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

---

 

This month in preprint news – here at The Company of Biologists, set just outside Cambridge in the UK, we’re hiring a new ‘Preprints Community Manager’. You can find out more here. It’s a great opportunity to get in to science communication and publishing, and of course preprints!

 

And this month in preprints, we found platypuses and pigeons, xenotransplants and reoriented axes,  CRISPR tools and liquid droplets. The preprints were hosted on bioRxiv, PeerJ, and arXiv. Use these links to get to the section you want:

 

Developmental biology

| Patterning & signalling

| Morphogenesis & mechanics

| Genes & genomes

| Stem cells, regeneration & disease modelling

Evo-devo & evo

Cell biology

Modelling

Tools & resources

| Imaging etc.

| Genome tools

Research practice

Why not…

 

Developmental biology

| Patterning & signalling

Reorientation of the primary body axis by ectopic embryonic cWnt signaling. Mark Q Martindale, Naveen Wijesena

 

 

High fidelity lineage tracing in mouse pre-implantation embryos using primed conversion of photoconvertible proteins. Maaike Welling,  Manuel A. Mohr, Aaron Ponti, Lluc R. Sabater, Andrea Boni, Prisca Liberali, Pawel Pelczar, Periklis Pantazis

 

 

Caudal counter-represses Hunchback to regulate even-skipped stripe 2 expression in Drosophila embryos. Ben J Vincent, Max V Staller, Francheska Lopez-Rivera, Meghan DJ Bragdon, Zeba Wunderlich, Javier Estrada, Angela H DePace

 

A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila. Berta Verd, Erik Clark, Karl R. Wotton, Hilde Janssens, Eva Jimenez-Guri, Anton Crombach, Johannes Jaeger

 

From pioneer to repressor: Bimodal foxd3 activity dynamically remodels neural crest regulatory landscape in vivo. Daria Gavriouchkina, Ruth M Williams, Martyna Lukoseviciute, Tatiana Hochgreb-Hagele, Upeka Senanayake, Vanessa Chong-Morrison, Supat Thongjuea, Emmanouela Repapi, Adam Mead, Tatjana Sauka-Spengler

 

Embryonic circular RNAs at tandem duplicated genes in zebrafish present new paradigm in gene expression. Vanessa Chong-Morrison, Tatjana Sauka-Spengler

 

 

Diversification of heart progenitor cells by EGF signaling and differential modulation of ETS protein activity. Benjamin Schwarz, Dominik Hollfelder, Katharina Scharf, Leonie Hartmann, Ingolf Reim

 

Single cell RNA-seq and ATAC-seq indicate critical roles of Isl1 and Nkx2-5 for cardiac progenitor cell transition states and lineage settlement. Guangshuai Jia, Jens Preussner, Stefan Guenther, Xuejun Yuan, Michail Yekelchyk, Carsten Kuenne, Mario Looso, Yonggang Zhou, Thomas Braun

 

Early Subset Of Cerebellar Nuclei Neurons Derived From Mesencephalon In Mice. Maryam Rahimi-Balaei, Xiaodan Jiao, Fiona Parkinson, Behzad Yeganeh, Hassan Marzban

 

Elevated and sustained reactive oxygen species levels facilitate mesoderm formation during early Xenopus development. Yue Han, Yaoyao Chen, Nick R Love, Shoko Ishibashi, Enrique Amaya

 

 

Ca2+-induced mitochondrial ROS regulate the early embryonic cell cycle. Yue Han, Shoko Ishibashi, Javier Iglesias-Gonzalez, Yaoyao Chen, Nick R Love, Enrique Amaya

 

Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg. Marc Stuart Presler, Elizabeth Van Itallie, Allon M. Klein, Ryan Kunz, Peg Coughlin, Leonid Peshkin, Steven Gygi, Martin Wühr, Marc Kirschner

 

Maternal proteins that are phospho-regulated upon egg activation include crucial factors for oogenesis, egg activation and embryogenesis in Drosophila melanogaster. Zijing Zhang, Amber R. Krauchunas, Stephanie Huang, Mariana F. Wolfner

 

Endodermal differentiation is reconstructed by coordination of two parallel signaling systems derived from the stele in roots. Pengxue Li, Qiaozhi Yu, Chunmiao Xu, Xu Gu, Shilian Qi, Hong Wang, Fenglin Zhong, Shuang Wu

 

Minimum requirements for reprogramming and maintaining cell fate in the Arabidopsis root. Colleen Drapek, Erin E. Sparks, Peter Marhavy, Tonni G. Andersen, Jessica H. Hennacy, Niko Geldner, Philip N. Benfey

 

LRX Proteins play a crucial role in pollen grain and pollen tube cell wall development. Tohnyui Ndinyanka Fabrice, Hannes Vogler, Christian Draeger, Gautam Munglani, Shibu Gupta, Aline Galatea Herger, Paul Knox, Ueli Grossniklaus, Christoph Ringli

 

Hominin-specific NOTCH2 paralogs expand human cortical neurogenesis through regulation of Delta/Notch interactions. Ikuo K Suzuki, David Gacquer, Roxane Van Heurck, Devesh Kumar, Marta Wojno, Angeline Bilheu, Adele Herpoel, Julian Cheron, Franck Polleux, Vincent Detours, Pierre Vanderhaeghen

 

Human-specific NOTCH-like genes in a region linked to neurodevelopmental disorders affect cortical neurogenesis. Ian T Fiddes, Gerrald A Lodewijk, Meghan M Mooring, Colleen M Bosworth, Adam D Ewing, Gary L Mantalas, Adam M Novak, Anouk van den Bout, Alex Bishara, Jimi L Rosenkrantz, Ryan Lorig-Roach, Andrew R Field, Maximillian Haeussler, Lotte Russo, Aparna Bhaduri, Tomasz J Nowakowski, Alex A Pollen, Max L Dougherth, Xander Nuttle, Marie-Claude Addor, Simon Zwolinski, Sol Katzman, Arnold Kreigstein, Evan E Eichler, Sofie R Salama, Frank MJ Jacobs, David Haussler

 

Skeletal muscle fibro-adipogenic progenitors of dystrophic mice are insensitive to NOTCH-dependent regulation of adipogenesis. Milica Marinkovic, Francesca Sacco, Filomena Spada, Lucia Lisa Petrilli, Claudia Fuoco, Elisa Micarelli, Theodora Pavlidou, Luisa Castagnoli, Matthias Mann, Cesare Gargioli, Gianni Cesareni

 

NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence. Aled J Parry, Matthew Hoare, Dóra Bihary, Robert Hänsel-Hertsch, Stephen Smith, Kosuke Tomimatsu, Shankar Balasubramanian, Hiroshi Kimura, Shamith Samarajiwa, Masashi Narita

 

 

Altered hsrω lncRNA levels in activated Ras background further enhance Ras activity in Drosophila eye and induces more R7 photoreceptors. Subhash C Lakhotia, Mukulika Ray

 

An atlas of Caenorhabditis elegans chemoreceptor expression. Berta Vidal, Ulkar Aghayeva, Haosheng Sun, Chen Wang, Lori Glenwinkel, Emily Bayer, Oliver Hobert

 

Bidirectional Cycling Dynamics of Living Neuronal Networks in Vitro. Arseniy Gladkov, Oleg Grinchuk, Yana Pigareva, Irina Mukhina, Victor Kazantsev, Alexey Pimashkin

 

Loss of Wt1 in the murine spinal cord alters interneuron composition and locomotion. Danny Schnerwitzki, Sharn Perry, Anna Ivanova, Fabio Viegas Caixeta, Paul Cramer, Sven Guenther, Kathrin Weber, Atieh Tafreshiha, Lore Becker, Ingrid L. Vargas Panesso, Thomas Klopstock, Martin Hrabe de Angelis, Manuela Schmidt, Klas Kullander, Christoph Englert

 

Smad9 is a key player of follicular selection in goose via keeping the balance of LHR transcription. Daolun Yu, Fanghui Chen, Li Zhang, Hejian Wang, Jie Chen, Zongmeng Zhang, Jie Li, Chaofeng Xing, Honglin Li, Jun Li, Yafei Cai

 

