August in preprints
Posted by the Node, on 8 September 2021
Welcome to our monthly scamper through the preprints on developmental biology and stem cells (and other related topics). Bumper section this month is the Genes & genomes section
The preprints this month are hosted on bioRxiv, arXiv and preprints.org – use these links to get to the section you want.
- Patterning & signalling
- Morphogenesis & mechanics
- Genes & genomes
- Stem cells, regeneration & disease modelling
- Plant development
- Evo-devo
Developmental biology
| Patterning & signalling
Adar-mediated A-to-I editing is required for establishment of embryonic body axes in zebrafish
Katarzyna Niescierowicz, Leszek Pryszcz, Cristina Navarrete, Eugeniusz Tralle, Marta Elzbieta Kasprzyk, Karim Abu Nahia, Katarzyna Misztal, Matthias Bochtler, Cecilia Winata
Strength of interactions in the Notch gene regulatory network determines patterning and fate in the notochord
Héctor Sánchez-Iranzo, Aliaksandr Halavatyi, Alba Diz-Muñoz
Co-option of immune effectors by the hormonal signalling system triggering metamorphosis in Drosophila melanogaster
Catarina Nunes, Takashi Koyama, Elio Sucena
SOX transcription factors direct TCF-independent WNT/beta-catenin transcription.
Shreyasi Mukherjee, David M Luedeke, Leslie Brown, Aaron Zorn
Superovulation does not alter calcium oscillations following fertilization
Virginia Savy, Paula Stein, Min Shi, Carmen J. Williams
Sufu regulation of Hedgehog signaling in P19 cells is required for proper glial cell differentiation
Danielle M. Spice, Joshua Dierolf, Gregory M. Kelly
TWIST1 interacts with adherens junction proteins during neural tube development and regulates fate transition in cranial neural crest cells
Jessica W. Bertol, Shelby Johnston, Rabia Ahmed, Victoria K. Xie, Kelsea M. Hubka, Lissette Cruz, Larissa Nitschke, Marta Stetsiv, Jeremy P. Goering, Paul Nistor, Sally Lowell, Hanne Hoskens, Peter Claes, Seth M. Weinberg, Irfan Saadi, Mary C. Farach-Carson, Walid D. Fakhouri
Spatial and temporal expression of PORCN is highly dynamic in the developing mouse cochlea
Brianna L. Oliver, Caryl A. Young, Vidhya Munnamalai
Patterning the embryonic pulmonary mesenchyme
Katharine Goodwin, Jacob M. Jaslove, Hirotaka Tao, Min Zhu, Sevan Hopyan, Celeste M. Nelson
Fatty acid-binding proteins and fatty acid synthase influence glial reactivity and promote the formation of Müller glia-derived progenitor cells in the avian retina
Warren A. Campbell, Allen Tangeman, Heithem M. El-Hodiri, Evan C. Hawthorn, Maddie Hathoot, Thanh Hoang, Seth Blackshaw, Andy J. Fischer
Self-organization of human dorsal-ventral forebrain structures by light induced SHH
Riccardo De Santis, Fred Etoc, A. Edwin Rosado-Olivieri, Ali H. Brivanlou
Src acts with WNT/FGFRL signaling to pattern the planarian anteroposterior axis
Nicolle A. Bonar, David I. Gittin, Christian P. Petersen
Phase transition specified by a binary code patterns the vertebrate eye cup
Revathi Balasubramanian, Xuanyu Min, Peter M.J. Quinn, Quentin Lo Giudice, Chenqi Tao, Karina Polanco, Neoklis Makrides, John Peregrin, Michael Bouaziz, Yingyu Mao, Qian Wang, Bruna L Costa, Diego Buenaventura, Fen Wang, Liang Ma, Stephen H Tsang, Pierre J. Fabre, Xin Zhang
Mechanisms underlying the cooperation between loss of epithelial polarity and Notch signaling during neoplastic growth in Drosophila
Rémi Logeay, Charles Géminard, Patrice Lassus, Diala Kantar, Lisa Héron-Milhavet, Bettina Fischer, Sarah J. Bray, Jacques Colinge, Alexandre Djiane
Lineage-specific control of convergent differentiation by a Forkhead repressor
Karolina Mizeracka, Julia M. Rogers, Jonathan D. Rumley, Shai Shaham, Martha L. Bulyk, John I. Murray, Maxwell G. Heiman
Noncanonical Notch signals have opposing roles during cardiac development
Matthew Miyamoto, Peter Andersen, Edrick Sulistio, Xihe Liu, Sean Murphy, Suraj Kannan, Lucy Nam, William Miyamoto, Emmanouil Tampakakis, Narutoshi Hibino, Hideki Uosaki, Chulan Kwon
Multi-layered regulation of neuroectoderm differentiation by retinoic acid in a primitive streak-like context
Luigi Russo, Hanna L. Sladitschek, Pierre A. Neveu
Transitions in the proteome and phospho-proteome during Xenopus laevis development
Elizabeth Van Itallie, Marian Kalocsay, Martin Wühr, Leonid Peshkin, Marc W. Kirschner
Spatial organisation and homeostasis of epithelial lineages at the gastroesophageal junction is regulated by the divergent Wnt mucosal microenvironment
Naveen Kumar, Rajendra Kumar Gurumurthy, Pon Ganish Prakash, Shilpa Mary Kurian, Christian Wentland, Volker Brinkmann, Hans-Joachim Mollenkopf, Tobias Krammer, Christophe Toussaint, Antoine-Emmanuel Saliba, Matthias Biebl, Christian Juergensen, Bertram Wiedenmann, Thomas F Meyer, Cindrilla Chumduri
A role for Hmga2 in the early-stage transition of neural stem-progenitor cell properties during mouse neocortical development
Naohiro Kuwayama, Yusuke Kishi, Yurie Maeda, Yurie Nishiumi, Yutaka Suzuki, Haruhiko Koseki, Yusuke Hirabayashi, Yukiko Gotoh
A Self-Limiting Circuit Regulates Mammary Cap Cell Plasticity Through TGF-beta Signaling
Armelle Le Guelte, Ian G. Macara
Sphingosine 1-Phosphate Mediates Adiponectin Receptor Signaling Essential For Lipid Homeostasis and Embryogenesis
Mario Ruiz, Ranjan Devkota, Dimitra Panagaki, Per-Olof Bergh, Delaney Kaper, Marcus Henricsson, Ali Nik, Kasparas Petkevicius, Johanna L. Höög, Mohammad Bohlooly-Y, Peter Carlsson, Jan Borén, Marc Pilon
Independently paced calcium oscillations in progenitor and differentiated cells in an ex vivo epithelial organ
Anna A. Kim, Amanda Nguyen, Marco Marchetti, Denise Montell, Beth. L. Pruitt, Lucy Erin O’Brien
Retinoic acid treatment recruits macrophages and increases axonal regeneration after optic nerve injury in the frog Rana pipiens
Valeria De La Rosa-Reyes, Mildred V. Duprey-Díaz, Jonathan M. Blagburn, Rosa E. Blanco
Apelin signaling dependent endocardial protrusions promote cardiac trabeculation in zebrafish
Didier Y.R. Stainier, Jialing Qi, Annegret Rittershaus, Rashmi Priya, Shivani Mansingh, Christian S.M. Helker
Context dependent activation and repression of enhancers by Hunchback binding sites in Drosophila embryo
