation Enables Selective Niche Retention Of One Daughter Cell In Intestinal Crypts And Is Facilitated By Interkinetic Nuclear Migration And Basal Tethering. Thomas Carroll, Alastair J. Langlands, James M. Osborne, Ian P. Newton, Paul L. Appleton, Inke Nathke

 

Aubergine And piRNAs Repress The Proto-Oncogene Cbl For Germline Stem Cell Self-Renewal. Patricia Rojas-Rios, Aymeric Chartier, Martine Simonelig

 

Ratiometric Distribution Of OCT4 During Stem Cell Division Controls The Balance Between Self-Renewal And Differentiation. Samuel C. Wolff, Raluca Dumitru, Cierra D. Dungee, Katarzyna M. Kedziora, Rachel A. Haggerty, JrGang Cheng, Adriana S. Beltran, Jeremy E. Purvis

 

The Abrogation Of Condensin Function Provides Independent Evidence For Defining The Self-Renewing Population Of Pluripotent Stem Cells. Alvina Lai, Nobuyoshi Kosaka, Prasad Abnave, Sounak Sahu, Aziz Aboobaker

 

Silencing Of Transposable Elements May Not Be A Major Driver Of Regulatory Evolution In Primate Induced Pluripotent Stem Cells. Michelle C. Ward, Siming Zhao, Kaixuan Luo, Bryan J. Pavlovic, Mohammad M. Karimi, Matthew Stephens, Yoav Gilad

 

Geometrical confinement guides Brachyury self-patterning in embryonic stem cells. Guillaume Blin, Catherine Picart, Manuel Thery, Michel Puceat

 

A Comparative Study Of Endoderm Differentiation In Humans And Chimpanzees. Lauren E. Blake, Samantha M. Thomas, John D. Blischak, Chiaowen Joyce Hsiao, Claudia Chavarria, Marsha Myrthil, Yoav Gilad, Bryan J. Pavlovic

 

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

 

Regulating prospero mRNA Stability Determines When Neural Stem Cells Stop Dividing. Lu Yang, Tamsin J. Samuels, Yoav Arava, Francesca Robertson, Aino I. Järvelin, Ching-Po Yang, Tzumin Lee, David Ish-Horowicz, Ilan Davis

 

Imp/Syp Temporal Gradients Govern Decommissioning Of Drosophila Neural Stem Cells. Ching-Po Yang, Tamsin J. Samuels, Yaling Huang, Lu Yang, David Ish-Horowicz, Ilan Davis, Tzumin Lee

 

OCT4 Impedes Cell Fate Redirection By The Melanocyte Lineage Master Regulator MITF. Danna Sheinboim, Itay Maza, Iris Dror, Shivang Parikh, Vladislav Krupalnik, Rachel E. Bell, Asaf Zviran, Yusuke Suita, Ofir Hakim, Yael Mandel Gutfreund, Mehdi Khaled, Jacob H. Hanna, Carmit Levy

 

Mammary organoids from Virtakoivu, et al.’s preprint

 

Vimentin Plays A Functional Role In Mammary Gland Regeneration. Reetta Virtakoivu, Emilia Peuhu, Anja Mai, Anni Warri, Johanna Ivaska

 

Deletion Of EP4 In S100a4-Lineage Cells Reduces Scar Tissue Formation During Early But Not Later Stages Of Tendon Healing. Jessica E. Ackerman, Katherine T. Best, Regis J. O’Keefe, Alayna Loiselle

 

Loss Of lrrk2 Impairs Cell Proliferation And Neuronal Regeneration In The Zebrafish Brain. Stefano Suzzi, Reiner Ahrendt, Stefan Hans, Svetlana A. Semenova, Saygin Bilican, Shady Sayed, Sylke Winkler, Sandra Spiess, Jan Kaslin, Pertti Panula, Michael Brand

 

PI3K Activation In Neural Stem Cells Drives Tumorigenesis Which Can Be Suppressed By Targeting CREB. Paul Daniel, Gulay Filiz, Daniel Brown, Michael Christie, Paul Waring, Yi Zhang, John Haynes, Colin Pouton, Dustin Flanagan, Elizabeth Vincan, Terrance Johns, Karen Montgomery, Wayne Phillips, Theo Mantamadiotis

 

Astrocytes from Julia TCW, et al.’s preprint

 

An Efficient Platform For Astrocyte Differentiation From Human Induced Pluripotent Stem Cells. Julia TCW, Minghui Wang, Anna Pimenova, Kathryn Bowles, Brigham Hartley, Emre Lacin, Saima Machlovi, Rawan Abdelaal, Celeste Karch, Hemali Phatnani, Paul Slesinger, Bin Zhang, Alison Goate, Kristen Brennand

 

Acquisition of cell migration defines NK cell differentiation from hematopoietic stem cell precursors. Barclay J Lee, Emily M Mace

 

Overexpression Of Hypoxia-Inducible Factor 1 Alpha Improves Immunomodulation By Dental Mesenchymal Stem Cells. Victor G. Martinez, Imelda Ontoria-Oviedo, Carolina P. Ricardo, Sian E. Harding, Rosa Sacedon, Alberto Varas, Agustin Zapata, Pilar Sepulveda, Angeles Vicente

 