Widespread dynamic and pleiotropic expression of the melanocortin-1-receptor (MC1R) system is conserved across chick, mouse and human embryonic development. Anna Thomas, Pauline Heux, Chloe Santos, Wisenave Arulvasan, Nita Solanky, Magalie E. Carey, Dianne Gerrelli, Veronica A. Kinsler, Heather C. Etchevers

 

 

| Morphogenesis & mechanics

Size-reduced embryos reveal a gradient scaling based mechanism for zebrafish somite formation. Kana Ishimatsu, Tom W Hiscock, Zach M Collins, Dini Wahyu Kartika Sari, Kenny Lischer, David L. Richmond, Yasumasa Bessho, Takaaki Matsui, Sean G Megason

 

Spatio-temporal elasticity patterns in extracellular matrix during Hydra morphogenesis. Mariam Veschgini, Hendrik O Petersen, Wasim Abuillan, Fernanda F Rossetti, Suat Özbek, Manfred Burghammer, Thomas W Holstein, Motomu Tanaka

 

 

Selective Filopodia Adhesion Ensures Robust Cell Matching in the Drosophila Heart. ShaoBo Zhang, Christopher Amourda, Timothy Saunders

 

Junction-based lamellipodia drive endothelial cell rearrangements in vivo via a VE-cadherin/F-actin based oscillatory ratchet mechanism. Ilkka Paatero, Loic Sauteur, MInkyoung Lee, Anne Karine Lagendijk, Daniel Heutschi, Dimitri Bieli, Benjamin M. Hogan, Markus Affolter, Heinz-Georg Belting

 

 

Actomyosin contractility modulates Wnt signaling through adherens junction stability. Eric T. Hall, Elizabeth A. Hoesing, Endre D. Sinkovics, Esther M. Verheyen

 

PI(4,5)P2 forms dynamic cortical structures and directs actin distribution and cell polarity in C. elegans embryos. Melina J. Scholze, Kevin S. Barbieux, Alessandro De Simone, Mathilde Boumasmoud, Camille C. N. Suess, Ruijia Wang, Pierre Gonczy

 

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

 

 

Cerebellar granule cell precursors can extend processes, undergo short migratory movements and express postmitotic markers before mitosis in the chick EGL. Michalina Hanzel, Richard JT Wingate

 

Axons from the trigeminal ganglia are the earliest afferent projections to the mouse cerebellum. Hassan Marzban, Maryam Rahimi Balaei, Richard Hawkes

 

 

Formin3 regulates dendritic architecture via microtubule stabilization and is required for somatosensory nociceptive behavior. Ravi Das, Jamin M Letcher, Jenna M Harris, Istvan Foldi, Sumit Nanda, Hansley M Bobo, József Mihály, Giorgio A Ascoli, Daniel N Cox

 

Effects of mutating α-tubulin lysine 40 on sensory dendrite development. Brian Jenkins, Harriet A. J. Saunders, Helena L. Record, Dena M. Johnson-Schlitz, Jill Wildonger

 

Anisotropic Cellular Mechanoresponse for Radial Size Maintenance of Developing Epithelial Tubes. Tsuyoshi Hirashima, Taiji Adachi

 

Live imaging of heart tube development in mouse reveals alternating phases of cardiac differentiation and morphogenesis. Kenzo Ivanovitch, Susana Temino, Miguel Torres

 

| Genes & genomes

 

 

Transgenerational Epigenetic Inheritance Factors Localize to Spatially and Temporally Ordered Liquid Droplet Assemblages. Gang Wan, Brandon Fields, George Spracklin, Carolyn Phillips, Scott Kennedy

 

Olig2 and Hes regulatory dynamics during motor neuron differentiation revealed by single cell transcriptomics. Andreas Sagner, Zachary Gaber, Julien Delile, Jennifer H. Kong, David L. Rousso, Caroline A. Pearson, Steven E. Weicksel, Manuela Melchionda, Neda Mousavy Gharavy, James Briscoe, Bennett Novitch

 

 

Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast. Giuliano G Stirparo, Thorsten Boroviak, Ge Guo, Jennifer Nichols, Austin Smith, Paul Bertone

 

Allele-specific control of replication timing and genome organization during development. Juan Carlos Rivera-Mulia, Andrew Dimond, Daniel Vera, Claudia Trevilla-Garcia, Takayo Sasaki, Jared Zimmerman, Catherine Dupont, Joost Gribnau, Peter Fraser, David M Gilbert

 

The conserved LEM-3/Ankle1 nuclease is involved in the combinatorial regulation of meiotic recombination repair and chromosome segregation in Caenorhabditis elegans. YE HONG, Maria Velkova, Nicola Silva, Marlene Jagut, Viktor Scheidt, Karim Labib, Verena Jantsch, Anton Gartner

 

Re-arrangements in the cytoplasmic distribution of small RNAs following the maternal-to-zygotic transition in Drosophila embryos. Mehmet Ilyas Cosacak, Hatice Yigit, Bunyamin Akgul

 

Smg5 is required for multiple nonsense-mediated mRNA decay pathways in Drosophila. Jonathan O. Nelson, Dominique Foerster, Kimberly Frizzell, Stefan Luschnig, Mark M. Metzstein

 

Quantitative RNAseq Meta Analysis Of Alternative Exon Usage In C. elegans. Nicolas J. Tourasse, Jonathan R. M. Millet, Denis Dupuy

 

Dynamic reorganization of nuclear architecture during human cardiogenesis. Paul A Fields, Vijay Ramani, Giancarlo Bonora, Galip Gurkan Yardimci, Alessandro Bertero, Hans Reinecke, Lil Pabon, William S Noble, Jay Shendure, Charles Murry

 

Transcriptional profiling reveals extraordinary diversity among skeletal muscle tissues. Erin E. Terry, Xiping Zhang, Christy Hoffmann, Laura D. Hughes, Scott A. Lewis, Jiajia Li, Lance Riley, Nicholas F. Lahens, Ming Gong, Francisco Andrade, Karyn A. Esser, Michael E. Hughes

 

Deciphering cis-regulatory logic with 100 million synthetic promoters. Carl de Boer, Ronen Sadeh, Nir Friedman, Aviv Regev

 

Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic. Peter A. Combs, Hunter B. Fraser

 

Determinants of Transcription Initiation Directionality in Metazoans. Mahmoud M Ibrahim, Aslihan Karabacak, Alexander Glahs, Ena Kolundzic, Antje Hirsekorn, Alexa Carda, Baris Tursun, Robert P Zinzen, Scott A Lacadie, Uwe Ohler

 

Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter encoded enhancer activities. Sarah Rennie, Maria Dalby, Marta Lloret-Llinares, Stylianos Bakoulis, Christian Dalager Vaagenso, Torben Heick Jensen, Robin Andersson

 

Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus. Sofia A Quinodoz, Noah Ollikainen, Barbara Tabak, Ali Palla, Jan Marten Schmidt, Elizabeth Detmar, Mason Lai, Alexander Shishkin, Prashant Bhat, Vickie Trinh, Erik Aznauryan, Pamela Russell, Christine Cheng, Marko Jovanovic, Amy Chow, Patrick McDonel, Manuel Garber, Mitchell Guttman

 

CHRAC/ACF Contribute to the Repressive Ground State of Chromatin. Alessandro Scacchetti, Laura Brueckner, Dhawal Jain, Tamas Schauer, Xu Zhang, Frank Schnorrer, Bas van Steensel, Tobias Straub, Peter B. Becker

 

Strong binding activity of few transcription factors is a major determinant of open chromatin. Bei Wei, Arttu Jolma, Biswajyoti Sahu, Lukas M. Orre, Fan Zhong, Fangjie Zhu, Teemu Kivioja, Inderpreet Kaur Sur, Janne Lehtio, Minna Taipale, Jussi Taipale

 

Chromatin-release of the long ncRNA A-ROD is required for transcriptional activation of its target gene DKK1. Evgenia Ntini, Julia Liz, Jose M Muino, Annalisa Marsico, Ulf Andersson Oerom

 

LEM-3 is a midbody-tethered DNA nuclease that resolves chromatin bridges during cytokinesis. YE HONG, Remi Sonneville, Bin Wang, Viktor Scheidt, Bettina Meier, Alexander Woglar, Sarah Demetriou, Karim Labib, Verena Jantsch, Anton Gartner

 

Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules. Kelsey A. Maher, Marko Bajic, Kaisa Kajala, Mauricio Reynoso, Germain Pauluzzi, Donnelly A. West, Kristina Zumstein, Margaret Woodhouse, Kerry Bubb, Mike Dorrity, Christine Queitsch, Julia Bailey-Serres, Neelima Sinha, Siobhan M. Brady, Roger B. Deal

 

 

Chromatin accessibility changes between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks. Paja Sijacic, Marko Bajic, Elizabeth C. McKinney, Richard B. Meagher, Roger B. Deal

 

Distinct types of short open reading frames are translated in plant cells. Igor Fesenko, Ilya Kirov, Andrey Kniazev, Regina Khazigaleeva, Vassili Lazarev, Daria Kharlampieva, Ekaterina Grafskaia, Viktor Zgoda, Ivan Butenko, Georgy Arapidi, Anna Mamaeva, Vadim Ivanov, Vadim Govorun

 

Distinct stimulatory mechanisms regulate the catalytic activity of Polycomb Repressive Complex 2 (PRC2). Chul-Hwan Lee, Marlene Holder, Daniel Grau, Ricardo Saldana-Meyer, Rais Ahmad Ganai, Jenny Zhang, Miao Wang, Marc-Werner Dobenecker, Danny Reinberg, Karim-Jean Armache

 

Functional redundancy of variant and canonical histone H3 lysine 9 modification in Drosophila. Taylor J. R. Penke, Daniel J. McKay, Brian D. Strahl, A. Gregory Matera, Robert J. Duronio

 

The function of the prereplicative complex and SCF complex components during Drosophila wing development. Hidetsugu Kohzaki

 

 

PWO1 interacts with PcG proteins and histones to regulate Arabidopsis flowering and development. Mareike L Hohenstatt, Pawel Mikulski, Olga Komarynets, Constanze Klose, Ina Kycia, Albert Jeltsch, Sara Farrona, Daniel Schubert

 

PWWP INTERACTOR OF POLYCOMBS (PWO1) links PcG-mediated gene repression to the nuclear lamina in Arabidopsis. Pawel Mikulski, Mareike L Hohenstatt, Sara Farrona, Cezary Smaczniak, Kerstin Kaufmann, Gerco Angenent, Daniel Schubert

 

The HoxD Cluster is a Dynamic and Resilient TAD Boundary Controling the Segregation of Antagonistic Regulatory Landscapes. Eddie Rodriguez-Carballo, Lucille Lopez-Delisle, Ye Zhan, Pierre Fabre, Leonardo Beccari, Imane El-Idrissi, Thi Hahn Nguyen Huynh, Hakan Ozadam, Job Dekker, Denis Duboule

 

Cohesin facilitates zygotic genome activation in zebrafish. Michael Meier, Jenny Grant, Amy Dowdle, Amarni Thomas, Jennifer E. Gerton, Philippe Collas, Justin M. O’Sullivan, Julia A. Horsfield

 

CTCF mediated genome architecture regulates the dosage of mitotically stable mono-allelic expression of autosomal genes. Keerthivasan Raanin Chandradoss, Kuljeet Singh Sandhu

 

Interdependent and separable functions of C. elegans MRN-C complex members couple formation and repair of meiotic DSBs. Chloe Girard, Baptiste Roelens, Karl A. Zawadzki, Anne M. Villeneuve

 

LINE-2 transposable elements shape post-transcriptional gene regulation in the human brain. Rebecca Petri, Per Ludvik Brattås, Marie E. Jönsson, Karolina Pircs, Johan Bengzon, Johan Jakobsson

 

No kissing in the nucleus: Unbiased analysis reveals no evidence of trans chromosomal regulation of mammalian immune development. Timothy M Johanson, Hannah D Coughlan, Aaron TL Lun, Naiara G Bediaga, Gaetano Naselli, Alexandra L Garnham, Leonard C Harrison, Gordon K Smyth, Rhys S Allan

 

The Transcriptional Logic of Mammalian Neuronal Diversity. Ken Sugino, Erin Clark, Anton Schulmann, Yasuyuki Shima, Lihua Wang, David L. Hunt, Bryan M. Hooks, Dimitri Trankner, Jayaram Chandrashekar, Serge Picard, Andrew Lemire, Nelson Spruston, Adam Hantman, Sacha B. Nelson

 

 

| Stem cells, regeneration & disease modelling

 

Signaling-dependent control of apical membrane size and self-renewal in rosette-stage human neuroepithelial stem cells. Jan-Philip Medelnik, Kathleen Roensch, Satoshi Okawa, Antonio del Sol, Osvaldo Chara, Levan Mchedlishvili, Elly Tanaka

 

Fractone bulbs derive from ependymal cells and their laminin composition influence the stem cell niche in the subventricular zone. Marcos Assis Nascimento, Lydia Sorokin, Tatiana Coelho-Sampaio

 

Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPS cells. Kai Fu, Constantinos Chronis, Abdenour Soufi, Giancarlo Bonora, Miguel Edwards, Steve Smale, Kenneth Zaret, Kathrin Plath, Matteo Pellegrini

 

Differentiation of primate primordial germ cell-like cells following transplantation into the adult gonadal niche. Enrique Sosa, Di Chen, Ernesto J Rojas, Jon Hennebold, Karen Peters, Zhuang Wu, Truong N Lam, Jennifer Mitchell, Ramesh Tailor, Marvin Meistrich, Kyle Orwig, Gunapala Shetty, Amander T Clark

 

Temporal epigenomic profiling identifies AHR as dynamic super-enhancer controlled regulator of mesenchymal multipotency. Deborah Gerard, Florian Schmidt, Aurelien Ginolhac, Martine Schmitz, Rashi Halder, Peter Ebert, Marcel H. Schulz, Thomas Sauter, Lasse Sinkkonen

 

Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells. Natalia Pietrosemoli, Sebastien Mella, Siham Yennek, Meryem Baghdadi, Hiroshi Sakai, Ramkumar Sambasivan, Francesca Pala, DANIELA DI GIROLAMO, Shahragim Tajbakhsh

 

Single-cell quantitative analysis of skeletal muscle cell population dynamics during regeneration and ageing. Lucia Lisa Petrilli, Filomena Spada, Claudia Fuoco, Elisa Micarelli, Alessio Reggio, Marco Rosina, Cesare Gargioli, Luisa Castagnoli, Gianni Cesareni

 

Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli are Altered with Age. Mati Mann, Arnav Mehta, Carl de Boer, Monika S. Kowalczyk, Kevin Lee, Noga Rogel, Abigail R. Knecht, Daneyal Farouq, Aviv Regev, David Baltimore

 

T helper cells modulate intestinal stem cell renewal and differentiation. Moshe Biton, Adam Haber, Semir Beyaz, Noga Rogel, Christopher Smillie, Karthik Shekhar, Alexandra Schnell, Zuojia Chen, Chuan Wu, Jose Ordovas-Montanes, David Alvarez, Rebecca H. Herbst, Itay Tirosh, Grace Burgin, Danielle Dionne, Michael E. Xifaras, Mei Zhang, Alex K. Shalek, Ulrich H. von Andrian, Daniel B. Graham, Orit Rozenblatt-Rosen, Hai Ning Shi, Vijay Kuchroo, Omer Yilmaz, Aviv Regev, Ramnik J. Xavier

 

The CD11a and EPCR marker combination simplifies and improves the purification of mouse hematopoietic stem cells. Alborz Karimzadeh, Vanessa Scarfone, Connie Chao, Karin Grathwohl, John W. Fathman, David Fruman, Thomas Serwold, Matthew Inla

 

Instructive starPEG-Heparin biohybrid 3D cultures for modeling human neural stem cell plasticity, neurogenesis, and neurodegeneration. Christos Papadimitriou, Mehmet I Cosacak, Violeta Mashkaryan, Hilal Celikkaya, Laura Bray, Prabesh Bhattarai, Heike Hollak, Xin Chen, Shuijin He, Christopher L Antos, Alvin Thomas, Jens Friedrichs, Andreas Dahl, Yixin Zhang, Uwe Freudenberg, Carsten Werner, Caghan Kizil

 

