June in preprints
Posted by the Node, on 5 July 2019
Welcome to our monthly trawl for developmental biology (and related) preprints.
Another big haul this month covering everything from great ape cerebral organoids to collectively contracting choanoflagellates, the genes that control iris development to the signals and forces making boundaries in the hindbrain. The preprints were hosted on bioRxiv, PeerJ, and arXiv. Let us know if we missed anything, and use these links to get to the section you want:
Developmental biology
| Stem cells, regeneration & disease modelling
Evo-devo & evo
Cell biology
Modelling
Tools & resources
Research practice & education
Why not…
Developmental biology
| Patterning & signalling
Coordination between stochastic and deterministic specification in the Drosophila visual system
Maximilien Courgeon, Claude Desplan
Regulation of Numb during planar cell polarity establishment in the Drosophila eye
Pedro M Domingos, Andreas Jenny, David del Alamo, Marek Mlodzik, Hermann Steller, Bertrand Mollereau
Drosophila Aop imposes a delay on E(spl)-mediated repression of Ato during R8 specification
Adam T. Majot, Lucas M. Jozwick, Clifton P. Bishop, Ashok P. Bidwai
Multimodal transcriptional control of pattern formation in embryonic development
Nicholas C Lammers, Vahe Galstyan, Armando Reimer, Sean A Medin, Chris H Wiggins, Hernan G Garcia
hunchback Promoters Can Readout Morphogenetic Positional Information in Less Than a Minute
Jonathan Desponds, Massimo Vergassola, Aleksandra M. Walczak
Cell elimination strategies upon identity switch via modulation of apterous in Drosophila wing disc
Olga Klipa, Fisun Hamaratoglu
The yellow gene influences Drosophila male mating success through sex comb melanization
Jonathan H. Massey, Daayun Chung, Igor Siwanowicz, David L. Stern, Patricia J. Wittkopp
Drosophila Trpm mediates calcium influx during egg activation
Qinan Hu, Mariana F. Wolfner
Motoneuron-derived Activinβ regulates Drosophila body size and tissue-scaling during larval growth and adult development
Lindsay Moss-Taylor, Ambuj Upadhyay, Xueyang Pan, Myung-Jun Kim, Michael B. O’Connor
Activated Ras/JNK driven Dilp8 in imaginal discs adversely affects organismal homeostasis during early pupal stage in Drosophila, a new checkpoint for development
Mukulika Ray, Subhash C. Lakhotia
Context-specific functions of Notch in Drosophila blood cell progenitors
DM Blanco-Obregon, MJ Katz, L Durrieu, L Gándara, P Wappner
Notch signaling is required for survival of the germline stem cell lineage in testes of Drosophila melanogaster
Chun L. Ng, Qian Yue, Schulz Cordula
Feedback regulation of BMP signaling by C. elegans cuticle collagens
Uday Madaan, Lionel Faure, Albar Chowdhury, Shahrear Ahmed, Emma J. Ciccarelli, Tina L. Gumienny, Cathy Savage-Dunn
Developmental myelination is modified by microglial pruning
Alexandria N. Hughes, Bruce Appel
A mesoderm-independent role for Nodal signaling in convergence & extension gastrulation movements
Margot L.K. Williams, Lilianna Solnica-Krezel
Pre-Border Gene Foxb1 Regulates the Differentiation Timing and Autonomic Neuronal Potential of Human Neural Crest Cells
Alan W. Leung, Francesc López-Giráldez, Cayla Broton, Kaixuan Lin, Maneeshi S. Prasad, Jacqueline C. Hernández, Andrew Z. Xiao, Martín I. Garcia-Castro
BMP7 functions predominantly as a heterodimer with BMP2 or BMP4 during mammalian embryogenesis
Hyung-Seok Kim, Judith Neugebauer, Autumn McKnite, Anup Tilak, Jan L. Christian
TEAD4/YAP1/WWTR1 prevent the premature onset of pluripotency prior to the 16-cell stage
Tristan Frum, Jennifer Watts, Amy Ralston
A new role for Notch in the control of polarity and asymmetric cell division of developing T cells
Mirren Charnley, Mandy Ludford-Menting, Kim Pham, Sarah M. Russell
Jag1 modulates an oscillatory Dll1-Notch-Hes1 signaling module to coordinate growth and fate of pancreatic progenitors
Philip A. Seymour, Caitlin A. Collin, Anuska l. R. Egeskov-Madsen, Mette C. Jørgensen, Hiromi Shimojo, Itaru Imayoshi, Kristian H. de Lichtenberg, Raphael Kopan, Ryoichiro Kageyama, Palle Serup
ΔN-Tp63 mediates Wnt/β-catenin-induced inhibition of differentiation in basal stem cells of mucociliary epithelia
Maximilian Haas, José Luis Gómez Vázquez, Dingyuan Iris Sun, Hong Thi Tran, Magdalena Brislinger, Alexia Tasca, Orr Shomroni, Kris Vleminckx, Peter Walentek
The Eya1 phosphatase mediates Shh-driven symmetric cell division of cerebellar granule cell precursors
Daniel J. Merk, Pengcheng Zhou, Samuel M. Cohen, Maria F. Pazyra-Murphy, Grace H. Hwang, Kristina J. Rehm, Jose Alfaro, Xuesong Zhao, Eunyoung Park, Pin-Xian Xu, Jennifer A. Chan, Michael J. Eck, Kellie J. Nazemi, Rosalind A. Segal
Slug/Snail2 is involved in the repression of proliferation genes by TGF-β in bronchial epithelial progenitor cells and is deregulated in abnormal epithelium
Chamseddine Ben Brahim, Charlotte Courageux, Ariane Jolly, Bérengère Ouine, Aurélie Cartier, Pierre de la Grange, Leanne de Koning, Pascale Leroy
Cyp26b1 is required for proper airway epithelial differentiation during lung development
Edward Daniel, Gabrielle I. Sutton, Yadanar Htike, Ondine Cleaver
Islet vascularization is regulated by primary endothelial cilia via VEGF-A dependent signaling
Yan Xiong, M. Julia Scerbo, Anett Seelig, Francesco Volta, Nils O’Brien, Andrea Dicker, Daniela Padula, Heiko Lickert, Jantje M. Gerdes, Per-Olof Berggren
Insulin-like growth factor 1 receptor signaling in tenocytes is required for adult tendon growth
Nathaniel P Disser, Kristoffer B Sugg, Jeffrey R Talarek, Dylan C Sarver, Brennan J Rourke, Christopher L Mendias
FOXC1 negatively regulates BMP-SMAD activity and Id1 expression during osteoblast differentiation
Jordan. C. Caddy, Leiah. M. Luoma, Fred. B. Berry
Autophagy-related genes atg7 and beclin1 are essential for energy metabolism and survival during the larval-to-juvenile transition stage of zebrafish
Suzan Attia Mawed, Jin Zhang, Fan Ren, Jie Mei
In the chick embryo, estrogen can induce chromosomally male ZZ left gonad epithelial cells to form an ovarian cortex, which supports oogenesis
Silvana Guioli, Debiao Zhao, Sunil Nandi, Michael Clinton, Robin Lovell-Badge
| Morphogenesis & mechanics
