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1 Dynamic aspects of plant water potential revealed by a microtensiometer 1 Vinay Pagay1* 2 1 School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, PMB 1, 3 Glen Osmond, SA 5064, Australia 4 * Correspondence: vinay.pagay@adelaide.edu.au 5 Abstract 6 Water potential i...
2021
Dynamic aspects of plant water potential revealed by a microtensiometer
10.1101/2021.06.23.449675
null
creative-commons
1 Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma Jeff DeMartino1,2,*, Michael T. Meister1,2,*, Lindy Visser1*, Mariël Brok1,2, Marian J. A. Groot Koerkamp1,2, Laura S. Hiemcke-Jiwa1,3, Terezinha de Souza1,2, Johannes H. M. Merks1, Frank ...
2022
Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma
10.1101/2022.07.15.497944
[ "DeMartino Jeff", "Meister Michael T.", "Visser Lindy", "Brok Mariël", "Groot Koerkamp Marian J. A.", "Hiemcke-Jiwa Laura S.", "de Souza Terezinha", "Merks Johannes H. M.", "Holstege Frank C. P.", "Margaritis Thanasis", "Drost Jarno" ]
creative-commons
Deeper than you think: partisan-dependent brain response Noa Katabi1, Hadas Simon2, Sharon Yakim2, Inbal Ravreby2,3, Yaara Yeshurun1,2 1 Sagol School of Neuroscience and 2 School of Psychological Sciences, Tel-Aviv University, Tel Aviv, Israel 3 Department of Neurobiology, Weizmann Institue of Science, Rehovot, Isr...
2021
Deeper than you think: partisan-dependent brain response
10.1101/2021.11.23.469735
[ "Katabi Noa", "Simon Hadas", "Yakim Sharon", "Ravreby Inbal", "Yeshurun Yaara" ]
null
Nuclear lamina strain states revealed by intermolecular force biosensor Brooke E. Danielsson1, Bobin George Abraham2*, Elina Mäntylä2*, Jolene I. Cabe1, Carl R Mayer1, Anna Rekonen2, Frans Ek2, Daniel E. Conway1¶, Teemu O. Ihalainen2¶ * Contributed equally ¶ Co-corresponding authors: dconway@vcu.edu, teemu.iha...
2022
Nuclear lamina strain states revealed by intermolecular force biosensor
10.1101/2022.03.07.483300
[ "Danielsson Brooke E.", "Abraham Bobin George", "Mäntylä Elina", "Cabe Jolene I.", "Mayer Carl R", "Rekonen Anna", "Ek Frans", "Conway Daniel E.", "Ihalainen Teemu O." ]
null
1 Paired high-throughput, in-situ imaging and high-throughput sequencing illuminate acantharian abundance and vertical distribution Margaret Mars Brisbin1*, Otis Davey Brunner1, Mary Matilda Grossmann1, Satoshi Mitarai1 5 1Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan...
2020
Paired high-throughput, in-situ imaging and high-throughput sequencing illuminate acantharian abundance and vertical distribution
10.1101/2020.02.27.967349
[ "Mars Brisbin Margaret", "Brunner Otis Davey", "Grossmann Mary Matilda", "Mitarai Satoshi" ]
creative-commons
PHYLOGENETIC SYNECDOCHE & OPTIMIZED SUBSAMPLING Title Phylogenetic Synecdoche Demonstrates Optimality of Subsampling and Improves Recovery of the Blaberoidea Phylogeny AUTHORS Dominic A. Evangelista1, 2, 9, Sabrina Simon3, Megan M. Wilson4, Akito Y. Kawahara5, Manpreet K. Kohli4, Jessica L. Ware4, Benjamin Wip...
2019
Phylogenetic Synecdoche Demonstrates Optimality of Subsampling and Improves Recovery of the Blaberoidea Phylogeny
10.1101/601237
[ "Evangelista Dominic A.", "Simon Sabrina", "Wilson Megan M.", "Kawahara Akito Y.", "Kohli Manpreet K.", "Ware Jessica L.", "Wipfler Benjamin", "Béthoux Olivier", "Grandcolas Philippe", "Legendre Frédéric" ]
creative-commons
Cas9 fusions for precision in vivo editing Ryan R. Richardson, Marilyn Steyert, Saovleak N. Khim, Andrea J. Romanowski, Jeffrey Inen, Bekir Altas, Alexandros Poulopoulos Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA Corresponding author: AP, apoulopoulos@som.umaryland.edu 67...
2022
Cas9 fusions for precision editing
10.1101/2020.07.15.199620
[ "Richardson Ryan R.", "Steyert Marilyn", "Khim Saovleak N.", "Romanowski Andrea J.", "Inen Jeffrey", "Altas Bekir", "Poulopoulos Alexandros" ]
creative-commons
1 Mutational analysis unveils the temporal and spatial distribution of G614 genotype of 2 SARS-CoV-2in different Indian states and its association with case fatality rate of 3 COVID-19 4 5 Ballamoole Krishna Kumar1#*, Bakilapadavu Venkatraja2#, Kattapuni Suresh 6 Prithvisagar1, Praveen Rai1, Anusha Rohit3, Madhura ...
2020
Mutational analysis unveils the temporal and spatial distribution of G614 genotype of SARS-CoV-2in different Indian states and its association with case fatality rate of COVID-19
10.1101/2020.07.27.222562
[ "Kumar Ballamoole Krishna", "Venkatraja Bakilapadavu", "Prithvisagar Kattapuni Suresh", "Rai Praveen", "Rohit Anusha", "Hegde Madhura Nagesh", "Karunasagar Indrani", "Karunasagar Iddya" ]
null
1 MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools Madeleine Ernst1,2*, Kyo Bin Kang1,3, Andrés Mauricio Caraballo-Rodríguez1, Louis-Felix Nothias1, Joe Wandy4, Mingxun Wang1, Simon Rogers5, Marnix H. Medema6, Pieter C. Dorrestein 1,7,8, Ju...
2019
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools
10.1101/654459
[ "Ernst Madeleine", "Kang Kyo Bin", "Caraballo-Rodríguez Andrés Mauricio", "Nothias Louis-Felix", "Wandy Joe", "Wang Mingxun", "Rogers Simon", "Medema Marnix H.", "Dorrestein Pieter C.", "van der Hooft Justin J.J." ]
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Supply-driven evolution: mutation bias and trait-fitness distributions can drive macro-evolutionary dynamics Zhun Ping (Julian) Xue1*, Leonid Chindelevich2, Fr´ed´eric Guichard3, 1 Faculty of Medicine, McGill University, Montreal, Quebec, Canada 2 MRC Centre for Global Infectious Disease Analysis, Imperial College, Lon...
2022
Supply-driven evolution: mutation bias and trait-fitness distributions can drive macro-evolutionary dynamics
10.1101/2022.07.18.500397
[ "(Julian) Xue Zhun Ping", "Chindelevich Leonid", "Guichard Frédéric" ]
creative-commons
! 1! Enlarged Ingroup Effect: How a Shared Culture Shapes In-Group Perception Paola Rigo1, Bindiya L. Ragunath 2 , Marc H. Bornstein 3,4 , Gianluca Esposito 2,5,6* 1 Department of Developmental 78 Psychology and Socialisation, University of Padua, Padua, Italy 2 Psychology Program, School of Social Sciences, Nanyan...
2020
Enlarged Ingroup Effect: How a Shared Culture Shapes In-Group Perception
10.1101/2020.06.12.148601
[ "Rigo Paola", "Ragunath Bindiya L.", "Bornstein Marc H.", "Esposito Gianluca" ]
creative-commons
DNA Supercoiling Drives a Transition between Collective Modes of Gene Synthesis Purba Chatterjee, Nigel Goldenfeld, and Sangjin Kim Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Loomis Laboratory of Physics, 1110 West Green Street, Urbana, Illinois 61801, ...
2021
DNA Supercoiling Drives a Transition between Collective Modes of Gene Synthesis
10.1101/2021.03.19.436182
[ "Chatterjee Purba", "Goldenfeld Nigel", "Kim Sangjin" ]
creative-commons
1 Subjective assessment and taste strips testing of gustatory function, at home, and in the lab Tomer Green¹, Anne Wolf², Anna Oleszkiewicz³, Anna Aronis¹, Thomas Hummel², Marta Y Pepino4 and *Masha Y Niv¹ Affiliations ¹Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusa...
2022
Subjective assessment and taste strips testing of gustatory function, at home, and in the lab
10.1101/2022.09.11.507407
[ "Green Tomer", "Wolf Anne", "Oleszkiewicz Anna", "Aronis Anna", "Hummel Thomas", "Pepino Marta Y", "Niv Masha Y" ]
null
1 The Envelope Protein of SARS-CoV-2 Inhibits Viral Protein Synthesis and Infectivity of Human Immunodeficiency Virus type 1 (HIV-1) Wyatt Henke, Hope Waisner, Sachith Polpitiya Arachchige, Maria Kalamvoki, and Edward Stephens# Department of Microbiology, ...