Intestinal crypts recover rapidly from focal damage with coordinated motion of stem cells that is impaired by aging. Jiahn Choi, Nikolai Rakhilin, Poornima Gadamsetty, Daniel J. Joe, Tahmineh Tabrizian, Steven M. Lipkin, Derek Huffman, Xiling Shen, Nozomi Nishimura

 

 

Generation of Mouse-Zebrafish Hematopoietic Tissue Chimeric Embryos for Hematopoiesis and Host-Pathogen Interaction Studies. Margarita M. Parada-Kusz, Anne Clatworthy, Elliott J. Hagedorn, Cristina Penaranda, Anil V. Nair, Jonathan E. Henninger, Christoph Ernst, Brian Li, Raquel Riquelme, Humberto Jijon, Eduardo J. Villablanca, Leonard I. Zon, Deborah Hung, Miguel Allende

 

Continuous high-resolution in vivo imaging reveals tumor-specific dissemination in an embryonic zebrafish xenograft model. Nandini Asokan, Stephan Daetwyler, Stefanie Nadine Bernas, Christopher Schmied, Steffen Volger, Katrin Lambert, Manja Wobus, Martin Wermke, Gerd Kempermann, Jan Huisken, Michael Brand, Martin Bornhaeuser

 

 

Mutations in C11ORF70 cause primary ciliary dyskinesia with randomization of left/right body asymmetry due to outer and inner dynein arm defects. Inga M Höben, Rim Hjeij, Heike Olbrich, Gerard W Dougherty, Tabea Menchen, Isabella Aprea, Diana Frank, Petra Pennekamp, Bernd Dworniczak, Julia Wallmeier, Johanna Raidt, Kim G Nielsen, Maria C Philipsen, Francesca Santamaria, Laura Venditto, Israel Amirav, Freerk Prenzel, Kaman Wu, Miriam Schmidts, Niki T Loges, Heymut Omran

 

A phase separated organelle at the root of motile ciliopathy. Ryan Huizar, Chanjae Lee, Alexander Boulgakov, Amjad Horani, Fan Tu, Kevin Drew, Edward Marcotte, Steven Brody, John Wallingford

 

Phenotyping ciliary dynamics and coordination in response to CFTR-modulators in Cystic Fibrosis respiratory epithelial cells. Maurizio Chioccioli, Luigi Feriani, Jurij Kotar, Preston E. Bratcher,  Pietro Cicuta

 

Gene expression in cord blood links genetic risk for neurodevelopmental disorders with maternal psychological distress and adverse childhood outcomes. Michael S. Breen, Aliza P. Wingo, Nastassja Koen, Kirsten A. Donald, Heather J. Zar, Kerry J. Ressler, Joseph D. Buxbaum, Dan J. Stein

 

Developmental And Genetic Regulation Of The Human Cortex Transcriptome In Schizophrenia. Andrew E Jaffe, Richard E Straub, Joo Heon Shin, Ran Tao, Yuan Gao, Leonardo Collado Torres, Tony Kam-Thong, Hualin S Xi, Jie Quan, Qiang Chen, Carlo Colantuoni, William S Ulrich, Brady J Maher, Amy Deep-Soboslay, The BrainSeq Consortium, Alan Cross, Nicholas J Brandon, Jeffrey T Leek, Thomas M Hyde, Joel E Kleinman, Daniel R Weinberger

 

Gene expression imputation across multiple brain regions reveals schizophrenia risk throughout development. Laura M Huckins, Amanda Dobbyn, Douglas Ruderfer, Gabriel Hoffman, Weiqing Wang, Antonio F Pardinas, Veera M Rajagopal, Thomas D Als, Hoang Tan Hoang, Kiran Girdhar, James Boocock, Panagiotis Roussos, Menachem Fromer, Robin Kramer, Enrico Domenici, Eric Gamazon, Shaun Purcell, CommonMind Consortium, Schizophrenia Working Group of the Psychiatric Gen, iPSYCH-GEMS Schizophrenia Working Group, Ditte Demontis, Anders Borglum, James Walters, Michael O’Donovan, Patrick F Sullivan, Micahel Owen, Bernie Devlin, Solveig K Sieberts, Nancy Cox, Hae Kyung Im, Pamela Sklar, Eli Ayumi Stahl

 

Germ line aging and regional epigenetic instability: age prediction using human sperm DNA methylation signatures. Timothy G Jenkins, Kenneth I Aston, Douglas T Carrell

 

Aging and neurodegeneration are associated with increased mutations in single human neurons. Michael A Lodato, Rachel E Rodin, Craig L Bohrson, Michael E Coulter, Alison R Barton, Minseok Kwon, Maxwell A Sherman, Carl M Vitzhum, Lovelace J Luquette, Chandri Yandava, Pengwei Yang, Thomas W Chittenden, Nicole E Hatem, Steven C Ryu, Mollie B Woodworth, Peter J Park, Christopher A Walsh

 

Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins. Yunzhang Wang, Robert Karlsson, Erik Lampa, Qian Zhang, Åsa K. Hedman, Malin Almgren, Catarina Almqvist, Allan F. McRae, Riccardo Marioni, Erik Ingelsson, Peter M. Visscher, Ian J. Deary, Lars Lind, Tiffany Morris, Stephan Beck, Nancy L. Pedersen, Sara Hägg

 

 

Identification of key pathways and metabolic fingerprints of longevity in C. elegans. Arwen Gao, Reuben Smith, Michel Van Weeghel, Rashmi Kamble, Riekelt Houtkooper

 

An essential post-developmental role for Lis1 in mice. Timothy J Hines, Xu Gao, Subhshri Sahu, Meghann M Lange, Jill R Turner, Jeffery L Twiss, Deanna S Smith

 

A urine-dependent human urothelial organoid offers a promising alternative to rodent models of infection. Harry Horsley, Dhanuson Dharmasena, James Malone-Lee, Jennifer L. Rohn

 

Germline loss of MBD4 predisposes to leukaemia due to a mutagenic cascade driven by 5mC. Mathijs A. Sanders, Edward Chew, Christoffer Flensburg, Annelieke Zeilemaker, Sarah E. Miller, Adil al Hinai, Ashish Bajel, Bram Luiken, Melissa Rijken, Tamara Mclennan, Remco M. Hoogenboezem, François G. Kavelaars, Marnie E. Blewitt, Eric M. Bindels, Warren S. Alexander, Bob Löwenberg, Andrew W. Roberts, Peter J. M. Valk, Ian Majewski

 

An Essential Role for Argonaute 2 in EGFR-KRAS Signaling in Pancreatic Cancer Development. Sunita Shankar, Jean Tien, Ronald F Siebenaler, Vijaya L Dommeti, Sylvia Zelenka-Wang, Kristin M Juckette, Alice Xu, Malay Mody, Andrew Goodrum, Grace Tsaloff, Ingrid J Apel, Lisha Wang, Javed Siddiqui, Jiaqi Shi, Chandan Kumar-Sinha, Arul M Chinnaiyan

 

 

Neutrophil adhesion in brain capillaries contributes to cortical blood flow decreases and impaired memory function in a mouse model of Alzheimer’s disease. Jean C. Cruz Hernandez, Oliver Bracko, Calvin J. Kersbergen, Victorine Muse, Mohammad Haft-Javaherian, Maxime Berg, Laibaik Park, Lindsay K. Vinarcsik, Iryna Ivasyk, Yiming Kang, Marta Cortes-Canteli, Myriam Peyrounette, Vincent Doyeux, Amy Smith, Joan Zhou, Gabriel Otte, Jeffrey D. Beverly, Elizabeth Davenport, Yohan Davit, Sidney Strickland, Costantino Iadecola, Sylvie Lorthois, Nozomi Nishimura, Chris B. Schaffer

 

PPARD regulation in gastric progenitor cells drives gastric tumorigenesis in mice. Xiangsheng Zuo, Yasunori Deguchi, Weiguo Xu, Daoyan Wei, Rui Tian, Weidong Chen, Micheline J. Moussalli, Yi Liu, Fei Mao, Min Xu, Yaying Yang, Shen Gao, Jonathan C. Jaoude, Fuyao Liu, Mihai Gagea, Russell Broaddus, Keping Xie, Imad Shureiqi

 