Actomyosin regulation by Eph receptor signaling couples boundary cell formation to border sharpness
Jordi Cayuso, Qiling Xu, Megan Addison, David G. Wilkinson
Multiple steps mediate ventricular layer attrition to form the adult mouse spinal cord central canal
Marco A. Cañizares, Aida Rodrigo Albors, Gail Singer, Nicolle Suttie, Metka Gorkic, Paul Felts, Kate G. Storey
The C. elegans plectin homologue VAB-10 acts as a hemidesmosome mechanosensor
Shashi Kumar Suman, Csaba Daday, Teresa Ferraro, Thanh Vuong-Brender, Saurabh Tak, Sophie Quintin, François Robin, Frauke Gräter, Michel Labouesse
Expansion of apical extracellular matrix underlies the morphogenesis of a recently evolved structure
Sarah Jacquelyn Smith, Lance A. Davidson, Mark Rebeiz
Matrix metalloproteinase 1 modulates invasive behavior of tracheal branches during ingression into Drosophila flight muscles
Julia Sauerwald, Wilko Backer, Till Matzat, Frank Schnorrer, Stefan Luschnig
Cellular contractility coordinates cytoskeletal dynamics and cell behaviour during Drosophila abdominal morphogenesis
Pau Pulido Companys, Anneliese Norris, Marcus Bischoff
Assembly of a persistent apical actin network by the formin Frl/Fmnl tunes epithelial cell deformability
Benoit Dehapiot, Raphaël Clément, Gabriella Gazsó-Gerhát, Jean-Marc Philippe, Thomas Lecuit
An emergent flow of the nuclear array in syncytial embryos
Zhiyi Lv, Jan Rosenbaum, Stephan Mohr, Xiaozhu Zhang, Helen Preiß, Sebastian Kruss, Karen Alim, Timo Aspelmeier, Jörg Großhans
HTT is a repressor of ABL activity required for APP induced axonal growth
Claire Marquilly, Germain Busto, Brittany S. Leger, Edward Giniger, James A. Walker, Lee G. Fradkin, Jean-Maurice Dura
Connexin 43 impacts the chick premigratory cranial neural crest cell population without affecting the neural crest cell epithelial-to-mesenchymal transition
Karyn Jourdeuil, Lisa Taneyhill
Pax2a regulates angiogenesis to facilitate fusion of the optic fissure
Megan L. Weaver, W. P Piedade, N.N Meshram, J.K. Famulski
Cell and tissue morphology determine actin-dependent nuclear migration mechanisms in neuroepithelia
Iskra Yanakieva, Anna Erzberger, Marija Matejčić, Carl D. Modes, Caren Norden
Sensory neurogenesis depends on vascular-neuronal filopodia contacts and blood flow
Laura Taberner, Aitor Bañón, Berta Alsina
GATA2 controls lymphatic endothelial cell junctional integrity and lymphovenous valve morphogenesis through miR-126
Md. Riaj Mahamud, Xin Geng, Yen-Chun Ho, Boksik Cha, Yuenhee Kim, Jing Ma, Lijuan Chen, Greggory Myers, Sally Camper, Debbie Mustacich, Marlys Witte, Dongwon Choi, Young-Kwon Hong, Hong Chen, Gaurav Varshney, James Douglas Engel, Shusheng Wang, Tae-Hoon Kim, Kim-Chew Lim, R. Sathish Srinivasan
Gli2 is necessary for migration of ventral Neural Stem Cells to demyelinated lesions
Daniel Z. Radecki, Heather Messling, James R. Haggerty-Skeans, Jayshree Samanta, James L. Salzer
Effects of abnormal muscle forces on prenatal joint morphogenesis in mice
Vivien Sotiriou, Rebecca A Rolfe, Paula Murphy, Niamh C Nowlan
Motility induced fracture reveals a ductile to brittle crossover in the epithelial tissues of a simple animal
Vivek N. Prakash, Matthew S. Bull, Manu Prakash
| Genes & genomes
Transcriptomic Analysis of the Neurogenesis Signature suggests Continued but Minimal Neurogenesis in the Adult Human Hippocampus
Ashutosh Kumar, Vikas Pareek, Muneeb A. Faiq, Pavan Kumar, Chiman Kumari, Himanshu N. Singh, Sanjib K. Ghosh
Single cell RNA-Seq analysis identifies molecular mechanisms controlling hypothalamic patterning and differentiation
Dong Won Kim, Parris Whitney Washington, Zoe Qianyi Wang, Sonia Lin, Changyu Sun, Lizhi Jiang, Seth Blackshaw
Translatomic database of cortical astroglia across male and female mouse development reveals two distinct developmental phenotypes
Gareth M. Rurak, Stephanie Simard, Amanda Van Geel, John Stead, Barbara Woodside, Gianfilippo Coppola, Natalina Salmaso
Single-cell genomic atlas of great ape cerebral organoids uncovers human-specific features of brain development
Sabina Kanton, Michael James Boyle, Zhisong He, Malgorzata Santel, Anne Weigert, Fatima Sanchis Calleja, Leila Sidow, Jonas Fleck, Patricia Guijarro, Dingding Han, Zhengzong Qian, Michael Heide, Wieland Huttner, Philipp Khaitovich, Svante Pääbo, Barbara Treutlein, J. Gray Camp
Single Cell Profiling Reveals Sex, Lineage and Regional Diversity in the Mouse Kidney
Andrew Ransick, Nils O. Lindström, Jing Liu, Zhu Qin, Jin-Jin Guo, Gregory F. Alvarado, Albert D. Kim, Hannah G. Black, Junhyong Kim, Andrew P. McMahon
Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of lineage specification during murine embryonic limb development
Natalie H. Kelly, Nguyen P.T. Huynh, Farshid Guilak
A Human Liver Cell Atlas: Revealing Cell Type Heterogeneity and Adult Liver Progenitors by Single-Cell RNA-sequencing
Nadim Aizarani, Antonio Saviano, Sagar, Laurent Mailly, Sarah Durand, Patrick Pessaux, Thomas F. Baumert, Dominic Grün
Single-cell chromatin accessibility analysis of mammary gland development reveals cell state transcriptional regulators and cellular lineage relationships
Chi-Yeh Chung, Zhibo Ma, Christopher Dravis, Sebastian Preissl, Olivier Poirion, Gidsela Luna, Xiaomeng Hou, Rajshekhar R. Giraddi, Bing Ren, Geoffrey M. Wahl
T Lymphopoiesis from Pluripotent Stem Cells by Defined Transcription Factors at Single Cell Resolution
Rongqun Guo, Fangxiao Hu, Qitong Weng, Cui Lv, Hongling Wu, Lijuan Liu, Zongcheng Li, Yang Zeng, Zhijie Bai, Mengyun Zhang, Yuting Liu, Xiaofei Liu, Chengxiang Xia, Tongjie Wang, Peiqing Zhou, Kaitao Wang, Yong Dong, Yuxuan Luo, Xiangzhong Zhang, Yuxian Guan, Yang Geng, Juan Du, Yangqiu Li, Yu Lan, Jiekai Chen, Bing Liu, Jinyong Wang
Single-Cell Signalling Analysis of Heterocellular Organoids
Xiao Qin, Jahangir Sufi, Petra Vlckova, Pelagia Kyriakidou, Sophie E. Acton, Vivian S. W. Li, Mark Nitz, Christopher J. Tape
A Single Cell Transcriptomic Atlas Characterizes Aging Tissues in the Mouse
The Tabula Muris consortium, Angela Oliveira Pisco, Nicholas Schaum, Aaron McGeever, Jim Karkanias, Norma F. Neff, Spyros Darmanis, Tony Wyss-Coray, Stephen R. Quake