Stefano Ceolin, Monika Hanf, Max Schnepf, Ulrich Unnerstall, Christophe Jung, Ulrike Gaul
Metabolic regulation of species-specific developmental rates
Margarete Diaz-Cuadros, Teemu P Miettinen, Dylan Sheedy, Carlos Manlio Diaz-Garcia, Svetlana Gapon, Alexis Hubaud, Gary Yellen, Scott R Manalis, William Oldham, Olivier Pourquie
Endothelial cell signature in muscle stem cells showed by VEGFA-FLT1-AKT1 axis for muscle stem cell survival
Mayank Verma, Yoko Asakura, Xuerui Wang, Kasey Zhou, Mahmut Ünverdi, Allison P. Kann, Robert S. Kraus, Atsushi Asakura
The growth and expansion of meningeal lymphatic networks are affected in craniosynostosis
Phillip Ang, Matt Matrongolo, Max A Tischfield
Wear and Tear of the Intestinal Visceral Musculature by Intrinsic and Extrinsic Factors
Ho D. Kim, Eric So, Jiae Lee, Yi Wang, Vikram S. Gill, Anna Gorbacheva, Hee Jin Han, Katelyn G.-L. Ng, Ken Ning, Inez K.A. Pranoto, Alejandra J.H. Cabrera, Dae Seok Eom, Young V. Kwon
Spatial and temporal expression of PORCN is highly dynamic in the developing mouse cochlea
Brianna L. Oliver, Caryl A. Young, Vidhya Munnamalai
Signaling and transcriptional networks governing late synovial joint development
Qin Bian, Yu-Hao Cheng, Emily Y. Su, Yuqi Tan, Dong Won Kim, Hong Wang, Sooyeon Yoo, Seth Blackshaw, Patrick Cahan
| Morphogenesis & mechanics
Ergodic patterns of cell state transitions underlie the reproducibility of embryonic development
Scott Holley, Miriam Genuth, Yasuhiro Kojima, Dörthe Jülich, Hisanori Kiryu
Developmental timing of Drosophila pachea pupae is robust to temperature changes
Bénédicte M. Lefèvre, Michael Lang
Tracheal tube fusion in Drosophila involves release of exosomes from multivesicular bodies
Carolina Camelo, Anna Koerte, Thea Jacobs, Peter Robin Hiesinger, Stefan Luschnig
A robust ex vivo system to study cellular dynamics underlying mouse peri-implantation development
Takafumi Ichikawa, Hui Ting Zhang, Laura Panavaite, Anna Erzberger, Dimitri Fabrèges, Rene Snajder, Adrian Wolny, Ekaterina Korotkevich, Nobuko Tsuchida-Straeten, Lars Hufnagel, Anna Kreshuk, Takashi Hiiragi
Ethology of morphogenesis reveals the design principles of cnidarian size and shape development
Anniek Stokkermans, Aditi Chakrabarti, Ling Wang, Prachiti Moghe, Kaushikaram Subramanian, Petrus Steenbergen, Gregor Mönke, Takashi Hiiragi, Robert Prevedel, L. Mahadevan, Aissam Ikmi
Size and shape regional differentiation during the development of the spine in the nine-banded armadillo (Dasypus novemcinctus)
Jillian D. Oliver, Katrina E. Jones, Stephanie E. Pierce, Lionel Hautier
Highly scaled measurements of C. elegans development suggest that physical constraints guide growth trajectories and animal shape
Joy Nyaanga, Christina Goss, Gaotian Zhang, Hannah N. Ahmed, Elliot J. Andersen, Isabella R. Miller, Justine K. Rozenich, Iris L. Swarthout, Jordan A. Vaughn, Erik C. Andersen, Niall M. Mangan, Sasha Shirman
Embryonic and aglomerular kidney development in the bay pipefish, Syngnathus leptorhynchus
Bianca R. Maters, Emily Stevenson, Peter D. Vize
Autophagy coordinates chondrocyte development and early joint formation in zebrafish
Joanna J. Moss, Martina Wirth, Sharon A. Tooze, Jon D. Lane, Chrissy L. Hammond
The cell surface hyaluronidase TMEM2 plays an essential role in mouse neural crest cell development and survival
Toshihiro Inubushi, Yuichiro Nakanishi, Makoto Abe, Yoshifumi Takahata, Riko Nishimura, Hiroshi Kurosaka, Fumitoshi Irie, Takashi Yamashiro, Yu Yamaguchi
Loss of the extracellular matrix protein DIG-1 causes glial fragmentation, dendrite breakage, and dendrite extension defects
Megan K. Chong, Elizabeth R. Cebul, Karolina Mizeracka, Maxwell G. Heiman
The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth
Giulia L. M. Boezio, Josephine Gollin, Shengnan Zhao, Rashmi Priya, Shivani Mansingh, Stefan Guenther, Nana Fukuda, Felix Gunawan, Didier Y. R. Stainier
Snrpb, the gene mutated in CCMS, is haploinsufficient and required for proper morphogenesis and splicing
Sabrina Shameen Alam, Shruti Kumar, Marie-Claude Beauchamp, Eric Bareke, Alexia Boucher, Nadine Nzirorera, Reinnier Padilla, Si Jing Zhang, Jacek Majewski, Loydie A. Jerome-Majewska
Vinculin recruitment to α-catenin halts the differentiation and maturation of enterocyte progenitors to maintain homeostasis of the Drosophila intestine
Jérôme Bohère, Buffy L. Eldridge-Thomas, Golnar Kolahgar
Topological morphogenesis of neuroepithelial organoids
Keisuke Ishihara, Arghyadip Mukherjee, Elena Gromberg, Jan Brugués, Elly M. Tanaka, Frank Jülicher
Local mechanical stimuli shape tissue growth in vertebrate joint morphogenesis
Ester Comellas, Johanna E Farkas, Giona Kleinberg, Katlyn Lloyd, Thomas Mueller, Timothy J Duerr, Jose J Muñoz, James R Monaghan, Sandra J Shefelbine
Co-option of immune effectors by the hormonal signalling system triggering metamorphosis in Drosophila melanogaster
Catarina Nunes, Takashi Koyama, Élio Sucena
| Genes & genomes
A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency
Xin Huang, Nazym Bashkenova, Yantao Hong, Diana Guallar, Zhe Hu, Vikas Malik, Dan Li, Xiaohua Shen, Hongwei Zhou, Jianlong Wang
Calpain DEK1 acts as a developmental switch gatekeeping cell fate transitions
Viktor Demko, Tatiana Belova, Maxim Messerer, Torgeir R. Hvidsten, Pierre-Francois Perroud, Klaus F. X. Mayer, Odd-Arne Olsen, Daniel Lang
Inferring and perturbing cell fate regulomes in human cerebral organoids
Jonas S. Fleck, Sophie M.J. Jansen, Damian Wollny, Makiko Seimiya, Fides Zenk, Malgorzata Santel, Zhisong He, J. Gray Camp, Barbara Treutlein
Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration
Yingxi Cao, Yu Xia, Joseph B. Balowski, Jianhong Ou, Lingyun Song, Alexias Safi, Timothy Curtis, Gregory E. Crawford, Kenneth D. Poss, Jingli Cao
Polycomb Repressive Complex 2 shields naïve human pluripotent cells from trophectoderm differentiation
Banushree Kumar, Carmen Navarro, Nerges Winblad, John P Schell, Cheng Zhao, Fredrik Lanner, Simon J Elsässer
Acquisition of cell identity in the brown alga Ectocarpus: which of time, cell shape or position matters most?
