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developmental and stem cell biologists

September in preprints

Posted by , on 3 October 2017

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


 

This month features butterfly eyespots, brain development in vivo and in silico, lots on cell commitment in embryos and dishes, a diverse selection of modelling preprints, and, right at the end in our ‘Why not…’ section, some algorithmic science art inspired by sand-bubbler crabs!

The preprints were hosted on bioRxivPeerJ, arXiv and Wellcome Open Research. Use these links to get to the section you want:

 

Developmental biology

Patterning & signalling

Morphogenesis & mechanics

Genes & genomes

Stem cells, regeneration & disease modelling

Evo-devo & evo
Cell biology
Modelling
Tools & resources

| Imaging etc.

| Genome tools

Research practice
Why not…

 

Developmental biology

| Patterning & signalling

 

Cultured blastocysts from Miller, et al.’s preprint

 

Transcriptional control by Sall4 in blastocysts facilitates lineage commitment of inner cell mass cells. Anzy Miller, Sarah Gharbi, Charles Etienne-Dumeau, Ryuichi Nishinakamura, Brian Hendrich

 

Dephosphorylation of the NPR2 guanylyl cyclase contributes to inhibition of bone growth by fibroblast growth factor. Leia C. Shuhaibar, Jerid W. Robinson, Ninna P. Shuhaibar, Jeremy R. Egbert, Giulia Vigone, Valentina Baena, Deborah Kaback, Siu-Pok Yee, Robert Feil, Melanie C. Fisher, Caroline N. Dealy, Lincoln R. Potter, Laurinda A. Jaffe

 

Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming.  Geoffrey Schiebinger, Jian Shu, Marcin Tabaka, Brian Cleary, Vidya Subramanian, Aryeh Solomon, Siyan Liu, Stacie Lin, Peter Berube, Lia Lee, Jenny Chen, Justin Brumbaugh, Philippe Rigollet, Konrad Hochedlinger, Rudolf Jaenisch, Aviv Regev, Eric Lander

 

MCAM contributes to the establishment of cell autonomous polarity in myogenic and chondrogenic differentiation. Artal Moreno-Fortuny, Laricia Bragg, Giulio Cossu, Urmas Roostalu

 

Early worm embryos from Liro, et al.’s preprint

 

The kinases PIG-1 and PAR-1 act in redundant pathways to regulate asymmetric division in the EMS blastomere of C. elegans. Malgorzata J. Liro, Diane G. Morton, Lesilee S. Rose

 

In vivo relevance of intercellular calcium signaling in Drosophila wing development. Qinfeng Wu, Pavel Aleksandrovich Brodskiy, Francisco Javier Huizar, Jamison John Jangula, Cody Narciso, Megan Kathleen Levis, Teresa Brito-Robinson, Jeremiah J. Zartman

 

Intercellular calcium signaling is regulated by morphogens during Drosophila wing development. Pavel A. Brodskiy, Qinfeng Wu, Francisco J. Huizar, Dharsan K. Soundarrajan, Cody Narciso, Megan Levis, Ninfamaria Arredondo-Walsh, Jianxu Chen, Peixian Liang, Danny Z. Chen, Jeremiah James Zartman

 

The hominoid-specific gene DSCR4 is involved in regulation of human leukocyte migration. Morteza Mahmoudi Saber, Marziyeh Karimiavargani, Nilmini Hettiarachchi, Michiaki Hamada, Takanori Uzawa, Yoshihiro Ito, Naruya Saitou

 

Ldb1 and Rnf12-dependent regulation of Lhx2 controls the relative balance between neurogenesis and gliogenesis in retina. Jimmy de Melo, Anand Venkataraman, Cristina Zibetti, Brian S. Clark, Seth Blackshaw

 

Tracking microvillous sensory neuron origins, from Aguillon, et al.’s preprint

 

Cell-type heterogeneity in the zebrafish olfactory placode is generated from progenitors within preplacodal ectoderm. Raphaël Aguillon, Julie Batut, Pascale Dufourcq, Romain Madelaine, Arul Subramanian, Thomas F. Schilling, Patrick Blader

 

Developmental diversification of cortical inhibitory interneurons. Christian Mayer,Christoph Hafemeister, Rachel C Bandler, Robert Machold, Kathryn Allaway, Xavier Jaglin, Renata Batista Brito, Andrew Butler, Gord Fishell, Rahul Satija

 

Modulation of apoptosis controls inhibitory interneuron number in the cortex. Myrto Denaxa, Guilherme Neves, Adam Rabinowitz, Sarah Kemlo, Petros Liodis, Juan Burrone, Vassilis Pachnis

 

Paupar LncRNA Promotes KAP1 Dependent Chromatin Changes And Regulates Subventricular Zone Neurogenesis. Ioanna Pavlaki, Farah Alammari, Bin Sun, Neil Clark, Tamara Sirey, Sheena Lee, Dan J. Woodcock, Chris P. Ponting, Francis G. Szele, Keith W. Vance

 

Single-cell transcriptomic profiling of progenitors of the oligodendrocyte lineage reveals transcriptional convergence during development. Sueli Marques, Darya Vanichkina, David van Bruggen, Elisa Floriddia, Hermany Munguba, Leif Varemo, Stefania Giacomello, Ana Mendanha Falcao, Mandy Meijer, S Samudyata, Simone Codeluppi, Asa Bjorklund, Sten Linnarsson, Jens Hjerling-Leffler, Ryan Taft, Goncalo Castelo-Branco

 

Embryonic and postnatal neurogenesis produce functionally distinct subclasses of dopaminergic neuron.Elisa Galliano, Eleonora Franzoni, Marine Breton, Annisa N. Chand, Darren J. Byrne, Venkatesh N. Murthy, Matthew S. Grubb

 

ELMOD1 stimulates ARF6-GTP hydrolysis to stabilize apical structures in developing vestibular hair cells. Jocelyn F Krey, Rachel A Dumont, Philip A Wilmarth, Larry L David, Kenneth R Johnson, Peter G Barr-Gillespie

 

Tracking mouse gonad development in mice, from Stevant, et al.’s preprint

 

Deciphering cell lineage specification during male sex determination with single-cell RNA sequencing. Isabelle Stevant, Yasmine Neirijnck, Christelle Borel, Jessica Escoffier, Lee B Smith, Stylianos E Antonarakis, Emmanouil T Dermitzakis, Serge Nef

 

Tissue specific auxin biosynthesis regulates leaf vein patterning. Irina Kneuper, William David Teale, Jonathan Edward Dawson, Ryuji Tsuggeki, Klaus Palme, Eleni Katifori, Franck Anicet Ditengou

 

Cross-species functional diversity within the PIN auxin efflux protein family. Devin Lee O’Connor, Samuel Elton, Fabrizio Ticchiarelli, Mon Mandy Hsia, John Vogel, Ottoline Leyser

 

The ERA-related GTPase AtERG2 associated with mitochondria 18S RNA is essential for early embryo development in Arabidopsis. Pengyu Cheng, Hongjuan Li, Linlin Yuan, Huiyong Li, Lele Xi, Junjie Zhang, Jin Liu, Yingdian Wang, Heping Zhao, Huixin Zhao, Shengcheng Han

 