L-tyrosine supplementation is not therapeutic for skeletal muscle dysfunction in zebrafish and mouse models of dominant skeletal muscle α-actin nemaline myopathy. Adriana M. Messineo, Charlotte Gineste, Tamar E. Sztal, Elyshia L McNamara, Christophe Vilmen, Augustin C. Ogier, Dorothee Hahne, David Bendahan, Nigel G. Laing, Robert J. Bryson-Richardson, Julien Gondin, Kristen J. Nowak

 

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes. David A. Knowles, Courtney K. Burrows, John D. Blischak, Kristen M. Patterson, Carole Ober, Jonathan K. Pritchard, Yoav Gilad

 

Endothelial Cell-Specific MCPIP Deletion Causes Endothelial Dysfunction and Impairs Post-ischemic Angiogenesis in Vivo. Jianli Niu, Nidhi Kapoor, Jian Liang, Zhuqing Jin, Edilu Becerra, Pappachan E. Kolattukudy

 

PKD2 is an essential ion channel subunit in the primary cilium of the renal collecting duct epithelium. Xiaowen Liu, Thuy Vien, Jingjing Duan, Shu-Hsien Sheu, Paul G. DeCaen, David E. Clapham

 

Cadmium exposure inhibits branching morphogenesis and causes alterations consistent with HIF-1α inhibition in human primary breast organoids. Sabrina A. Rocco, Lada Koneva, Lauren Y. M. Middleton, Tasha Thong, Sumeet Solanki, Sarah Karram, Kowit Nambunmee, Craig Harris, Laura S. Rozek, Maureen A. Sartor, Yatrik M. Shah, Justin Colacino

 

Genomic Locus Modulating Corneal Thickness in the Mouse Identifies POU6F2 as a Potential Risk of Developing Glaucoma. Rebecca King, Felix L. Struebing, Ying Li, Jiaxing Wang, Allison Ashley Koch, Jessica Cooke Bailey, Puya Gharahkhan, Stuart MacGregor, R. Rand Allingham, Michael A. Hauser, Janey L. Wiggs, Eldon E. Geisert

 

Clonal analysis of newborn hippocampal dentate granule cell proliferation and development in temporal lobe epilepsy. Shatrunjai P. Singh, Candi L. LaSarge, Amen An, John J. McAuliffe, Steve C. Danzer

 

Evo-devo & evo

Hox genes pattern the primary body axis of an anthozoan cnidarian prior to gastrulation. Timothy Q. DuBuc, Thomas B. Stephenson, Amber N. Rock, Mark Q. Martindale

 

 

Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution. Sebastian Kittelmann, Alexandra D. Buffry, Isabel Almudi, Marianne Yoth, Gonzalo Sabaris, Franziska A. Franke, Juan Pablo Couso, Maria D. S. Nunes, Nicolas Frankel, Jose Luis Gomez-Skarmeta, Jose Pueyo-Marques, Saad Arif, Alistair P. McGregor

 

 

Duplication and divergence of Sox genes in spiders. Christian L. B. Paese, Daniel J. Leite, Anna Schoenauer, Alistair P. McGregor, Steven Russell

 

Pervasive correlated evolution in gene expression shapes cell type transcriptomes. Cong Liang, Jacob M. Musser, Alison Cloutier, Richard Prum, Gunter Wagner

 

How morphological development can guide evolution. Sam Kriegman, Nick Cheney, Josh Bongard

 

Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages. Dennis Kostka, Alisha K. Holloway, Katherine Pollard

 

Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex. Marta Florio, Michael Heide, Holger Brandl, Anneline Pinson, Sylke Winkler, Pauline Wimberger, Wieland B. Huttner, Michael Hiller

 

Developmental constraints on genome evolution in four bilaterian model species. Jialin Liu, Marc Robinson-Rechavi

 

 

The role of chromosomal inversions in speciation. Zachary Fuller, Christopher Leonard, Randee Young, Stephen Schaeffer, Nitin Phadnis

 

Gene regulatory network rewiring by an adaptively evolving microRNA cluster in Drosophila. Yang Lyu, Zhongqi Liufu, Juan Xiao, Yuxin Chen, Chung-I Wu, Tian Tang

 

Rapid evolution of gained essential developmental functions of a young gene via interactions with other essential genes. Yuh Chwen G Lee, Iuri M Ventura, Gavin R Rice, Don-Yuan Chen, Manyuan Long

 

The asexual genome of Drosophila. Stephan Schiffels, Ville Mustonen, Michael Lässig

 

Improved genome assembly and annotation for the rock pigeon (Columba livia). Carson Holt, Michael Campbell, David Keays, Nathaniel Edelman, Aurelie Kapusta, Emily Maclary, Eric Domyan, Alexander Suh, Wesley Warrenb, Mark Yandell, Thomas Gilbert, Michael D. Shapiro

 

Hemimetabolous genomes reveal molecular basis of termite eusociality. Mark C. Harrison, Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Johannes Gowin, Carolin Greiner, Yi Han, Haofu Hu, Daniel S. T. Hughes, Ann-Kathrin Huylmans, Carsten Kemena, Lukas P. M. Kremer, Sandra L. Lee, Alberto Lopez-Ezquerra, Ludovic Mallet, Jose M. Monroy-Kuhn, Annabell Moser, Shwetha C. Murali, Donna M. Muzny, Saria Otani, Maria-Dolors Piulachs, Monica Poelchau, Jiaxin Qu, Florentine Schaub, Ayako Wada-Katsumata, Kim C. Worley, Qiaolin Xie, Guillem Ylla, Michael Poulsen, Richard A. Gibbs, Coby Schal, Stephen Richards, Xavier Belles, Judith Korb, Erich Bornberg-Bauer

 

 

Insights into platypus population structure and history from whole-genome sequencing. Hilary C Martin, Elizabeth M Batty, Julie Hussin, Portia Westall, Tasman Daish, Stephen Kolomyjec, Paolo Piazza, Rory Bowden, Margaret Hawkins, Tom Grant, Craig Moritz, Frank Grutzner, Jaime Gongora, Peter Donnelly

 

Reduction in major transcription factor binding domain families during the evolution of the avian lineage. Allie M. Graham, Jason S. Presnell

 

Host shifts result in parallel genetic changes when viruses adapt to closely related species. Ben Longdon, Jonathan P Day, Joel M Alves, Sophia CL Smith, Thomas M Houslay, John E McGonigle, Lucia Tagliaferri, Francis M Jiggins

 

Overlooked polyploidies in lycophytes generalize their roles during the evolution of vascular plants. Jinpeng Wang, Jigao Yu, Pengchuan Sun, Chao Li, Xiaoming Song, Tianyu Lei, Yuxian Li, Jiaqing Yuan, Sangrong Sun, Hongling Ding, Xueqian Duan, Shaoqi Shen, Yanshuang Shen, Jing Li, Fanbo Meng, Yangqin Xie, Jianyu Wang, Yue Hou, Jin Zhang, Xianchun Zhang, Xiyin Wang

 

A primitive starfish ancestor from the Early Ordovician of Morocco reveals the origin of crown group Echinodermata. Aaron W. Hunter, Javier Ortega-Hernandez

 

Russian Doll Genes and Complex Chromosome Rearrangements in Oxytricha trifallax. Jasper Braun, Lukas Nabergall, Rafik Neme, Laura F Landweber, Masahico Saito, Natasha Jonoska

 

Nearly Neutral Evolution Across the Drosophila melanogaster Genome. David Castellano, Jennifer James, Adam Eyre-Walker

 

 

Cell biology

Formation and disassembly of a contractile actomyosin network mediates content release from large secretory vesicles. Dagan Segal, Assaf Zaritsky, Eyal D. Schejter, Ben Zion Shilo

 

 

Variation in traction forces during cell cycle progression. Benoit Vianay, Fabrice Senger, Simon Alamos, Maya Anjur-Dietrich, Elizabeth Bearce, Bevan Cheeseman, Lisa Lee, Manuel Thery

 

Cell size control driven by the circadian clock and environment in cyanobacteria. Bruno M. C. Martins, Amy K. Tooke, Philipp Thomas, James C. W. Locke

 

RodZ promotes MreB polymer formation and curvature localization to determine the cylindrical uniformity of E. coli shape. Randy M Morgenstein, Benjamin P Bratton, Joshua W Shaevitz, Zemer Gitai

 