Bernard Billoud, Denis Saint-Marcoux, Sabine Chenivesse, Carole Duchêne, Camille Noûs, Jane A. Langdale, Bénédicte Charrier
Widespread translational control regulates retinal development in mouse
Kaining Chen, Congying Chen, Huihui Li, Jiaqi Yang, Mengqing Xiang, Hongwei Wang, Zhi Xie
Tomato CRABS CLAW paralogues interact with chromatin remodelling factors to mediate carpel development and floral determinacy
Laura Castañeda, Estela Giménez, Benito Pineda, Begoña García-Sogo, Ana Ortiz-Atienza, Rosa Micol-Ponce, Trinidad Angosto, Juan Capel, Vicente Moreno, Fernando J. Yuste-Lisbona, Rafael Lozano
DPPA2 and DPPA4 are dispensable for mouse zygotic genome activation and preimplantation development
Zhiyuan Chen, Zhenfei Xie, Yi Zhang
Lifelong single-cell profiling of cranial neural crest diversification
Peter Fabian, Kuo-Chang Tseng, Mathi Thiruppathy, Claire Arata, Hung-Jhen Chen, Joanna Smeeton, Nellie Nelson, J. Gage Crump
Heterozygous loss of ZBTB38 leads to early embryonic lethality in mice via suppressing Nanog and Sox2
Miki Nishio, Takuya Matsuura, Shunya Hibi, Shiomi Ohta, Chio Oka, Noriaki Sasai, Yasumasa Ishida, Eishou Matsuda
The PAF1 complex cell-autonomously promotes oogenesis in Caenorhabditis elegans
Yukihiro Kubota, Natsumi Ota, Hisashi Takatsuka, Takuma Unno, Shuichi Onami, Asako Sugimoto, Masahiro Ito
A gene regulatory network for neural induction
Katherine E. Trevers, Hui-Chun Lu, Youwen Yang, Alexandre Thiery, Anna C. Strobl, Božena Pálinkášová, Nidia M. M. de Oliveira, Irene M. de Almeida, Mohsin A. F. Khan, Natalia Moncaut, Nicholas M. Luscombe, Leslie Dale, Andrea Streit, Claudio D. Stern
A micro-evolutionary change in target binding sites as key determinant of Ultrabithorax function in Drosophila
Soumen Khan, Saurabh J. Pradhan, Guillaume Giraud, Françoise Bleicher, Rachel Paul, Samir Merabet, LS Shashidhara
A nuclear role for the Argonaute protein AGO2 in mammalian gametogenesis
Kimberly N Griffin, Haixin Li, Benjamin William Walters, Huafeng Wang, Carolyn B Kaya, Jean Kanyo, TuKiet Lam, Andy L Cox, Jean-Ju Chung, Bluma J Lesch
The Nab2 RNA binding protein promotes sex-specific splicing of Sex lethal in Drosophila neuronal tissue
Binta Jalloh, J. Christopher Rounds, Brianna E. Brown, Carly L. Lancaster, Sara W. Leung, Ayan Banerjee, Derrick J. Morton, Rick S. Bienkowski, Isaac J. Kremsky, Milo B. Fasken, Anita H. Corbett, Kenneth H. Moberg
Dynamics of maternal gene expression in Rhodnius prolixus
Agustina Pascual, Rolando Rivera Pomar
Sequential in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster
Ana Rita Amândio, Leonardo Beccari, Lucille Lopez-Delisle, Bénédicte Mascrez, Jozsef Zakany, Sandra Gitto, Denis Duboule
A temporally controlled sequence of X-chromosome inactivation and reactivation defines female mouse in vitro germ cells with meiotic potential
Jacqueline Severino, Moritz Bauer, Tom Mattimoe, Niccolò Arecco, Luca Cozzuto, Patricia Lorden, Norio Hamada, Yoshiaki Nosaka, So Nagaoka, Holger Heyn, Katsuhiko Hayashi, Mitinori Saitou, Bernhard Payer
The small and large intestine contain transcriptionally related mesenchymal stromal cell subsets that derive from embryonic Gli1+ mesothelial cells
Simone Isling Pærregaard, Sophie Schussek, Line Wulff, Kristoffer Niss, Urs Mörbe, Johan Jendholm, Kerstin Wendland, Anna T. Andrusaite, Kevin F. Brulois, Robert J. B. Nibbs, Katarzyna Sitnik, Allan McI Mowat, Eugene C. Butcher, Søren Brunak, William W. Agace
Pre-Implantation Alcohol Exposure Induces Lasting Sex-Specific DNA Methylation Programming Errors in the Developing Forebrain
LM Legault, K Doiron, M Breton-Larrivée, A Langford-Avelar, A Lemieux, M Caron, LA Jerome-Majewska, D Sinnett, S McGraw
Cleavage of histone H2A during embryonic stem cell differentiation destabilizes nucleosomes to counteract gene activation
Mariel Coradin, Joseph Cesare, Yemin Lan, Zhexin Zhu, Peder J. Lund, Simone Sidoli, Yekaterina Kori, Congcong Lu, Elizabeth G. Porter, Charles W. M. Robert, Benjamin A. Garcia
Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish
Damir Baranasic, Matthias Hörtenhuber, Piotr Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Varnai, Yavor Hadzhiev, Ada Jimenez-Gonzalez, Nan Li, Joseph Wragg, Fabio D’Orazio, Noelia Díaz, Benjamín Hernández-Rodríguez, Zelin Chen, Marcus Stoiber, Michaël Dong, Irene Stevens, Samuel E. Ross, Anne Eagle, Ryan Martin, Pelumi Obasaju, Sepand Rastegar, Alison C. McGarvey, Wolfgang Kopp, Emily Chambers, Dennis Wang, Hyejeong R. Kim, Rafael D. Acemel, Silvia Naranjo, Maciej Lapinski, Vanessa Chong, Sinnakaruppan Mathavan, Bernard Peers, Tatjana Sauka-Spengler, Martin Vingron, Piero Carninci, Uwe Ohler, Scott Allen Lacadie, Shawn Burgess, Cecilia Winata, Freek van Eeden, Juan M. Vaquerizas, José Luis Gómez-Skarmeta, Daria Onichtchouk, Ben James Brown, Ozren Bogdanovic, Monte Westerfield, Fiona C. Wardle, Carsten O. Daub, Boris Lenhard, Ferenc Müller
The miR-430 locus with extreme promoter density is a transcription body organizer, which facilitates long range regulation in zygotic genome activation
Yavor Hadzhiev, Lucy Wheatley, Ledean Cooper, Federico Ansaloni, Celina Whalley, Zelin Chen, Stefano Gustincich, Remo Sanges, Shawn Burgess, Andrew Beggs, Ferenc Müller
Evidence from combined analysis of single cell RNA-Seq and ATAC-Seq data of regulatory toggles operating in native and iPS-derived murine retina
Anouk Georges, Arnaud Lavergne, Michiko Mandai, Fanny Lepiemme, Latifa Karim, Loic Demeulenaere, Diego Aguilar, Michael Schyns, Sébastien Dupont, Laurent Nguyen, Jean-Marie Rakic, Masayo Takahashi, Michel Georges, Haruko Takeda
Neuromesodermal progenitor origin of trunk neural crest in vivo
Martyna Lukoseviciute, Sarah Mayes, Tatjana Sauka-Spengler
Extent and complexity of RNA processing in the development of honey bee queen and worker castes revealed by Nanopore direct RNA sequencing
Xu Jiang He, Andrew B. Barron, Liu Yang, Hu Chen, Yu Zhu He, Li Zhen Zhang, Qiang Huang, Zi Long Wang, Xiao Bo Wu, Wei Yu Yan, Zhi Jiang Zeng
Segregation of neural crest specific lineage trajectories from a heterogeneous neural plate border territory only emerges at neurulation
Ruth M Williams, Martyna Lukoseviciute, Tatjana Sauka-Spengler, Marianne E Bronner
A red herring in zebrafish genetics: allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