A murine aging cell atlas reveals cell identity and tissue-specific trajectories of aging
Jacob C. Kimmel, Lolita Penland, Nimrod D. Rubinstein, David G. Hendrickson, David R. Kelley, Adam Z. Rosenthal
Genomic structure of Hstx2 modifier of Prdm9-dependent hybrid male sterility in mice
Diana Lustyk, Slavomír Kinský, Kristian Karsten Ullrich, Michelle Yancoskie, Lenka Kašíková, Václav Gergelits, Radislav Sedláček, Yingguang Frank Chan, Linda Odenthal-Hesse, Jiří Forejt, Petr Jansa
The temporal transcription factor E93 controls dynamic enhancer activity and chromatin accessibility during development
Spencer L Nystrom, Matthew J Niederhuber, Daniel J McKay
Essential roles of Hdac1 and 2 in lineage development and genome-wide DNA methylation during mouse preimplantation development
Panpan Zhao, Huanan Wang, Han Wang, Yanna Dang, Lei Luo, Shuang Li, Yan Shi, Lefeng Wang, Shaohua Wang, Jesse Mager, Kun Zhang
Restricted and non-essential redundancy of RNAi and piRNA pathways in mouse oocytes
Eliska Taborska, Josef Pasulka, Radek Malik, Filip Horvat, Irena Jenickova, Zoe Jelić Matošević, Petr Svoboda
Direct evidence for transport of RNA from the mouse brain to the germline and offspring
Elizabeth A. O’Brien, Kathleen S. Ensbey, Bryan W. Day, Paul A. Baldock, Guy Barry
Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption
Xuan G. Luong, Enrico Maria Daldello, Gabriel Rajkovic, Cai-Rong Yang, Marco Conti
The Lid/KDM5 histone demethylase complex activates a critical effector of the oocyte-to-zygote transition
Daniela Torres-Campana, Shuhei Kimura, Guillermo A. Orsi, Béatrice Horard, Gérard Benoit, Benjamin Loppin
CHD4-NURD controls spermatogonia survival and differentiation
Rodrigo O. de Castro, Victor Goitea, Luciana Previato, Agustin Carbajal, Courtney T. Griffin, Roberto J. Pezza
Sperm DNA damage causes genomic instability in early embryonic development
Sjors Middelkamp, Helena T.A. van Tol, Diana C.J. Spierings, Sander Boymans, Victor Guryev, Bernard A.J. Roelen, Peter M. Lansdorp, Edwin Cuppen, Ewart W. Kuijk
Polycomb contraction differentially regulates terminal human hematopoietic differentiation programs
A. Lorzadeh, C. Hammond, D.J.H.F. Knapp, Q. Cao, F Wang, A. Heravi-Moussavi, M Wong, M. Bilenky, M. Moksa, Z. Sharafian, P.M. Lavoie, C.J. Eaves, M. Hirst
Genomic architecture of Shh dependent cochlear morphogenesis
Victor Muthu, Alex. M. Rohacek, Yao Yao, Staci M. Rakowiecki, Alexander S. Brown, Ying-Tao Zhao, James Meyers, Kyoung-Jae Won, Shweta Ramdas, Christopher D. Brown, Kevin A. Peterson, Douglas J. Epstein
TWIST1 homo- and heterodimers orchestrate specificity control in embryonic stem cell lineage differentiation and craniofacial development
Xiaochen Fan, Ashley J Waardenberg, Madeleine Demuth, Pierre Osteil, Jane Sun, David A.F. Loebel, Mark Graham, Patrick P.L. Tam, Nicolas Fossat
Large-scale dissection suggests that ultraconserved elements are dispensable for mouse embryonic stem cell survival and fitness
Aksana Schneider, Michael Hiller, Frank Buchholz
The role of maternal pioneer factors in predefining first zygotic responses to inductive signals
George E. Gentsch, Thomas Spruce, Nick D. L. Owens, James C. Smith
miR-92a-3p controls cell cycle progression in zebrafish
Christopher E. Presslauer, Teshome T. Bizuayehu, Jorge M.O. Fernandes, Igor S. Babiak
Identification and characterization of cis-regulatory elements for photoreceptor type-specific transcription in zebrafish
Wei Fang, Yi Wen, Xiangyun Wei
The lncRNAs Implicated in Redox Regulation in Ybx1 Deficient Zebrafish Larvae
Chen Huang, Bo Zhu, Dongliang Leng, Wei Ge, Xiaohua Douglas Zhang
DREAM Interrupted: Severing MuvB from DREAM’s pocket protein impairs gene repression but not DREAM assembly on chromatin
Paul D. Goetsch, Susan Strome
LST-1 acts in trans with a conserved RNA-binding protein to maintain stem cells
Kimberly A. Haupt, Amy L. Enright, Ahlan S. Ferdous, Aaron M. Kershner, Heaji Shin, Marvin Wickens, Judith Kimble
Germline maintenance through the multifaceted activities of GLH/Vasa in Caenorhabditis elegans P granules
Elisabeth A. Marnik, J. Heath Fuqua, Catherine S. Sharp, Jesse D. Rochester, Emily L. Xu, Sarah E. Holbrook, Dustin L. Updike
POT-1 telomere binding protein promotes a novel form of Transgenerational Epigenetic Inheritance
Evan H. Lister-Shimauchi, Michael Dinh, Paul Maddox, Shawn Ahmed
A reproductive arrest program triggered by defects in Piwi and germ granules
Maya Spichal, Bree Heestand, Katherine Kretovich Billmyre, Stephen Frenk, Shawn Ahmed
Stress Resets Transgenerational Small RNA Inheritance
Leah Houri-Ze’evi, Guy Teichman, Hila Gingold, Oded Rechavi
Neuronal TORC1 modulates longevity via AMPK and cell nonautonomous regulation of mitochondrial dynamics in C. elegans
Yue Zhang, Anne Lanjuin, Suvagata Roy Chowdhury, Meeta Mistry, Carlos G. Silva Garcia, Heather J. Weir, Chia-Lin Lee, Caroline C. Escoubas, Emina Tabakovic, William B. Mair
Natural variants in C. elegans atg-5 3’UTR uncover divergent effects of autophagy on polyglutamine aggregation in different tissues
J Alexander-Floyd, S Haroon, M Ying, AA Entezari, C Jaeger, M Vermulst, T Gidalevitz
An atlas of transcription factors expressed in the Drosophila melanogaster pupal terminalia
Ben J. Vincent, Gavin R. Rice, Gabriella M. Wong, William J. Glassford, Kayla I. Downs, Jessica L. Shastay, Kenechukwu Charles-Obi, Malini Natarajan, Madelaine Gogol, Julia Zeitlinger, Mark Rebeiz
Natural genetic variation screen in Drosophila identifies Wnt signaling, mitochondrial metabolism, and redox homeostasis genes as modifiers of apoptosis
Rebecca A.S. Palu, Elaine Ong, Kaitlyn Stevens, Shani Chung, Katie G. Owings, Alan G. Goodman, Clement Y. Chow
Targeting of the dosage-compensated male X-chromosome during early Drosophila development
LE Rieder, WT Jordan III, EN Larschan
| Stem cells, regeneration & disease modelling
Homo- and heterodimerization of bHLH transcription factors balance stemness and bipotential differentiation
Aleix Puig-Barbé, Joaquín de Navascués
Control iPSC lines with clinically annotated genetic variants for versatile multi-lineage differentiation