2022
The Envelope Protein of SARS-CoV-2 Inhibits Viral Protein Synthesis and Infectivity of Human Immunodeficiency Virus type 1 (HIV-1)
10.1101/2022.03.23.485576
[ "Henke Wyatt", "Waisner Hope", "Arachchige Sachith Polpitiya", "Kalamvoki Maria", "Stephens Edward" ]
null
1 NAD kinase promotes Staphylococcus aureus pathogenesis by 1 supporting production of virulence factors and protective enzymes 2 3 Clarisse Leseigneur1, Laurent Boucontet2, Magalie Duchateau3, Javier Pizarro-Cerda1, 4 Mariette Matondo3, Emma Colucci-Guyon2, Olivier Dussurget1* 5 6 1Institut Pasteur, ...
2022
NAD kinase promotes pathogenesis by supporting production of virulence factors and protective enzymes
10.1101/2021.08.09.455706
[ "Leseigneur Clarisse", "Boucontet Laurent", "Duchateau Magalie", "Pizarro-Cerda Javier", "Matondo Mariette", "Colucci-Guyon Emma", "Dussurget Olivier" ]
null
1 Research Article 1 2 Adaptive divergence of meiotic recombination rate in ecological speciation 3 4 5 6 Swatantra Neupane and Sen Xu* 7 8 Department of Biology, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019 9 10 *Correspondence author: Sen Xu, email: sen.xu@u...
2020
Adaptive divergence of meiotic recombination rate in ecological speciation
10.1101/2020.07.24.219576
[ "Neupane Swatantra", "Xu Sen" ]
null
Chemophototherapy Overcomes Doxorubicin Resistance in Human Ovarian Cancer Cells 1 2 Sanjana Ghosha, Upendra Chitgupia,b, Ulas Sunarc and Jonathan F. Lovella* 3 aDepartment of Biomedical Engineering, University at Buffalo, State University of New York, 4 Buffalo, New York, 14260, USA 5 bNektar Therapeutics, ...
2022
Chemophototherapy Overcomes Doxorubicin Resistance in Human Ovarian Cancer Cells
10.1101/2022.02.14.480412
[ "Ghosh Sanjana", "Chitgupi Upendra", "Sunar Ulas", "Lovell Jonathan F." ]
creative-commons
1 Transneuronal interactions facilitate axonal compartment formation Authors: Bavat Bornstein1, Idan Alyagor1, Victoria Berkun1, Hagar Meltzer1, Fabienne Reh2, 5 Hadas Keren-Shaul3,4, Eyal David3, Thomas Riemensperger2 and Oren Schuldiner1* 1Department of Molecular Cell Biology, Weizmann Institute of Sc...
2019
Transneuronal interactions facilitate axonal compartment formation
10.1101/834515
[ "Bornstein Bavat", "Alyagor Idan", "Berkun Victoria", "Meltzer Hagar", "Reh Fabienne", "Keren-Shaul Hadas", "David Eyal", "Riemensperger Thomas", "Schuldiner Oren" ]
null
PEPseq Quantifies Transcriptome-Wide Changes in Protein Occupancy and Reveals Selective Translational Repression After Translational Stress Jakob Trendel1,2, Etienne Boileau3,4, Marco Jochem2, Christoph Dieterich3,4,§,+ & Jeroen Krijgsveld2,5,§,+ [1] European Molecular Biology Laboratory (EMBL), Heidelberg, Germany ...
2022
PEPseq Quantifies Transcriptome-Wide Changes in Protein Occupancy and Reveals Selective Translational Repression After Translational Stress
10.1101/2022.07.28.501819
[ "Trendel Jakob", "Boileau Etienne", "Jochem Marco", "Dieterich Christoph", "Krijgsveld Jeroen" ]
creative-commons
Title 1 2 Identification of a transcriptional signature found in multiple models of ASD and related disorders 3 4 Authors 5 6 Samuel Thudiuma,b, Katherine Palozolaa,b, Eloise L’Hera,b, Erica Korba,b,* 7 8 Author Affiliations 9 10 Department of Geneticsa, Epigenetics Instituteb, Perelman School...
2022
Identification of a transcriptional signature found in multiple models of ASD and related disorders
10.1101/2022.01.14.476375
[ "Thudium Samuel", "Palozola Katherine", "L’Her Eloise", "Korb Erica" ]
creative-commons
1 Methods Article Orientation of Directional Deep Brain Stimulation Leads on CT: Resolving the Ambiguity Rebecca Kurtev-Rittstiega, Stefan Achatza, Amir Nouriniaa, Stephan Mittermeyera a R&D Functional and Stereotactic Neurosurgery, Brainlab AG, Munich, Germany Short Title: automatic direc...
2020
Orientation of Directional Deep Brain Stimulation Leads on CT: Resolving the Ambiguity
10.1101/2020.09.16.298653
[ "Kurtev-Rittstieg Rebecca", "Achatz Stefan", "Nourinia Amir", "Mittermeyer Stephan" ]
creative-commons
1 ICER controls HIV-1 infection and replication in elite controllers 1 2 3 Zhenwu Luo1*, Min Li1, Taiwei Li2, Zongyang Lv3, 4, Zhiwei Ye5, William J. Cisneros6, Jie 4 Zhang5, Lingmin Yuan3, 4, Judd F. Hultquist6, Stephen A Migueles7, Jian Zhu2, Wei Jiang1,8* 5 6 7 1Department of Microbiology and Im...
2021
ICER controls HIV-1 infection and replication in elite controllers
10.1101/2021.06.30.450567
[ "Luo Zhenwu", "Li Min", "Li Taiwei", "Lv Zongyang", "Ye Zhiwei", "Cisneros William J.", "Zhang Jie", "Yuan Lingmin", "Hultquist Judd F.", "Migueles Stephen A", "Zhu Jian", "Jiang Wei" ]
null
Deciphering the language of antibodies using self-supervised learning Jinwoo Leem1*, Laura S. Mitchell1, James H.R. Farmery1, Justin Barton1, Jacob D. Galson1 1 Alchemab Therapeutics Ltd, East Side, Office 1.02, Kings Cross, London, N1C 4AX *Corresponding author: jin@alchemab.com Abstract An individual’s ...
2021
Deciphering the language of antibodies using self-supervised learning
10.1101/2021.11.10.468064
[ "Leem Jinwoo", "Mitchell Laura S.", "Farmery James H.R.", "Barton Justin", "Galson Jacob D." ]
creative-commons
1 Title Extended longevity geometrically-inverted proximal tubule organoids for protein uptake studies Authors Eric Parigoris1,2, Ji-Hoon Lee1,2, Amy Yunfan Liu1,2, Xueying Zhao3, Shuichi Takayama1,2,* 1 Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, Unit...
2022
Extended longevity geometrically-inverted proximal tubule organoids for protein uptake studies
10.1101/2022.03.24.485493
[ "Parigoris Eric", "Lee Ji-Hoon", "Liu Amy Yunfan", "Zhao Xueying", "Takayama Shuichi" ]
null
1 Evolution of degrees of carnivory and dietary specialization across Mammalia and their 1 effects on speciation 2 Matthew D. Pollard1,2 and Emily E. Puckett1,2 3 1Department of Biological Sciences, University of Memphis, Memphis, TN 38152 4 2Center for Biodiversity Research, University of Memphis, Memphis, ...
2022
Evolution of degrees of carnivory and dietary specialization across Mammalia and their effects on speciation
10.1101/2021.09.15.460515
[ "Pollard Matthew D.", "Puckett Emily E." ]
creative-commons
1 Induction of the HIF pathway: Differential regulation by chemical hypoxia and oxygen glucose deprivation Authors Alicia E. Novak1,2,3*, Susan M. Jones1,3, J. Paul Elliott1,2,3 Affiliations 1Neurotrauma Research, Swedish Medical Center, Englewood, Colorado, United States of America 2Colorado Neurologic...
2019
Induction of the HIF pathway: Differential regulation by chemical hypoxia and oxygen glucose deprivation
10.1101/525006
[ "Novak Alicia E.", "Jones Susan M.", "Elliott J. Paul" ]
null
ggcoverage: an R package to visualize and annotate genome coverage for various NGS data Yabing Song1,* and Jianbin Wang1,* 1School of Life Sciences, Tsinghua University, Beijing, China. *To whom correspondence should be addressed. Abstract Summary: Visualizing genome coverage is of vital importance to inspect...