Richard J White, Eirinn Mackay, Stephen W Wilson, Elisabeth M Busch-Nentwich
Somatic mutation rates scale with lifespan across mammals
Alex Cagan, Adrian Baez-Ortega, Natalia Brzozowska, Federico Abascal, Tim H. H. Coorens, Mathijs A. Sanders, Andrew R. J. Lawson, Luke M. R. Harvey, Shriram G. Bhosle, David Jones, Raul E. Alcantara, Timothy M. Butler, Yvette Hooks, Kirsty Roberts, Elizabeth Anderson, Edmund Flach, Simon Spiro, Inez Januszczak, Ethan Wrigglesworth, Matthew W. Perkins, Robert Deaville, Megan Druce, Ruzhica Bogeska, Michael D. Milsom, Björn Neumann, Frank Gorman, Fernando Constantino-Casas, Laura Peachey, Diana Bochynska, Ewan St. John Smith, Moritz Gerstung, Peter J. Campbell, Elizabeth P. Murchison, Michael R. Stratton, Iñigo Martincorena
Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin
Irene M. Kaplow, Daniel E. Schäffer, Morgan E. Wirthlin, Alyssa J. Lawler, Ashley R. Brown, Michael Kleyman, Andreas R. Pfenning
Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic stem cells
Parmentier Romuald, Moussy Alice, Chantalat Sophie, Racine Laëtitia, Sudharshan Ravi, Papili Gao Nan, Stockholm Daniel, Corre Guillaume, Fourel Geneviève, Deleuze Jean-François, Gunawan Rudiyanto, Paldi Andras
Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos
Ashley Albright, Michael Stadler, Michael Eisen
A 3D transcriptomics atlas of the mouse olfactory mucosa
Mayra L. Ruiz Tejada Segura, Eman Abou Moussa, Elisa Garabello, Thiago S. Nakahara, Melanie Makhlouf, Lisa S. Mathew, Filippo Valle, Susie S.Y. Huang, Joel D. Mainland, Michele Caselle, Matteo Osella, Stephan Lorenz, Johannes Reisert, Darren W. Logan, Bettina Malnic, Antonio Scialdone, Luis R. Saraiva
Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis
Dong Li, Fan Wu, Shuo Zhou, Xiao-Jun Huang, Hsiang-Ying Lee
HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations
Naama Hirsch, Idit Dahan, Eva D’haene, Matan Avni, Sarah Vergult, Marta Vidal-García, Pamela Magini, Claudio Graziano, Giulia Severi, Elena Bonora, Anna Maria Nardone, Francesco Brancati, Alberto Fernández-Jaén, Olson J. Rory, Benedikt Hallgrimsson, Ramon Y. Birnbaum
Integrated single-cell transcriptomic and epigenetic analyses of cell-state transition and lineage commitment in the embryonic mouse cerebellum
Nagham Khouri-Farah, Qiuxia Guo, Kerry Morgan, Jihye Shin, James Y.H. Li
Rapid redistribution and extensive binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates
Joyce J. Thompson, Daniel J. Lee, Apratim Mitra, Sarah Frail, Ryan Dale, Pedro P. Rocha
Multi-organ analysis of low-level somatic mosaicism reveals stage- and tissue-specific mutational features in human development
Hyeonju Son, Ja Hye Kim, Il Bin Kim, Myeong-Heui Kim, Nam Suk Sim, Dong-Seok Kim, Junehawk Lee, Jeong Ho Lee, Sangwoo Kim
Hydrozoan sperm-specific H2B histone variants stabilize chromatin and block transcription without enhancing chromatin condensation
Anna Torok, Martin JG Browne, Jordina C Vilar, Indu Patwal, Timothy Q DuBuc, F Febrimarsa, Erwan Atcheson, Andrew Flaus, Uri Frank, Sebastian G Gornik
The control of transcriptional memory by stable mitotic bookmarking
Maelle Bellec, Jeremy Dufourt, George Hunt, Helene Lenden-Hasse, Antonio Trullo, Amal Zine El Aabidine, Marie Lamarque, Marissa M Gaskill, Heloise Faure-Gautron, Mattias Mannervik, Melissa Harrison, Jean-Christophe Andrau, Cyril Favard, Ovidiu Radulescu, Mounia Lagha
Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification
Lukas Voortman, Caitlin Anderson, Elizabeth Urban, Mini Yuan, Sang Tran, Alexandra Neuhaus-Follini, Josh Derrick, Thomas Gregor, Robert J. Johnston Jr.
Profiling of N6-methyladenosine dynamics indicates regulation of oyster development by m6A-RNA epitranscriptomes
Lorane Le Franc, Bruno Petton, Pascal Favrel, Guillaume Riviere
Abundant small RNAs in the reproductive tissues of the honey bee, Apis mellifera, are a plausible mechanism for epigenetic inheritance and parental manipulation of gene expression
Owen T. Watson, Gabriele Buchmann, Paul Young, Kitty Lo, Emily J. Remnant, Boris Yagound, Mitch Shambrook, Andrew F. Hill, Benjamin P. Oldroyd, Alyson Ashe
| Stem cells, regeneration & disease modelling
Characterization of a novel Lbx1 loss of function mouse line
Lyvianne Decourtye, Jeremy McCallum-Loudeac, Sylvia Zellhuber-McMillan, Emma Young, Kathleen J Sircombe, Megan J Wilson
Hematopoiesis at single cell resolution spanning human development and maturation
Hojun Li, Jideofor Ezike, Anton Afanassiev, Laura Greenstreet, Stephen Y Zhang, Jennifer Whangbo, Vincent Butty, Enrico Moiso, Guinevere Connelly, Vivian Morris, Dahai Wang, George Q. Daley, Salil Garg, Stella Chou, Aviv Regev, Edroaldo Lummertz da Rocha, Geoffrey Schiebinger, Grant Rowe
Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis
Amritha V. Hanasoge Somasundara, Matthew A. Moss, Mary J. Feigman, Chen Chen, Samantha L. Cyrill, Michael F. Ciccone, Marygrace C. Trousdell, Macy Vollbrecht, Siran Li, Jude Kendall, Semir Beyaz, John E. Wilkinson, Camila O. dos Santos
Directed Differentiation of Human Pluripotent Stem Cells into Radial Glia and Astrocytes Bypasses Neurogenesis
Vukasin M. Jovanovic, Claire Malley, Carlos A. Tristan, Seungmi Ryu, Pei-Hsuan Chu, Elena Barnaeva, Pinar Ormanoglu, Jennifer Colon Mercado, Sam Michael, Michael E. Ward, Anton Simeonov, Ilyas Singeç
Novel roles of small extracellular vesicles in regulating the quiescence and proliferation of neural stem cells
Jingtian Zhang, Junki Uchiyama, Koshi Imami, Yasushi Ishihama, Ryoichiro Kageyama, Taeko Kobayashi
An early Shh-H2O2 feedback loop controls the progression of the regenerative program during adult zebrafish fin regeneration
Marion Thauvin, Rodolphe Matias de Sousa, Marine Alves, Michel Volovitch, Sophie Vriz, Christine Rampon
Direct reprogramming of human embryonic to trophoblast stem cells
Norah M.E. Fogarty, Ahmed Abdelbaki, Afshan McCarthy, Liani Devito, Alice E. Chen, Prabhakaran Munusamy, Paul Blakeley, Kay Elder, Phil Snell, Leila Christie, Paul Serhal, Rabi A. Odia, Mahesh Sangrithi, Kathy K. Niakan
Targeted gene correction and functional recovery in achondroplasia patient-derived iPSCs
Huan Zou, Mingfeng Guan, Yundong Li, Fang Luo, Wenyuan Wang, Yiren Qin
Nucleoporin107 mediates female sexual differentiation via Dsx