Matthew R Hildebrandt, Miriam S Reuter, Wei Wei, Naeimeh Tayebi, Jiajie Liu, Sazia Sharmin, Jaap Mulder, L Stephen Lesperance, Patrick M Brauer, Caroline Kinnear, Alina Piekna, Asli Romm, Jennifer Howe, Peter Pasceri, Rebecca S Mok, Guoliang Meng, Matthew Rozycki, Deivid de Carvalho Rodrigues, Elisa C Martinez, Michael J Szego, Juan Carlos Zúñiga-Pflücker, Michele K Anderson, Steven A Prescott, Norman D Rosenblum, Binita M Kamath, Seema Mital, Stephen W Scherer, James Ellis
Context-dependent requirement of H3K9 methyltransferase activity during cellular reprogramming to iPSCs
Simon Vidal, Alexander Polyzos, Jorge Morales Valencia, Hongsu Wang, Emily Swanzey, Ly-sha Ee, Bhishma Amlani, Shengjiang Tu, Yixiao Gong, Valentina Snetkova, Jane A. Skok, Aristotelis Tsirigos, Sangyong Kim, Effie Apostolou, Matthias Stadtfeld
Recurrent genetic abnormalities in human pluripotent stem cells: definition and routine detection in culture supernatant by targeted droplet digital PCR
Said Assou, Nicolas Girault, Mathilde Plinet, Julien Bouckenheimer, Caroline Sansac, Marion Combe, Joffrey Mianné, Chloé Bourguignon, Mathieu Fieldes, Engi Ahmed, Thérèse Commes, Anthony Boureux, Jean-Marc Lemaître, John De Vos
Long-term single-cell passaging of human iPSCs fully supports pluripotency and high-efficient trilineage differentiation capacity
Estela Cruvinel, Isabella Ogusuku, Rosanna Cerioni, Jéssica Gonçalves, Maria Elisa Góes, Anderson Carlos Silva, Alexandre Pereira, Rafael Dariolli, Marcos Valadares, Diogo Biagi
Prospective Isolation of Chondroprogenitors from Human iPSCs Based on Cell Surface Markers Identified using a CRISPR-Cas9-Generated Reporter
Amanda Dicks, Chia-Lung Wu, Nancy Steward, Shaunak S. Adkar, Charles A. Gersbach, Farshid Guilak
Canonical Wnt pathway controls mESCs self-renewal through inhibition of spontaneous differentiation via β-catenin/TCF/LEF functions
Francesco Aulicino, Francesco Sottile, Elisa Pedone, Frederic Lluis, Lucia Marucci, Maria Pia Cosma
Injury stimulates stem cells to resist radiation-induced apoptosis
Divya A Shiroor, Tisha E Bohr, Carolyn E Adler
Critical role for P53 in regulating the cell cycle of ground state embryonic stem cells
Menno ter Huurne, Tianran Peng, Guoqiang Yi, Guido van Mierlo, Hendrik Marks, Hendrik G. Stunnenberg
Two distinct functional axes of positive feedback-enforced PRC2 recruitment in mouse embryonic stem cells
Matteo Perino, Guido van Mierlo, Sandra M.T. Wardle, Hendrik Marks, Gert Jan C. Veenstra
Oct4 mediated inhibition of Lsd1 activity promotes the active and primed state of pluripotency enhancers
Lama AlAbdi, Debapriya Saha, Ming He, Mohd Saleem Dar, Sagar M. Utturkar, Putu Ayu Sudyanti, Stephen McCune, Brice H. Spears, James A. Breedlove, Nadia A. Lanman, Humaira Gowher
Chd1 regulates repair of promoter-proximal DNA breaks to sustain hypertranscription in embryonic stem cells
Aydan Bulut-Karslioglu, Hu Jin, Marcela Guzman-Ayala, Andrew JK Williamson, Miroslav Hejna, Anthony D Whetton, Jun S. Song, Miguel Ramalho-Santos
KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency
Dafne Campigli Di Giammartino, Andreas Kloetgen, Alexander Polyzos, Yiyuan Liu, Daleum Kim, Dylan Murphy, Abderhman Abuhashem, Paola Cavaliere, Boaz Aronson, Veevek Shah, Noah Dephoure, Matthias Stadtfeld, Aristotelis Tsirigos, Effie Apostolou
Optogenetic control of Wnt signaling for modeling early embryogenic patterning with human pluripotent stem cells
Nicole A. Repina, Xiaoping Bao, Joshua A. Zimmermann, David A. Joy, Ravi S. Kane, David V. Schaffer
NF-κB-c-REL impairment drives human stem cells into the oligodendroglial fate
Lucia M Ruiz-Perera, Johannes FW Greiner, Christian Kaltschmidt, Barbara Kaltschmidt
Lineage hierarchies and stochasticity ensure the long-term maintenance of adult neural stem cells
Emmanuel Than-Trong, Bahareh Kiani, Nicolas Dray, Sara Ortica, Benjamin Simons, Steffen Rulands, Alessandro Alunni, Laure Bally-Cuif
Towards automated control of embryonic stem cell pluripotency
Mahmoud Khazim, Lorena Postiglione, Elisa Pedone, Dan L. Rocca, Carine Zahra, Lucia Marucci
Gastruloid development competence discriminates different states of pluripotency between naïve and primed
Federica Cermola, Cristina D’Aniello, Rosarita Tatè, Dario De Cesare, Alfonso Martinez-Arias, Gabriella Minchiotti, Eduardo Jorge Patriarca
Unique Epigenetic Programming Distinguishes Regenerative Spermatogonial Stem Cells in the Developing Mouse Testis
Keren Cheng, I-Chung Chen, Benjamin J. Hale, Brian P. Hermann, Christopher B. Geyer, Jon M. Oatley, John R. McCarrey
Differentiation of Urine-Derived Induced Pluripotent Stem Cells to Neuron, Astrocyte and Microvascular Endothelial Cells from a Diabetic Patient
Wan Liu, Ping Zhang, Jing Tan, Yongzhong Lin
Early Stem Cell Aging in the Mature Brain
Albina Ibrayeva, Maxwell Bay, Elbert Pu, David Jörg, Lei Peng, Heechul Jun, Naibo Zhang, Daniel Aaron, Congrui Lin, Galen Resler, Mi-Hyeon Jang, Benjamin D. Simons, Michael A. Bonaguidi
Neogenin-1 distinguishes between myeloid-biased and balanced Hoxb5+ mouse long-term hematopoietic stem cells
Gunsagar S. Gulati, Monika Zukowska, Joseph Noh, Allison Zhang, Rahul Sinha, Benson M. George, Daniel J. Wesche, Irving L. Weissman, Krzysztof Szade
Regeneration is a partial redeployment of the embryonic gene network
Jacob F. Warner, Aldine R. Amiel, Hereroa Johnston, Eric Röttinger
Dynamics and variability in regenerative potential of neuronal subtypes in the Nematostella nerve net
Jamie A. Havrilak, Layla Al-Shaer, Nesli Akinci, Aldine Amiel, Eric Röttinger, Michael J. Layden
A subset of SMN complex members have a specific role in tissue regeneration via ERBB pathway-mediated proliferation
Wuhong Pei, Lisha Xu, Zelin Chen, Claire C Slevin, Kade P Pettie, Stephen Wincovitch, NISC Comparative Sequencing Program, Shawn M Burgess
Region-specific regulation of stem cell-driven regeneration in tapeworms
Tania Rozario, Edward B. Quinn, Jianbin Wang, Richard E. Davis, Phillip A. Newmark
Midkine-a is required for cell cycle progression of Müller glia during neuronal regeneration
Mikiko Nagashima, Travis S. D’Cruz, Doneen Hesse, Christopher J. Sifuentes, Pamela A. Raymond, Peter F. Hitchcock
Zebrafish spinal cord repair is accompanied by transient tissue stiffening