2022
: an R package to visualize and annotate genome coverage for various NGS data
10.1101/2022.09.01.503744
[ "Song Yabing", "Wang Jianbin" ]
creative-commons
CpG-creating Mutations are Costly in Many Human Viruses Victoria R. Caudill1, Sarina Qin1, Ryan Winstead1, Jasmeen Kaur1, Kaho Tisthammer1, E. Geo Pineda1, Oana Carja2, Rosalind M Eggo.3, Katia Koelle7, Katrina Lythgoe8, Scott Roy1, Nicole Allen1, Milo Aviles1, Brittany A. Baker1, William Bauer1, Shannel Bermudez1, Cor...
2019
CpG-creating Mutations are Costly in Many Human Viruses
10.1101/702175
[ "Caudill Victoria R.", "Qin Sarina", "Winstead Ryan", "Kaur Jasmeen", "Tisthammer Kaho", "Pineda E. Geo", "Carja Oana", "Eggo Rosalind M", "Koelle Katia", "Lythgoe Katrina", "Roy Scott", "Allen Nicole", "Aviles Milo", "Baker Brittany A.", "Bauer William", "Bermudez Shannel", "Carlson...
creative-commons
1 Intact rDNA arrays of Potentilla-origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer László Barthaa1, Terezie Mandákováb, Aleš Kovaříkc, Paul-Adrian Bulzud, Nathalie Roddee, Václav Mahelkaf, Martin A. Lysakb, Margaux-Alison Fustiere, Jan Šafářg, Petr Cápalg, Luj...
2021
Intact rDNA arrays of -origin detected in nucleus suggest recent eudicot-to-monocot horizontal transfer
10.1101/2021.12.15.472635
[ "Bartha László", "Mandáková Terezie", "Kovařík Aleš", "Bulzu Paul-Adrian", "Rodde Nathalie", "Mahelka Václav", "Lysak Martin A.", "Fustier Margaux-Alison", "Šafář Jan", "Cápal Petr", "Keresztes Lujza", "Banciu Horia L." ]
creative-commons
Antibiotics modulate attractive interactions in bacterial colonies affecting survivability under combined treatment Short title: Antibiotics modulate attractive interactions in bacterial colonies Tom Cronenberg*, Marc Hennes*, Isabelle Wielert, Berenike Maier$ Institute for Biological Physics, University of Col...
2020
Antibiotics modulate attractive interactions in bacterial colonies affecting survivability under combined treatment
10.1101/2020.12.14.422681
[ "Cronenberg Tom", "Hennes Marc", "Wielert Isabelle", "Maier Berenike" ]
creative-commons
Adaptation Within Embryonic and Neonatal Heart Environment Reveals Alternative Fates for Adult c-Kit+ Cardiac Interstitial Cells Bingyan J. Wang MS, Roberto Alvarez Jr. PhD, Alvin Muliono, Sharon Sengphanith, Megan M. Monsanto, Joi Weeks MS, Roberto Sacripanti, Mark A. Sussman PhD* SDSU Heart Institute, San Die...
2019
Adaptation Within Embryonic and Neonatal Heart Environment Reveals Alternative Fates for Adult c-Kit Cardiac Interstitial Cells
10.1101/758516
[ "Wang Bingyan J.", "Alvarez Roberto", "Muliono Alvin", "Sengphanith Sharon", "Monsanto Megan M.", "Weeks Joi", "Sacripanti Roberto", "Sussman Mark A." ]
null
1 Cell-­‐type  specific  concentration  regulation  of  the  basal  transcription  factor  TFIIH       Authors:     Lise-­‐Marie  Donnio1,  Catherine  Miquel2,  Wim  Vermeulen3,  Giuseppina  Giglia-­‐Mari1*,  Pierre-­‐Olivier   Mari1*     1  :  Institut  Neu...
2019
Cell-type specific concentration regulation of the basal transcription factor TFIIH
10.1101/613281
[ "Donnio Lise-Marie", "Miquel Catherine", "Vermeulen Wim", "Giglia-Mari Giuseppina", "Mari Pierre-Olivier" ]
null
1 Deciphering copper coordination in the animal prion protein amyloidogenic domain 1 2 Giulia Salzano1, Martha Brennich2, Giordano Mancini3,4, Thanh Hoa Tran1, Giuseppe 3 Legname1,5, Paola D’Angelo6* and Gabriele Giachin7* 4 5 1 Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzat...
2018
Deciphering copper coordination in the animal prion protein amyloidogenic domain
10.1101/507624
[ "Salzano Giulia", "Brennich Martha", "Mancini Giordano", "Tran Thanh Hoa", "Legname Giuseppe", "Angelo Paola D’", "Giachin Gabriele" ]
null
Live-cell STED microscopy of mitochondrial cristae Till Stephana,c, Axel Roescha,c, Dietmar Riedelb, Stefan Jakobsa,c aDepartment of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; bLaboratory of Electron Microscopy, Max Planck Institute for Biophysical Chemistry,...
2019
Live-cell STED microscopy of mitochondrial cristae
10.1101/640920
[ "Stephan Till", "Roesch Axel", "Riedel Dietmar", "Jakobs Stefan" ]
creative-commons
1 Dynamic evolution of de novo DNA methyltransferases in rodent and primate genomes Antoine Molaro1,4, Harmit S. Malik1,2 and Deborah Bourc’his3 1Division of Basics Sciences & 2Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; 3Institut Curie, PSL University, ...
2019
Dynamic evolution of DNA methyltransferases in rodent and primate genomes
10.1101/786863
[ "Molaro Antoine", "Malik Harmit S.", "Bourc’his Deborah" ]
creative-commons
Sugar-rich larval diet promotes lower adult pathogen load and higher 1 survival after infection in a polyphagous fly 2 Hue Dinh1, Ida Lundbäck1, Sheemal Kumar1, Anh The Than1,2, Juliano Morimoto1,3,4, Fleur Ponton1 3 1. School of Natural Sciences, Macquarie University, Australia 4 2. Department of Entomology, ...
2021
Sugar-rich larval diet promotes lower adult pathogen load and higher survival after infection in a polyphagous fly
10.1101/2021.12.16.473033
[ "Dinh Hue", "Lundbäck Ida", "Kumar Sheemal", "Than Anh The", "Morimoto Juliano", "Ponton Fleur" ]
creative-commons
A deep generative model of the SARS-CoV-2 spike protein predicts future variants Rahul M. Dhodapkar School of Medicine Yale University New Haven, CT 06510, USA Correspondence to: rahul.dhodapkar@yale.edu ABSTRACT SARS-CoV-2 has demonstrated a robust ability to adapt in response to environ- mental pressures—increasing v...
2023
A deep generative model of the SARS-CoV-2 spike protein predicts future variants
10.1101/2023.01.17.524472
null
creative-commons
1 Biodegradation of polyester polyurethane by 2 Aspergillus flavus G10 3 Sehroon Khan1, 2†, Sadia Nadir †1,2,3, Yang Dong †4,5 , Douglas A. Schaefer2* , Peter E. 4 Mortimer1, Heng Gui1,2, Afsar Khan6, Mingming Yu7, Shahid Iqbal1, 2, Jun Sheng4, 5 5 Jianchu Xu1,2* 6 1 Key Laboratory for Plant Biodiversity and Bio...
2020
Biodegradation of polyester polyurethane by G10
10.1101/2020.06.25.170654
[ "Khan Sehroon", "Nadir Sadia", "Dong Yang", "Schaefer Douglas A.", "Mortimer Peter E.", "Gui Heng", "Khan Afsar", "Yu Mingming", "Iqbal Shahid", "Sheng Jun", "Xu Jianchu" ]
creative-commons
1 The characterisation of phytoene synthase-1 and 2, and 1-D-deoxy-xylulose 5-phosphate synthase genes from red chilli pepper (Capsicum annuum) Harriet M. Berry1, Nan Zhou2, Daniel V. Rickett2, Charles J. Baxter2, Eugenia M. A. Enfissi1 and Paul D. Fraser1* 1School of Biological Sciences, Royal Holloway, Univ...
2023
The characterisation of phytoene synthase-1 and 2, and 1-D-deoxy-xylulose 5-phosphate synthase genes from red chilli pepper ()
10.1101/2023.01.25.525515
[ "Berry Harriet M.", "Zhou Nan", "Rickett Daniel V.", "Baxter Charles J.", "Enfissi Eugenia M. A.", "Fraser Paul D." ]
creative-commons
1 Rapid pacing by circulating traveling waves improves maturation of 1 hiPSC-derived cardiomyocytes in self-organized tissue ring 2 3 Junjun Li1,2#, Lu Zhang3#, Leqian Yu2, Itsunari Minami4, Marcel Hörning2,9, Ji Dong5, Jing 4 Qiao2, Nanae Fujimoto1,2, Yuji Shiba6, Yang Zhao7, Fuchou Tang5, Shigeru Miyagawa...