Tikva Shore, Tgst Levi, Rachel Kalifa, Amatzia Dreifuss, Dina Rekler, Ariella Weinberg-Shukron, Yuval Nevo, Tzofia Bialistoky, Victoria Moyal, Merav Yaffa Gold, Shira Leebhoff, David Zangen, Girish Deshpande, Offer Gerlitz
microRNA Expression Levels Change in Neonatal Patients During and After Exposure to Cardiopulmonary Bypass
Lance Hsieh, Lan Tu, Alison Paquette, Nataliya Kibiryeva, Jennifer Marshall, Douglas Bittel, James O’Brien, Kasey Vickers, Peter Pastuszko, Vishal Nigam
DDX41 is needed for pre-and post-natal hematopoietic stem cell differentiation in mice
Jing Ma, Nadim Mahmud, Maarten C. Bosland, Susan R. Ross
Ecdysone exerts biphasic control of regenerative signaling, coordinating the completion of regeneration with developmental progression
Faith Karanja, Subhshri Sahu, Sara Weintraub, Rajan Bhandari, Rebecca Jaszczak, Jason Sitt, Adrian Halme
Role of YAP in early ectodermal specification and a Huntington’s Disease model of human neurulation
Francesco M. Piccolo, Nathaniel R. Kastan, Tomomi Haremaki, Qingyun Tian, Tiago L. Laundos, Riccardo De Santis, Thomas S. Carroll, Ji-Dung Luo, Ksenia Gnedeva, Fred Etoc, A. J. Hudspeth, Ali H. Brivanlou
A Drosophila RNAi screen reveals conserved glioblastoma-related adhesion genes that regulate collective cell migration
Nirupama Kotian, Katie M. Troike, Kristen N. Curran, Justin D. Lathia, Jocelyn A. McDonald
Mesoderm-Derived PDGFRA+ Cells Regulate the Emergence of Hematopoietic Stem Cells in the Dorsal Aorta
Vashe Chandrakanthan, Prunella Rorimpandey, Fabio Zanini, Diego Chacon, Young Chan Kang, Kathy Knezevic, Yizhou Huang, Qiao Qiao, Rema A. Oliver, Ashwin Unnikrishnan, Daniel R. Carter, Brendan Lee, Chris Brownlee, Carl Power, Simon Mendez-Ferrer, Grigori Enikolopov, William Walsh, Berthold Göttgens, Samir Taoudi, Dominik Beck, John E. Pimanda
Regeneration of the larval sea star nervous system by wounding induced respecification to the sox2 lineage
Minyan Zheng, Olga Zueva, Veronica F. Hinman
Examining the effect of chronic intranasal oxytocin administration on the neuroanatomy and behavior of three autism-related mouse models
Zsuzsa Lindenmaier, Jacob Ellegood, Monique Stuive, Kaitlyn Easson, Jane Foster, Evdokia Anagnostou, Jason P. Lerch
A human stem cell resource to decipher the biochemical and cellular basis of neurodevelopmental defects in Lowe Syndrome
Bilal M. Akhtar, Priyanka Bhatia, Shubhra Acharya, Sanjeev Sharma, Yojet Sharma, BS Aswathy, Kavina Ganapathy, Anil Vasudevan, Padinjat Raghu
Myostatin is a negative regulator of adult neurogenesis in zebrafish
Vishnu Muraleedharan Saraswathy, Lili Zhou, Brooke Burris, Deepika Dogra, Sven Reischauer, Mayssa H. Mokalled
Metabolic control of adult neural stem cell self-renewal by the mitochondrial protease YME1L
Gulzar A. Wani, Hans-Georg Sprenger, Kristiano Ndoci, Srikanth Chandragiri, Richard James Acton, Désirée Schatton, Sandra M.V. Kochan, Vignesh Sakthivelu, Milica Jevtic, Jens M. Seeger, Stefan Müller, Patrick Giavalisco, Elena I. Rugarli, Elisa Motori, Thomas Langer, Matteo Bergami
Clonal dynamics of haematopoiesis across the human lifespan
Emily Mitchell, Michael Spencer Chapman, Nicholas Williams, Kevin Dawson, Nicole Mende, Emily F Calderbank, Hyunchul Jung, Thomas Mitchell, Tim Coorens, David Spencer, Heather Machado, Henry Lee-Six, Megan Davies, Daniel Hayler, Margarete Fabre, Krishnaa Mahbubani, Fede Abascal, Alex Cagan, George Vassiliou, Joanna Baxter, Inigo Martincorena, Michael R Stratton, David Kent, Krishna Chatterjee, Kourosh Saeb Parsy, Anthony R Green, Jyoti Nangalia, Elisa Laurenti, Peter J Campbell
The spatio-temporal program of liver zonal regeneration
Shani Ben-Moshe, Tamar Veg, Rita Manco, Stav Dan, Aleksandra A. Kolodziejczyk, Keren Bahar Halpern, Eran Elinav, Shalev Itzkovitz
Human Deep Cortical Neurons Promote Regeneration and Recovery After Cervical Spinal Cord Injury
Vanessa M. Doulames, James Weimann, Giles W. Plant
Lung injury induces alveolar type 2 cell hypertrophy and polyploidy with implications for repair and regeneration
Anthea Weng, Mariana Maciel-Herrerias, Satoshi Watanabe, Lynn Welch, Annette S. Flozak, Rogan Grant, Raul Piseaux Aillon, Laura Dada, Seung Hye Han, Monique Hinchcliff, Alexander Misharin, GR Scott Budinger, Cara J. Gottardi
Necrosis-induced apoptosis promotes regeneration in Drosophila wing imaginal discs
Jacob Klemm, Michael J. Stinchfield, Robin E. Harris
High temperature perception in leaves promotes vascular regeneration in distant tissues
Phanu T. Serivichyaswat, Kai Bartusch, Martina Leso, Constance Musseau, Akira Iwase, Yu Chen, Keiko Sugimoto, Marcel Quint, Charles W. Melnyk
Gene regulatory networks controlling temporal patterning, neurogenesis, and cell fate specification in the mammalian retina
Pin Lyu, Thanh Hoang, Clayton P. Santiago, Eric D. Thomas, Andrew E. Timms, Haley Appel, Megan Gimmen, Nguyet Le, Lizhi Jiang, Dong Won Kim, Siqi Chen, David Espinoza, Ariel E. Telger, Kurt Weir, Brian S. Clark, Timothy J. Cherry, Jiang Qian, Seth Blackshaw
Renal Interstitial Cells Promote Nephron Regeneration by Secreting Prostaglandin E2
Xiaoliang Liu, Ting Yu, Xiaoqin Tan, Daqing Jin, Jiangping Zhang, Yunfeng Zhang, Shuyi Liao, Wenmin Yang, Jinghong Zhao, Tao P Zhong, Chi Liu
Loss of Elp1 disrupts trigeminal ganglion neurodevelopment in a model of Familial Dysautonomia
Carrie E. Leonard, Frances Lefcort, Lisa A. Taneyhill
Cell tip growth underlies injury response of marine macroalgae
Maki Shirae-Kurabayashi, Tomoya Edzuka, Masahiro Suzuki, Gohta Goshima
Inability to switch from ARID1A-BAF to ARID1B-BAF impairs exit from pluripotency and commitment towards neural crest formation in ARID1B-related neurodevelopmental disorders
Luca Pagliaroli, Patrizia Porazzi, Alyxandra T. Curtis, Chiara Scopa, Harald M.M. Mikkers, Christian Freund, Lucia Daxinger, Sandra Deliard, Sarah A. Welsh, Sarah Offley, Connor A. Ott, Bruno Calabretta, Samantha A. Brugmann, Gijs W.E. Santen, Marco Trizzino
| Plant development
Asymmetric Redundancy of Soybean Nodule Inception (NIN) Genes in Root Nodule Symbiosis
Mengdi Fu, Jiafeng Sun, Xiaolin Li, Yuefeng Guan, Fang Xie
Liquid-liquid phase separation of florigen activation complex induces flowering