Karrikin-sensing protein KAI2 is a new player in regulating root growth patterns. Stephanie M. Swarbreck, Yannick Guerringue, Elsa Matthus, Fiona J. C. Jamieson, Julia M. Davies

 

The CLAVATA receptor FASCIATED EAR2 responds to different CLE peptides by signaling through different downstream effectors. Byoung Il Je, Fang Xu, Qingyu Wu, Lei Liu, Robert Meeley, David Jackson

 

Mouse brain vasculature from Di Giovanna, et al.’s preprint

 

Whole-brain vasculature reconstruction at the single capillary level. Antonino Paolo Di Giovanna, Alessandro Tibo, Ludovico Silvestri, Marie Caroline Muellenbroich, Irene Costantini, Anna Letizia Allegra Mascaro, Leonardo Sacconi, Paolo Frasconi, Francesco Saverio Pavone

 

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

 

Worm oocyte development from Lee, et al.’s preprint

 

CYK-4 functions independently of its centralspindlin partner ZEN-4 to cellularize oocytes in germline syncytia. Kian-Yong Lee, Rebecca A. Green, Edgar Gutierrez, J. Sebastian Gomez-Cavazos, Irina Kolotuev, Shaohe Wang, Arshad Desai, Alex Groisman, Karen Oegema

 

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

 

C. elegans DBL-1/BMP Regulates Lipid Accumulation via Interaction with Insulin Signaling. James Clark, Michael Meade, Gehan Ranepura, David H Hall, Cathy Savage-Dunn

 

 

| Morphogenesis & mechanics

Motility-gradient induced elongation of the vertebrate embryo. Ido Regev, Karine Guevorkian, Olivier Pourquie, L. Mahadevan

 

Drosophila egg chambers from Sallak, et al.’s preprint

 

Src42A required for collective border cell migration in vivo. Yasmin Sallak, Alba Yurani Torres, Hongyan Yin, Denise Montell

 

A “molecular guillotine” reveals an interphase function of Kinesin-5. Zhiyi Lv, Jan Rosenbaum, Timo Aspelmeier, Jorg Grosshans

 

Drosophila beta-Tubulin 97EF is upregulated at low temperature and stabilizes microtubules. Faina Myachina, Fritz Bosshardt, Johannes Bischof, Moritz Kirschmann, Christian F. Lehner

 

Microglia remodel synapses by presynaptic trogocytosis and spine head filopodia induction. Laetitia Weinhard, Urte Neniskyte, Giulia di Bartolomei, Giulia Bolasco, Pedro Machado, Nicole Schieber, Melanie Exiga, Auguste Vadisiute, Angelo Raggioli, Andreas Schertel, Yannick Schwab, Cornelius T. Gross

 

Centrosomes in the worm embryo, from Medley, et al.’s preprint

 

APC/CFZR-1 Controls SAS-5 Levels to Regulate Centrosome Duplication in Caenorhabditis elegans. Jeffrey C. Medley, Lauren E. DeMeyer, Megan M. Kabara, Mi Hye Song

 

Re-evaluating functional landscape of the cardiovascular system during development. Norio Takada, Madoka Omae, Fumihiko Sagawa, Neil Chi, Satsuki Endo, Satoshi Kozawa, Thomas N Sato

 

Role of midbody remnant in meiosis II creating tethered polar bodies. Alex McDougall, Celine Hebras, Gerard Pruliere, David Burgess, Vlad Costache, Remi Dumollard, Janet Chenevert

 

Non-Elastic Remodeling of the 3D Extracellular Matrix by Cell-Generated Forces. Andrea Malandrino, Michael Mak, Xavier Trepat, Roger D. Kamm

 

Depth Dependent Nanomechanical Analysis of Extracellular Matrix in Multicell Spheroids. Varun Vyas, Melani Solomon, Gerard G. M. D’Souza, Bryan D. Huey

 

 

| Genes & genomes

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

 

Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo. Jenna E. Haines, Michael B. Eisen

 

dmrad51/spnA mutant exhibit defects during somatic stages of developmental and show enhanced genomic damage, cell death and low temperature sensitivity. Chaitali Khan, Sonia Muliyil, Champakali Ayyub, Basuthkar J. Rao

 

Chromatin organization changes during the establishment and maintenance of the postmitotic state. Yiqin Ma, Laura Buttitta

 

 

Rendered OPT hearts, from Sun, et al.’s preprint

 

Cardiac enriched BAF chromatin remodeling complex subunit Baf60c regulates gene expression programs essential for heart development and function. Xin Sun, Swetansu Hota, Yu-Qing Zhou, Stefanie Novak, Dario Miguel-Perez, Danos Christodoulou, Christine Seidman, Jonathan Seidman, Carol Gregorio, Mark Henkelman, Janet Rossant, Benoit Bruneau

 

Nkx2.5-dependent alterations of the embryonic heart DNA methylome identify novel cis-regulatory elements in cardiac development. Bushra Gorsi, Timothy Mosbruger, Megan Smith, Jonathon Hill, H. Joseph Yost

 

Gene neighbourhood integrity disrupted by CTCF loss in vivo. Dominic Lee, Wilson Tan, George Anene, Peter Li, Tuan Danh, Zenia Tiang, Shi Ling Ng, Motakis Efthymios, Matias Autio, Jianming Jiang, Melissa Fullwood, Shyam Prabhakar, Roger Foo

 

Nonparametric Bayesian inference of transcriptional branching and recombination identifies regulators of early human germ cell development. Christopher Andrew Penfold, Anastasiya Sybirna, John Reid, Yun Huang, Lorenz Wernisch, Zoubin Ghahramani, Murray Grant, M. Azim Surani

 

The FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Jennifer Frost, M. Yvonne Kim, Guen-Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel Lin, Hyunjin Yoo, Jaemyung Choi, Yoko Ikeda, Tetsu Kinoshita, Yeonhee Choi, Daniel Zilberman, Robert L. Fischer

 

Genetic Identification of Novel Separase regulators in Caenorhabditis elegans. Michael Melesse, Dillon E. Sloan, Joseph T. Benthal, Quincey Caylor, Krishen Gosine, Xiaofei Bai, Joshua N. Bembenek

 

Pleiotropy in enhancer function is encoded through diverse genetic architectures. Ella Preger-Ben Noon, Gonzalo Sabarís, Daniela Ortiz, Jonathan Sager, Anna Liebowitz, David L. Stern, Nicolas Frankel

 

Small RNAs are trafficked from the epididymis to developing mammalian sperm. Upasna Sharma, Fengyun Sun, Brian Reichholf, Veronika Herzog, Stefan Ameres, Oliver Rando

 

Ploidy changes, centrosomes and spindles from Yaguchi, et al.’s preprint

 

Uncoordinated centrosome duplication cycle underlies the instability of non-diploid states in mammalian somatic cells. Kan Yaguchi, Ryo Matsui, Takahiro Yamamoto, Yuki Tsukada, Atsuko Shibanuma, Keiko Kamimura, Toshiaki Koda, Ryota Uehara

 

Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation. Ethan Edward Ford, Matthew R. Grimmer, Sabine Stolzenburg, Ozren Bogdanovic, Alex de Mendoza, Peggy J. Farnham, Pilar Blancafort, Ryan Lister

 

Arabidopsis in different temperatures from Tasset, et al.’s preprint

 