2019
Rapid pacing by circulating traveling waves improves maturation of hiPSC-derived cardiomyocytes in self-organized tissue ring
10.1101/717108
[ "Li Junjun", "Zhang Lu", "Yu Leqian", "Minami Itsunari", "Hörning Marcel", "Dong Ji", "Qiao Jing", "Fujimoto Nanae", "Shiba Yuji", "Zhao Yang", "Tang Fuchou", "Miyagawa Shigeru", "Chen Yong", "Sawa Yoshiki", "Tang Chao", "Liu Li" ]
null
1 Root carbon interaction with soil minerals is dynamic, leaving a legacy of microbially-derived residues Rachel A. Neuratha,b, Jennifer Pett-Ridgec, Ilexis Chu-Jacobya, Donald Hermana, Thea Whitmand, Peter Nicoe, Andrew S. Liptonf, Jennifer Kylef, Malak M. Tfailyg, Alison Thompsonf, Mary K. Firestonea ...
2021
Root carbon interaction with soil minerals is dynamic, leaving a legacy of microbially-derived residues
10.1101/2021.03.23.436628
[ "Neurath Rachel A.", "Pett-Ridge Jennifer", "Chu-Jacoby Ilexis", "Herman Donald", "Whitman Thea", "Nico Peter", "Lipton Andrew S.", "Kyle Jennifer", "Tfaily Malak M.", "Thompson Alison", "Firestone Mary K." ]
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Identification of Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids Authors: Yuling Han1, #, Liuliu Yang1, #, Xiaohua Duan1, 11#, Fuyu Duan2, #, Benjamin E. Nilsson- Payant 3, #, Tomer M. Yaron4, 5#, Pengfei Wang6, Xuming Tang1, Tuo Zhang7, Zeping Zhao1, Yaron Bram8,9, David Redmond10, Sean Houghton10...
2020
Identification of Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids
10.1101/2020.05.05.079095
[ "Han Yuling", "Yang Liuliu", "Duan Xiaohua", "Duan Fuyu", "Nilsson-Payant Benjamin E.", "Yaron Tomer M.", "Wang Pengfei", "Tang Xuming", "Zhang Tuo", "Zhao Zeping", "Bram Yaron", "Redmond David", "Houghton Sean", "Nguyen Duc", "Xu Dong", "Wang Xing", "Uhl Skyler", "Huang Yaoxing", ...
null
1 Spatial accumulation of salicylic acid is regulated by RBOHD in potato immunity against viruses Tjaša Lukan1,*, Maruša Pompe-Novak1,*, Špela Baebler1,*, Magda Tušek-Žnidarič1, Aleš Kladnik2, Maja Križnik1, Andrej Blejec1, Maja Zagorščak1, Katja Stare1, Barbara Dušak1, Anna Coll1, Stephan Pollmann3, Karolina...
2020
Spatial accumulation of salicylic acid is regulated by RBOHD in potato immunity against viruses
10.1101/2020.01.06.889998
[ "Lukan Tjaša", "Pompe-Novak Maruša", "Baebler Špela", "Tušek-Žnidarič Magda", "Kladnik Aleš", "Križnik Maja", "Blejec Andrej", "Zagorščak Maja", "Stare Katja", "Dušak Barbara", "Coll Anna", "Pollmann Stephan", "Morgiewicz Karolina", "Hennig Jacek", "Gruden Kristina" ]
creative-commons
1 Assembly intermediates of orthoreovirus captured in the cell Geoff Sutton1,*, Dapeng Sun2*, Xiaofeng Fu2,‡,*, Abhay Kotecha1,#,*, Corey W. Hecksel3,†, Daniel K. Clare3, Peijun Zhang1,2,3, David I. Stuart1,3 & Mark Boyce1 1. Division of Structural Biology, Wellcome Centre for Human Genetics, University...
2020
Assembly intermediates of orthoreovirus captured in the cell
10.1101/2020.06.10.144998
[ "Sutton Geoff", "Sun Dapeng", "Fu Xiaofeng", "Kotecha Abhay", "Hecksel Corey W.", "Clare Daniel K.", "Zhang Peijun", "Stuart David I.", "Boyce Mark" ]
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1 1 Is proton magnetic resonance spectroscopy a valid method to quantify muscle carnosine in humans? 1 2 Vinicius da Eira Silva1, Vitor de Salles Painelli1, Samuel Katsuyuki Shinjo2, Eduardo Maffud Cilli5, Craig 3 Sale4, Bruno Gualano1, Maria Concepción Otaduy3, Guilherme Giannini Artioli1 4 5 1 Appli...
2019
Is proton magnetic resonance spectroscopy a valid method to quantify muscle carnosine in humans?
10.1101/568923
[ "da Eira Silva Vinicius", "de Salles Painelli Vitor", "Shinjo Samuel Katsuyuki", "Cilli Eduardo Maffud", "Sale Craig", "Gualano Bruno", "Otaduy Maria Concepción", "Artioli Guilherme Giannini" ]
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DRAFT Lineage recording reveals dynamics of cerebral organoid regionalization Zhisong He1,*, Tobias Gerber2,*, Ashley Maynard1,*, Akanksha Jain1,*, Rebecca Petri1,*, Malgorzata Santel1, Kevin Ly1, Leila Sidow2, Fatima Sanchis Callejal1, Stephan Riesenberg2, J. Gray Camp3,4,�, and Barbara Treutlein1,2,� 1Department of B...
2020
Lineage recording reveals dynamics of cerebral organoid regionalization
10.1101/2020.06.19.162032
[ "He Zhisong", "Gerber Tobias", "Maynard Ashley", "Jain Akanksha", "Petri Rebecca", "Santel Malgorzata", "Ly Kevin", "Sidow Leila", "Callejal Fatima Sanchis", "Riesenberg Stephan", "Camp J. Gray", "Treutlein Barbara" ]
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1 Stimulation of platelet P2Y1 receptors by different endogenous nucleotides leads to 1 functional selectivity via biased signalling 2 Running header: P2Y1 agonists have biased activity on platelet function. 3 4 Kate L Arkless,1 Dingxin Pan,1 Manu Shankar-Hari,2,3 Richard T. Amison1, Clive P. Page,1 Khonda...
2022
Stimulation of platelet P2Y receptors by different endogenous nucleotides leads to functional selectivity via biased signalling
10.1101/2022.08.16.504096
[ "Arkless Kate L", "Pan Dingxin", "Shankar-Hari Manu", "Amison Richard T.", "Page Clive P.", "Rahman Khondaker Miraz", "Pitchford Simon C." ]
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Elucidating the structural features of ABCA1 in its heterogeneous membrane environment. Sunidhi S.a,1, Sukriti Sachera,1, Parth Garga, Arjun Raya,∗ aDepartment of Computational Biology, Indraprastha Institute of Information Technology, Delhi, India Abstract ABCA1 plays an integral part in Reverse Cholesterol Transport ...
2021
Elucidating the structural features of ABCA1 in its heterogeneous membrane environment
10.1101/2021.05.23.445323
[ "Sunidhi S.", "Sacher Sukriti", "Garg Parth", "Ray Arjun" ]
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1 Automated neuronal reconstruction with super- multicolour fluorescence imaging Marcus N. Leiwe1,2, Satoshi Fujimoto1,2, Toshikazu Baba1,2, Daichi Moriyasu1, Biswanath Saha1, Richi Sakaguchi1, Shigenori Inagaki1, & Takeshi Imai1,2* Affiliations: 1 Graduate School of Medical Sciences, Kyushu University, Fukuoka...
2022
Automated neuronal reconstruction with super-multicolour fluorescence imaging
10.1101/2022.10.20.512984
[ "Leiwe Marcus N.", "Fujimoto Satoshi", "Baba Toshikazu", "Moriyasu Daichi", "Saha Biswanath", "Sakaguchi Richi", "Inagaki Shigenori", "Imai Takeshi" ]
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1 Title: Optogenetic control of excitatory post-synaptic differentiation through neuroligin-1 tyrosine phosphorylation Authors: Mathieu Letellier1,2, Matthieu Lagardère1,2,$, Béatrice Tessier1,2,$, Harald Janovjak3, Olivier Thoumine1,2,* 1. University of Bordeaux, Interdisciplinary Institute for Neuroscience, UM...
2019
Optogenetic control of excitatory post-synaptic differentiation through neuroligin-1 tyrosine phosphorylation
10.1101/788638
[ "Letellier Mathieu", "Lagardère Matthieu", "Tessier Béatrice", "Janovjak Harald", "Thoumine Olivier" ]
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Structure of Mpro from COVID-19 virus and discovery of its inhibitors 1 Zhenming Jin1,2,10, Xiaoyu Du2,10, Yechun Xu3,10, Yongqiang Deng4,10, Meiqin Liu5,10, Yao 2 Zhao1, Bing Zhang1, Xiaofeng Li4, Leike Zhang5, Chao Peng6, Yinkai Duan1, Jing Yu1, Lin 3 Wang1, Kailin Yang7, Fengjiang Liu1, Rendi Jiang5, Xinglou Y...