Stephanie Möllmert, Maria A. Kharlamova, Tobias Hoche, Anna V. Taubenberger, Shada Abuhattum, Veronika Kuscha, Thomas Kurth, Michael Brand, Jochen Guck
Combinatorial proteomics and transcriptomics identify AMPK in the control of the axonal regeneration programme of DRG sensory neurons after spinal injury
Guiping Kong, Luming Zhou, Elisabeth Serger, Ilaria Palmisano, Francesco De Virgiliis, Thomas H Hutson, Eilidh Mclachlan, Anja Freiwald, Paolo La Montanara, Kirill Shkura, Radhika Puttagunta, Simone Di Giovanni
Pre-existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish
Marcos Sande-Melón, Inês J. Marques, María Galardi-Castilla, Xavier Langa, María Pérez-López, Marius Botos, Gabriela Guzmán-Martínez, David Miguel Ferreira-Francisco, Dinko Pavlinic, Vladimir Benes, Remy Bruggmann, Nadia Mercader
Single-cell analysis of the muscle stem cell hierarchy identifies heterotypic communication signals involved in skeletal muscle regeneration
Andrea J. De Micheli, Paula Fraczek, Sharon Soueid-Baumgarten, Hiranmayi Ravichandran, Iwijn De Vlaminck, Olivier Elemento, Benjamin D. Cosgrove
A high-content in vivo screen to identify microRNA epistasis in the repopulating mouse liver
Adam M. Zahm, Amber W. Wang, Yue J. Wang, Jonathan Schug, Kirk J. Wangensteen, Klaus H. Kaestner
The dynamic chromatin architecture of the regenerating liver
Amber W. Wang, Yue J. Wang, Adam M. Zahm, Ashleigh R. Morgan, Kirk J. Wangensteen, Klaus H. Kaestner
A temporal map of gene expression pattern during zebrafish liver regeneration
Urmila Jagtap, Ambily Sivadas, Sandeep Basu, Ankit Verma, Sridhar Sivasubbu, Vinod Scaria, Chetana Sachidanandan
Evaluation of Open Hollow Hydroxyapatite Microsphere on Bone Regeneration in Rat Calvarial Defects
Youqu Shen, Mohamed Rahaman, Yongxian Liu, Yue-Wern Huang
Real-time monitoring of mechanical cues in the regenerative niche reveal dynamic strain magnitudes that enhance bone repair
Brett S. Klosterhoff, Jarred Kaiser, Bradley D. Nelson, Salil S. Karipott, Marissa A. Ruehle, Scott J. Hollister, Jeffrey A. Weiss, Keat Ghee Ong, Nick J. Willett, Robert E. Guldberg
Adaptive and Innate Immune Cell Responses in Tendons and Lymph Nodes After Tendon Injury and Repair
Andrew C Noah, Thomas M Li, Leandro M Martinez, Susumu Wada, Jacob B Swanson, Nathaniel P Disser, Kristoffer B Sugg, Scott A Rodeo, Theresa T Lu, Christopher L Mendias
Electric-induced reversal of morphogenesis in Hydra
Erez Braun, Hillel Ori
The expanded BXD family of mice: A cohort for experimental systems genetics and precision medicine
David George Ashbrook, Danny Arends, Pjotr Prins, Megan K Mulligan, Suheeta Roy, Evan G Williams, Cathleen M Lutz, Alicia Valenzuela, Casey J Bohl, Jesse F Ingels, Melinda McCarty, Arthur Centeno, Reinmar Hager, Johan Auwerx, Saunak Sen, Lu Lu, Robert W. Williams
Zebrafish Dscaml1 is Essential for Retinal Patterning and Function of Oculomotor Subcircuits
Manxiu Ma, Alexandro D. Ramirez, Tong Wang, Rachel L. Roberts, Katherine E. Harmon, David Schoppik, Avirale Sharma, Christopher Kuang, Stephanie L. Goei, James A. Gagnon, Steve Zimmerman, Shengdar Q. Tsai, Deepak Reyon, J. Keith Joung, Emre R. F. Aksay, Alexander F. Schier, Y. Albert Pan
Zebrafish mbnl mutants model molecular and physical phenotypes of human MBNL loss of function disorders
Melissa N. Hinman, Jared I. Richardson, Rose A. Sockol, Eliza D Aronson, Sarah J. Stednitz, Katrina N. Murray, J. Andrew Berglund, Karen Guillemin
GABAergic cell loss in mice lacking autism-associated gene Sema6A
Karlie Menzel, Gábor Szabó, Yuchio Yanagawa, Turhan Cocksaygan, Céline Plachez
Multiparametric phenotyping of compound effects on patient derived organoids
Johannes Betge, Niklas Rindtorff, Jan Sauer, Benedikt Rauscher, Clara Dingert, Haristi Gaitantzi, Frank Herweck, Thilo Miersch, Erica Valentini, Veronika Hauber, Tobias Gutting, Larissa Frank, Sebastian Belle, Timo Gaiser, Inga Buchholz, Ralf Jesenofsky, Nicolai Härtel, Tianzuo Zhan, Bernd Fischer, Katja Breitkopf-Heinlein, Elke Burgermeister, Matthias P. Ebert, Michael Boutros
| Plant development
Transcriptional Activation of Arabidopsis Zygotes Is Required for Their Initial Division
Ping Kao, Michael Nodine
Auxin promotion of seedling growth via ARF5 is dependent on the brassinosteroid-regulated transcription factors BES1 and BEH4
Anahit Galstyan, Jennifer L Nemhauser
Epistatic Transcription Factor Networks Differentially Modulate Arabidopsis Growth and Defense
Baohua Li, Michelle Tang, Céline Caseys, Ayla Nelson, Marium Zhou, Xue Zhou, Siobhan M. Brady, Daniel J. Kliebenstein
The Arabidopsis Diacylglycerol Kinase 4 is involved in nitric oxide-dependent pollen tube guidance and fertilization
Aloysius Wong, Lara Donaldson, Maria Teresa Portes, Jörg Eppinger, José Feijó, Christoph Gehring
Proteomic studies of the Arabidopsis TRAPP complexes reveal conserved organization and a novel plant-specific component with a role in plant development
Veder J. Garcia, Shou-Ling Xu, Raksha Ravikumar, Wenfei Wang, Liam Elliott, Mary Fesenko, Melina Altmann, Pascal Falter-Braun, Ian Moore, Farhah F. Assaad, Zhi-Yong Wang
Root development is maintained by specific bacteria-bacteria interactions within a complex microbiome
Omri M. Finkel, Isai Salas-González, Gabriel Castrillo, Theresa F. Law, Jonathan M. Conway, Paulo José Pereira Lima Teixeira, Corbin D. Jones, Jeffery L. Dangl
CRISPR-TSKO facilitates efficient cell type-, tissue-, or organ-specific mutagenesis in Arabidopsis
Ward Decaestecker, Rafael Andrade Buono, Marie L. Pfeiffer, Nick Vangheluwe, Joris Jourquin, Mansour Karimi, Gert Van Isterdael, Tom Beeckman, Moritz K. Nowack, Thomas B. Jacobs
Integration of a FT expression cassette into CRISPR/Cas9 construct enables fast generation and easy identification of transgene-free mutants in Arabidopsis
Yuxin Cheng, Na Zhang, Saddam Hussain, Sajjad Ahmed, Wenting Yang, Shucai Wang
Cellular heterogeneity in pressure and growth emerges from tissue topology and geometry
Yuchen Long, Ibrahim Cheddadi, Vincent Mirabet, Gabriella Mosca, Mathilde Dumond, Jan Traas, Christophe Godin, Arezki Boudaoud
TaAPO-A1, an ortholog of rice ABERRANT PANICLE ORGANIZATION 1, is associated with total spikelet number per spike in elite hexaploid winter wheat varieties (Triticum aestivum L.)