POWERDRESS-mediated histone deacetylation is essential for thermomorphogenesis in Arabidopsis thaliana. Celine Tasset, Avilash Singh Yadav, Sridevi Sureshkumar, Rupali Singh, Lennard van der Woude, Maxim Nekrasov, David Tremethick, Martijn van Zanten, Sureshkumar Balasubramanian

 

Telomere repeats induce domains of H3K27 methylation in Neurospora. Kirsty Jamieson, Kevin J McNaught, Tereza Ormsby, Neena A. Leggett, Shinji Honda, Eric U Selker

 

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

 

NF90/ILF3 is a transcription factor that promotes proliferation over differentiation by hierarchical regulation in K562 erythroleukemia cells. Ting-Hsuan Wu, Lingfang Shi, Jessika Adrian, Minyi Shi, Ramesh V. Nair, Michael P. Snyder, Peter N. Kao

 

Insights into the molecular changes associated with postnatal human brain development: an integrated transcriptomics and proteomics study. Michael S. Breen, Sureyya Ozcan, Jordan M. Ramsey, Nitin Rustogi, Michael G. Gottshalk, Maree J. Webster, Cyndi Shannon Weickert, Joseph D. Buxbaum, Sabine Bahn

 

Mating can cause transgenerational gene silencing in Caenorhabditis elegans. Sindhuja Devanapally, Samual Allgood, Antony M. Jose

 

 

| Stem cells, regeneration & disease modelling

CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo. Gabriel N Aughey, Alicia Estacio Gomez, Jamie Thomson, Hang Yin, Tony D Southall

 

High-Resolution Dissection of Conducive Reprogramming Trajectory to Ground State Pluripotency. Asaf Zviran, Nofar Mor, Yoach Rais, Hila Gingold, Shani Peles, Elad Chomsky, Sergey Viukov, Jason D. Buenrostro, Leehee Weinberger, Yair S. Manor, Vladislav Krupalnik, Mirie Zerbib, Hadas Hezroni, Diego Adhemar Jaitin, David Larastiaso, Shlomit Gilad, Sima Benjamin, Awni Mousa, Muneef Ayyash, Daoud Sheban, Jonathan Bayerl, Alejandro Aguilera Castrejon, Rada Massarwa, Itay Maza, Suhair Hanna, Ido Amit, Yonatan Stelzer, Igor Ulitsky, William J. Greenleaf, Yitzhak Pilpel, Noa Novershtern, Jacob H. Hanna

 

SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells. Özgen Deniz, Lorenzo de la Rica, Kevin C. L. Cheng, Dominik Spensberger, Miguel R. Branco

 

Sox4 drives intestinal secretory differentiation toward tuft and enteroendocrine fates. Adam Gracz, Matthew J. Fordham, Danny C. Trotier, Bailey Zwarycz, Yuan-Hung Lo, Katherine Bao, Joshua Starmer, Noah F. Shroyer, Richard L. Reinhardt, Scott T. Magness

 

FACT sets a barrier for cell fate reprogramming in C. elegans and Human. Ena Kolundzic, Andreas Ofenbauer, Bora Uyar, Anne Sommermeier, Stefanie Seelk, Mei He, Guelkiz Baytek, Altuna Akalin, Sebastian Diecke, Scott Allen Lacadie, Baris Tursun

 

Polymorphic dynamics of ribosomal proteins gene expression during somatic cell reprogramming and their differentiation into specialized cells-types. Prashanth Kumar Guthikonda, Sumitha Prameela Bharathan, Janakiram Rayabaram, Trinadha Rao Sornapudi, Sailu R Yellaboina, Shaji R Velayudhan, Sreenivasulu Kurukuti

 

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

 

Loss of MECP2 leads to induction of p53 and cell senescence. William E Lowry, Minori Ohashi, Peiyee Lee, Kai Fu, Benni Vargas, Denise E. Allen, Elena Korsakova, Jessica K Cinkornpumin, Carlos Salas, Jennifer C Park, Igal Germanguz, Konstantinos Chronis, Edward Kuoy, Stephen Tran, Xinshu Xiao, Matteo Pellegrini, Kathrin Plath

 

The U2AF homology motif kinase 1 (UHMK1) is upregulated upon hematopoietic cell differentiation. Isabella Barbutti, Joao Agostinho Machado-Neto, Vanessa Cristina Arfelli, Paula de Melo Campos, Fabiola Traina, Sara Teresinha Olalla Saad, Leticia Froehlich Archangelo

 

Integrated transcriptome and epigenome analyses identify alternative splicing as a novel candidate linking histone modifications to embryonic stem cell fate decision. Yungang Xu, Guangxu Jin, Liang Liu, Dongmin Guo, Xiaobo Zhou

 

Coronal sections of mice brains from Sullivan & Armstrong’s preprint

 

Transplanted Adult Neural Stem Cells Express Sonic Hedgehog In Vivo and Suppress White Matter Neuroinflammation After Experimental Traumatic Brain Injury. Genevieve M. Sullivan, eRegina C. Armstrong

 

Intraocular injection of ES cell-derived neural progenitors improve visual function in retinal ganglion cell-depleted mouse models. Divya Mundackal Sivaraman, Rasheed Vazhanthodi Abdul, Tiffany Schmidt, Lalitha Soundararajan, Samer Hattar, Jackson James

 

Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with signatures from post mortem adult brains. Gabriel E. Hoffman, Brigham J. Hartley, Erin Flaherty, Ian Ladran, Peter Gochman, Douglas Ruderfer,Eli A. Stahl, Judith Rapoport, Pamela Sklar, Kristen J. Brennand

 

Part of Daniszewski, et al.’s experimental workflow

 

Single Cell RNA Sequencing of stem cell-derived retinal ganglion cells. Maciej Daniszewski, Anne Senabouth, Quan Nguyen, Duncan E Crombie, Samuel W Lukowski, Tejal Kulkarni, Donald J Zack, Alice Pebay, Joseph E Powell, Alex Hewitt

 

JIP2 haploinsufficiency contributes to neurodevelopmental abnormalities in human pluripotent stem cell-derived neural progenitors and cortical neurons. Reinhard Roessler, Johanna Goldmann, Chikdu Shivalila, Rudolf Jaenisch

 

LRP1 Regulates Peroxisome Biogenesis and Cholesterol Homeostasis in Oligodendrocytes and is Required in CNS Myelin Development and Repair. Jing-Ping Lin, Yevgeniya A Mironova, Peter Shrager, Roman J Giger

 

Effects of mechanical loading on cortical defect repair using a novel mechanobiological model of bone healing. Chao Liu, Robert Carrera, Vittoria Flamini, Lena Kenny, Pamela Cabahug-Zuckerman, Benson George, Daniel Hunter, Bo Liu, Gurpreet Singh, Philipp Leucht, Kenneth A Mann, Jill A Helms, Alesha B Castillo

 

Tracking responses to spinal cord injury in rats, from Didangelos, et al.’s preprint

 

Rats and axolotls share a common molecular signature after spinal cord injury enriched in collagen-1. Athanasios Didangelos, Katalin Bartus, Jure Tica, Michele Puglia, Bernd Roschitzki, Elizabeth Bradbury

 