2020
Structure of M from COVID-19 virus and discovery of its inhibitors
10.1101/2020.02.26.964882
[ "Jin Zhenming", "Du Xiaoyu", "Xu Yechun", "Deng Yongqiang", "Liu Meiqin", "Zhao Yao", "Zhang Bing", "Li Xiaofeng", "Zhang Leike", "Peng Chao", "Duan Yinkai", "Yu Jing", "Wang Lin", "Yang Kailin", "Liu Fengjiang", "Jiang Rendi", "Yang Xinglou", "You Tian", "Liu Xiaoce", "Yang Xi...
null
1 Evolution within a given virulence phenotype (pathotype) is driven 1 by changes in aggressiveness: a case study of French wheat leaf rust 2 populations 3 4 Cécilia Fontyn, Kevin JG Meyer, Anne-Lise Boixel, Ghislain Delestre, Emma Piaget, Corentin 5 Picard, Frédéric Suffert, Thierry C Marcel*, Henriette ...
2022
Evolution within a given virulence phenotype (pathotype) is driven by changes in aggressiveness: a case study of French wheat leaf rust populations
10.1101/2022.08.29.505401
[ "Fontyn Cécilia", "Meyer Kevin JG", "Boixel Anne-Lise", "Delestre Ghislain", "Piaget Emma", "Picard Corentin", "Suffert Frédéric", "Marcel Thierry C", "Goyeau Henriette" ]
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Elastase treatment of tendon specifically impacts the mechanical 1 properties of the interfascicular matrix 2 3 Marta S. Godinho1, Chavaunne T. Thorpe2, Steve E. Greenwald3, Hazel R. 4 C. Screen1* 5 6 1 Institute of Bioengineering, School of Engineering and Materials Science, Queen Mary 7 University of...
2020
Elastase treatment of tendon specifically impacts the mechanical properties of the interfascicular matrix
10.1101/2020.09.18.303081
[ "Godinho Marta S.", "Thorpe Chavaunne T.", "Greenwald Steve E.", "Screen Hazel R. C." ]
null
Phase Transition of RNA-protein Complexes into Ordered Hollow Condensates Ibraheem Alshareedah§a, Mahdi Muhammad Moosa§a, Muralikrishna Rajub, Davit Potoyan*b, Priya R. Banerjee*a aDepartment of Physics, University at Buffalo, Buffalo NY 14260, USA bDepartment of Chemistry, Iowa State University, Ames IA 500...
2020
Phase Transition of RNA-protein Complexes into Ordered Hollow Condensates
10.1101/2020.01.10.902353
[ "Alshareedah Ibraheem", "Moosa Mahdi Muhammad", "Raju Muralikrishna", "Potoyan Davit", "Banerjee Priya R." ]
null
1 1 Elemental analysis of Moringa oleifera seeds by Laser Induced Breakdown 2 Spectroscopy (LIBS) and its anti-cancer and anti-microbial studies 3 4 R. K. Aldakheela,b , S. Rehmanc , Firdos A. Khand, A. Mostafae , M. A. Almessierea, 5 M. A. Gondalf*1, A. Baykalg 6 7 aDepartment of Biophysics, cDepartment of Epidemic ...
2020
Elemental analysis of seeds by Laser Induced Breakdown Spectroscopy (LIBS) and its anti-cancer and anti-microbial studies
10.1101/2020.04.15.042663
[ "Aldakheel R. K.", "Rehman S.", "Khan Firdos A.", "Mostafa A.", "Almessiere M. A.", "Gondal M. A.", "Baykal A." ]
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1 Title: Dynamics of brain-fluid circulation are altered in the mature-onset Tet-off APP mouse model of amyloidosis Author list: Inès R.H. Ben-Nejma1#*, Aneta J. Keliris1#*, Verdi Vanreusel1,3, Peter Ponsaerts2, Annemie Van der Linden1, Georgios A. Keliris1* Author affiliations: 1Bio-Imaging Lab, University of ...
2022
Dynamics of brain-fluid circulation are altered in the mature-onset Tet-off APP mouse model of amyloidosis
10.1101/2022.03.11.483807
[ "Ben-Nejma Inès R.H.", "Keliris Aneta J.", "Vanreusel Verdi", "Ponsaerts Peter", "Van der Linden Annemie", "Keliris Georgios A." ]
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An Activator Locks Kv7.1 Channels Open by Electro-Mechanical Uncoupling and Allosterically Modulates its Pore Running title: RL3 Binding and Activation Melina Möller1,*, Julian A. Schreiber1,2,*, Mark Zaydman3, Zachary Beller3, Sebastian Becker1, Nadine Ritter1,4, Eva Wrobel1, Nathalie Strutz-Seebohm1, Nie...
2021
An Activator Locks Kv7.1 Channels Open by Electro-Mechanical Uncoupling and Allosterically Modulates its Pore
10.1101/2021.02.11.430741
[ "Möller Melina", "Schreiber Julian A.", "Zaydman Mark", "Beller Zachary", "Becker Sebastian", "Ritter Nadine", "Wrobel Eva", "Strutz-Seebohm Nathalie", "Decher Niels", "Cui Jianmin", "Schmitt Nicole", "Düfer Martina", "Wünsch Bernhard", "Seebohm Guiscard" ]
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RL-118 and 11β-HSD1 target engagement through TAPS assay: behaviour and molecular analysis Puigoriol-Illamola, D.1,2, Companys-Alemany, J.1,2, Homer, N.3, Leiva, R.4, Vázquez, S.4, Mole, D.5, Griñán-Ferré, C.1,2, Pallàs, M1,2. RL-118 and 11β-HSD1 target engagement through TAPS assay: behaviour and molecular analysi...
2020
RL-118 and 11β-HSD1 target engagement through TAPS assay: behaviour and molecular analysis
10.1101/2020.10.27.356881
[ "Puigoriol-Illamola D.", "Companys-Alemany J.", "Homer N.", "Leiva R.", "Vázquez S.", "Mole D.", "Griñán-Ferré C.", "Pallàs M." ]
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Disruption of the autism-associated gene SCN2A alters synaptic development and neuronal signaling in patient iPSC-glutamatergic neurons Chad O. Brown1,5, Jarryll Uy3,4, Nadeem Murtaza1,5, Elyse Rosa1, Alexandria Alfonso1, Sansi Xing1, Biren M. Dave2,4, Savannah Kilpatrick1,5, Annie A. Cheng5, Sean H. White1, St...
2021
Disruption of the autism-associated gene alters synaptic development and neuronal signaling in patient iPSC-glutamatergic neurons
10.1101/2021.09.14.460368
[ "Brown Chad O.", "Uy Jarryll", "Murtaza Nadeem", "Rosa Elyse", "Alfonso Alexandria", "Xing Sansi", "Dave Biren M.", "Kilpatrick Savannah", "Cheng Annie A.", "White Sean H.", "Scherer Stephen W.", "Lu Yu", "Singh Karun K." ]
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The Bayesian Superorganism III: externalised memories facilitate distributed 1 sampling 2 Edmund R. Hunt1, Nigel R. Franks1, Roland J. Baddeley2 3 1School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, 4 BS8 1TQ, UK 5 2School of Experimental Psychology, Uni...
2018
The Bayesian Superorganism III: externalised memories facilitate distributed sampling
10.1101/504241
[ "Hunt Edmund R.", "Franks Nigel R.", "Baddeley Roland J." ]
null
1 Lung epithelial stem cells express SARS-CoV-2 entry factors: implications for COVID- 19 Anna A. Valyaeva1, Anastasia A. Zharikova1,2, Artem S. Kasianov2, Yegor S. Vassetzky3,4 ✉ and Eugene V. Sheval1,5,6 ✉ 1Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia. ...
2020
Lung epithelial stem cells express SARS-CoV-2 entry factors: implications for COVID-19
10.1101/2020.05.23.107334
[ "Valyaeva Anna A.", "Zharikova Anastasia A.", "Kasianov Artem S.", "Vassetzky Yegor S.", "Sheval Eugene V." ]
creative-commons
Cross-modal temporal biases emerge during early sensitive periods Stephanie Badde1,2,*, Pia Ley1, Siddhart S Rajendran 1,3, Idris Shareef1,3, Ramesh Kekunnaya3, & Brigitte Röder1 1 Biological Psychology and Neuropsychology, University of Hamburg, Hamburg, Germany 2 Department of Psychology and Center of Ne...