Quddoos H. Muqaddasi, Jonathan Brassac, Ravi Koppolu, Jörg Plieske, Martin W. Ganal, Marion S. Röder
Reprogramming of 24nt siRNAs in rice gametes
Chenxin Li, Hengping Xu, Fang-Fang Fu, Scott D. Russell, Venkatesan Sundaresan, Jonathan I. Gent
De novo Transcriptome Characterization of Royal Iris (Iris section Oncocyclus) and Identification of Flower Development Genes
Yamit Bar-Lev, Esther Senden, Metsada Pasjmanik-Chor, Yuval Sapir
Evo-devo & evo
Multiple roles of the polycistronic gene tarsaless/mille-pattes/polished-rice during embryogenesis of the kissing bug Rhodnius prolixus
Vitória Tobias-Santos, Diego Guerra-Almeida, Flavia Mury, Lupis Ribeiro, Mateus Berni, Helena Araujo, Carlos Logullo, Natália Martins Feitosa, Jackson de Souza-Menezes, Evenilton Pessoa Costa, Rodrigo Nunes-da-Fonseca
Genetic, morphometric, and molecular analyses of interspecies differences in head shape and hybrid developmental defects in the wasp genus Nasonia
Lorna B Cohen, Rachel Edwards, Dyese Moody, Deanna Arsala, Jack H Werren, Jeremy A Lynch
Doublesex mediates the development of sex-specific pheromone organs in Bicyclus butterflies via multiple mechanisms
Anupama Prakash, Antónia Monteiro
tartan underlies the evolution of male Drosophila genital morphology
Joanna F. D. Hagen, Cláudia C. Mendes, Amber Blogg, Alex Payne, Kentaro M. Tanaka, Pedro Gaspar, Javier Figueras Jimenez, Maike Kittelmann, Alistair P. McGregor, Maria Daniela S. Nunes
An ancestral apical brain region contributes to the central complex under the control of foxQ2 in the beetle Tribolium castaneum
Bicheng He, Marita Buescher, Max Stephen Farnworth, Frederic Strobl, Ernst Stelzer, Nikolaus Dieter Bernhard Koniszewski, Dominik Mühlen, Gregor Bucher
Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation
Jonathan E. Valencia, Roberto Feuda, Dan O. Mellott, Robert D. Burke, Isabelle S. Peter
A set of endogenous control genes for use in quantitative real-time PCR experiments reveal that the wild-type formin Ldia2 is enriched in the early pond snail embryo
Harriet F. Johnson, Angus Davison
ABC-transporter activity and autocrine eicosanoid-signaling are required for germ cell migration a basal chordate
Susannah H. Kassmer, Delany Rodriguez, Anthony DeTomaso
Diverse cell junctions with unique molecular composition in tissues of a sponge (Porifera)
Jennyfer M. Mitchell, Scott A. Nichols
Par protein localization during the early development of Mnemiopsis leidyi suggests different modes of epithelial organization in Metazoa
Miguel Salinas-Saavedra, Mark Q Martindale
Neurogenin regulates effectors of migratory neuron cell behaviors in Ciona
Susanne Gibboney, Kwantae Kim, Florian Razy-Krajka, Wei Wang, Alberto Stolfi
Phenotypic plasticity as an important mechanism of cave colonization and adaptation in Astyanax cavefish
Helena Bilandžija, Breanna Hollifield, Mireille Steck, Guanliang Meng, Mandy Ng, Andrew D. Koch, Romana Gračan, Helena Ćetković, Megan L. Porter, Kenneth J. Renner, William R. Jeffery
Light-regulated collective contractility in a multicellular choanoflagellate
Thibaut Brunet, Ben T. Larson, Tess A. Linden, Mark J. A. Vermeij, Kent McDonald, Nicole King
Biophysical principles of choanoflagellate self-organization
Ben T. Larson, Teresa Ruiz-Herrero, Stacey Lee, Sanjay Kumar, L. Mahadevan, Nicole King
A chronology of multicellularity evolution in cyanobacteria
Katrin Hammerschmidt, Giddy Landan, Fernando Domingues Kümmel Tria, Tal Dagan
A Systems Biology perspective of Dynamical Patterning Modules in the transition to multicellularity: lessons from an aggregative bacteria
Alejandra Guzmán-Herrera, Juan A. Arias Del Angel, Natsuko Rivera-Yoshida, Mariana Benítez, Alessio Franci
A burst of genetic innovation in actin-related proteins (Arps) for testis-specific function in a Drosophila lineage
Courtney M. Schroeder, John Valenzuela, Glen M. Hocky, Harmit S. Malik
Cell biology
Caveolae coupling of melanocytes signaling and mechanics is required for human skin pigmentation
Lia Domingues, Ilse Hurbain, Floriane Gilles-Marsens, Nathalie André, Melissa Dewulf, Maryse Romao, Christine Viaris de Lesegno, Cédric Blouin, Christelle Guéré, Katell Vié, Graça Raposo, Christophe Lamaze, Cédric Delevoye
Prolonged ovarian storage of mature Drosophila oocytes dramatically increases meiotic spindle instability
Ethan J. Greenblatt, Rebecca Obniski, Claire Mical, Allan C. Spradling
Arp2/3 and Unc45 maintain heterochromatin stability in Drosophila polytene chromosomes
George Dialynas, Laetitia Delabaere, Irene Chiolo
Extramacrochaete promotes branch and bouton number via the sequestration of Daughterless in the cytoplasm of neurons
Edward A. Waddell, Jennifer M. Viveiros, Erin L. Robinson, Michal A. Sharoni, Nina K. Latcheva, Daniel R. Marenda
Dynamic centriolar relocalization of Polo kinase and Centrobin in early mitosis primes centrosome asymmetry in fly neural stem cells
Emmanuel Gallaud, Anjana Ramdas Nair, Nicole Horsley, Arnaud Monnard, Priyanka Singh, Tri Thanh Pham, David Salvador Garcia, Alexia Ferrand, Clemens Cabernard
Multiscale activity imaging in the mammary gland reveals how oxytocin enables lactation
Alexander J. Stevenson, Gilles Vanwalleghem, Teneale A. Stewart, Nicholas D. Condon, Bethan Lloyd-Lewis, Natascia Marino, James W. Putney, Ethan K
Telophase correction refines division orientation in stratified epithelia
Kendall J. Lough, Kevin M. Byrd, Carlos P. Descovich, Danielle C. Spitzer, Abby J. Bergman, Gerard M. Beaudoin III, Louis F. Reichardt, Scott E. Williams