DNAJB1-PRKACA fusion kinase drives tumorigenesis and interacts with β-catenin and the liver regenerative response. Edward R Kastenhuber, Gadi Lalazar, Darjus F Tschaharganeh, Shauna L Houlihan, Timour Baslan, Chi-Chao Chen, David Requena, Sha Tian, Benedikt Bosbach, John E Wilkinson, Sanford M Simon, Scott W Lowe

 

Bcl11b is a Newly Identified Regulator of Vascular Smooth Muscle Phenotype and Arterial Stiffness. Jeff Arni Valisno, Pavania Elavalakanar, Christopher Nicholson, Kuldeep Singh, Dorina Avram, Richard A. Cohen, Gary F. Mitchell, Kathleen G. Morgan, Francesca Seta

 

Chromatin accessibility profiling uncovers genetic- and T2D disease state-associated changes in cis-regulatory element use in human islets. Shubham Khetan, Romy Kursawe, Ahrim Youn, Nathan Lawlor, Eladio Marquez, Duygu Ucar, Michael L Stitzel

 

Drosophila larval brain neoplasms present tumour-type dependent genome instability. Fabrizio Rossi, Camille Stephan-Otto Attolini, Jose Luis Mosquera, Cayetano Gonzalez

 

Pervasive epistasis in cell proliferation pathways modulates neurodevelopmental defects of autism-associated 16p11.2 deletion. Janani Iyer, Mayanglambam Dhruba Singh, Matthew Jensen, Payal Patel, Lucilla Pizzo, Emily Huber, Haley Koerselman, Alexis T. Weiner, Paola Lepanto, Komal Vadodaria, Alexis Kubina, Qingyu Wang, Abigail Talbert, Sneha Yennawar, Jose Badano, J. Robert Manak, Melissa M. Rolls, Arjun Krishnan, Santhosh Girirajan

 

Targeting histone deacetylase activity to arrest cell growth and promote neural differentiation in Ewing sarcoma. Barbara Kunzler Souza, Patricia Luciana da Costa Lopez, Pamela Rossi Menegotto, Igor Araujo Vieira, Nathalia Kersting, Ana Lucia Abujamra, Andre T. Brunetto, Algemir L. Brunetto, Lauro Gregianin, Caroline Brunetto de Farias, Carol J. Thiele, Rafael Roesler

 

Fibroblast-derived HGF drives acinar lung cancer cell polarization through integrin-dependent RhoA-ROCK1 inhibition. Anirban Datta, Emma Sandilands, Keith E. Mostov, David M. Bryant

 

A Rational Drug Combination Design to Inhibit Epithelial-Mesenchymal Transition in a Three-Dimensional Microenvironment. Farnaz Barneh, Mehdi Mirzaie, Payman Nickchi, Tuan Zea Tan, Jean Paul Thiery, Mehran Piran, Mona Salimi, Fatemeh Goshadrou, Amir Reza Aref, Mohieddin Jafari

 

Telomerase mutant zebrafish from from Scahill, et al.’s preprint

 

The age of heterozygous telomerase mutant parents influences the adult phenotype of their offspring irrespective of genotype in zebrafish. Catherine M. Scahill1, Zsofia Digby, Ian M. Sealy, Richard J. White, John E. Collins, Elisabeth M. Busch-Nentwich

 

Evo-devo & evo

 

Distalless and engrailed expression in butterflies, from Connahs, et al.’s preprint

 

Disrupting different Distal-less exons leads to ectopic and missing eyespots accurately modeled by reaction-diffusion mechanisms. Heidi Connahs, Sham Tlili, Jelle van Creij, Tricia Y. J. Loo, Tirtha Banerjee, Timothy E. Saunders, Antonia Monteiro

 

The Complex Simplicity of the Brittle Star Nervous System. Olga Zueva, Maleana Khoury, Thomas Heinzeller, Daria Mashanova, Vladimir Mashanov

 

Early developmental morphology reflects independence from parents in social beetles. Kyle M. Benowitz, Madeline E. Sparks, Elizabeth C. McKinney, Patricia J. Moore, Allen J. Moore

 

A zombie LIF gene in elephants is up-regulated by TP53 to induce apoptosis in response to DNA damage. Juan Manuel Vazquez, Michael Sulak, Sravanthi Chigurupati, Vincent J. Lynch

 

Microinjection to deliver protein and mRNA into zygotes of the cnidarian endosymbiosis model Aiptasia sp. Madeline Bucher, Victor Arnold Shivas Jones, Elizabeth Ann Hambleton, Annika Guse

 

A core signaling mechanism at the origin of animal nociception. Oscar M. Arenas, Emanuela E. Zaharieva, Alessia Para, Constanza Vasquez-Doorman, Christian P. Petersen, Marco Gallio

 

Sphaeroforma arctica from Ondracka & Ruiz-Trillo’s preprint

 

Decoupling of the nuclear division cycle and cell size control in the coenocytic cycle of the ichthyosporean Sphaeroforma arctica. Andrej Ondracka, Iñaki Ruiz-Trillo

 

Pan-arthropod analysis reveals somatic piRNAs as an ancestral TE defence. Samuel H. Lewis, Kaycee A. Quarles, Yujing Yang, Melanie Tanguy, Lise Frezal, Stephen A. Smith, Prashant P. Sharma, Richard Cordaux, Clement Gilbert, Isabelle Giraud, David H. Collins, Phillip D. Zamore, Eric A. Miska, Peter Sarkies, Francis M. Jiggins

 

Multispecies coalescent analysis unravels the non-monophyly and controversial relationships of Hexapoda. Lucas A. Freitas, Beatriz Mello, Carlos G. Schrago

 

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. David Thybert, Maša Roller, Fábio C. P. Navarro, Ian Fiddes, Ian Streeter, Christine Feig, David Martin-Galvez, Mikhail Kolmogorov, Václav Janoušek, Wasiu Akanni, Bronwen Aken, Sarah Aldridge, Varshith Chakrapani, William Chow, Laura Clarke, Carla Cummins, Anthony Doran, Matthew Dunn, Leo Goodstadt, Kerstin Howe, Matthew Howell, Ambre-Aurore Josselin, Robert C. Karn, Christina M. Laukaitis, Lilue Jingtao, Fergal Martin, Matthieu Muffato, Michael A. Quail, Cristina Sisu, Mario Stanke, Klara Stefflova, Cock Van Oosterhout, Frederic Veyrunes, Ben Ward, Fengtang Yang, Golbahar Yazdanifar, Amonida Zadissa, David Adams, Alvis Brazma, Mark Gerstein, Benedict Paten, Son Pham, Thomas Keane, Duncan T. Odom, Paul Flicek

 

Draft genome of the Eutardigrade Milnesium tardigradum sheds light on ecdysozoan evolution. Felix Mathias Bemm, Laura Burleigh, Frank Foerster, Roland Schmucki, Martin Ebeling, Christian Janzen, Thomas Dandekar, Ralph Schill, Ulrich Certa, Joerg Schultz

 

Bombyx mori from Qiao, et al.’s preprint

 

Melanism patches up the defective cuticular morphological traits through promoting the up-regulation of cuticular protein-coding genes in Bombyx mori. Liang Qiao, Ri-xin Wang, You-jin Hao, Hai Hu, Gao Xiong, Song-zhen He, Jiang-bo Song, Kun-peng Lu, James Mallet, Ya-qun Xin, Bin Chen, Fang-yin Dai

 