2019
Cross-modal temporal biases emerge during early sensitive periods
10.1101/839514
[ "Badde Stephanie", "Ley Pia", "Rajendran Siddhart S", "Shareef Idris", "Kekunnaya Ramesh", "Röder Brigitte" ]
creative-commons
1 Structure of the Inmazeb cocktail and resistance to escape against Ebola virus Author list: Vamseedhar Rayaprolu1,5, Ben Fulton2, Ashique Rafique2, Emilia Arturo1,9, Dewight Williams3, Chitra Hariharan1, Heather Callaway1, Amar Parvate1,6, Sharon L. Schendel1, Diptiben Parekh1, Sean Hui1,7, Kelly Shaffer1,8...
2022
Structure of the Inmazeb cocktail and resistance to escape against Ebola virus
10.1101/2022.10.11.511805
[ "Rayaprolu Vamseedhar", "Fulton Ben", "Rafique Ashique", "Arturo Emilia", "Williams Dewight", "Hariharan Chitra", "Callaway Heather", "Parvate Amar", "Schendel Sharon L.", "Parekh Diptiben", "Hui Sean", "Shaffer Kelly", "Pascal Kristen", "Wloga Elzbieta", "Giordano Stephanie", "Copin R...
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Modeling SARS-CoV-2 nsp1–5’-UTR complex via the extended ensemble simulations Shun Sakuraba,∗,† Xie Qilin,‡ Kota Kasahara,¶ Junichi Iwakiri,§ and Hidetoshi Kono† †Institute for Quantum Life Science, National Institutes for Quantum and Radiological Research and Technology, 8-1-7 Umemi-dai, Kizu, Kyoto 619-0215 ‡College ...
2021
Modeling SARS-CoV-2 nsp1–5’-UTR complex via the extended ensemble simulations
10.1101/2021.02.24.432807
[ "Sakuraba Shun", "Qilin Xie", "Kasahara Kota", "Iwakiri Junichi", "Kono Hidetoshi" ]
creative-commons
Studies on the Biosorption Potential of Copper by Rhizopus arrhizus Biomass Jyoti Chauhan,1 Ishan Saini,1 and Prashant Kaushik2* 1Department of Botany, Kurukshetra University Kurukshetra, Kurukshetra 136119, India 2Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de Valèn...
2020
Studies on the Biosorption Potential of Copper by Biomass
10.1101/2020.07.13.201566
[ "Chauhan Jyoti", "Saini Ishan", "Kaushik Prashant" ]
creative-commons
The role of Selenoprotein N in the differentiation of erythroid progenitors during stress erythropoiesis Robert F. Paulson1*, Shaneice Nettleford1, Chang Liao1, Yuanting Chen1, Siyang Hao1, Mireille Baltzinger2, Mélanie Thami-Braye2, Alain Lescure2*, and K. Sandeep Prabhu1* 1Department of Veterinary and Biomedical ...
2018
The role of Selenoprotein N in the differentiation of erythroid progenitors during stress erythropoiesis
10.1101/506345
[ "Paulson Robert F.", "Nettleford Shaneice", "Liao Chang", "Chen Yuanting", "Hao Siyang", "Baltzinger Mireille", "Thami-Braye Mélanie", "Lescure Alain", "Prabhu K. Sandeep" ]
creative-commons
The influence of stimulus duration on olfactory identity Praveen Kuruppath* and Leonardo Belluscio Developmental Neural Plasticity Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892, USA. Correspondence: Praveen Kuruppath (praveen.k...
2020
The influence of stimulus duration on olfactory identity
10.1101/2020.09.07.286773
[ "Kuruppath Praveen", "Belluscio Leonardo" ]
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1 Glyoxylic acid overcomes 1-MCP-induced blockage of fruit ripening in Pyrus communis L. var. ‘D’Anjou’ Seanna Louise Hewitt1,2 and Amit Dhingra1,2* 1-Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 2-Department of Horticulture, Washington State University, Pullman, WA ...
2019
Glyoxylic acid overcomes 1-MCP-induced blockage of fruit ripening in . var. ‘D’Anjou’
10.1101/852954
[ "Hewitt Seanna Louise", "Dhingra Amit" ]
creative-commons
To be submitted as Registered Report to PLOS Biology Number of words in the manuscript: 9511 words Number of figures: 9 figures Decomposing age effects in EEG alpha power AUTHORS: Marius Tröndle1,2,3*, Tzvetan Popov1,2, Andreas Pedroni1,2, Christian Pfeiffer1, Zofia Barańczuk-Turska1,2,4, Nicolas Langer1,2,3 AFFILIATI...
2021
Decomposing age effects in EEG alpha power
10.1101/2021.05.26.445765
[ "Tröndle Marius", "Popov Tzvetan", "Pedroni Andreas", "Pfeiffer Christian", "Barańczuk-Turska Zofia", "Langer Nicolas" ]
creative-commons
1 Tomato spotted wilt virus benefits its thrips vector by modulating metabolic and plant defense pathways in tomato Punya Nachappa1*, Jean Challacombe2, David C. Margolies3, James R. Nechols3, Anna E. Whitfield4 and Dorith Rotenberg4* 1Department of Agricultural Biology, Colorado State University, Fort...
2020
Tomato spotted wilt virus benefits its thrips vector by modulating metabolic and plant defense pathways in tomato
10.1101/2020.08.10.244665
[ "Nachappa Punya", "Challacombe Jean", "Margolies David C.", "Nechols James R.", "Whitfield Anna E.", "Rotenberg Dorith" ]
creative-commons
PARNAS: Objectively Selecting the Most Representative Taxa on a Phylogeny Alexey Markin1,∗, Sanket Wagle2, Siddhant Grover2, Amy L. Vincent Baker1, Oliver Eulenstein2, and Tavis K. Anderson1,∗ 1 Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA 2 Department of Computer Scienc...
2022
PARNAS: Objectively Selecting the Most Representative Taxa on a Phylogeny
10.1101/2022.09.12.507613
[ "Markin Alexey", "Wagle Sanket", "Grover Siddhant", "Vincent Baker Amy L.", "Eulenstein Oliver", "Anderson Tavis K." ]
creative-commons
1 Journal: https://www.mdpi.com/journal/genes/special_issues/metagenomics_insitu 1 2 3 Tree Lab: Portable genomics for early detection of plant viruses and pests in Sub-Saharan Africa 4 5 6 7 Laura M. Boykin1, Peter Sseruwagi2, Titus Alicai3, Elijah Ateka4, Ibrahim Umar Mohammed5, Jo-Ann L. 8 S...
2019
Tree Lab: Portable genomics for early detection of plant viruses and pests in Sub-Saharan Africa
10.1101/702613
[ "Boykin Laura M.", "Sseruwagi Peter", "Alicai Titus", "Ateka Elijah", "Mohammed Ibrahim Umar", "Stanton Jo-Ann L.", "Kayuki Charles", "Mark Deogratius", "Fute Tarcisius", "Erasto Joel", "Bachwenkizi Hilda", "Muga Brenda", "Mumo Naomi", "Mwangi Jenniffer", "Abidrabo Phillip", "Okao-Okuj...
creative-commons
Expanded Asgard archaea shed new light on the origin of eukaryotes and support a 2- 1 domain tree of life 2 3 Ruize Xie1,#, Yinzhao Wang2,#, Danyue Huang1, Jialin Hou2, Liuyang Li2, Haining Hu2, 4 Xiaoxiao Zhao2, Fengping Wang1,2,3* 5 6 1School of Oceanography, Shanghai Jiao Tong University, 1954 Huashan R...
2021
Expanded Asgard archaea shed new light on the origin of eukaryotes and support a 2-domain tree of life
10.1101/2021.02.04.429862
[ "Xie Ruize", "Wang Yinzhao", "Huang Danyue", "Hou Jialin", "Li Liuyang", "Hu Haining", "Zhao Xiaoxiao", "Wang Fengping" ]
creative-commons
Pirayre et al. RESEARCH Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducing Trichoderma reesei strain Rut-C30 Aur´elie Pirayre1*, Laurent Duval2,1, Corinne Blugeon3, Cyril Firmo3, Sandrine Perrin3, Etienne Jourdier1, Antoine Margeot1 and Fr´ed´erique Bidar...
2020
Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducing strain Rut-C30
10.1101/2020.10.02.324319
[ "Pirayre Aurélie", "Duval Laurent", "Blugeon Corinne", "Firmo Cyril", "Perrin Sandrine", "Jourdier Etienne", "Margeot Antoine", "Bidard Frédérique" ]
creative-commons
Stoll et al. RESEARCH UPMaBoSS: a novel framework for dynamic cell population modeling Gautier Stoll1,2*, Aur´elien Naldi3, Vincent No¨el4, Eric Viara5, Emmanuel Barillot4, Guido Kroemer1,2, Denis Thie↵ry3 and Laurence Calzone4 Abstract One of the aims of mathematical modeling is to understand and simulate the e↵ects o...