Daam2 Driven Degradation Of VHL Promotes Gliomagenesis. Wenyi Zhu, Saritha Krishna, Cristina Garcia, Chia-Ching John Lin, Ken L. Scott, Carrie Mohila, Chad Creighton, Seung-Hee Yoo, Hyun Kyoung Lee, Benjamin Deneen

 

In Vivo Phenotyping Of Parkinson-Specific Stem Cells Reveals Increased a-Synuclein Levels But No Spreading. Kathrin Hemmer, Lisa M. Smits, Silvia Bolognin, Jens C. Schwamborn

 

Zfp423, A Joubert Syndrome Gene, Is A Domain-Specific Regulator Of Cell Cycle Progression, DNA Damage Response And Purkinje Cell Development In The Cerebellar Primordium. Filippo Casoni, Laura Croci, Camilla Bosone, Roberta D’Ambrosio, Aurora Badaloni, Davide Gaudesi, Valeria Barili, Justyna R. Sarna, Lino Tessarollo, Ottavio Cremona, Richard Hawkes, Soren Warming, Gian Giacomo Consalez

 

Tacrolimus Rescues Endothelial ALK1 Loss-Of-Function Signaling And Improves HHT Vascular Pathology. Santiago Ruiz, Pallavi Chandakkar, Haitian Zhao, Julien Papoin, Prodyot K. Chatterjee, Erica Christen, Christine N. Metz, Lionel Blanc, Fabien Campagne, Philippe Marambaud

 

Inducible And Reversible Phenotypes In A Novel Mouse Model Of Friedreich’s Ataxia. Vijayendran Chandran, Kun Gao, Vivek Swarup, Revital Versano, Hongmei Dong, Maria C. Jordan, Daniel H. Geschwind

 

A Possible Role Of Microglia In Zika Virus Infection Of The Fetal Human Brain. Julien Muffat, Yun Li, Attya Omer, Ann Durbin, Irene Bosch, Grisilda Bakiasi, Edward Richards, Aaron Meyer, Lee Gehrke, Rudolf Jaenisch

 

Infected tissues from Nguyen, et al.’s preprint

 

Highly Efficient Maternal-Fetal Zika Virus Transmission in Pregnant Rhesus Macaques. Sydney M Nguyen, Kathleen M Antony, Dawn M Dudley, Sarah Kohn, Heather Simmons, Bryce Wolfe, M Shahriar Salamat, Leandro BC Teixeira, Gregory J Wiepz, Troy H Thoong, Matthew T Aliota, Andrea M Weiler, Gabrielle L Barry, Kim L Weisgrau, Logan J Vosler, Mariel S Mohns, Meghan E Breitbach, Laurel M Stewart, Mustafa N Rasheed, Christina M Newman, Michael E Graham, Oliver E Wieben, Patrick A Turski, Kevin M Johnson, Jennifer Post, Jennifer M Hayes, Nancy Schultz-Darken, Michele L Schotzko, Josh A Eudailey, Sallie R Permar, Eva G Rakasz, Emma L Mohr, Saverio Capuano III, Alice F Tarantal, Jorge E Osorio, Shelby L O’Connor, Thomas C Friedrich, David H O’Connor, Thaddeus G Golos

 

Systematic Characterization Of Human 21st Chromosome Orthologs In Caenorhabditis elegans. Sarah Nordquist, Allison Griffith, Jonathan Pierce

 

Drosophila CaV2 Channels Harboring Human Migraine Mutations Cause Synapse Hyperexcitability That Can Be Suppressed By Inhibition Of A Ca2+ Store Release Pathway. Douglas J. Brusich, Ashlyn M. Spring, Thomas D. James, Timothy H. Helms, C. Andrew Frank

 

Super-Resolution Microscopy Reveals That Disruption Of Ciliary Transition Zone Architecture Is A Cause Of Joubert Syndrome. Xiaoyu Shi, Galo Garcia III, Julie C. Van De Weghe, Ryan McGorty, Gregory J. Pazour, Dan Doherty, Bo Huang, Jeremy F. Reiter

 

 

| Plant development

An Inference Approach Combines Spatial And Temporal Gene Expression Data To Predict Gene Regulatory Networks In Arabidopsis Stem Cells. Maria Angels de Luis Balaguer, Adam P. Fisher, Natalie M. Clark, Maria Guadalupe Fernandez-Espinosa, Barbara Moller, Dolf Weijers, Jan U. Lohmann, Cranos Williams, Oscar Lorenzo, Rosangela Sozzani

 

Sargassum muticum apices from Linardić & Braybrook’s preprint

 

Towards An Understanding Of Spiral Patterning In The Sargassum muticum Shoot Apex. Marina Linardić, Siobhan A. Braybrook

 

The Proteolytic Landscape Of An Arabidopsis Separase-Deficient Mutant Reveals Novel Substrates Associated With Plant Development. Chen Liu, Simon Stael, Kris Gevaert, Frank Van Breusegem, Peter Bozhkov, Panagiotis Moschou

 

Spatial Specificity Of Auxin Responses Coordinates Wood Formation. Klaus Brackmann, Virginie Jouannet, Jiyan Qi, Theresa Schlamp, Karin Gruenwald, Pablo Sanchez, Thomas Greb

 