Genetic architectures of larval pigmentation and color pattern in the redheaded pine sawfly (Neodiprion lecontei). Catherine Linnen, Claire T. O’Quin, Taylor Shackleford, Connor R. Sears, Carita Lindstedt

 

Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution. Sahin Naqvi, Daniel W Bellott, Kathy S Lin, David C Page

 

Radical changes persist longer in the absence of sex. Joel Sharbrough, Meagan Luse, Jeffrey L Boore, John M Logsdon Jr., Maurine Neiman

 

Gene transfers, like fossils, can date the Tree of Life. Adrian A. Davin, Eric Tannier, Tom A. Williams, Bastien Boussau, Vincent Daubin, Gergely J. Szollosi

 

Virtual Genome Walking: Generating gene models for the salamander Ambystoma mexicanum. Teri Evans, Andrew D. Johnson, Matthew D. Loose

 

Conflict between heterozygote advantage and hybrid incompatibility in haplodiploids (and sex chromosomes). Ana-Hermina Ghenu, Alexandre Blanckaert, Roger K. Butlin, Jonna Kulmuni, Claudia Bank

 

EVOLUTIONARY ANALYSIS OF CANDIDATE NON-CODING ELEMENTS REGULATING NEURODEVELOPMENTAL GENES IN VERTEBRATES. Francisco J. Novo

 

Dramatic evolution of body length due to post-embryonic changes in cell size in a newly discovered close relative of C. elegans. Gavin C. Woodruff, Patrick C. Phillips

 

The crowns have eyes: Multiple opsins found in the eyes of the Crown-of-Thorns Starfish Acanthaster planci including the first r-opsin utilized by a deuterostome eye. Elijah K. Lowe, Anders Garm, Esther Ullrich-Luter, Maria Ina Arnone

 

Evidence for “inter- and intraspecific horizontal genetic transfers” between anciently asexual bdelloid rotifers is explained by cross-contamination. Christopher G Wilson, Reuben W Nowell, Timothy G Barraclough

 

Cyanobacteria cell cize dynamics from Martins, et al.’s preprint

 

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

 

Cell biology

 

Wild type cilia from apical to basal, from Stevenson, et al.’s preprint

 

Regulator of calcineurin-2 is a ciliary protein with a role in cilia length control. Nicola Stevenson, Dylan Bergen, Amadeus Xu, Emily Wyatt, Freya Henry, Janine McCaughey, Laura Vuolo, Chrissy Hammond, David Stephens

 

Dynamics of the IFT Machinery at the Ciliary Tip. Alexander Chien, Sheng Min Shih, Raqual Bower, Douglas Tritschler, Mary E. Porter, Ahmet Yildiz

 

Dynamic Spatiotemporal Organization of Exocytosis During Cellular Shape Change. Fabio Urbina, Shawn Gomez, Stephanie L. Gupton

 

Microtubule regulation of integrin-based adhesions is mediated by myosin-IIA. Yukako Nishimura, Nisha Mohd Rafiq, Sergey V. Plotnikov, Zhen Zhang, Visalatchi Thiagarajan, Meenubharathi Natarajan, Gareth E. Jones, Pakorn Kanchanawong, Alexander D. Bershadsky

 

Force dependence of filopodia adhesion: involvement of myosin II and formins. Naila O. Alieva, Artem K. Efremov, Shiqiong Hu, Dongmyung Oh, Zhongwen Chen, Meenubharathi Natarajan, Hui Ting Ong, Antoine Jegou, Guillaume Romet-Lemonne, Jay T. Groves, Michael P. Sheetz, Jie Yan, Alexander D. Bershadsky

 

The lamellipodium is a myosin independent mechanosensor. Patrick W. Oakes, Tamara C. Bidone, Yvonne Beckham, Austin V. Skeeters, Guillermina R. Ramirez-San Juan, Stephen P. Winter, Gregory A. Voth, Margaret L. Gardel

 

Architecture of mammalian centriole distal appendages accommodates distinct blade and matrix functional elements. T. Tony Yang, Weng Man Chong, Won-Jing Wang, Gregory Mazo, Barbara Tanos, Zhengmin Chen, Minh Nguyet Thi Tran, Yi-De Chen, Rueyhung Roc Weng, Chia-En Huang, Wann-Neng Jane, Meng-Fu Bryan Tsou, Jung-Chi Liao

 

Spatial and temporal translocation of PKCα in single endothelial cell in response to focal mechanical stimulus. Masataka Arai, Toshihiro Sera, Takumi Hasegawa, Susumu Kudo

 

A Plk1 FRET reporter in action from Cascales, et al.’s preprint

 

Cyclin A2 localises in the cytoplasm at the S/G2 transition to activate Plk1. Helena Silva Cascales, Kamila Burdova, Erik Mullers, Henriette Stoy, Patrick von Morgen, Libor Macurek, Arne Lindqvist

 

CDK1 and PLK1 co-ordinate the disassembly and re-assembly of the Nuclear Envelope in vertebrate mitosis. Ines J de Castro, Raquel Sales Gil, Lorena Ligammari, Maria Laura Di Giacinto, Paola Vagnarelli

 

Phosphatase PP2A and microtubule pulling forces disassemble centrosomes during mitotic exit. Stephen J. Enos, Martin Dressler, Beatriz Ferreira Gomes, Anthony A. Hyman, Jeffrey B. Woodruff

 

Resolving ESCRT-III spirals at the intercellular bridge of dividing cells using 3D STORM imaging. Inna Goliand, Tali Dadosh, Natalie Elia

 

Reconstructing nuclear pores in Otsuka, et al.’s preprint

 

Postmitotic Nuclear Pore Assembly Proceeds By Radial Dilation Of Small ER Membrane Openings. Shotaro Otsuka, Anna M. Steyer, Martin Schorb, Jean-Karim Heriche, M. Julius Hossain, Suruchi Sethi, Moritz Kueblbeck, Yannick Schwab, Martin Beck, Jan Ellenberg

 

Nano-scale size holes in ER sheets provide an alternative to tubules for highly-curved membranes. Lena K. Schroeder, Andrew E.S. Barentine, Sarah Schweighofer, David Baddeley, Joerg Bewersdorf, Shirin Bahmanyar

 

Human replication licensing factor Cdt1 directly links mitotic kinetochores to spindle microtubules. Shivangi Agarwal, Kyle Smith, Yizhuo Zhou, Aussie Suzuki, Richard McKenney, Dileep Varma

 

Mutant worms from Beacham, et al.’s preprint

 

NECAPs are negative regulators of the AP2 clathrin adaptor complex. Gwendolyn M Beacham, Edward A Partlow, Jeffrey J Lange, Gunther Hollopeter

 

MDCK cells from Vivian Wang’s preprint

 

Propagating actomyosin-generated force to intercellular junction. Vivian W. Tang

 

Distinct prophase arrest mechanisms in human male meiosis. Sabrina Z. Jan, Aldo Jongejan, Cindy M. Korver, Saskia K. M. van Daalen, Ans M. M. van Pelt, Sjoerd Repping, Geert Hamer

 

ATR is a multifunctional regulator of male mouse meiosis. Alexander Widger, Shantha K Mahadevaiah, Julian Lange, Elias ElInati, Jasmin Zohren, Takayuki Hirota, Marcello Stanzione, Obah Ojarikre, Valdone Maciulyte, Dirk de Rooij, Attila Toth, Scott Keeney, James MA Turner