2020
UPMaBoSS: a novel framework for dynamic cell population modeling
10.1101/2020.05.31.126094
[ "Stoll Gautier", "Naldi Aurélien", "Noël Vincent", "Viara Eric", "Barillot Emmanuel", "Kroemer Guido", "Thieffry Denis", "Calzone Laurence" ]
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1 Pseudomonas two-partner secretion toxin Exolysin contributes to insect 1 killing 2 3 Viviana Job1, Stéphanie Bouillot1, Erwan Gueguen2, Mylène Robert-Genthon1, Peter Panchev1, Sylvie 4 Elsen1 and Ina Attrée1* 5 6 1Université Grenoble Alpes, Bacterial Pathogenesis and Cellular Responses team, CNRS ERL...
2019
two-partner secretion toxin Exolysin contributes to insect killing
10.1101/807867
[ "Job Viviana", "Bouillot Stéphanie", "Gueguen Erwan", "Robert-Genthon Mylène", "Panchev Peter", "Elsen Sylvie", "Attrée Ina" ]
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1 Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for 1 more efficient SNP identification 2 Zenaida V. Magbanua1*, Chuan-Yu Hsu1, Olga Pechanova1, Mark Arick II1, Corrinne E. Grover2, Daniel G. 3 Peterson1 4 1 Institute for Genomics, Biocomputing and Biotechnology,...
2022
Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for more efficient SNP identification
10.1101/2022.09.06.506835
[ "Magbanua Zenaida V.", "Hsu Chuan-Yu", "Pechanova Olga", "Arick Mark", "Grover Corrinne E.", "Peterson Daniel G." ]
creative-commons
1 Title: Tracking niche change through time: simultaneous inference of ecological 1 niche evolution and estimation of contemporary niches 2 3 Abstract: 4 1. The ecological niche of species is often studied from two different perspectives. 5 Environmental niche modelling (ENM) infers a species’ current nic...
2021
Tracking niche change through time: simultaneous inference of ecological niche evolution and estimation of contemporary niches
10.1101/2019.12.29.890608
[ "Hua Xia", "Cardillo Marcel", "Bromham Lindell" ]
null
stainlib: a python library for augmentation and normalization of histopathology H&E images. Sebastian Ot´aloraa,e, Niccol´o Marinia,e, Damian Podareanub, Ruben Heksterb, David Tellezc, Jeroen Van Der Laakc, Henning M¨ullera, Manfredo Atzoria,d aInformation Systems Institute, University of Applied Sciences Western Switz...
2022
stainlib: a python library for augmentation and normalization of histopathology H&E images
10.1101/2022.05.17.492245
[ "Otálora Sebastian", "Marini Niccoló", "Podareanu Damian", "Hekster Ruben", "Tellez David", "Van Der Laak Jeroen", "Müller Henning", "Atzori Manfredo" ]
creative-commons
1 Cryptic genetic variations of alanine:glyoxylate aminotransferase shape its fitness and dynamics Mirco Dindo1, Stefano Pascarelli1, Davide Chiasserini2, Silvia Grottelli2, Claudio Costantini2, Gen-Ichiro Uechi1, Giorgio Giardina3*, Paola Laurino1*, Barbara Cellini2* 1Protein Engineering and Evolution Uni...
2021
Cryptic genetic variations of alanine:glyoxylate aminotransferase shape its fitness and dynamics
10.1101/2021.05.24.445519
[ "Dindo Mirco", "Pascarelli Stefano", "Chiasserini Davide", "Grottelli Silvia", "Costantini Claudio", "Uechi Gen-Ichiro", "Giardina Giorgio", "Laurino Paola", "Cellini Barbara" ]
creative-commons
Haplotype Reconstruction in Connected Tetraploid F1 1 Populations 2 Chaozhi Zheng∗, Rodrigo R. Amadeu, Patricio R. Munoz, Jeffrey B. Endelman 3 December 9, 2020 4 Running head: Haplotype Reconstruction in Tetraploids 5 Key words: multiparental population, hidden Markov model, tetraploid potato, double reduc- 6 tion, QT...
2020
Haplotype Reconstruction in Connected Tetraploid F1 Populations
10.1101/2020.12.18.423519
[ "Zheng Chaozhi", "Amadeu Rodrigo R.", "Munoz Patricio R.", "Endelman Jeffrey B." ]
creative-commons
Control over patch encounters changes foraging behaviour Sam Hall-McMaster1,2,*, Peter Dayan3,4, Nicolas W. Schuck1,2 1Max Planck Institute for Human Development, Berlin, Germany 2Max Planck UCL Centre for Computational Psychiatry and Ageing Research, Berlin, Germany and London, United Kingdom 3Max ...
2021
Control over patch encounters changes foraging behaviour
10.1101/2021.01.19.426950
[ "Hall-McMaster Sam", "Dayan Peter", "Schuck Nicolas W." ]
creative-commons
Optical interrogation of sympathetic neuronal effects on macroscopic cardiac monolayer dynamics Burton R.A.B1*., Tomek, J2*., Ambrosi, C.M3., Larsen H.E2., Sharkey, A.R2., Capel, R.A1., Bilton, S2., Klimas, A3., Stephens, G2., Li, D2., Gallone, G2., Herring, N2., Mann, E2., Kumar, A4., Kramer H2., Entcheva E3., Pat...
2019
Optical interrogation of sympathetic neuronal effects on macroscopic cardiac monolayer dynamics
10.1101/717991
[ "Burton R.A.B.", "Tomek J.", "Ambrosi C.M.", "Larsen H.E.", "Sharkey A.R.", "Capel R.A.", "Bilton S.", "Klimas A.", "Stephens G.", "Li D.", "Gallone G.", "Herring N.", "Mann E.", "Kumar A.", "Kramer H.", "Entcheva E.", "Paterson D.J.", "Bub G." ]
creative-commons
1 The coordination of terminal differentiation and cell cycle exit is mediated through the regulation of chromatin accessibility Yiqin Ma 1, Daniel J. McKay 2 and Laura Buttitta 1* 1. University of Michigan, Dept. of Molecular Cellular and Developmental Biology, Ann Arbor, MI 2. University of North Carolina, ...
2018
The coordination of terminal differentiation and cell cycle exit is mediated through the regulation of chromatin accessibility
10.1101/488387
[ "Ma Yiqin", "McKay Daniel J.", "Buttitta Laura" ]
creative-commons
1 Myogenetic oligodeoxynucleotide (myoDN) recovers the differentiation of 1 skeletal muscle myoblasts deteriorated by diabetes mellitus 2 3 Shunichi Nakamura1, Shinichi Yonekura2,3, Takeshi Shimosato1,2,3, 4 Tomohide Takaya1,2,3* 5 6 1Department of Agriculture, Graduate School of Science and Technol...
2021
Myogenetic oligodeoxynucleotide (myoDN) recovers the differentiation of skeletal muscle myoblasts deteriorated by diabetes mellitus
10.1101/2021.03.10.434717
[ "Nakamura Shunichi", "Yonekura Shinichi", "Shimosato Takeshi", "Takaya Tomohide" ]
creative-commons
A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys Jiao Qu1,#, Fa Yang1,#, Tao Zhu1,#, Yingshuo Wang2,#, Wen Fang1, Yan Ding1, Xue Zhao1, Xianjia Qi3, Qiangmin Xie2, Qiang Xu1, Yicheng Xie2,*, Yang Sun1,4,* and Dijun Chen1,* 1State Key Laboratory of Pharmaceutical Biotechnology, Schoo...
2022
A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys
10.1101/2022.01.22.477221
[ "Qu Jiao", "Yang Fa", "Zhu Tao", "Wang Yingshuo", "Fang Wen", "Ding Yan", "Zhao Xue", "Qi Xianjia", "Xie Qiangmin", "Xu Qiang", "Xie Yicheng", "Sun Yang", "Chen Dijun" ]
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1 Pro-IL-18 secreted by keratinocytes detects the group A 1 streptococcal protease SpeB 2 3 4 Anders F. Johnson1*, Jenna S. Sands1*, Keya Trivedi1, Raedeen Russell1, Doris L. LaRock1, Christopher N. 5 LaRock1# 6 7 1Department of Microbiology and Immunology and Department of Medicine, Emory School o...
2021
Pro-IL-18 secreted by keratinocytes detects the group A streptococcal protease SpeB
10.1101/2021.08.22.457234
[ "Johnson Anders F.", "Sands Jenna S.", "Trivedi Keya", "Russell Raedeen", "LaRock Doris L.", "LaRock Christopher N." ]
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1 1 Structural basis for activation of DNMT1 2 3 Amika Kikuchi1†, Hiroki Onoda1†, Kosuke Yamaguchi2, Satomi Kori1, Shun Matsuzawa1, Yoshie 4 Chiba3, Shota Tanimoto3, Sae Yoshimi1, Hiroki Sato1, Atsushi Yamagata4, Mikako Shirouzu4, 5 Naruhiko Adachi5, Jafar Sharif6, Haruhiko Koseki6, Atsuya Nishiyama3, Ma...