CRootBox: A Structural-Functional Modelling Framework For Root Systems. Andrea Schnepf, Daniel Leitner, Magdalena Landl, Guillaume Lobet, Trung Hieu Mai, Shehan Morandage, Cheng Sheng, Mirjam Zoerner, Jan Vanderborght, Harry Vereecken

 

Root Interactions And Plant Growth In A Tomato/Potato Onion Intercropping System Under Different Phosphorus Levels. Hongjie Yu, Shaocan Chen, Xingang Zhou, Fengzhi Wu

 

Leaf morphometrics from Migicovsky, et al.’s preprint

 

Morphometrics Reveals Complex And Heritable Apple Leaf Shapes. Zoë Migicovsky, Mao Li, Daniel H. Chitwood, Sean Myles

 

Systematic Analysis Of RNA-Seq-Based Gene Co-Expression Across Multiple Plants. Hua Yu, Bingke Jiao, Chengzhi Liang

 

A Small RNA Pathway Mediates Global Allelic Dosage In Endosperm. Robert M. Erdmann, P.R. V. Satyaki, Maja Klosinska, Mary Gehring

 

Plant miRNA Regulation Is Environmentally And Developmentally-Sensitive. Patrick von Born, Ignacio Rubio-Somoza

 

Over-Expression Of The RieskeFeS Protein Increases Electron Transport Rates And Yield In Arabidopsis. Andrew Simkin, Lorna McAusland, Tracy Lawson, Christine A. Raines

 

Genome-Wide Characterization Of Isoform Switching In Arabidopsis thaliana. Dries Vaneechoutte, April Roberts Estrada, Ying-Chen Lin, Ann Loraine, Klaas Vandepoele

 

Characterization Of Imprinted Genes In Rice Reveals Post-Fertilization Regulation And Conservation At Some Loci Of Imprinting In Plant Species. Chen Chen, Tingting Li, Shan Zhu, Zehou Liu, Zhenyuan Shi, Xiaoming Zheng, Rui Chen, Jianfeng Huang, Yi Shen, Shiyou Luo, Lei Wang, Qiao-Quan Liu, Zhiguo E

 

The Peach RGF/GLV Signalling Peptide pCTG134 Is Involved In A Regulatory Circuit That Sustains Auxin And Ethylene Actions. Nicola Busatto, Umberto Salvagnin, Francesca Resentini, Silvia Quaresimin, Lorella Navazio, Oriano Marin, Maria Pellegrini, Fabrizio Costa, Dale F. Mierke, Livio Trainotti

 

MutS-Homolog2 Silencing Generates Tetraploid Meiocytes In Tomato (Solanum lycopersicum). Supriya Sarma, Arun Kumar Pandey, Maruthachalam Ravi, Yellamaraju Sreelakshmi, Rameshwar Sharma

 

Coordinated Shifts In Allocation Among Reproductive Tissues Across 14 Coexisting Plant Species. Elizabeth Hedi Wenk, Konrad Abramowicz, Mark Westoby, Daniel Stein Falster

 

Evo-devo & evo

An FGF-Driven Coherent Feed-Forward Circuit Patterns The Cardiopharyngeal Mesoderm Of A Simple Chordate In Space And Time. Florian Razy-Krajka, Basile Gravez, Lionel Christiaen

 

RNase reverses segment sequence in the anterior of a beetle egg (Callosobruchus maculatus, Coleoptera). Jitse Michiel van der Meer

 

Olfactory Receptors Are Required For Social Behavior And Neural Plasticity In Ants, As Evidenced By CRISPR-Mediated Gene Knockout. Hua Yan, Comzit Opachaloemphan, Giacomo Mancini, Huan Yang, Matthew Gallitto, Jakub Mlejnek, Kevin Haight, Majid Ghaninia, Lucy Huo, Alexandra Leibholz, Jesse Slone, Xiaofan Zhou, Maria Traficante, Clint A. Penick, Kelly Dolezal, Kaustubh Gokhale, Kelsey Stevens, Ingrid Fetter-Pruneda, Roberto Bonasio, Laurence J. Zwiebel, Shelley Berger, Juergen Liebig, Danny Reinberg, Claude Desplan

 

Giardia cells from Krtkova, et al.’s preprint

 

14-3-3 Negatively Regulates Actin Filament Formation In The Deep Branching Eukaryote Giardia lamblia. Jana Krtkova, Jennifer Xu, Marco Lalle, Melissa Steele-Ogus, Germain C. M. Alas, David Sept, Alexander R. Paredez

 

Distinct Core Promoter Codes Drive Transcription Initiation At Key Developmental Transitions In A Marine Chordate. Gemma B. Danks, Pavla Navratilova, Boris Lenhard, Eric Thompson

 

Ascidians diagrams from Harada’s preprint

 

Deciphering The Developmental Program In The Ascidian Ciona intestinalis Just Prior To Gastrulation. Yoshito Harada

 

An Aphrodisiac Produced By Vibrio fischeri Stimulates Mating In The Closest Living Relatives Of Animals. Arielle Woznica, Joseph P. Gerdt, Ryan Hulett, Jon Clardy, Nicole King

 

Ophiuroid Phylotranscriptomics Enables Discovery Of Novel Echinoderm Representatives Of Bilaterian Neuropeptide Families And Reconstruction Of Neuropeptide Precursor Evolution Over ~270 Million Years. Meet Zandawala, Ismail Moghul, Luis Alfonso Yanez Guerra, Jerome Delroisse, Nikara Abylkassimova, Andrew F. Hugall, Timothy D. O’Hara, Maurice R. Elphick