 

Non-canonical circadian oscillations in Drosophila S2 cells drive gene-expression cycles coupled to metabolic oscillations. Guillaume Rey, Nikolay B. Milev, Utham K. Valekunja, Ratnasekhar Ch, Sandipan Ray, Mariana Silva Dos Santos, Andras D. Nagy, Robin Antrobus, James I. MacRae, Akhilesh B. Reddy

 

The Cell-Cycle Transcriptional Network Generates and Transmits a Pulse of Transcription Once Each Cell Cycle. Chun-Yi Cho, Christina M. Kelliher, Steven B. Haase

 

Activation of Rho-kinase and focal adhesion kinase regulates the organization of stress fibers and focal adhesions in the central part of fibroblasts. Kazuo Katoh

 

Cell contraction induces long-ranged stress stiffening in the extracellular matrix. Yu Long Han, Pierre Ronceray, Guoqiang Xu, Andrea Malandrino, Roger Kamm, Martin Lenz, Chase P. Broedersz, Ming Guo

 

 

Modelling

Approximate Bayesian computation reveals the importance of repeated measurements for parameterising cell-based models of growing tissues. Jochen Kursawe, Ruth E. Baker, Alexander George Fletcher

 

Inferring parameters for a lattice-free model of cell migration and proliferation using experimental data. Alexander Browning, Scott W. McCue, Rachelle N. Binny, Michael J. Plank, Esha T. Shah, Matthew J. Simpson

 

Reprogramming, oscillations and transdifferentiation in epigenetic landscapes. Bivash Kaity, Ratan Sarkar, Buddhapriya Chakrabarti, Mithun K. Mitra

 

Modelling epigenetic dynamics, from Michieletto, et al.’s preprint

 

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

 

Optimal quantification of contact inhibition in cell populations. David J. Warne, Ruth E. Baker, Matthew J. Simpson

 

In silico mechanobiochemical modeling of morphogenesis in cell monolayers. Hongyan Yuan, Bahador Marzban

 

Bifurcations in valveless pumping techniques from a coupled fluid-structure-electrophysiology model in heart development. Nicholas A. Battista, Laura A. Miller

 

Theory of epithelial cell shape transitions induced by mechanoactive chemical gradients. Kinjal Dasbiswas, Edouard Hannezo, Nir. S. Gov

 

Growing brains in silico, fromVerner & Garikipati’s preprint

 

A computational study of growth-driven folding patterns on shells, with application to the developing brain. S. N. Verner, K. Garikipati

 

Simulating insect wing shapes, from Ishimoto & Sugimura’s preprint

 

A mechanical model for diversified insect wing margin shapes. Yukitaka Ishimoto, Kaoru Sugimura

 

Analysis of biochemical mechanisms provoking differential spatial expression in Hh target genes. Manuel Cambón

 

The importance of geometry in the corneal micropocket assay. James A Grogan, Anthony J Connor, Joe M Pitt-Francis, Philip K Maini, Helen M Byrne

 

Functional Modeling of Plant Growth Dynamics. Yuhang Xu, Yumou Qiu, James Schnable

 

Integration of anatomy ontologies and Evo-Devo using structured Markov chains suggests a new framework for modeling discrete phenotypic traits. Sergei Tarasov

 

Spatial cytoskeleton organization supports targeted intracellular transport. Anne E. Hafner, Heiko Rieger

 

Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets. Stefan Wyder, Michael T Raissig, Ueli Grossniklaus

 

Replication Timing Networks: a novel class of gene regulatory networks. Juan Carlos Rivera-Mulia, Sebo Kim, Haitham Gabr, Tamer Kahveci, David M Gilbert

 

 

Tools & resources

| Imaging etc.

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering. Isaac Nuñez, Tamara Matute, Roberto Herrera, Juan Keymer, Tim Marzullo, Tim Rudge, Fernan Federici

 

PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems. Ahmadreza Ghaffarizadeh, Samuel H. Friedman, Shannon M. Mumenthaler, Paul Macklin

 

Hemodynamic forces can be accurately measured in vivo with optical tweezers. Sebastien Harlepp, Fabrice Thalmann, Gautier Follain, Jacky G. Goetz

 

Tracking chromosome dynamics from Ma, et al.’s preprint

 

CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics. Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Yu-Chieh Chung, David Grunwald, Shaojie Zhang, Thoru Pederson

 

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

 

Obtaining 3D Super-resolution Information from 2D Super-resolution Images through a 2D-to-3D Transformation Algorithm. Andrew Ruba, Joseph Kelich, Wangxi Luo, Weidong Yang

 

Hydrogel encapsulation of living organisms for long-term microscopy. Kyra Burnett, Eric Edsinger, Dirk R. Albrecht

 

Quantification of cellular distribution as Poisson process in 3D matrix using a multiview light-sheet microscope. Warren Colomb, Matthew Osmond, Charles Durfee, Melissa D. Krebs, Susanta K. Sarkar

 

Replication domains from Xiang, et al.’s preprint

 

Correlative live and super-resolution imaging reveals the dynamic structure of replication domains. Wanqing Xiang, M. Julia Roberti, Jean-Karim Heriche, Sebastian Huet, Stephanie Alexander, Jan Ellenberg

 

Coupling optogenetics and light-sheet microscopy to study signal transduction in vivo. Prameet Kaur, Timothy E. Saunders, Nicholas Stanislaw Tolwinski

 

Arabidopsis phenotyping through Geometric Morphometrics. Carlos A. Manacorda, Sebastian Asurmendi

 

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

 

vU-net: accurate cell edge segmentation in time-lapse fluorescence live cell images based on convolutional neural network. Chuangqi Wang, Xitong Zhang, Yenyu Chen, Kwonmoo Lee

 

ChromoTrace: Reconstruction of 3D Chromosome Configurations by Super-Resolution Microscopy. Carl Barton, Sandro Morganella, Oeyvind Oedegaard, Stephanie Alexander, Jonas Ries, Tomas Fitzgerald, Jan Ellenberg, Ewan Birney

 

PlantCV v2.0: Image analysis software for high-throughput plant phenotyping. Malia A Gehan, Noah Fahlgren​​, Arash Abbasi, Jeffrey C Berry, Steven T Callen, Leonardo Chavez, Andrew N Doust, Max J Feldman, Kerrigan B Gilbert, John G Hodge, J Steen Hoyer, Andy Lin, Suxing Liu, César Lizárraga, Argelia Lorence, Michael Miller, Eric Platon, Monica Tessman, Tony Sax

 

Segmented plants with help from Rasberry Pi, from Tovar, et al.’s prperint

 

Raspberry Pi Powered Imaging for Plant Phenotyping. Jose Tovar, John Steen Hoyer, Andy Lin, Allison Tielking, Steven Callen, Elizabeth Castillo, Michael Miller, Monica Tessman, Noah Fahlgren, James Carrington, Dmitri Nusinow, Malia A. Gehan

 

Segmenting Calcium flashes in Reynolds, et al.’s preprint

 

ABLE: an Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data. Stephanie Reynolds, Therese Abrahamsson, Renaud Schuck, P. Jesper Sjöström, Simon R Schultz, Pier Luigi Dragotti

 