Giant flagellins form thick flagellar filaments in two species of marine Gammaproteobacteria. Nicholas Maitland Thomson, Josie L Ferreira, Teige R Matthews-Palmer, Morgan Beeby, Mark J Pallen

 

Uncoupling Intraflagellar Transport and Primary Cilia Formation Demonstrates Deep Integration of IFT in Hedgehog Signaling. Thibaut Eguether, Fabrice P Cordelieres, Gregory J Pazour

 

 

CDC20B is required for deuterosome-mediated centriole production in multiciliated cells. Diego R. Revinski, Laure-Emmanuelle Zaragosi, Camille Boutin, Sandra Ruiz-Garcia, Marie Deprez, Olivier Rosnet, Virginie Thome, Olivier Mercey, Agnes Paquet, Nicolas Pons, Brice Marcet, Laurent Kodjabachian, Pascal Barbry

 

Structural centrosome aberrations promote non-cell-autonomous invasiveness. Olivier Ganier, Dominik Schnerch, Philipp Oertle, Roderick Y. H. Lim, Marija Plodinec, Erich A. Nigg

 

A robust and tunable mitotic oscillator in artificial cells. Ye Guan, Zhengda Li, Shiyuan Wang, Patrick M. Barnes, Xuwen Liu, Haotian Xu, Minjun Jin, Allen P. Liu, Qiong Yang

 

Exportin Crm1 is repurposed as a docking protein to generate microtubule organizing centers at the nuclear pore. Xun Bao, Christos Spanos, Tomoko Kojidani, Eric Lynch, Juri Rappsilber, Yasushi Hiraoka, Tokuko Haraguchi, Kenneth Sawin

 

Endocytosis caused by liquid-liquid phase separation of proteins. Louis-Philippe Bergeron-Sandoval, Hossein Khadivi Heris, Adam G. Hendricks, Allen J. Ehrlicher, Paul Francois, Rohit V. Pappu, Stephen W. Michnick

 

Systematic analysis of the molecular architecture of endocytosis reveals a nanoscale actin nucleation template that drives efficient vesicle formation. Markus Mund, Johannes Albertus van der Beek, Joran Deschamps, Serge Dmitrieff, Jooske Louise Monster, Andrea Picco, Francois Nedelec, Marko Kaksonen, Jonas Ries

 

The contributions of the actin machinery to endocytic membrane bending and vesicle formation. Andrea Picco, Wanda Kukulski, Hetty E. Manenschijn, Tanja Specht, John A. G. Briggs, Marko Kaksonen

 

 

CYRI (FAM49) proteins are local inhibitors of Scar/WAVE induced lamellipodia that bind directly to active Rac1. Loic Fort, Jose Batista, Peter A Thomason, Heather J Spence, Jennifer Greaves, Kirsty J Martin, Kurt I Anderson, Peter Brown, Sergio Lilla, Matthwe P Neilson, Petra Tafelmeyer, Sara Zanivan, Shehab Ismail, Nicholas C.O. Tomkinson, Luke H Chamberlain, Robert H Insall, Laura M Machesky

 

Dynein dynamics at the microtubule plus-ends and cortex during division in the C. elegans zygote. Ruddi Rodriguez-Garcia, Laurent Chesneau, Sylvain Pastezeur, Julien Roul, Marc Tramier, Jacques Pecreaux

 

The tumor suppressor APC is an attenuator of spindle-pulling forces during C. elegans asymmetric cell division. Kenji Sugioka, Lars-Eric Fielmich, Kota Mizumoto, Bruce Bowerman, Sander van den Heuvel, Akatsuki Kimura, Hitoshi Sawa

 

Dissecting single cell molecular spatiotemporal mobility and clustering at Focal Adhesions in polarised cells by fluorescence fluctuation spectroscopy methods. Jorge Bernardino de la Serna, Esther Garcia

 

Stopping Transformed Growth with Cytoskeletal Proteins: Turning a Devil into an Angel. Bo Yang, Haguy Wolfenson, Naotaka Nakazawa, Shuaimin Liu, Junqiang Hu, Michael Sheetz

 

 

Modelling

 

 

Model reduction permits Turing instability analysis of arbitrary reaction-diffusion models. Stephen Smith, Neil Dalchau

 

The phenomenon of growing surface interference explains the rosette pattern of jaguar. Michäel Dougoud, Christian Mazza, Beat Schwaller, Laszlo Pecze

 

 

Dynamic gradient scaling as a critical point of growth control. Daniel Aguilar Hidalgo, Steffen Werner, Ortrud Wartlick, Marcos González-Gaitán, Benjamin Friedrich, Frank Jülicher

 

Temporal precision of regulated gene expression. Shivam Gupta, Julien Varennes, Hendrik C. Korswagen, Andrew Mugler

 

A biophysical model explains the spontaneous bursting behavior in the developing retina. Dora Karvouniari, Lionel Gil, Olivier Marre, Serge Picaud, Bruno Cessac

 

An efficient gene regulatory network inference algorithm for early Drosophila melanogaster embryogenesis. Hirotaka Matsumoto, Hisanori Kiryu, Yasuhiro Kojima, Suguru Yaginuma, Itoshi Nikaido

 

 

Turbulent dynamics of epithelial cell cultures. C. Blanch-Mercader, V. Yashunsky, S. Garcia, G. Duclos, L. Giomi, P. Silberzan

 

 

Mechanical characterisation of disordered and anisotropic cellular monolayers. Alexander Nestor-Bergmann, Emma Johns, Sarah Woolner, Oliver E. Jensen

 

Do cells sense time by number of divisions? Zeev Schuss, Kimsy Tor, David Holcman

 

Euplotid: A quantized geometric model of the eukaryotic cell. Diego Borges-Rivera

 

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

 

A biophysical dynamic module for the polarisation of auxin efflux carriers PIN-FORMED (PIN). Valeria Hernandez-Hernandez, Rafael A. Barrio, Mariana Benitez, Naomi Nakayama, Jose Roberto Romero-Arias, Carlos Villarreal

 

Discrete and continuum approximations for collective cell migration in a scratch assay with cell size dynamics. Oleksii M Matsiaka, Catherine Penington, Ruth E Baker, Matthew Simpson

 

Shaping Epigenetic Memory via Genomic Bookmarking. Davide Michieletto, Michael Chiang, Davide Coli, Argyris Papantonis, Enzo Orlandini, Peter R. Cook, Davide Marenduzzo

 

Subtle alteration in microRNA dynamics accounts for differential nature of cellular proliferation. Dola Sengupta, Vinodhini Govindaraj, Sandip Kar

 

Mathematics at the eve of a historic transition in biology. Guo-Wei Wei

 

Tools & resources

| Imaging etc.

 

 

EpiGraph: an open-source platform to quantify epithelial organization. Pablo Vicente-Munuera, Pedro Gomez-Galvez, Antonio Tagua, Marta Letran, Yanlan Mao, Luis M. Escudero

 

 

An adaptable chromosome preparation methodology for use in invertebrate research organisms. Longhua Guo, Alice Accorsi, Shuonan He, Carlos Guerrero-Hernández, Shamilene Sivagnanam, Sean McKinney, Matthew Gibson, Alejandro Sánchez Alvarado

 

Combined flow cytometry and high throughput image analysis for the study of essential genes in Caenorhabditis elegans. Blanca Hernando-Rodríguez, Annmary Paul Erinjeri, María Jesús Rodríguez-Palero, Val Millar, Sara González-Hernández, María Olmedo, Bettina Schulze, Ralf Baumeister, Manuel J. Muñoz, Peter Askjaer, Marta Artal-Sanz

 

A method to keep the excitation light sheet in focus in selective plane illumination microscopy. Liang Gao

 

Topography and refractometry of sperm cells using SLIM. Lina Liu, Mikhail E Kandel, Marcello Rubessa, Sierra Schreiber, Mathew Wheeler, Gabriel Popescu

 

Simultaneously measuring image features and resolution in live-cell STED images. Andrew E. S. Barentine, Lena K. Schroeder, Michael Graff, David Baddeley, Joerg Bewersdorf

 

 

 

3D label-free imaging and analysis of Pinus pollen grains using optical diffraction tomography. Geon Kim, SangYun Lee, Seungwoo Shin, YongKeun Park

 