 

Double Maternal Effect: Duplicated Nucleoplasmin 2 Genes, npm2a And npm2b, Are Shared By Fish And Tetrapods, And Have Distinct And Essential Roles In Early Embryogenesis. Caroline T. Cheung, Jeremy Pasquier, Aurelien Bouleau, Thao-Vi Nguyen, Franck Chesnel, Yann Guiguen, Julien Bobe

 

Extensive Sexual Wing Shape Dimorphism In Drosophila melanogaster, Ceratitis capitata, And Musca domestica. Natalia Siomava, Ernst A. Wimmer, Nico Posnien

 

Allele specific expression and methylation in the bumblebee, Bombus terrestris. Zoe N Lonsdale, Kate D Lee, Maria Kyriakidou, Harindra E Amarasinghe, Despina Nathanael, Eamonn B Mallon

 

Excretion through digestive tissues predates the evolution of excretory organs. Carmen Andrikou, Daniel Thiel, Juan Antonio Ruiz-Santiesteban, Andreas Hejnol

 

Duplication And Sub/Neofunctionalization Of malvolio, An Insect Homolog Of Nramp, In The Subsocial Beetle Nicrophorus vespilloides. Elijah C. Mehlferber, Kyle M. Benowitz, Eilleen M. Roy-Zokan, Elizabeth C. McKinney, Christopher B. Cunningham, Allen J. Moore

 

De Novo Assembly And Annotation Of The Eastern Fence Lizard (Sceloporus undulatus ) Transcriptome. Mariana B. Grizante, Marc Tollis, Juan J. Rodriguez, Ofir Levy, Michael J. Angilletta Jr., Kenro Kusumi

 

The Nuclear And Mitochondrial Genomes Of The Facultatively Eusocial Orchid Bee Euglossa dilemma. Philipp Brand, Nicholas Saleh, Hailin Pan, Cai Li, Karen Kapheim, Santiago Ramirez

 

Development of a high-density, ~2M SNP genotyping array and 670k SNP imputation array for the domestic horse. Robert J Schaefer, Mikkel Schubert, Ernest Bailey, Danika L. Bannasch, Eric Barrey, Gila Kahila Bar-Gal, Gottfried Brem, Samantha A. Brooks, Ottmar Distl, Ruedi Fries, Carrie J. Finno, Vinzenz Gerber, Bianca Haase, Vidhya Jagannathan, Ted Kalbfleisch, Tosso Leeb, Gabriella Lindgren, Maria Susana Lopes, Nuria Mach, Artur da Câmara Machado, James N. MacLeod, Annette McCoy, Julia Metzger, Cecilia Penedo, Sagi Polani, Stefan Rieder, Imke Tammen, Jens Tetens, Georg Thaller, Andrea Verini-Supplizi, Claire M. Wade, Barbara Wallner, Ludovic Orlando, James R. Mickelson, Molly E. McCue

 

First de-novo transcriptome assembly of a South American frog, Oreobates cruralis, enables population genomic studies of Neotropical amphibians. Santiago Montero-Mendieta​, Manfred Grabherr, Henrik Lantz, Ignacio De la Riva, Jennifer A Leonard, Matthew T Webster, Carles Vilà

 

Cichlids from Malinsky, et al.’s preprint

 

Whole Genome Sequences Of Malawi Cichlids Reveal Multiple Radiations Interconnected By Gene Flow. Milan Malinsky, Hannes Svardal, Alexandra M. Tyers, Eric A. Miska, Martin J. Genner, George F. Turner, Richard Durbin

 

New genes and functional innovation in mammals. Jose Luis Villanueva-Canas, Jorge Ruiz-Orera, M. Isabel Agea, Maria Gallo, David Andreu, M. Mar Alba

 

Meiotic Genes In Colpodean Ciliates Support Secretive Sexuality. Micah Dunthorn, Rebecca A. Zufall, Jingyun Chi, Konrad Paszkiewicz, Karen Moore, Frederic Mahe

 

Juvenile Hormone, But Not Nutrition Or Social Cues, Affects Reproductive Maturation In Solitary Alkali Bees (Nomia melanderi). Karen M. Kapheim, Makenna M. Johnson

 

 

Cell biology

The Human Cell Atlas. Aviv Regev, Sarah Teichmann, Eric S. Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy, Hans Clevers, Bart Deplancke, Ian Dunham, James Eberwine, Roland Eils, Wolfgang Enard, Andrew Farmer, Lars Fugger, Berthold Gottgens, Nir Hacohen, Muzlifah Haniffa, Martin Hemberg, Seung K. Kim, Paul Klenerman, Arnold Kriegstein, Ed Lein, Sten Linnarsson, Joakim Lundeberg, Partha Majumder, John Marioni, Miriam Merad, Musa Mhlanga, Martijn Nawijn, Mihai Netea, Garry Nolan, Dana Pe’er, Anthony Philipakis, Chris P. Ponting, Stephen R. Quake, Wolf Reik, Orit Rozenblatt-Rosen, Joshua R. Sanes, Rahul Satija, Ton Shumacher, Alex K. Shalek, Ehud Shapiro, Padmanee Sharma, Jay Shin, Oliver Stegle, Michael Stratton, Michael J. T. Stubbington, Alexander van Oudenaarden, Allon Wagner, Fiona M. Watt, Jonathan S. Weissman, Barbara Wold, Ramnik J. Xavier, Nir Yosef

