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SDB 78th Annual Meeting 2019

A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.

List by Alex Eve

Preprints:

Moana: A robust and scalable cell type classification framework for single-cell RNA-Seq data

Florian Wagner, Itai Yanai

https://www.biorxiv.org/content/10.1101/456129v1

Presented by Itai Yanai in the Satellite Symposium: Machine Learning for Developmental Biology.

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

Juan C. Caicedo, Jonathan Roth, Allen Goodman, Tim Becker, Kyle W Karhohs, Matthieu Broisin, Molnar Csaba, Claire McQuin, Shantanu Singh, Fabian Theis, Anne E. Carpenter

https://www.biorxiv.org/content/10.1101/335216v4

Presented by Juan Caicedo in the Satellite Symposium: Machine Learning for Developmental Biology.

FIN-Seq: Transcriptional profiling of specific cell types in frozen archived tissue from the human central nervous system

Ryoji Amamoto, Emanuela Zuccaro, Nathan C. Curry, Sonia Khurana, Hsu-Hsin Chen, Constance L. Cepko, Paola Arlotta

https://www.biorxiv.org/content/10.1101/602847v1

Presented by Constance Cepko in the “Development: from Deconstruction to Reconstruction” session.

Daisy quorum drives for the genetic restoration of wild populations

John Min, Charleston Noble, Devora Najjar, Kevin M. Esvelt

https://www.biorxiv.org/content/10.1101/115618v2

Presented by Kevin Esvelt in the “Genome Editing: from Transgenesis to CRISPR” (CS I-1) session.

Size control of the inner ear via hydraulic feedback

Kishore R. Mosaliganti, Ian A. Swinburne, Chon U Chan, Nikolaus D. Obholzer, Amelia A. Green, Shreyas Tanksale, L. Mahadevan, Sean G. Megason

https://www.biorxiv.org/content/10.1101/349381v1

Presented by Akankshi Munjal in the “Morphogenesis: from Camera Lucida to In Toto Imaging” (CS I-2) session.

Hydraulic control of embryo size, tissue shape and cell fate

Chii Jou Chan, Maria Costanzo, Teresa Ruiz-Herrero, Gregor Mönke, Ryan J. Petrie, L. Mahadevan, Takashi Hiiragi

https://www.biorxiv.org/content/10.1101/389619v1

Presented by Chii Chan in the “Morphogenesis: from Camera Lucida to In Toto Imaging” (CS I-2) session. Now published in Nature.

Lumen expansion facilitates epiblast-primitive endoderm fate specification in the mouse blastocyst formation

Allyson Quinn Ryan, Chii Jou Chan, François Graner, Takashi Hiiragi

https://www.biorxiv.org/content/10.1101/575282v1

Presented by Chii Chan in the “Morphogenesis: from Camera Lucida to In Toto Imaging” (CS I-2) session.

Satellite DNA-containing gigantic introns in a unique gene expression program during Drosophila spermatogenesis

Jaclyn M Fingerhut, Jessica V. Moran, Yukiko M Yamashita

https://www.biorxiv.org/content/10.1101/493254v1

Presented by Jaclyn Fingerhut in the “RNA: from siRNA to lnRNA” (CS I-3) session. Now published in PLoS Genetics.

The role of lineage, hemilineage and temporal identity in establishing neuronal connectivity in the Drosophila larval CNS

Brandon Mark, Sen-Lin Lai, Aref Arzan Zarin, Laurina Manning, Albert Cardona, James W. Truman, Chris Q. Doe

https://www.biorxiv.org/content/10.1101/617936v2

Presented by Christopher Doe in the “Developmental Timing: from Heterochronic Genes to Aging” (CS I-6) session.

Latent developmental potential to form limb-like skeletal structures in zebrafish

M. Brent Hawkins, Katrin Henke, Matthew P. Harris

https://www.biorxiv.org/content/10.1101/450619v1

Presented by Michael Brent Hawkins in the “Evolution: from HOX genes to Floral Evolution” (CS I-4) session.

The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids

Natalie Turner, Deimante Mikalauskaite, Krista Barone, Kathleen Flaherty, Gayani Senevirathne, Noritaka Adachi, Neil H Shubin, Tetsuya Nakamura

https://www.biorxiv.org/content/10.1101/644062v1

Presented by Tetsuya Nakamura in “Evolution: from HOX genes to Floral Evolution” (CS I-4) session.

Dissecting mechanisms of human islet differentiation and maturation through epigenome profiling

Juan R. Alvarez-Dominguez, Julie Donaghey, Jennifer H. R. Kenty, Niloofar Rasouli, Aharon Helman, Jocelyn Charlton, Juerg R. Straubhaar, Alexander Meissner, Douglas A. Melton

https://www.biorxiv.org/content/10.1101/613026v1

Presented by Doug Melton in the “Reprogramming: from Cloning to Curing Disease” plenary session.

Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids

Sapna Chhabra, Lizhong Liu, Ryan Goh, Aryeh Warmflash

https://www.biorxiv.org/content/10.1101/440164v2

Presented by Aryeh Warmflash in the “Human Development: from Analysis to Organoids” (CS II-3) session.