Three dimensional cross-modal image inference: label-free methods for subcellular structure prediction. Chek Ounkomol, Daniel A. Fernandes, Sharmishtaa Seshamani, Mary M. Maleckar, Forrest Collman, Gregory R. Johnson

 

Optical crosstalk in SPAD arrays for high-throughput single-molecule fluorescence spectroscopy. Antonino Ingargiola, Maya Segal, Angelo Gulinatti, Ivan Rech, Ivan Labanca, Piera Maccagnani, Massimo Ghioni, Shimon Weiss, Xavier Michalet

 

Recording neural activity in unrestrained animals with 3D tracking two photon microscopy. Doycho Karagyozov, Mirna Mihovilovic Skanata, Amanda Lesar, Marc Gershow

 

 

A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein. Yi Shen, Hod Dana, Ahmed S. Abdelfattah, Ronak Patel, Jamien Shea, Rosana S. Molina, Bijal Rawal, Vladimir Rancic, Yu-Fen Chang, Lanshi Wu, Yingche Chen, Yong Qian, Matthew D. Wiens, Nathan Hambleton, Klaus Ballanyi, Thomas E. Hughes, Mikhail Drobizhev, Douglas S. Kim, Minoru Koyama, Eric R. Schreiter, Robert E. Campbell

 

A FRET based biosensor for measuring Gα13 activation in single cells. Marieke Mastop, Nathalie R. Reinhard, Cristiane R. Zuconelli, Fenna Terwey, Theodorus W. J. Gadella Sr., Jakobus van Unen, Merel J. W. Adjobo-Hermans, Joachim Goedhart

 

Understanding boundary effects and confocal optics enables quantitative FRAP analysis in the confined geometries of animal, plant, and fungal cells. James L Kingsley, Jeffrey P Bibeau, Iman Mousavi, Cem Unsal, Zhilu Chen, Xinming Huang, Luis Vidali, Erkan Tuzel

 

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos. Vikas Trivedi, Harry M. T. Choi, Scott E. Fraser, Niles A. Pierce

 

Single-molecule fluorescent amplification of RNA using clampFISH probes. Sara H Rouhanifard, Margaret Dunagin, Ian A Mellis, Sareh Bayatpour, Orsolya Symmons, Allison Cote, Arjun Raj

 

An optimized pipeline for parallel image-based quantification of gene expression and genotyping after in situ hybridization. Tomasz Dobrzycki, Monika Krecsmarik, Florian Bonkhofer, Roger K Patient, Rui Monteiro

 

Quantitative methods to investigate the 4D dynamics of heterochromatic repair sites in Drosophila cells. Christopher P Caridi, Laetitia Delabaere, Harianto Tjong, Hannah Hopp, Devika Das, Frank Alber, Irene Chiolo

 

In vivo multiphoton fluorescence imaging with polymer dots. Ahmed M Hassan, Xu Wu, Jeremy W Jarrett, Shihan Xu, David R Miller, Jiangbo Yu, Evan P Perillo, Yen-Liang Liu, Daniel T Chiu, Hsin-Chih Yeh, Andrew K Dunn

 

 

Eukaryotically expressed encapsulins as orthogonal compartments for multiscale molecular imaging. Felix Sigmund, Christoph Massner, Philipp Erdmann, Anja Stelzl, Hannes Rolbieski, Helmut Fuchs, Martin Hrabe de Angelis, Mitul Desai, Sarah Bricault, Alan Jasanoff, Vasilis Ntziachristos, Juergen Plitzko, Gil Gregor Westmeyer

 

Brillouin microscopy, what is it really measuring? Pei-Jung Wu, Irina Kabakova, Jeffrey Ruberti, Joseph M. Sherwood, Iain E. Dunlop, Carl Paterson, Peter Török, Darryl R. Overby

 

REASSESSING THE REVOLUTIONS RESOLUTIONS. Marin van Heel, Michael Schatz

 

Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy. Massimiliano Bonomi, Riccardo Pellarin, Michele Vendruscolo

 

ShuTu: Open-Source Software for Efficient and Accurate Reconstruction of Dendritic Morphology. Dezhe Z. Jin, Ting Zhao, David Hunt, Rachel Pearcy, Ching-Lung Hsu, Nelson Spruston

 

 

Automated 3D Neuron Tracing with Precise Branch Erasing and Confidence Controlled Back-Tracking. Siqi Liu, Donghao Zhang, Yang Song, Hanchuan Peng, Weidong Cai

 

MICCS: A Fully Programmable Multipurpose Integrated Cell Culture System. Timothy Kassis, Paola M. Perez, Chloe J. W. Yang, Luis R. Soenksen, David L. Trumper, Linda G. Griffith

 

Visual Representation of Experimental Protocols. James Scott-Brown, Antonis Papachristodoulou

 

Protein structures as shapes: Analysing protein structure variation using geometric morphometrics. Jose Sergio Hleap, Christian Blouin

 

Which line to follow? The utility of different line-fitting methods to capture the mechanism of morphological scaling. Alexander W. Shingleton

 

A Cautionary Tail: Changes in Integrin Behavior with Labeling. Catherine G. Galbraith, Michael W. Davidson, James A. Galbraith

 

Exploring biological networks in 3D, stereoscopic 3D and immersive 3D with iCAVE. Selim Kalayci, Zeynep H. Gumus

 

Quantitative imaging of chromatin decompaction in living cells. Elisa Dultz, Roberta Mancini, Guido Polles, Pascal Vallotton, Frank Alber, Karsten Weis

 

| Genome tools

CRISPys: Optimal sgRNA design for editing multiple members of a gene family using the CRISPR system. Gal Hyams, Shiran Abadi, Adi Avni, Eran Halperin, Eilon Shani, Itay Mayrose

 

Potential high-frequency off-target mutagenesis induced by CRISPR/Cas9 in Arabidopsis and its prevention. Qiang Zhang, Hui-Li Xing, Zhi-Ping Wang, Hai-Yan Zhang, Fang Yang, Xue-Chen Wang, Qi-Jun Chen

 

CRISPR-Cas12a target binding unleashes single-stranded DNase activity. Janice S Chen, Enbo Ma, Lucas B Harrington, Xinran Tian, Jennifer A Doudna

 

SgTiler: a fast method to design tiling sgRNAs for CRISPR/Cas9 mediated screening. Musaddeque Ahmed, Housheng Hansen He

 

Easy quantification of template-directed CRISPR/Cas9 editing. Eva Karina Brinkman, Arne Nedergaard Kousholt, Tim Harmsen, Christ Leemans, Tao Chen, Jos Jonkers, Bas van Steensel

 

Covalent linkage of the DNA repair template to the CRISPR/Cas9 complex enhances homology-directed repair. Natasa Savic, Femke Ringnalda, Katja Bargsten, Yizhou Li, Christian Berk, Jonathan Hall, Dario Neri, Martin Jinek, Gerald Schwank

 

Rapid, modular, and cost-effective generation of donor DNA constructs for CRISPR-based gene knock-in. Yi-Jiun Chen, Weikang Wang, Xiao-Jiun Tian, Daniel E. Lefever, David A. Taft, Jianhua Xing

 

Transgenic mouse lines expressing the 3xFLAG-dCas9 protein for enChIP analysis. Toshitsugu Fujita, Fusako Kitaura, Asami Oji, Naoki Tanigawa, Miyuki Yuno, Masahito Ikawa, Ichiro Taniuchi, Hodaka Fujii

 

A suite of transgenic driver and reporter mouse lines with enhanced brain cell type targeting and functionality. Tanya L Daigle, Linda Madisen, Travis A Hage, Matthew T Valley, Ulf Knoblich, Rylan S Larsen, Marc M Takeno, Lawrence Huang, Hong Gu, Rachael Larsen, Maya Mills, Alice Bosma-Moody, La’Akea Siverts, Miranda Walker, Lucas T Graybuck, Zizhen Yao, Olivia Fong, Emma Garren, Garreck Lenz, Mariya Chavarha, Julie Pendergraft, James Harrington, Karla E Hirokawa, Julie A Harris, Medea McGraw, Douglas R Ollerenshaw, Kimberly Smith, Baker A Baker, Jonathan T Ting, Susan M Sunkin, Jerome Lecoq, Michael Z Lin, Edward S Boyden, Gabe J Murphy, Nuno da Costa, Jack Waters, Lu Li, Bosiljka Tasic, Hongkui Zeng