 

TIRF-M images and associated kymographs from Tan, et al.’s preprint

 

Cooperative Accumulation Of Dynein-Dynactin At Microtubule Minus-Ends Drives Microtubule Network Reorganization. Ruensern Tan, Peter J. Foster, Daniel J. Needleman, Richard J. McKenney

 

Role of Membrane-tension Gated Ca Flux in Cell Mechanosensation. Lijuan He, Jiaxiang Tao, Fangwei Si, Yi Wu, Tiffany Wu, Vishnu Prasath, Denis Wirtz, Sean X. Sun

 

Two-Step Interphase Microtubule Disassembly Aids Spindle Morphogenesis. Nunu Mchedlishvili, Helen K. Matthews, Adam Corrigan, Buzz Baum

 

Spindle assembly checkpoint strength is governed by cell size and PAR-mediated cell fate determination in C. elegans. Abigail Gerhold

 

Microtubules following cold shock, from Pitaval, et al.’s preprint

 

Microtubule stabilization drives 3D centrosome migration to initiate primary ciliogenesis. Amandine Pitaval, Fabrice Senger, Gaelle Letort, Xavier Gidrol, James Sillibourne, Manuel THERY

 

Analysis Of Interphase Node Proteins In Fission Yeast By Quantitative And Super Resolution Fluorescence Microscopy. Matthew Akamatsu, Yu Lin, Joerg Bewersdorf, Thomas D. Pollard

 

Time-Course Analysis Of Early Meiotic Prophase Events Informs Mechanisms Of Homolog Pairing And Synapsis In Caenorhabditis elegans. Susanna Mlynarczyk-Evans, Anne M. Villeneuve

 

Meiotic Crossover Patterning In The Absence Of ATR: Loss Of Interference And Assurance But Not The Centromere Effect. Morgan M Brady, Susan McMahan, Jeff Sekelsky

 

A Single Checkpoint Pathway Eliminates Mouse Oocytes With DNA Damage Or Chromosome Synapsis Failure. Vera Rinaldi, Ewelina Bolcun-Filas, Hiroshi Kogo, Hiroki Kurahashi, John Schimenti

 

Loss Of PTEN Promotes Formation Of Signaling-Specific Clathrin-Coated Pits. Luciana K. Rosselli-Murai, Joel A. Yates, Sei Yoshida, Julia T. Bourg, Kenneth K. Y. Ho, Megan White, Julia Prisby, Xinyu Tan, Megan Altemus, Liwei Bao, Zhi-Fen Wu, Sarah L. Veatch, Joel A. Swanson, Sofia D. Merajver, Allen P. Liu

 

Intercellular mRNA Trafficking Via Membrane Nanotubes In Mammalian Cells. Gal Haimovich, Christopher M. Ecker, Margaret C. Dunagin, Elliot Eggan, Arjun Raj, Jeffrey E. Gerst, Robert H. Singer

 

Cell Mechanosensing and Avoidance of Strain Gradients. Sophie Chagnon-Lessard, Hubert Jean-Ruel, Michel Godin, Andrew E. Pelling

 

The Human Cytoplasmic Dynein Interactome Reveals Novel Activators Of Motility. William B. Redwine, Morgan E. DeSantis, Ian Hollyer, Zaw M. Htet, Phuoc T. Tran, Selene K. Swanson, Laurence Florens, Michael P. Washburn, Samara L. Reck-Peterson

 

DNA Damage Checkpoint Dynamics Drive Cell Cycle Phase Transitions. Hui Xiao Chao, Cere E. Poovey, Ashley A. Privette, Gavin D. Grant, Jean G. Cook, Jeremy E. Purvis

 

Mitochondria Are Physiologically Maintained At Close To 50 C. Dominique Chretien, Paule Benit, Hyung-Ho Ha, Susanne Keipert, Riyad El-Khoury, Young-Tae Chang, Martin Jastroch, Howard Jacobs, Pierre Rustin, Malgorzata Rak

 

 

Modelling

Organoid And Tissue Patterning Through Phase Separation: Use Of A Vertex Model To Relate Dynamics Of Patterning To Underlying Biophysical Parameters. William Waites, Matteo Cavaliere, Elise Cachat, Vincent Danos, Jamie A. Davies

 

Modelling cells from Fisher, Strutt and Fletcher’s preprint

 

Integrating Planar Polarity And Tissue Mechanics In Computational Models Of Epithelial Morphogenesis. Katherine H. Fisher, David Strutt, Alexander G. Fletcher

 

Drosophila embryos and aspect ratios, from Atia, et al.’s preprint

 

Universal geometric constraints during epithelial jamming. Lior Atia, Dapeng Bi, Yasha Sharma, Jennifer A. Mitchel, Bomi Gweon, Stephan Koehler, Stephen J. DeCamp, Bo Lan, Rebecca Hirsch, Adrian F. Pegoraro, Kyu Ha Lee, Jacqueline Starr, David A. Weitz, Adam C. Martin, Jin-Ah Park, James P. Butler, Jeffrey J. Fredberg

 