Ken-ichiro Taoka, Hiroyuki Tsuji, Suai Anzawa, Mayu Enomoto, Yuka Koizumi, Juri Nakamura, Mari Tanaka, Akiko Fujita, Kyoko Furuita, Takashi S. Kodama, Masaru Fujimoto, Kazuo Kurokawa, Takashi Okamoto, Toshimichi Fujiwara, Akihiko Nakano, Chojiro Kojima
B1L regulates lateral root development by exocytic vesicular trafficking-mediated polar auxin transport in Arabidopsis
Gang Yang, Bi-xia Chen, Tao Chen, Jia-hui Chen, Rui Sun, Cong-cong Liu, Jiao Jia, Xiu-le Yue, Li-zhe An, Hua Zhang
Overexpression of HOP2 induces developmental defects and compromises growth in Arabidopsis
Ameth N. Garrido, Therese Francom, Sakina Divan, Mohamad Kesserwan, Jenya Daradur, C. Daniel Riggs
Sorbitol in loquat promotes early flower bud differentiation via the MADS-box transcription factor EjCAL
Hongxia Xu, Ting Chen, Meng Qi, Xiaoying Li, Junwei Chen
Endogenous auxin directs development of embryonic stem cells into somatic proembryos in Arabidopsis
Omid Karami, Cheryl Philipsen, Arezoo Rahimi, Annisa Ratna Nurillah, Kim Boutilier, Remko Offringa
Cytokinin-CLAVATA crosstalk is an ancient mechanism regulating shoot meristem homeostasis in land plants
Joseph Cammarata, Christopher Morales Farfan, Michael Scanlon, Adrienne HK Roeder
RNA Pol IV has antagonistic parent-of-origin effects on Arabidopsis endosperm
Prasad R.V. Satyaki, Mary Gehring
Defining the components of the miRNA156-SPL-miR172 aging pathway in pea and their expression relative to changes in leaf morphology
J.K. Vander Schoor, V. Hecht, G. Aubert, J. Burstin, J.L. Weller
3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves
Michael C. Tross, Mathieu Gaillard, Mackenzie Zweiner, Chenyong Miao, Ryleigh J. Grove, Bosheng Li, Bedrich Benes, James C. Schnable
doi: https://doi.org/10.
| Evo-devo
An ancient dental signalling centre supports homology of an enamel knot in sharks
Alexandre P. Thiery, Ariane S. I. Standing, Rory L. Cooper, Gareth J. Fraser
DEVELOPMENTAL AND EVOLUTIONARY COMPARATIVE ANALYSIS OF A HOXD REGULATORY LANDSCAPE IN MAMMALS AND BIRDS
Aurélie Hintermann, Isabel Guerreiro, Christopher Chase Bolt, Sandra Gitto, Denis Duboule, Leonardo Beccari
On the edge: Evolution of polarity protein BASL and the capacity for stomatal lineage asymmetric divisions
Ido Nir, Gabriel O. Amador, Yan Gong, Nicole K. Smoot, Le Cai, Hagai Shohat, Dominique C. Bergmann
A novel regulatory gene promotes novel cell fate by suppressing ancestral fate in the sea anemone Nematostella vectensis
Leslie S Babonis, Camille Enjolras, Joseph F Ryan, Mark Q Martindale
Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene
Jian Ming Khor, Jennifer Guerrero-Santoro, Charles A. Ettensohn
Evolutionary analyses of visual opsin genes in anurans reveals diversity and positive selection suggestive of functional adaptation to distinct light environments
Ryan K Schott, Leah Perez, Matthew A Kwiatkowski, Vance Imhoff, Jennifer M Gumm
Cell Biology
Zebrafish heme oxygenase 1a is necessary for normal development and macrophage migration
Kaiming Luo, Masahito Ogawa, Anita Ayer, Warwick J Britton, Roland Stocker, Kazu Kikuchi, Stefan H Oehlers
Characterization of the composition and functioning of the Crumbs complex in C. elegans
Victoria G Castiglioni, João J Ramalho, Jason Kroll, Riccardo Stucchi, Hanna van Beuzekom, Ruben Schmidt, Maarten Altelaar, Mike Boxem
Arf6 anchors Cdr2 nodes at the cell cortex to control cell size at division
Hannah E. Opalko, Kristi E. Miller, Hyun-Soo Kim, Cesar Vargas-Garcia, Abhyudai Singh, Michael-Christopher Keogh, James B. Moseley
Microtubule deacetylation reduces cell stiffness to allow the onset of collective cell migration in vivo
CL Marchant, AN Malmi-Kakkada, JA Espina, EH Barriga
Nuclear SUN1 stabilizes endothelial cell junctions to regulate blood vessel formation
Danielle B Buglak, Ariel L Gold, Allison P Marvin, Shea N Ricketts, Morgan Oatley, Natalie T Tanke, Bryan N Johnson, Victoria L Bautch
Stress-dependent inhibition of cell polarity through unbalancing the GEF/GAP regulation of Cdc42
Clàudia Salat-Canela, Mercè Carmona, Rebeca Martín-García, Pilar Pérez, José Ayté, Elena Hidalgo
DAAM mediates the assembly of long-lived, treadmilling stress fibers in collectively migrating epithelial cells in Drosophila
Kristin M Sherrard, Maureen Cetera, Sally Horne-Badovinac
A mechanosensing mechanism mediated by IRSp53 controls plasma membrane shape homeostasis at the nanoscale
Xarxa Quiroga, Nikhil Walani, Albert Chavero, Alexandra Mittens, Andrea Disanza, Francesc Tebar, Xavier Trepat, Robert G. Parton, Giorgio Scita, Maria Isabel Geli, Marino Arroyo, Anabel-Lise Le Roux, Pere Roca-Cusachs
Dynamics of mitochondrial mRNA abundance and poly(A) tail during the mammalian oocyte-to-embryo transition
Yusheng Liu, Yiwei Zhang, Zhonghua Liu, Falong Lu, Jiaqiang Wang
Conservation and divergence of poly(A) tail regulation during the mammalian oocyte-to-embryo transition
Yusheng Liu, Juexue Jin, Yiwei Zhang, Le-Yun Wang, Chuanxin Zhang, Zhenzhen Hou, Wei Li, Zhonghua Liu, Falong Lu, Jiaqiang Wang
Poly(A) tail length is a major regulator of maternal gene expression during the mammalian oocyte-to-embryo transition
Yusheng Liu, Hu Nie, Chuanxin Zhang, Zhenzhen Hou, Jiaqiang Wang, Falong Lu
Dynamics of poly(A) tail length and non-A residues during the human oocyte-to-embryo transition
Yusheng Liu, Keliang Wu, Fanghong Shao, Hu Nie, Jingye Zhang, Cheng Li, Zhenzhen Hou, Jiaqiang Wang, Bing Zhou, Han Zhao, Falong Lu
Abundant non-A residues in the poly(A) tail orchestrate the mouse oocyte-to-embryo transition
Yusheng Liu, Hu Nie, Le-Yun Wang, Shuang Wu, Wei Li, Qi Zhou, Jiaqiang Wang, Falong Lu
Re-polyadenylation occurs predominantly on maternal mRNA degradation intermediates during mammalian oocyte-to-embryo transition
Yusheng Liu, Yiwei Zhang, Hu Nie, Zhonghua Liu, Jiaqiang Wang, Falong Lu
Tip growth in the brown alga Ectocarpus is controlled by a RHO-GAP-BAR domain protein independently from F-actin organisation
Zofia Nehr, Sabine Chenivesse, Bernard Billoud, Sabine Genicot, Nathalie Desban, Ioannis Theodorou, Adeel Nasir, Aude Le Bail, Hervé Rabillé, Olivier Godfroy, Christos Katsaros, Bénédicte Charrier
Modelling
Recursive feedforward regulatory logic underlies robustness of the specification-to-differentiation transition and fidelity of terminal cell fate during C. elegans endoderm development