Edge Detection of Cryptic Lamellipodia Assisted by Deep Learning. Chuangqi Wang, Shawn Kang, Eunice Kim, Xitong Zhang, Hee June Choi, Aaron Choi, Kwonmoo Lee

 

Mapping nonapoptotic caspase activity with a transgenic reporter in mice. Peter Nicholls, Thomas Pack, Nikhil Urs, Sunil Kumar, Gabor Turu, Evan Calabrese, Wendy Roberts, Ping Fan, Valeriy Ostapchenko, Monica Guzman, Flavio Beraldo, Vania Prado, Marco Prado, Ivan Spasojevic, Joshua Snyder, Kafui Dzirasa, G. Allan Johnson, Marc Caron

 

Development of an Intrinsic Skin Sensor for Blood Glucose Level with CRISPR-mediated Genome Editing in Epidermal Stem Cells. Jiping Yue, Yuanyuan Li, Xuewen Gou, Xiaoyang Wu

 

Mini-ring approach for high-throughput drug screenings in 3D tumor models. Nhan Phan, Bobby Tofig, Deanna Janzen, Jin Huang, Sanaz Memarzadeh, Robert Damoiseaux, Alice Soragni

 

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

 

| Genome tools

Employing single-stranded DNA donors for the high-throughput production of conditional knockout alleles in mice. Denise G. Lanza, Angelina Gaspero, Isabel Lorenzo, Lan Liao, Ping Zheng, Ying Wang, Yu Deng, Chonghui Cheng, Chuansheng Zhang, Matthew N. Rasband, John R. Seavitt, Francisco J. DeMayo, Jianming Xu, Mary E. Dickinson, Arthur L. Beaudet, Jason D. Heaney

 

Generation and validation of homozygous fluorescent knock-in cells using genome editing. Birgit Koch, Bianca Nijmeijer, Moritz Kueblbeck, Yin Cai, Nike Walther, Jan Ellenberg

 

Precision genome-editing with CRISPR/Cas9 in human induced pluripotent stem cells. John P. Budde, Rita Martinez, Simon Hsu, Natalie Wen, Jason A. Chen, Giovanni Coppola, Alison M. Goate, Carlos Cruchaga, Celeste Karch

 

Unexpected CRISPR off-target mutation pattern in vivo are not typically germline-like. Zhiting Wei, Funan He, Guohui Chuai, Hanhui Ma, Zhixi Su, Qi Liu

 

Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage. Peter Istvan Kulcsar, Andras Talas, Krisztina Huszar, Zoltan Ligeti, Eszter Toth, Nora Weinhardt, Elfrieda Fodor, Ervin Welker

 

High-throughput creation and functional profiling of eukaryotic DNA sequence variant libraries using CRISPR/Cas9. Xiaoge Guo, Alejandro Chavez, Angela Tung, Yingleong Chan, Ryan Cecchi, Santiago Lopez Garnier, Christian Kaas, Eric Kelsic, Max Schubert, James DiCarlo, James Collins, George Church

 

FlashFry: a fast and flexible tool for large-scale CRISPR target design. Aaron McKenna, Jay Shendure

 

CRISPRd Arabidopsis from Hodgens, et al.’s preprint

 

indCAPS: A tool for designing screening primers for CRISPR/Cas9 mutagenesis events. Charles Hodgens, Zachary Nimchuk, Joseph Kieber

 

Integrated design, execution, and analysis of arrayed and pooled CRISPR genome editing experiments. Matthew C. Canver, Maximilian Haeussler, Daniel E. Bauer, Stuart H. Orkin, Neville E. Sanjana, Ophir Shalem, Guo-Cheng Yuan, Feng Zhang, Jean-Paul Concordet, Luca Pinello

 

Mechanisms of improved specificity of engineered Cas9s revealed by single molecule analysis. Digvijay Singh, Yanbo Wang, John Mallon, Olivia Yang, Jingyi Fei, Anustup Poddar, Damon Ceylan, Scott Bailey, Taekjip Ha

 

Characterization and Validation of a Novel Group of Type V, Class 2 Nucleases for in vivo Genome Editing. Matthew B Begemann, Benjamin N Gray, Emma January, Anna Singer, Dylan C Kesler, Yonghua He, Haijun Liu, Hongjie Guo, Alex Jordan, Thomas P Brutnell, Todd C Mockler, Mohammed Oufattole

 

High-resolution genome-wide functional dissection of transcriptional regulatory regions in human. Xinchen Wang, Liang He, Sarah Goggin, Alham Saadat, Li Wang, Melina Claussnitzer, Manolis Kellis

 

Multi-platform​ ​ discovery​ ​ of​ ​ haplotype-resolved structural​ ​ variation​ ​ in​ ​ human​ ​ genomes. Mark J.P. Chaisson, Ashley D. Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J. Gardner, Oscar Rodriguez, Li Guo, Ryan L. Collins, Xian Fan, Jia Wen, Robert E. Handsaker, Susan Fairley, Zev N. Kronenberg, Xiangmeng Kong, Fereydoun Hormozdiari, Dillon Lee, Aaron M. Wenger, Alex Hastie, Danny Antaki, Peter Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T. Chuang, Deanna M. Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, Gorkin David, Madhusudan Gujral, Victor Guryev, William Haynes-Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Patrick Marks, Karine Valud-Martinez, Sascha Meiers, Katherine M. Munson, Fabio Navarro, Bradley J. Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy Pang, Yunjiang Qiu, Gabriel Rosanio, Mallory Ryan, Adrian Stutz, Diana C.J. Spierings, Alistair Ward, AnneMarie E. Welsch, Ming Xiao, Wei Xu, Chengsheng Zhang, Qihui Zhu, Xiangqun Zheng-Bradley, Goo Jun, Li Ding, Chong​ ​ Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B. Gerstein, Pui-Yan Kwok, Peter M. Lansdorp, Gabor Marth, Jonathan Sebat, Xinghua Shi, Ali Bashir, Kai Ye, Scott E. Devine, Michael Talkowski, Ryan E. Mills, Tobias Marschall, Jan Korbel, Evan E. Eichler, Charles Lee

 

Successful optimization of CRISPR/Cas9-mediated defined point mutation knock-in using allele-specific PCR assays in zebrafish. Sergey V. Prykhozhij, Charlotte Fuller, Shelby L. Steele, Chansey J. Veinotte, Babak Razaghi, Christopher McMaster, Adam Shlien, David Malkin, Jason N. Berman

 

Profiling DNA Methylation Differences Between Inbred Mouse Strains on the Illumina Human Infinium MethylationEPIC Microarray. Hemant Gujar, Jane W Liang, Nicholas C Wong, Khyobeni Mozhui

 

From trash to treasure: detecting unexpected contamination in unmapped NGS data. llaria Granata​​, Mara Sangiovanni​​, Amarinder Singh Thind, Mario Rosario Guarracino.