An Anisotropic Attraction Model For The Diversity And Robustness Of Cell Arrangement In Nematodes. Kazunori Yamamoto, Akatsuki Kimura

 

A Theory That Predicts Behaviors Of Disordered Cytoskeletal Networks. Julio Belmonte, Maria Leptin, Francois Nedelec

A Model For Adult Organ Resizing Demonstrates Stem Cell Scaling Through A Tunable Commitment Rate. XinXin Du, Lucy Erin O’Brien, Ingmar Riedel-Kruse

 

Single-Cell Reprogramming Of Mouse Embryo Development Through A Critical Transition State. Masa Tsuchiya, Alessandro Giuliani, Kenichi Yoshikawa

 

Predicting Morphological Disparities In Sea Urchin Skeleton Growth And Form. Maria Abou Chakra, Miroslav Lovric, Jon R. Stone

 

Role of distal enhancers in shaping 3D-folding patterns and defining human-specific features of interphase chromatin architecture in embryonic stem cells. Gennadi Glinsky

 

 

Tools & resources

 

On-chip high-resolution imaging of the same cells in the same worms throughout larval development, from Shivers, Uppaluri and Brangwynne’s preprint

 

Microfluidic Immobilization And Subcellular Imaging Of Developing Caenorhabditis elegans. Jordan Shivers, Sravanti Uppaluri, Clifford P. Brangwynne

 

High-density superresolution microscopy with an incoherent light source and a conventional epifluorescence microscope setup. Kirti Prakash

 

3D Single-Molecule Super-Resolution Microscopy With A Tilted Light Sheet. Anna-Karin Gustavsson, Petar N. Petrov, Maurice Y. Lee, Yoav Shechtman, W. E. Moerner

 

Poor man’s two photon imaging: Scanning Laser Upconversion Microscopy. Cecilia Sorbello, Roberto Etchenique

 

A High Resolution Whole Brain Imaging Using Oblique Light Sheet Tomography. Arun Narasimhan, Kannan  Umadevi Venkataraju, Judith Mizrachi, Dinu F. Albeanu, Pavel Osten

 

Boosting The Localization Precision Of dSTORM By Biocompatible Metal-Dielectric Coated Glass Coverslips. Hannah Sophie Heil, Benjamin Schreiber, Monika Emmerling, Sven Hoefling, Martin Kamp, Markus Sauer, Katrin Gertrud Heinze

 

Aberration-corrected high-NA open-top selective-plane illumination microscopy for biological imaging. Ryan McGorty, Dan Xie, Bo Huang

 

Serial Crystallography with Multi-stage Merging of 1000’s of Images. Herbert J. Bernstein, Lawrence C. Andrews, James Foadi, Martin R. Fuchs, Jean Jakoncic, Sean McSweeney, Dieter K. Schneider, Wuxian Shi, John Skinner, Alexei Soares, Yusuke Yamada

 

Achieving Better Than 3 Å Resolution By Single Particle Cryo-EM At 200 keV. Mark A. Herzik Jr., Mengyu Wu, Gabriel C. Lander

 

sfCherry2 labelling different compartments of the cell, from Feng, et al’s preprint

 

Improved Split Fluorescent Proteins For Endogenous Protein Labeling. Siyu Feng, Sayaka Sekine, Veronica Pessino, Han Li, Manuel D. Leonetti, Bo Huang

 

A safer, urea-based in situ hybridization method improves detection of gene expression
in diverse animal species. Chiara Sinigaglia, Daniel Thiel, Andreas Hejnol, Evelyn Houliston, Lucas Leclere

 

Micropatterned Substrates To Promote And Dissect Reprogramming Of Human Somatic Cells. Jared Carlson-Stevermer, Ty Harkness, Ryan Prestil, Stephanie Seymour, Gavin Knight, Randolph Ashton, Krishanu Saha

 

Control of microtubule dynamics using an optogenetic microtubule plus end-F-actin cross-linker. Rebecca C Adikes, Ryan A Hallett, Brian F Saway, Brian Kuhlman, Kevin C Slep

 

Filopodyan: An Open-Source Pipeline For The Analysis Of Filopodia. Vasja Urbančič, Richard Butler, Benjamin Richier, Manuel Peter, Julia Mason, Christine E. Holt, Jennifer L. Gallop

 

Deconvolution Of Subcellular Protrusion Heterogeneity And The Underlying Actin Regulator Dynamics From Live Cell Imaging. Chuangqi Wang, Hee June Choi, Sung-Jin Kim, Yongho Bae, Kwonmoo Lee

 

Aberrant Cortical Activity In Multiple GCaMP6-Expressing Transgenic Mouse Lines. Nicholas A. Steinmetz, Christina Buetfering, Jerome Lecoq, Christian R. Lee, Andrew J. Peters,Elina A. K. Jacobs, Philip Coen, Douglas R. Ollerenshaw, Matthew T. Valley, Saskia E. J. de Vries, Marina Garrett, Jun Zhuang, Peter A. Groblewski, Sahar Manavi, Jesse Miles, Casey White, Eric Lee, Fiona Griffin, Joshua D. Larkin, Kate Roll, Sissy Cross, Thuyanh V. Nguyen, Rachael Larsen, Julie Pendergraft, Tanya Daigle, Bosiljka Tasic, Carol L. Thompson, Jack Waters, Shawn Olsen, David J. Margolis,Hongkui Zeng, Michael Hausser, Matteo Carandini, Kenneth D. Harris