 

A versatile genetic tool for post-translational control of gene expression in Drosophila melanogaster. Sachin Sethi, Jing W. Wang

 

Saturating Single-Cell Datasets. Aparna Bhaduri, Tomasz J. Nowakowski, Alex A. Pollen, Arnold R. Kriegstein

 

Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data. Nelly Olova, Felix Krueger, Simon Andrews, David Oxley, Rebecca V Berrens, Miguel R Branco, Wolf Reik

 

Rapid high-resolution measurement of DNA replication timing by droplet digital PCR. Dzmitry G. Batrakou, Emma D. Heron, Conrad A. Nieduszynski

 

Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Change.Jigar Desai, Ryan C. Sartor, Lovely Mae Lawas, Krishna S. V. Jagadish, Colleen J. Doherty

 

Removing unwanted variation between samples in Hi-C experiments. Kipper Fletez-Brant, Yunjiang Qiu, David U Gorkin, Ming Hu, Kasper D Hansen

 

Binless normalization of Hi-C data provides significant interaction and difference detection independently of resolution. Yannick G. Spill, David Castillo, Marc A. Marti-Renom

 

Leveraging multiple transcriptome assembly methods for improved gene structure annotation. Luca Venturini, Shabhonam Caim, Gemy Kaithakottil, Daniel Lee Mapleson, David Swarbreck

 

Spliceosome profiling visualizes the operations of a dynamic RNP in vivo at nucleotide resolution. Jordan Burke, Adam Longhurst, Daria Merkurjev, Jade Sales-Lee, Beiduo Rao, James Moresco, John Yates III, Jingyi Jessica Li, Hiten D Madhani

 

Transcriptome-wide analysis of the functional intronome using spliceosome profiling. Weijun Chen, Jill Moore, Hakan Ozadam, Hennady P Shulha, Nicholas Rhind, Zhiping Weng, Melissa J. Moore

 

TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. Shubhada R. Kulkarni, Dries Vaneechoutte, Jan Van de Velde, Klaas Vandepoele

 

 

FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data. Josip Stefan Herman, Sagar Sagar, Dominic Grun

 

Cross-Site Comparison of Ribosomal Depletion Kits for Illumina RNAseq Library Construction. Zachary T Herbert, Jamie P Kershner, Vincent L Butty, Jyothi Thimmapuram, Sulbha Choudhari, Yuriy O Alekseyev, Jun Fan, Jessica W Podnar, Edward Wilcox, Jenny Gipson, Allison Gillaspy, Kristen Jepsen, Sandra Splinter BonDurant, Krystalynne Morris, Maura Berkeley, Ashley LeClerc, Stephen D. Simpson, Gary Sommerville, Leslie Grimmett, Marie Adams, Stuart S. Levine

 

An interlaboratory study of complex variant detection. Stephen E Lincoln, Justin M Zook, Shimul Chowdhury, Shazia Mahamdallie, Andrew Fellowes, Eric W Klee, Rebecca Truty, Catherine Huang, Farol L Tomson, Megan H Cleveland, Peter M Vallone, Yan Ding, Sheila Seal, Wasanthi DeSilva, Russell K Garlick, Marc Salit, Nazneen Rahman, Stephen F Kingsmore, Swaroop Aradhya, Robert L Nussbaum, Matthew J Ferber, Brian H Shirts

 

MEGAN-LR: New algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. Daniel Huson, Benjamin Albrecht, Caner Bagci, Irina Bessarab, Anna Gorska, Dino Jolic, Rohan B.H. Williams

 

CREAM: Clustering of genomic REgions Analysis Method. Seyed Ali Madani Tonekaboni, Parisa Mazrooei, Victor Kofia, Benjamin Haibe-Kains, Mathieu Lupien

 

The fractured landscape of RNA-seq alignment: The default in our STARs. Sara Ballouz, Alexander Dobin, Thomas R Gingeras, Jesse Gillis

 

miRAW: A deep learning approach to predict miRNA targets by analyzing whole miRNA transcripts. Albert Pla Planas, Xiangfu Zhong, Simon Rayner

 

Classifying cells with Scasat – a tool to analyse single-cell ATAC-seq. Syed Murtuza Baker, Connor Rogerson, Andrew Hayes, Andrew D. Sharrocks, Magnus Rattray

 

scmap – A tool for unsupervised projection of single cell RNA-seq data. Vladimir Yu. Kiselev, Andrew Yiu, Martin Hemberg

 

Expressed Exome Capture Sequencing (EecSeq): a method for cost-effective exome sequencing for all organisms with or without genomic resources. Jonathan B Puritz, Kathleen E Lotterhos

 

Tn5Prime, a Tn5 based 5′ Capture Method for Single Cell RNA-seq. Charles Cole, Ashley Byrne, Anna E. Beaudin, E. Camilla Forsberg, Christopher Vollmers

 

Mantis: A Fast, Small, and Exact Large-Scale Sequence Search Index. Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, Rob Patro

 

SpatialDE – Identification of spatially variable genes. Valentine Svensson, Sarah A. Teichmann, Oliver Stegle

 

Technology-independent estimation of cell type composition using differentially methylated regions. Stephanie C. Hicks, Rafael A. Irizarry

 

Revisiting criteria for plant miRNA annotation in the era of big data. Michael J. Axtell, Blake C. Meyers

 

OMGene: Mutual improvement of gene models through optimisation of evolutionary conservation. Michael Dunne, Steven Kelly

 

Research practice

Community-driven data analysis training for biology. Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Guéguen, Martin Čech, John Chilton, Dave Clements, Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Lariviere, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon Ryan, Florian Sigloch, Nicola Soranzo, Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Rolf Backofen, Anton Nekrutenko, Björn Grüning

 

How Changes in Common Practice Can Improve the Quality of Biomedical Science. Matthias Steinfath, Silvia Vogl, Norman Violet, Franziska Schwarz, Hans Mielke, Thomas Selhorst, Matthias Greiner, Gilbert Schoenfelder

 

The impact factor fallacy. Frieder Michel Paulus, Nicole Cruz, Soeren Krach

 

Explanation implies causation? Leslie Myint, Jeffrey T. Leek, Leah R. Jager

 

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

 

Manipulating the alpha level cannot cure significance testing – comments on “Redefine statistical significance”. Trafimow D, Amrhein V, Areshenkoff CN, Barrera-Causil C, Beh EJ, Bilgiç Y, Bono R, Bradley MT, Briggs WM, Cepeda-Freyre HA, Chaigneau SE, Ciocca DR, Carlos Correa J, Cousineau D, de Boer MR, Dhar SS, Dolgov I, Gómez-Benito J, Grendar M, Grice J, Guerrero-Gimenez ME, Gutiérrez A, Huedo-Medina TB, Jaffe K, Janyan A, Karimnezhad A, Korner-Nievergelt F, Kosugi K, Lachmair M, Ledesma R, Limongi R, Liuzza MT, Lombardo R, Marks M, Meinlschmidt G, Nalborczyk L, Nguyen HT, Ospina R, Perezgonzalez JD, Pfister R, Rahona JJ, Rodríguez-Medina DA, Romão X, Ruiz-Fernández S, Suarez I, Tegethoff M, Tejo M, van de Schoot R, Vankov I, Velasco-Forero S, Wang T, Yamada Y, Zoppino FC, Marmolejo-Ramos F.

 

Key steps to avoiding artistry with significance tests. C Patrick Doncaster, Thomas H G Ezard

 

If funders and libraries subscribed to open access: The case of eLife, PLOS, and BioOne. Willinsky J, Rusk M.

 

Oxford Nanopore sequencing in a research-based undergraduate course. Yi Zeng, Christopher Herbert Martin

 

 

Why not…

Dietary and behavioral inferences from dental pathology and non-masticatory wear on dentitions from a British medieval town. Ian Towle, Carole Davenport, Joel Irish, Isabelle De Groote

 

Cobwebbing in the city: urbanization-driven changes in web-building are decoupled from body size in an orb-web spider. Maxime Dahirel, Maarten De Cock, Pieter Vantieghem, Dries Bonte

(No Ratings Yet)
Loading...