Chee Kiang Ewe, Erica M Sommermann, Josh Kenchel, Sagen E Flowers, Morris F Maduro, Joel H. Rothman
Mathematical model reveals that heterogeneity in the number of ion transporters regulates the fraction of mouse sperm capacitation
Alejandro Aguado-García, Daniel A. Priego-Espinosa, Andrés Aldana, Alberto Darszon, Gustavo Martínez-Mekler
Phyllotaxis Models: from the Inhibition Potential to the Real Plant
Walch Jean-Paul
The origin of universal cell shape variability in a confluent epithelial monolayer
Souvik Sadhukhan, Saroj Kumar Nandi
Mechanics of Live Cell Elimination
Siavash Monfared, Guruswami Ravichandran, José E. Andrade, Amin Doostmohammadi
Computational modeling and quantitative cell physiology reveal central parameters for the brassinosteroid-regulated cell growth of the Arabidopsis root
Ruth Großeholz, Friederike Wanke, Nina Glöckner, Luiselotte Rausch, Leander Rohr, Stefan Scholl, Emanuele Scacchi, Amelie-Jette Spazierer, Lana Shabala, Sergey Shabala, Karin Schumacher, Ursula Kummer, Klaus Harter
Theory of branching morphogenesis by local interactions and global guidance
Mehmet Can Ucar, Dmitrii Kamenev, Kazunori Sunadome, Dominik Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, Edouard Hannezo
Maintaining the stem cell niche in multicellular models of epithelia
Claire Miller, Edmund Crampin, James Osborne
Space: The Re-visioning Frontier of Biological Image Analysis with Graph Theory, Computational Geometry, and Spatial Statistics
John R Jungck, Michael J Pelsmajer , Camron Chappel , Dylan Taylor
Reviews
Self-organization in embryonic development: myth and reality
Stuart A. Newman
Deep learning for bioimage analysis
Adrien Hallou, Hannah Yevick, Bianca Dumitrascu, Virginie Uhlmann
Perspective on Sex and Regeneration
Moshe Reuveni
Tools & Resources
Inferring kinetic parameters of oscillatory gene regulation from single cell time series data
Joshua Burton, Cerys S Manning, Magnus Rattray, Nancy Papalopulu, Jochen Kursawe
Deep learning-based algorithm for predicting the live birth potential of mouse embryos
Yuta Tokuoka, Takahiro G. Yamada, Daisuke Mashiko, Zenki Ikeda, Tetsuya J. Kobayashi, Kazuo Yamagata, Akira Funahashi
Expression Atlas of Avian Neural Crest Proteins: Neurulation to Migration
Brigette Y. Monroy, Carly J. Adamson, Alexis Camacho-Avila, Christian N. Guerzon, Camilo V. Echeverria Jr., Crystal D. Rogers
MorphoGraphX 2.0: Providing context for biological image analysis with positional information
Soeren Strauss, Adam Runions, Brendan Lane, Dennis Eschweiler, Namrata Bajpai, Nicola Trozzi, Anne-Lise Routier-Kierzkowska, Saiko Yoshida, Sylvia Rodrigues da Silveira, Athul Vijayan, Rachele Tofanelli, Mateusz Majda, Emillie Echevin, Constance Le Gloanec, Hana Bertrand-Rakusova, Milad Adibi, Kay Schneitz, George Bassel, Daniel Kierzkowski, Johannes Stegmaier, Miltos Tsiantis, Richard S. Smith
Live imaging YAP signaling in vivo with fusion reporter mice
Bin Gu, Brian Bradshaw, Min Zhu, Yu Sun, Sevan Hopyan, Janet Rossant
Direct reprogramming of human fibroblasts into insulin-producing cells by transcription factors
Marta Fontcuberta-PiSunyer, Ainhoa García-Alamán, Èlia Prades, Noèlia Téllez, Hugo Figueiredo, Rebeca Fernandez-Ruiz, Sara Cervantes, Carlos Enrich, Laura Clua, Javier Ramón-Azcón, Christophe Broca, Anne Wojtusciszyn, Anna Novials, Nuria Montserrat, Josep Vidal, Ramon Gomis, Rosa Gasa
Village in a dish: a model system for population-scale hiPSC studies
Drew R. Neavin, Angela M. Steinmann, Han Sheng Chiu, Maciej S. Daniszewski, Cátia Moutinho, Chia-Ling Chan, Mubarika Tyebally, Vikkitharan Gnanasambandapillai, Chuan E. Lam, Uyen Nguyen, Damián Hernández, Grace E. Lidgerwood, Alex W. Hewitt, Alice Pébay, Nathan J. Palpant, Joseph E. Powell
Python-Microscope: A new open source Python library for the control of microscopes
David Miguel Susano Pinto, Mick A Phillips, Nicholas Hall, Julio Mateos–Langerak, Danail Stoychev, Tiago Susano Pinto, Martin J Booth, Ilan Davis, Ian M Dobbie
A novel transposable element based authentication protocol for Drosophila cell lines
Daniel Mariyappa, Douglas B. Rusch, Shunhua Han, Arthur Luhur, Danielle Overton, David F. B. Miller, Casey M. Bergman, Andrew C. Zelhof
Vesalius: Tissue anatomy from spatial transcriptomic data
Patrick C.N. Martin, Cecilia Lövkvist, Byung-Woo Hong, Kyoung Jae Won
Whole genome analysis for 163 guide RNAs in Cas9 edited mice reveals minimal off-target activity
Kevin A. Peterson, Sam Khalouei, Joshua A. Wood, Denise G. Lanza, Lauri G. Lintott, Brandon J. Willis, John R. Seavitt, Nour Hanafi, Robert E. Braun, Mary E. Dickinson, Jacqueline K. White, K.C. Kent Lloyd, Jason D. Heaney, Stephen A. Murray, Arun Ramani, Lauryl M.J. Nutter
Generation of iPSCs from endangered Grevy’s zebra and comparative transcriptomic analysis of mammalian PSCs
Yoshinori Endo, Ken-ichiro Kamei, Koichi Hasegawa, Keisuke Okita, Hideyuki Ito, Shiho Terada, Miho Inoue-Murayama
Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas
Katy Börner, Sarah A. Teichmann, Ellen M. Quardokus, James Gee, Kristen Browne, David Osumi-Sutherland, Bruce W. Herr II, Andreas Bueckle, Hrishikesh Paul, Muzlifah A. Haniffa, Laura Jardine, Amy Bernard, Song-Lin Ding, Jeremy A. Miller, Shin Lin, Marc Halushka, Avinash Boppana, Teri A. Longacre, John Hickey, Yiing Lin, M. Todd Valerius, Yongqun He, Gloria Pryhuber, Xin Sun, Marda Jorgensen, Andrea J. Radtke, Clive Wasserfall, Fiona Ginty, Jonhan Ho, Joel Sunshine, Rebecca T. Beuschel, Maigan Brusko, Sujin Lee, Rajeev Malhotra, Sanjay Jain, Griffin Weber
A Library of Induced Pluripotent Stem Cells from Clinically Well-Characterized, Diverse Healthy Human Individuals
Christoph Schaniel, Priyanka Dhanan, Bin Hu, Yuguang Xiong, Teeya Raghunandan, David M. Gonzalez, Rafael Dariolli, Sunita L. D’Souza, Arjun S. Yadaw, Jens Hansen, Gomathi Jayaraman, Bino Mathew, Moara Machado, Seth I. Berger, Joseph Tripodi, Vesna Najfeld, Jalaj Garg, Marc Miller, Colleen S. Lynch, Katherine C. Michelis, Neelima C. Tangirala, Himali Weerahandi, David C. Thomas, Kristin G. Beaumont, Robert Sebra, Milind Mahajan, Eric Schadt, Dusica Vidovic, Stephan C. Schürer, Joseph Goldfarb, Evren U. Azeloglu, Marc R. Birtwistle, Eric A. Sobie, Jason C. Kovacic, Nicole C. Dubois, Ravi Iyengar
Who is the best surrogate for germ stem cell transplantation in fish?