 

A Comparison Between Single Cell RNA Sequencing And Single Molecule RNA FISH For Rare Cell Analysis. Eduardo A. Torre, Hannah Dueck, Sydney Shaffer, Janko Gospocic, Rohit Gupte, Roberto Bonasio, Junhyong Kim, John Murray, Arjun Raj

 

Ultra-Accurate Genome Sequencing And Haplotyping Of Single Human Cells. Wai Keung Chu, Peter Edge, Ho Suk Lee, Vikas Bansal, Vineet Bafna, Xiaohua Huang, Kun Zhang

 

Graphene Oxide-Quenching-Based Fluorescence In Situ Hybridization (G-FISH) To Detect RNA In Tissue: Simple And Fast Tissue RNA Diagnostics. Do Won Hwang, Yoo Ri Choi, Dohyun Kim, Hye Yoon Park, Kyu Wan Kim, Mee Young Kim, Chul-Kee Park, Dong Soo Lee

 

SCENIC: Single-Cell Regulatory Network Inference And Clustering. Sara Aibar, Carmen Bravo González-Blas, Thomas Moerman, Jasper Wouters, Vân Anh Huynh-Thu, Hana Imrichová, Zeynep Kalender Atak, Gert Hulselmans, Michael Dewaele, Florian Rambow, Pierre Geurts, Jan Aerts, Jean-Christophe Marine, Joost van den Oord, Stein Aerts

 

Bias, Robustness And Scalability In Differential Expression Analysis Of Single-Cell RNA-Seq Data. Charlotte Soneson, Mark D. Robinson

 

Reverse-Engineering Biological Networks From Large Data Sets. Joseph Lane Natale, David Hofmann, Damián G. Hernández, Ilya Nemenman

 

Accuracy, Reproducibility And Bias Of Next Generation Sequencing For Quantitative Small RNA Profiling: A Multiple Protocol Study Across Multiple Laboratories. Maria D. Giraldez, Ryan M. Spengler, Alton Etheridge, Paula Maria Godoy, Andrea J. Barczak, Srimeenakshi Srinivasan, Peter L. De Hoff, Kahraman Tanriverdi, Amanda Courtright, Shulin Lu, Joseph Khoory, Renee Rubio, David Baxter, Tom A. P. Driedonks, Hank P. J. Buermans, Esther N. M. Nolte-‘t Hoen, Hui Jiang, Kai Wang, Ionita Ghiran, Yaoyu Wang, Kendall Van Keuren-Jensen, Jane E. Freedman, Prescott G. Woodruff, Louise C. Laurent, David J. Erle, David J. Galas, Muneesh Tewari

 

Genome And Epigenome Engineering CRISPR Toolkit For Probing In Vivo cis-Regulatory Interactions In The Chicken Embryo. Ruth M. Williams, Upeka Senanayake, Mara Artibani, Gunes Taylor, Daniel Wells, Ahmed Ashour Ahmed, Tatjana Sauka-Spengler

 

Enhanced Guide-RNA Design And Targeting Analysis For Precise CRISPR Genome Editing Of Single And Consortia Of Industrially Relevant And Non-Model Organisms. Brian Mendoza, Cong T. Trinh

 

CRISPR/Cas9 screening using unique molecular identifiers. Bernhard Schmierer, Sandeep Kumar Botla, Jilin Zhang, Mikko Turunen, Teemu Kivioja, Jussi Taipale

 

The Kinetic Basis Of CRISPR-Cas Off-Targeting Rules. Misha Klein, Behrouz Eslami-Mossallam, Dylan Gonzalez Arroyo, Martin Depken

 

A thermostable Cas9 with increased lifetime in human plasma. Lucas Harrington, David Paez-Espino, Janice S. Chen, Enbo Ma, Brett T. Staahl, Nikos C. Kyrpides, Jennifer A. Doudna

 

Behavioural and morphological differences in P. pacificus strains, from Rödelsperger and Moreno’s preprint

 

Differential Variant Calling In Mutants From Diverse Genetic Backgrounds: A Case Study In The Nematode Pristionchus pacificus. Christian Rödelsperger, Eduardo Moreno

 

A Sequencer Coming Of Age: De Novo Genome Assembly Using MinION Reads. Carlos Victor de Lannoy,Dick de Ridder, Judith Risse

 

scImpute: Accurate And Robust Imputation For Single Cell RNA-Seq Data. Wei Vivian Li, Jingyi Jessica Li

 

High-throughput, image-based screening of genetic variant libraries. George Emanuel, Jeffrey R Moffitt, Xiaowei Zhuang

 

In Situ Genotyping Of A Pooled Strain Library After Characterizing Complex Phenotypes. Michael J. Lawson, Daniel Camsund, Jimmy Larsson, Ozden Baltekin, David Fange, Johan Elf

 

Targeting Repair Pathways With Small Molecules Increases Precise Genome Editing In Pluripotent Stem Cells. Stephan Riesenberg, Tomislav Maricic

 

A Simple Representation Of Three-Dimensional Molecular Structure. Seth D. Axen, Xi-Ping Huang, Elena L. Caceres, Leo Gendelev, Bryan L. Roth, Michael J. Keiser

 