An intact keratin network is crucial for mechanical integrity and barrier function in keratinocyte cell sheets
Susanne Karsch, Fanny Büchau, Thomas M. Magin, Andreas Janshoff
Enhanced cell-cell contact stability upon Fibroblast Growth factor Receptor/N-cadherin cross-talk
Thao Nguyen, Laurence Duchesne, Gautham Hari Narayama sankara, Nicole Boggetto, David Fernig, Chandrashekakr Uttamrao Murade, Benoit Ladoux, Rene-Marc Mege
Dynamics of Meiotic Sex Chromosome Inactivation and Pachytene Activation in Mice Spermatogenesis
Ábel Vértesy, Javier Frias-Aldeguer, Zeliha Sahin, Nicolas Rivron, Alexander van Oudenaarden, Niels Geijsen
RanGTP induces an effector gradient of XCTK2 and importin α/β for spindle microtubule cross-linking
Stephanie C. Ems-McClung, Mackenzie Emch, Stephanie Zhang, Serena Mahnoor, Lesley N. Weaver, Claire E. Walczak
Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis in the nematode lineage
Regina Rillo-Bohn, Renzo Adilardi, Barış Avşaroğlu, Lewis Stevens, Simone Köhler, Joshua Bayes, Clara Wang, Sabrina Lin, Kayla Baskevitch, Abby F. Dernburg
PACSIN2-dependent apical endocytosis regulates the morphology of epithelial microvilli
Meagan M. Postema, Nathan E. Grega-Larson, Leslie M. Meenderink, Matthew J. Tyska
ADAMTS-1 and Syndecan-4 intersect in the regulation of cell migration and angiogenesis
Jordi Lambert, Kate Makin, Sophia Akbareian, Robert Johnson, Stephen D Robinson, Dylan R. Edwards
Rupture of nuclear envelope in starfish oocytes proceeds by F-actin-driven segregation of pore-dense and pore-free membranes
Natalia Wesolowska, Pedro Machado, Ivan Avilov, Celina Geiss, Hiroshi Kondo, Masashi Mori, Yannick Schwab, Péter Lénárt
Modelling
Dynamic morphoskeletons in development
Mattia Serra, Sebastian Streichan, L. Mahadevan
Intrinsic noise, Delta-Notch signalling and delayed reactions promote sustained, coherent, synchronised oscillations in the presomitic mesoderm
Joseph W. Baron, Tobias Galla
Using a continuum model to decipher the mechanics of embryonic tissue spreading from time-lapse image sequences: An approximate Bayesian computation approach
Tracy L. Stepien, Holley E. Lynch, Shirley X. Yancey, Laura Dempsey, Lance A. Davidson
Accurate and efficient discretisations for stochastic models of cell migration and cell proliferation with crowding
Nabil T. Fadai, Ruth E. Baker, Matthew J. Simpson
A theoretical model of neural maturation during the spinal cord neurogenesis
Piyush Joshi, Isaac Skromne
Interkinetic nuclear movements promote apical expansion in pseudostratified epithelia at the expense of apicobasal elongation
Marina A. Ferreira, Evangeline Despin-Guitard, Fernando Duarte, Pierre Degond, Eric Theveneau
Multi-scale dynamical modelling of T-cell development from an early thymic progenitor state to lineage commitment
Victor Olariu, Mary A. Yui, Pawel Krupinski, Wen Zhou, Julia Deichmann, Ellen V. Rothenberg, Carsten Peterson
From spikes to intercellular waves: tuning the strength of calcium stimulation modulates organ size control
Ramezan Paravitorghabeh, Dharsan Soundarrajan, Jeremiah J. Zartman
Tools & resources
Negligible-Cost and Weekend-Free Chemically Defined Human iPSC Culture
Hui-Hsuan Kuo, Xiaozhi Gao, Jean-Marc DeKeyser, K. Ashley Fetterman, Emily A. Pinheiro, Carly J. Weddle, Michael V. Orman, Marisol Romero-Tejeda, Mariam Jouni, Malorie Blancard, Tarek Magdy, Conrad Epting, Alfred L. George Jr., Paul W. Burridge
CLIJ: Enabling GPU-accelerated image processing in Fiji
Robert Haase, Loic A. Royer, Peter Steinbach, Deborah Schmidt, Alexandr Dibrov, Uwe Schmidt, Martin Weigert, Nicola Maghelli, Pavel Tomancak, Florian Jug, Eugene W. Myers
An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion
Kizhakke Mattada Sathyan, Brian D. McKenna, Warren D. Anderson, Fabiana M. Duarte, Leighton Core, Michael J. Guertin
3D-Cell-Annotator: an open-source active surface tool for single cell segmentation in 3D microscopy images
Ervin A. Tasnadi, Timea Toth, Maria Kovacs, Akos Diosdi, Francesco Pampaloni, Jozsef Molnar, Filippo Piccinini, Peter Horvath
LongAxis: a MATLAB-based program for 3D quantitative analysis of epithelial cell shape and orientation
Keith R. Carney, Chase D. Bryan, Hannah B. Gordon, Kristen M. Kwan
Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy
Claudia Prahst, Parham Ashrafzadeh, Kyle Harrington, Lakshmi Venkatraman, Mark Richards, Ana Martins Russo, Kin-Sang Cho, Karen Chang, Thomas Mead, Dong Feng Chen, Douglas Richardson, Lena Claesson-Welsh, Claudio Franco, Katie Bentley
Accurate denoising of single-cell RNA-Seq data using unbiased principal component analysis
Florian Wagner, Dalia Barkley, Itai Yanai
Coolpup.py – a versatile tool to perform pile-up analysis of Hi-C data
Ilya M. Flyamer, Rob S. Illingworth, Wendy A. Bickmore
Modular and efficient pre-processing of single-cell RNA-seq
Páll Melsted, A. Sina Booeshaghi, Fan Gao, Eduardo da Veiga Beltrame, Lambda Lu, Kristján Eldjárn Hjorleifsson, Jase Gehring, Lior Pachter
Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
Joseph W. Foley, Chunfang Zhu, Philippe Jolivet, Shirley X. Zhu, Peipei Lu, Michael J. Meaney, Robert B. West
Inhibition of Histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing
Bin Liu, Siwei Chen, Anouk La Rose, Deng Chen, Fangyuan Cao, Dominik Kiemel, Manon Aïssi, FJ Dekker, HJ Haisma
Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells
Wesley A. Wierson, Brandon W. Simone, Zachary WareJoncas, Carla Mann, Jordan M. Welker, Bibekananda Kar, William A. C. Gendron, Michael A. Barry, Karl J. Clark, Drena L. Dobbs, Maura A. McGrail, Stephen C. Ekker, Jeffrey J. Essner
Optogenetic Control of Programmable Genome Editing by Photoactivatable CRISPR/Cas9 Nanosystem in the Second Near-Infrared Window
Xiaohong Chen, Yuxuan Chen, Huhu Xin, Tao Wan, Yuan Ping
Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing
Sundaram Acharya, Arpit Mishra, Deepanjan Paul, Asgar Hussain Ansari, Mohd. Azhar, Manoj Kumar, Riya Rauthan, Namrata Sharma, Meghali Aich, Dipanjali Sinha, Saumya Sharma, Shivani Jain, Arjun Ray, Suman Jain, Sivaprakash Ramalingam, Souvik Maiti, Debojyoti Chakraborty
GenEditID: an open-access platform for the high-throughput identification of CRISPR edited cell clones
Ying Xue, YC Loraine Tung, Rasmus Siersbaek, Anne Pajon, Chandra SR Chilamakuri, Ruben Alvarez-Fernandez, Richard Bowers, Jason Carroll, Matthew Eldridge, Alasdair Russell, Florian T. Merkle
CAMIO for deletion analysis of endogenous DNA sequences in multicellular organisms
Hui-Min Chen, Jorge Garcia Marques, Ken Sugino, Dingjun Wei, Rosa Linda Miyares, Tzumin Lee
Enhanced Golic+: Gene targeting with 100% recovery in Drosophila male germ cells
Hui-Min Chen, Xiaohao Yao, Qingzhong Ren, Chuan-Chie Chang, Ling-Yu Liu, Tzumin Lee
Serum-free culture system for spontaneous human mesenchymal stem cell spheroids formation
Guoyi Dong, Shengpeng Wang, Yuping Ge, Weihua Zhao, Qiuting Deng, Qi Cao, Quanlei Wang, Zhouchun Shang, Wenjie OuYang, Jing Li, Chao Liu, Jie Tang, Ying Gu
A Novel Tmem119-tdTomato Reporter Mouse Model for Studying Microglia in the Central Nervous System
Chunsheng Ruan, Linlin Sun, Alexandra Kroshilina, Lien Beckers, Philip L. De Jager, Elizabeth M. Bradshaw, Samuel Hasson, Guang Yang, Wassim Elyaman
An inducible Cre mouse line to sparsely target nervous system cells, including Remak Schwann cells
Darshan Sapkota, Joseph D. Dougherty
Generation of a Retina Reporter hiPSC Line to Label Progenitor, Ganglion, and Photoreceptor Cell Types
Phuong T. Lam, Christian Gutierrez, Katia Del Rio-Tsonis, Michael L. Robinson
Vascularized human cortical organoids model cortical development in vivo
Yingchao Shi, Le Sun, Jianwei Liu, Suijuan Zhong, Mengdi Wang, Rui Li, Peng Li, Lijie Guo, Ai Fang, Ruiguo Chen, Woo-Ping Ge, Qian Wu, Xiaoqun Wang
Cross-species blastocyst chimerism between nonhuman primates using iPSCs
Morteza Roodgar, Fabian P. Suchy, Vivek Bajpai, Jose G. Viches-Moure, Joydeep Bhadury, Angelos Oikonomopoulos, Joseph C. Wu, Joseph L. Mankowski, Kyle M. Loh, Hiromitsu Nakauchi, Catherine A. VandeVoort, Michael P. Snyder
Direct Visualization of Live Zebrafish Glycan via Single-step Metabolic Labeling with Fluorophore-tagged Nucleotide Sugars
Senlian Hong, Pankaj Sahai-Hernandez, Digantkumar Gopaldas Chapla, Kelley W. Moremen, David Traver, Peng Wu
NeuroPAL: A Neuronal Polychromatic Atlas of Landmarks for Whole-Brain Imaging in C. elegans
Eviatar Yemini, Albert Lin, Amin Nejatbakhsh, Erdem Varol, Ruoxi Sun, Gonzalo E. Mena, Aravinthan D.T. Samuel, Liam Paninski, Vivek Venkatachalam, Oliver Hobert
Tailoring cryo-electron microscopy grids by photo-micropatterning for in-cell structural studies
Mauricio Toro-Nahuelpan, Ievgeniia Zagoriy, Fabrice Senger, Laurent Blanchoin, Manuel Théry, Julia Mahamid
Aequorea victoria’s secrets
Gerard G. Lambert, Hadrien Depernet, Guillaume Gotthard, Darrin T. Schultz, Isabelle Navizet, Talley Lambert, Daphne S. Bindels, Vincent Levesque, Jennifer N. Moffatt, Anya Salih, Antoine Royant, Nathan C. Shaner
Exploration of cell development pathways through high dimensional single cell analysis in trajectory space
Denis Dermadi, Michael Bscheider, Kristina Bjegovic, Nicole H. Lazarus, Agata Szade, Husein Hadeiba, Eugene C. Butcher
Research practice & education
The effect of bioRxiv preprints on citations and altmetrics
Nicholas Fraser, Fakhri Momeni, Philipp Mayr, Isabella Peters
Gender and other potential biases in peer review: Analysis of 38,250 external peer review reports
Anna Severin, Joao Martins, François Delavy, Anne Jorstad, Matthias Egger, Rachel Heyard
Assessing the size of the affordability problem in scholarly publishing
Alexander Grossmann, Björn Brembs
Grant reviewer perceptions of panel discussion in face-to-face and virtual formats: lessons from team science?
Stephen A. Gallo, Karen B. Schmaling, Lisa A. Thompson, Scott R. Glisson
The Participation and Motivations of Grant Peer Reviewers: A Comprehensive Survey
Stephen A Gallo, Lisa A Thompson, Karen B Schmaling, Scott R Glisson
Knowledge and attitudes among life scientists towards reproducibility within journal articles
Evanthia Kaimaklioti Samota, Robert P. Davey
Long-term impact of intensive postgraduate laboratory training at the Cold Spring Harbor Neurobiology of Drosophila summer course
Sarah Ly, Karla Kaun, Chi-Hon Lee, David Stewart, Stefan R. Pulver, Alex C. Keene
Why not…
Sophisticated suction organs from insects living in raging torrents: Morphology and ultrastructure of the attachment devices of net-winged midge larvae (Diptera: Blephariceridae)
Victor Kang, Richard Johnston, Thomas van de Kamp, Tomáš Faragó, Walter Federle
Arm swapping autograft shows functional equivalency of five arms in sea stars
Daiki Wakita, Hitoshi Aonuma, Shin Tochinai
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