A novel self-organizing embryonic stem cell system reveals signaling logic underlying the patterning of human ectoderm

George Britton, Idse Heemskerk, Rachel Hodge, Amina A Qutub, Aryeh Warmflash

https://www.biorxiv.org/content/10.1101/518803v1

Presented by Aryeh Warmflash in the “Human Development: from Analysis to Organoids” (CS II-3) session.

TEAD4/YAP1/WWTR1 prevent the premature onset of pluripotency prior to the 16-cell stage

Tristan Frum, Jennifer Watts, Amy Ralston

https://www.biorxiv.org/content/10.1101/663005v1

Presented by Amy Ralston in the “Gene Regulation: from Enhancers to Single-cell transcriptomics” (CS II-1) session.

In vitro characterization of the human segmentation clock

Margarete Diaz-Cuadros, Daniel E Wagner, Christoph Budjan, Alexis Hubaud, Jonathan Touboul, Arthur Michaut, Ziad Al Tanoury, Kumiko Yoshioka-Kobayashi, Yusuke Niino, Ryoichiro Kageyama, Atsushi Miyawaki, Olivier Pourquié

https://www.biorxiv.org/content/10.1101/461822v1

Presented by Magarete Diaz Cuadros in the “Human Development: from Analysis to Organoids” (CS I-3) session.

Region-specific regulation of stem cell-driven regeneration in tapeworms

Tania Rozario, Edward B. Quinn, Jianbin Wang, Richard E. Davis, Phillip A. Newmark

https://www.biorxiv.org/content/10.1101/495234v2

Presented by Tania Rozario in the “Healing & Regeneration: from Phenomena to Mechanisms” (CS II-4) session.

Efficient Zygotic Genome Editing via RAD51-Enhanced Interhomolog Repair

Jonathan J. Wilde, Tomomi Aida, Martin Wienisch, Qiangge Zhang, Peimin Qi, Guoping Feng

https://www.biorxiv.org/content/10.1101/263699v3

Presented by Jonathan Wilde in the “Lineage: from Imaging to Barcoding” (CS II-2) session.

Lineage tracing on transcriptional landscapes links state to fate during differentiation

Caleb Weinreb, Alejo Rodriguez-Fraticelli, Fernando Camargo, Allon M Klein

https://www.biorxiv.org/content/10.1101/467886v2

Presented by Allon Klein in the “Gene Regulation: from Enhancers to Single-cell Transcriptomics” (CS II-2) session.

A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution

Jonathan S. Packer, Qin Zhu, Chau Huynh, Priya Sivaramakrishnan, Elicia Preston, Hannah Dueck, Derek Stefanik, Kai Tan, Cole Trapnell, Junhyong Kim, Robert H. Waterston, John I. Murray

https://www.biorxiv.org/content/10.1101/565549v2

Presented by Zhirong Bao in the “Lineage: from Imaging to Barcoding” (CS II-2) session.

A genetic, genomic, and computational resource for exploring neural circuit function

Fred P. Davis, Aljoscha Nern, Serge Picard, Michael B. Reiser, Gerald M. Rubin, Sean R. Eddy, Gilbert L. Henry

https://www.biorxiv.org/content/10.1101/385476v1

Presented by Claude Desplan in the “Pattern formation: from Organizers to Morphogens and Gene Regulatory Networks” plenary session.

Stem cell differentiation trajectories in Hydra resolved at single-cell resolution

Stefan Siebert, Jeffrey A. Farrell, Jack F. Cazet, Yashodara L. Abeykoon, Abby S. Primack, Christine E. Schnitzler, Celina E. Juliano

https://www.biorxiv.org/content/10.1101/460154v1

Presented by Celina Juliano in the “Development: from Old Questions to New Systems” (CS III-3) session.

Single cell analysis reveals modified hematopoietic cell composition affecting inflammatory and immunopathological responses in Astyanax mexicanus

Robert Peuß, Andrew C. Box, Yongfu Wang, Shiyuan Chen, Jaya Krishnan, Dai Tsuchiya, Brian Slaughter, Nicolas Rohner

https://www.biorxiv.org/content/10.1101/647255v3

Presented by Nicolas Rohner in the “Development: from Old Questions to New Systems” (CS III-3) session.

High-throughput, image-based flow cytometry and clustering method for phenotyping heterogeneous cell populations

Robert Peuß, Andrew C. Box, Alice Accorsi, Christopher Wood, Alejandro Sánchez Alvarado, Nicolas Rohner

https://www.biorxiv.org/content/10.1101/603035v1

Presented by Nicolas Rohner in the “Development: from Old Questions to New Systems” (CS III-3) session.

Apigenin as a Candidate Prenatal Treatment for Trisomy 21: Effects in Human Amniocytes and the Ts1Cje Mouse Model

Faycal Guedj, Jeroen LA Pennings, Ashley E Siegel, Fatimah Alsebaa, Lauren J Massingham, Umadevi Tantravahi, Diana W Bianchi

https://www.biorxiv.org/content/10.1101/495283v1

Presented by Diana Bianchi in the “Developmental Biology & Society: from Fundamental to Practical” plenary session.

Categories: developmental biology , evolutionary biology , neuroscience , plant biology

 

Posted on: 26 July 2019 , updated on: 10 February 2020

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