DNA.Land: A Digital Biobank Using A Massive Crowdsourcing Approach. Jie Yuan, Assaf Gordon, Daniel Speyer, Richard Aufrichtig,Dina Zielinski, Joseph Pickrell, Yaniv Erlich

 

MutPred2: inferring the molecular and phenotypic impact of amino acid variants. Vikas Pejaver, Jorge Urresti, Jose Lugo-Martinez, Kymberleigh A. Pagel, Guan Ning Lin, Hyun-Jun Nam, Matthew Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac

 

MotifMark: Finding Regulatory Motifs in DNA Sequences. Hamid Reza Hassanzadeh

 

CircMarker: A Fast and Accurate Algorithm for Circular RNA Detection. Xin Li, Chong Chu, Jingwen Pei, Ion Mandoiu, Yufeng Wu

 

piClusterBusteR: Software For Automated Classification And Characterization Of piRNA Cluster Loci. Patrick A. Schreiner, Peter Atkinson

 

Research practice

Cooperation And Liaison Between Universities And Editors (CLUE): Recommendations On Best Practice. Elizabeth Wager, Sabine Kleinert,Michele Garfinkel, Volker Bähr, Ksenija Baždarić, Michael Farthing, Chris Graf, Zoë Hammatt, Lyn Horn, Susan King, Debra Parrish, Bernd Pulverer, Paul Taylor, Gerrit van Meer

 

Overview of the two-part Manuscript 101 homework, from Halbisen and Ralston’s preprint

 

Manuscript 101: A Data-Driven Writing Exercise For Beginning Scientists. Michael A. Halbisen, Amy Ralston

 

Modeling Science Trustworthiness Under Publish Or Perish Pressure. David Robert Grimes, Chris T. Bauch, John P. A. Ioannidis

 

The Reproducibility Of Research And The Misinterpretation Of P Values.  David Colquhoun

 

A tale of two cores: a quantitative comparative analysis of the institutional and the open access models for flow research technology platforms. Anna Petrunkina, Reiner Schulte

 

Eyeballs On Science: Impact Is Not Just Citations, But How Big Is Readership? Kevin Winker

 

Interactive Biology Cloud Lab Enables Authentic Inquiry-Based Science Learning At MOOC Scale. Zahid Hossain, Engin Bumbacher, Alison Brauneis, Monica Diaz, Andy Saltarelli, Paulo Blikstein, Ingmar Riedel-Kruse

 

BioSharing: Harnessing Metadata Standards For The Data Commons. Susanna-Assunta Sansone,Alejandra Gonzalez-Beltran,Philippe Rocca-Serra, Peter McQuilton, Massimiliano Izzo, Allyson Lister, Milo Thurston

 

Marginal Returns And Levels Of Research Grant Support Among Scientists Supported By The National Institutes Of Health. Michael S. Lauer, Deepshikha Roychowdhury, Katie Patel, Rachael Walsh, Katrina Pearson

 

Opportunities And Obstacles For Deep Learning In Biology And Medicine. Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Wei Xie, Gail L. Rosen, Benjamin J. Lengerich, Johnny Israeli, Jack Lanchantin,Stephen Woloszynek, Anne E. Carpenter, Avanti Shrikumar, Jinbo Xu, Evan M. Cofer, David J. Harris, Dave DeCaprio, Yanjun Qi, Anshul Kundaje,Yifan Peng, Laura K. Wiley, Marwin H. S. Segler, Anthony Gitter, Casey S. Greene

 

Transparency In Authors’ Contributions And Responsibilities To Promote Integrity In Scientific Publication. Marcia McNutt, Monica Bradford, Jeffrey Drazen, R. Brooks Hanson, Bob Howard, Kathleen Hall Jamieson, Veronique Kiermer, Michael Magoulias, Emilie Marcus, Barbara Kline Pope, Randy Schekman, Sowmya Swaminathan,  Peter Stang, Inder Verma

 

bioPDFX: preparing PDF scientific articles for biomedical text mining. Shitij Bhargava, Tsung-Ting Kuo, Ankit Goyal, Vincent Kuri, Gordon Lin, Chun-Nan Hsu

 

Assessing value of biomedical digital repositories. Chun-Nan Hsu, Anita Bandrowski, Jeffrey S. Grethe, Maryann E. Martone

 

A persistent lack of International representation on editorial boards in biology. Johanna Espin, Sebastian Palmas-Perez, Farah Carrasco-Rueda, Kristina Riemer, Pablo Allen, Nathan Berkebile, Kirsten Hecht, Renita Kay Kastner-Wilcox, Mauricio Nunez-Regueiro, Candice Prince, Maria Constanza Rios-Marin, Erica P Ross, Bhagatveer Singha, Tia Tyler, Judit Ungvari Martin, Mariana Villegas, Tara Cataldo, Emilio Bruna

 

Gene annotation bias impedes biomedical research. Winston Haynes, Aurelie Tomczak, Purvesh Khatri

 

PaperBLAST: Text-mining papers for information about homologs. Morgan N Price, Adam P. Arkin

 

Why not…

To Beard, Or Not To Beard: Linking Sexual Selection On Masculinity, Embryonic Neural Crest Cells, And Human Self-Domestication. Ben Thomas Gleeson

 

Genetically Engineered Orange Petunias On The Market. Hany Bashandy, Teemu H. Teeri

 

 

 




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