 

Accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments. Viktor Petukhov, Jimin Guo, Ninib Baryawno, Nicolas Severe, David Scadden, Maria G. Samsonova, Peter V. Kharchenko

 

Gene synthesis allows biologists to source genes from farther away in the tree of life. Aditya Kunjapur, Philipp Pfingstag, Neil C Thompson

 

Curated compendium of human transcriptional biomarker data. Nathan P Golightly, Anna I Bischoff, Avery Bell, Parker D Hollingsworth, Stephen R Piccolo

 

One of Hansen,  et al.’s subcellular process networks

 

A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes. Jens Hansen, David Meretzky, Simeneh Woldesenbet, Gustavo Stolovitzky, Ravi Iyengar

 

Comparison of seven single cell Whole Genome Amplification commercial kits using targeted sequencing. Tamir Biezuner, Ofir Raz, Shiran Amir, Lilach Milo, Rivka Adar, Yael Fried, Elena Ainbinder, Ehud Shapiro

 

Biosensor libraries harness large classes of binding domains for allosteric transcription regulators. Javier F. Juarez, Begoña Lecube-Azpeitia, Stuart L. Brown, George M. Church

 

An automated model test system for systematic development and improvement of gene expression models. Alexander C Reis, Howard Salis

 

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution. Wenxiu Ma, Ferhat Ay, Choli Lee, Gunhan Gulsoy, Xinxian Deng, Savannah Cook, Jennifer Hesson, Christopher Cavanaugh, Carol B. Ware, Anton Krumm, Jay Shendure, C. Anthony Blau, Christine M. Disteche, William S. Noble, Zhijun Duan

 

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse. Alexander Lachmann, Denis Torre, Alexandra B. Keenan, Kathleen M. Jagodnik, Hyojin J. Lee, Moshe C. Silverstein, Lily Wang, Avi Ma’ayan

 

LeafCutter: Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

 

A sequence-based, deep learning model accurately predicts RNA splicing branchpoints. Joseph M. Paggi, Gill Bejerano

 

Superior ab initio Identification, Annotation and Characterisation of TEs and Segmental Duplications from Genome Assemblies. LU ZENG, R Daniel Kortschak, Joy M Raison, Terry Bertozzi, David L Adelson

 

DeepBlueR: Large-scale epigenomic analysis in R. Markus List, Felipe Albrecht, Christoph Bock, Thomas Lengauer

 

mosdepth: quick coverage calculation for genomes and exomes. Brent S. Pedersen, Aaron Quinlan

 

CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Peter J. Skene, Steven Henikoff

 

Real-time fluorescence and deformability cytometry – flow cytometry goes mechanics. Philipp Rosendahl, Katarzyna Plak, Angela Jacobi, Martin Kraeter, Nicole Toepfner, Oliver Otto, Christoph Herold, Maria Winzi, Maik Herbig, Yan Ge, Salvatore Girardo, Katrin Wagner, Buzz Baum, Jochen Guck

 

DAFi: A Directed Recursive Filtering and Clustering Approach to Data-Driven Identification of Cell Populations from Polychromatic Flow Cytometry Data. Alexandra J Lee, Ivan Chang, Julie G Burel, Cecilia S Lindestam Arlehamn, Daniela Weiskopf, Bjoern Peters, Alessandro Sette, Richard H Scheuermann, Yu Qian

 

Interactive Visual Analysis of Mass Cytometry Data by Hierarchical Stochastic Neighbor Embedding Reveals Rare Cell Types. Vincent van Unen, Thomas Hollt, Nicola Pezzotti, Na Li, Marcel J. T. Reinders, Elmar Eisemann, Anna Vilanova, Frits Koning, Boudewijn P. F. Lelieveldt

 

HyperTRIBE: Upgrading TRIBE with enhanced editing. Weijin Xu, Reazur Rahman, Michael Rosbash

 

plot2DO: a tool to assess the quality and distribution of genomic data. Răzvan V Chereji

 

Gene regulatory network inference from single-cell data using multivariate information measures. Thalia E Chan, Michael Stumpf, Ann C Babtie

 

A duplex MIPs-based biological-computational cell lineage discovery platform. Liming Tao, Ofir Raz, Zipora Marx, Tamir Biezuner, Shiran Amir, Lilach Milo, Rivka Adar, Amos Onn, Noa Chapal-Ilani, Veronika Berman, Ron Levy, Barak Oron, Ehud Shapiro

 

Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision. Yungang Xu, Yongcui Wang, Jiesi Luo, Weiling Zhao, Xiaobo Zhou

 

miRNAgFree: prediction and profiling of novel microRNAs without genome assembly. Ernesto L. Aparicio, Antonio Rueda, Bastian Fromm, Cristina Gómez-Martin, Ricardo Lebrón, Jose L Oliver, Juan A Marchal, Michail Kotsyfakis, Michael Hackenberg

 

Trendy: Segmented regression analysis of expression dynamics for high-throughput ordered profiling experiments. Rhonda Bacher, Ning Leng, Li-Fang Chu, James Thomson, Christina Kendziorski, Ron Stewart

 

MTopGO: a tool for module identification in PPI Networks. Danila Vella​, Simone Marini, Francesca Vitali, Riccardo Bellazzi

 

Research practice

Award or Reward? Which comes first, NIH funding or research impact? Lucas C Parra, Lukas Hirsch

 

Assessment of the impact of shared data on the scientific literature. Michael  Milham, Cameron Craddock, Michael Fleischmann, Jake Son, Jon Clucas, Helen Xu, Bonhwang Koo, Anirudh Krishnakumar, Bharat Biswal, Francisco Castellanos, Stan Colcombe, Adriana Di Martino, Xi-Nian Zuo, Arno Klein

 

IntelliEppi: Intelligent reaction monitoring and holistic data management system for the molecular biology lab. Arthur Neuberger, Zeeshan Ahmed, Thomas Dandekar

 

Findings of a retrospective, controlled cohort study of the impact of a change in Nature journals’ editorial policy for life sciences research on the completeness of reporting study design and execution. Malcolm Robert Macleod, The NPQIP Collaborative group

 

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

 

Idea farming: it is a good idea to have bad ideas in science. Christopher J Lortie

 

Imagining the ‘open’ university: Sharing scholarship to improve research and education. Erin C McKiernan

 

The Modern Research Data Portal: A design pattern for networked, data-intensive science. Kyle Chard, Eli Dart, Ian Foster​, David Shifflett, Steven Tuecke, Jason Williams

 

Can editors save peer review from peer reviewers? Rafael D’Andrea, James P O’Dwyer.

 

How to share data for collaboration. Shannon E Ellis, Jeffrey T Leek

 

An invitation to modeling: building a community with shared explicit practices. Kam D Dahlquist, Melissa L Aikens, Joseph T Dauer, Samuel S Donovan, Carrie Diaz Eaton, Hannah Callender Highlander, Kristin P Jenkins, John R Jungck, M Drew LaMar, Glenn Ledder, Robert L Mayes, Richard C Schugart

 

Down with ncRNA! Long live fRNA and jRNA! Dan Graur

 

What exactly is ‘N’ in cell culture and animal experiments? Stanley E Lazic, Charlie J Clarke-Williams, Marcus R Munafo

 

Estimating the scale of biomedical data generation using text mining. Gabriel Rosenfeld, Dawei Lin

 

Why not…

 

Sand-bubbler crab-inspired algorithm art from Hendrik Richter

 

Visual art inspired by the collective feeding behavior of sand-bubbler crabs. Hendrik Richter

 

The reality of “food porn”: Larger brain responses to food-related cues than to erotic images predict cue-induced eating. Francesco Versace, David W Frank, Elise M Stevens, Menton M Deweese, Michele Guindani, Susan M Schembre

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