the community site for and by developmental biologists

August in preprints

Posted by , 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.

Developmental biology

Cell Biology

Modelling

Reviews

Tools & Resources

Research practice & education

Developmental biology

| Patterning & signalling

Wild type and Adar MO injected zebrafish embryos from Niescierowicz, et al.

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

Formation of ectopic posterior eyes in the absence of Src in planarian from Bonar, et al.

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

Esophageal organoid (left panel) and stomach organoid from Kumar, et al.

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

Visceral musculature disruption phenotypes in Drosophila midguts from Kim, et al

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

atg13 knockout zebrafish line from Moss, et al.

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

Neuroepithelial organoids from Ishihara, et al.

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

 STITCH plots of scRNAseq and snATACseq datasets across the zebrafish lifetime from Fabian, et al.

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

 Kaplow, et al. used a CNN to predict brain OCR ortholog open chromatin status

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

Human blastocysts from Fogarty, et al.

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

Kotian, et al. screen for genes that regulate collective cell migration

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

Mouse lung section from Weng, et al.

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

Rice shoot apical meristems from Taoka, et al.

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

Shoot development in Physcomitrium patens from Cammarata, et al.

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

Developmental time-course of abaxial cotyledon epidermis from Nir, et al.

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

Xenopus laevis cephalic neural crest cells from Marchant, et al.

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 from Nehr, et al.

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

Modelling branching morphogenesis using zebrafish innervation from Ucar, et al.

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

Image analysis of an Arabidopisis thaliana ovule using MorphographX 2.0 from Strauss, et al.

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 in Cos7 cells from Bousmah, et al.

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

Imaging a mouse spinal cord using PySeq2500 from Pandit, et al.

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

Picasso embedding of the ex-utero mouse embryo E8.5 data fit to a world map boundary from Chari, et al.

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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