Roman Franěk, Yu Cheng, Michaela Fučíková, Vojtěch Kašpar, Xuan Xie, Mujahid Ali Shah, Otomar Linhart, Ivo Šauman, Martin Pšenička
Spatiotemporal dynamics of human microglia are linked with brain developmental processes across the lifespan
D.A. Menassa, T.A.O. Muntslag, M. Martin-Estebané, L. Barry-Carroll, M.A. Chapman, I. Adorjan, T. Tyler, B. Turnbull, M.J.J. Rose-Zerilli, J.A.R. Nicoll, Z. Krsnik, I. Kostovic, D. Gomez-Nicola
Fast 3D Clear: A Fast, Aqueous, Reversible Three-Day Tissue Clearing Method for Adult and Embryonic Mouse Brain and Whole Body
Stylianos Kosmidis, Adrian Negrean, Alex Dranovsky, Attila Losonczy, Eric R. Kandel
High-efficiency CRISPR gene editing in C. elegans using Cas9 integrated into the genome
Matthew L. Schwartz, M. Wayne Davis, Matthew S. Rich, Erik M. Jorgensen
tdLanYFP, a yellow, bright, photostable and pH insensitive fluorescent protein for live cell imaging and FRET-based sensing strategies
Yasmina Bousmah, Hana Valenta, Giulia Bertolin, Utkarsh Singh, Valérie Nicolas, Hélène Pasquier, Marc Tramier, Fabienne Merola, Marie Erard
Deep learning-enhanced morphological profiling predicts cell fate dynamics in real-time in hPSCs
Edward Ren, Sungmin Kim, Saad Mohamad, Samuel F. Huguet, Yulin Shi, Andrew R. Cohen, Eugenia Piddini, Rafael Carazo Salas
Development of an efficient single-cell cloning and expansion strategy for genome edited induced pluripotent stem cells
Nupur Bhargava, Priya Thakur, Thulasi Priyadharshini Muruganandam, Shashank Jaitly, Pragya Gupta, Neelam Lohani, Sangam Giri Goswami, Saurabh Kumar Bhattacharya, Suman Jain, Sivaprakash Ramalingam
Designing and interpreting 4D tumour spheroid experiments
Ryan J. Murphy, Alexander P. Browning, Gency Gunasingh, Nikolas K. Haass, Matthew J. Simpson
CellProfiler 4: Improvements in Speed, Utility and Usability
David R. Stirling, Madison J. Swain-Bowden, Alice M. Lucas, Anne E. Carpenter, Beth A. Cimini, Allen Goodman
CellDART: Cell type inference by domain adaptation of single-cell and spatial transcriptomic data
Sungwoo Bae, Kwon Joong Na, Jaemoon Koh, Dong Soo Lee, Hongyoon Choi, Young Tae Kim
Maternal mRNA deadenylation is defective in in vitro matured mouse and human oocytes
Yusheng Liu, Wenrong Tao, Yiwei Zhang, Hu Nie, Zhenzhen Hou, Jingye Zhang, Zhen Yang, Jiaqiang Wang, Falong Lu, Keliang Wu
Mutationathon: towards standardization in estimates of pedigree-based germline mutation rates
Lucie A. Bergeron, Søren Besenbacher, Tychele N. Turner, Cyril J. Versoza, Richard Wang, Alivia Lee Price, Ellie Armstrong, Meritxell Riera, Jedidiah Carlson, Hwei-yen Chen, Matthew W. Hahn, Kelley Harris, April Snøfrid Lo Natalie M Kleppe, Elora H. López-Nandam, Priya Moorjani, Susanne P. Pfeifer, George P. Tiley, Anne D. Yoder, Guojie Zhang, Mikkel H. Schierup
EVALUATION OF STED SUPER-RESOLUTION IMAGE QUALITY BY IMAGE CORRELATION SPECTROSCOPY (QuICS)
Elena Cerutti, Morgana D’Amico, Isotta Cainero, Gaetano Ivan Dellino, Mario Faretta, Giuseppe Vicidomini, Pier Giuseppe Pelicci, Paolo Bianchini, Alberto Diaspro, Luca Lanzano’
High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads
Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye
PySeq2500: An open source toolkit for repurposing HiSeq 2500 sequencing systems as versatile fluidics and imaging platforms
Kunal Pandit, Joana Petrescu, Miguel Cuevas, William Stephenson, Peter Smibert, Hemali Phatnani, Silas Maniatis
Long-Read Sequencing of the Zebrafish Genome Reorganizes Genomic Architecture
Yelena Chernyavskaya, Xiaofei Zhang, Jinze Liu, Jessica S. Blackburn
Locus-specific chromatin profiling of evolutionarily young transposable elements
Darren Taylor, Robert Lowe, Claude Philippe, Kevin C. L. Cheng, Gael Cristofari, Miguel R. Branco
BioCode: A Data-Driven Approach for Learning How Biological Networks Grow
Emre Sefer
New strategies to improve minimap2 alignment accuracy
Heng Li
CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis
David R. Stirling, Anne E. Carpenter, Beth A. Cimini
Research practice & education
PEERS – an open science “Platform for the Exchange of Experimental Research Standards” in biomedicine
Annesha Sil, Anton Bespalov, Christina Dalla, Chantelle Ferland-Beckham, Arnoud Herremans, Konstantinos Karantzalos, Martien J. Kas, Nikolaos Kokras, Michael J. Parnham, Pavlina Pavlidi, Kostis Pristouris, Thomas Steckler, Gernot Riedel, Christoph H. Emmerich
The Specious Art of Single-Cell Genomics
Tara Chari, Joeyta Banerjee, Lior Pachter
Peer teaching as bioinformatics training strategy: incentives, challenges, and benefits.
Nur-Taz Rahman, Caitlin Meyer, Durga Thakral, Wesley L Cai, Rolando Garcia-Milian, Ann T Chen, Razib Obaid
MITI Minimum Information guidelines for highly multiplexed tissue images
Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila M. Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, Jeremy Muhlich, Raquel Arias-Camison, Milen Nikolov, Madison Tyler, Jia-Ren Lin, Erik A. Burlingame, Sarah Arena, Human Tumor Atlas Network, Young H. Chang, Samouil L Farhi, Vésteinn Thorsson, Nithya Venkatamohan, Julia L. Drewes, Dana Pe’er, David A. Gutman, Markus D. Herrmann, Nils Gehlenborg, Peter Bankhead, Joseph T. Roland, John M. Herndon, Michael P. Snyder, Michael Angelo, Garry Nolan, Jason Swedlow, Nikolaus Schultz, Daniel T. Merrick, Sarah A. Mazzilli, Ethan Cerami, Scott J. Rodig, Sandro Santagata, Peter K. Sorger
Biologists need modern data infrastructure on campus
Andrey Andreev, Tom Morrell, Kristin Briney, Sandra Gesing, Uri Manor
Why multiple hypothesis test corrections provide poor control of false positives in the real world
Stanley E. Lazic
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