2022
Structural basis for activation of DNMT1
10.1101/2022.06.16.496385
[ "Kikuchi Amika", "Onoda Hiroki", "Yamaguchi Kosuke", "Kori Satomi", "Matsuzawa Shun", "Chiba Yoshie", "Tanimoto Shota", "Yoshimi Sae", "Sato Hiroki", "Yamagata Atsushi", "Shirouzu Mikako", "Adachi Naruhiko", "Sharif Jafar", "Koseki Haruhiko", "Nishiyama Atsuya", "Nakanishi Makoto", "...
creative-commons
Title: Complete genomes of clade G6 Saccharibacteria suggest a divergent ecological 1 niche and lifestyle 2 3 Author: Jonathon L. Baker1,* 4 1 Genomic Medicine Group 5 J. Craig Venter Institute 6 4120 Capricorn Lane 7 La Jolla, CA 92037 8 9 *Corresponding Author: JLB: jobaker@jcvi.org 10 11 ...
2021
Complete genomes of clade G6 Saccharibacteria suggest a divergent ecological niche and lifestyle
10.1101/2021.05.28.446221
null
creative-commons
Modeling the Opening SARS-CoV-2 Spike: an Investigation of its Dynamic Electro-Geometric Properties Anna Kucherovaa, Selma Strangoa, Shahar Sukenikb, Maxime Theillarda aDepartment of Applied Mathematics, University of California, Merced, California 95343, USA. bDepartment of Chemistry and Chemical Biology, University o...
2020
Modeling the Opening SARS-CoV-2 Spike: an Investigation of its Dynamic Electro-Geometric Properties
10.1101/2020.10.29.361261
[ "Kucherova Anna", "Strango Selma", "Sukenik Shahar", "Theillard Maxime" ]
creative-commons
1 A population-level statistic for assessing Mendelian behavior 1 of genotyping-by-sequencing data from highly duplicated 2 genomes 3 4 Lindsay V. Clark1*, Wittney Mays23, Alexander E. Lipka2, and Erik J. Sacks2 5 1Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL ...
2021
A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes
10.1101/2020.01.11.902890
[ "Clark Lindsay V.", "Mays Wittney", "Lipka Alexander E.", "Sacks Erik J." ]
creative-commons
Carbohydrate-Binding Protein from Stinging Nettle as Fusion Inhibitor for SARS-CoV-2 Variants of Concern Emiel Vanhulle1, Thomas D’huys1, Becky Provinciael1, Joren Stroobants1, Anita Camps1, Sam 1 Noppen1, Dominique Schols1, Els J.M. Van Damme2, Piet Maes3, Annelies Stevaert1 and Kurt 2 Vermeire1,* 3 1Labor...
2022
Carbohydrate-Binding Protein from Stinging Nettle as Fusion Inhibitor for SARS-CoV-2 Variants of Concern
10.1101/2022.07.08.499297
[ "Vanhulle Emiel", "D’huys Thomas", "Provinciael Becky", "Stroobants Joren", "Camps Anita", "Noppen Sam", "Schols Dominique", "Van Damme Els J.M.", "Maes Piet", "Stevaert Annelies", "Vermeire Kurt" ]
creative-commons
1 Path integration in large-scale space and with novel geometries: Comparing 1 Vector Addition and Encoding-Error Models 2 3 S. K. Harootonian1,2, R. C. Wilson2, L. Hejtmánek1,3, E. M. Ziskin1,2, A. D. Ekstrom1,2 4 5 1Center for Neuroscience, University of California Davis, Davis, CA 6 2Psychology De...
2019
Path integration in large-scale space and with novel geometries: Comparing Vector Addition and Encoding-Error Models
10.1101/809012
[ "Harootonian S. K.", "Wilson R. C.", "Hejtmánek L.", "Ziskin E. M.", "Ekstrom A. D." ]
creative-commons
1 Axonal Na+ channels detect and transmit levels of input synchrony in local brain circuits Mickaël Zbili1,3, Sylvain Rama1,3, Pierre Yger2, Yanis Inglebert1, Norah Boumedine-Guignon1, Laure Fronzaroli-Moliniere1, Romain Brette2, Michaël Russier1 & Dominique Debanne1 1 UNIS, INSE...
2019
Axonal Na channels detect and transmit levels of input synchrony in local brain circuits
10.1101/618710
[ "Zbili Mickaёl", "Rama Sylvain", "Yger Pierre", "Inglebert Yanis", "Boumedine-Guignon Norah", "Fronzaroli-Moliniere Laure", "Brette Romain", "Russier Michaёl", "Debanne Dominique" ]
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1 Highly social pinyon jays, but not less social Clark’s nutcrackers, modify 1 their food-storing behaviour when observed by a heterospecific. 2 Alizée Vernouillet1, Dawson Clary2 & Debbie M. Kelly1,2 3 1. Department of Biological Sciences, University of Manitoba 4 2. Department of Psychology, University of ...
2021
Highly social pinyon jays, but not less social Clark’s nutcrackers, modify their food-storing behaviour when observed by a heterospecific
10.1101/2021.02.28.433225
[ "Vernouillet Alizée", "Clary Dawson", "Kelly Debbie M." ]
creative-commons
Title: Of Rats and Men, a Translational Model to Understand Vancomycin 1 Pharmacokinetic/Toxicodynamic relationships. 2 3 Running Title: Translating Rat to Man in VIKI 4 5 Authors: Marc H. SCHEETZ1-3*, Gwendolyn PAIS1-2, Thomas P. LODISE4, Steven Y.C. TONG5-7, 6 Joshua S. DAVIS5, MBBS, PhD; J. Nicholas O...
2021
Of Rats and Men, a Translational Model to Understand Vancomycin Pharmacokinetic/Toxicodynamic relationships
10.1101/2021.04.22.437975
[ "Scheetz Marc H.", "Pais Gwendolyn", "Lodise Thomas P.", "Tong Steven Y.C.", "Davis Joshua S.", "O’Donnell J. Nicholas", "Liu Jiajun", "Neely Michael", "Prozialeck Walter C.", "Lamar Peter C.", "Rhodes N.Jim", "Holland Thomas", "Avedissian Sean N." ]
creative-commons
1 Main Manuscript for Work horse strain Clostridioides difficile 630Δerm is oblivious to its anaerobic lifestyle Daniel Troitzscha, Hao Zhangb, Silvia Dittmanna, Dorothee Düsterhöfta,c, Annika- Marisa Michelb, Lothar Jänschd, Katharina Riedela, José Manuel Borrero-de Acuñab,e, Dieter Jahnb,e, Susanne Sievers...
2020
Work horse strain 630Δ is oblivious to its anaerobic lifestyle
10.1101/2020.01.07.897181
[ "Troitzsch Daniel", "Zhang Hao", "Dittmann Silvia", "Düsterhöft Dorothee", "Michel Annika-Marisa", "Jänsch Lothar", "Riedel Katharina", "Borrero-de Acuña José Manuel", "Jahn Dieter", "Sievers Susanne" ]
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A novel computational method to design BH3-mimetic peptide inhibitors that can bind specifically to Mcl-1 or Bcl-XL C. Narendra Reddy1, Nishat Manzar1, Bushra Ateeq1,2 and Ramasubbu Sankararamakrishnan1,2,* 1Department of Biological Sciences and Bioengineering, 2Mehta Family Center for Enginee...
2020
A novel computational method to design BH3-mimetic peptide inhibitors that can bind specifically to Mcl-1 or Bcl-X
10.1101/2020.07.09.194662
[ "Reddy C. Narendra", "Manzar Nishat", "Ateeq Bushra", "Sankararamakrishnan Ramasubbu" ]
creative-commons
PERFECTO: Prediction of Extended Response and Growth Functions for Estimating Chemotherapy Outcomes in Breast Cancer Daria Kurz Interdisciplinary Breast Center Helios Klinikum Munich West Munich, Germany daria.kurz@helios-gesundheit.de Cristian Axenie Audi Konfuzius-Institut Ingolstadt Lab Technische Hochschule Ingolst...
2020
PERFECTO: Prediction of Extended Response and Growth Functions for Estimating Chemotherapy Outcomes in Breast Cancer
10.1101/2020.12.29.424759
[ "Kurz Daria", "Axenie Cristian" ]
creative-commons
Investigation of Capsule-Inspired Neural Network Approaches for DNA Methylation Joshua J. Levy*,1,2,3, Youdinghuan Chen1,2, Nasim Azizgolshani2, Curtis L. Peterson2,4, Alexander J. Titus5, Erika L. Moen4,6, Louis J. Vaickus3, Lucas A. Salas2,7, Brock C. Christensen2,7,8 Author Affiliations: 1. Program in Qua...
2020
Investigation of Capsule-Inspired Neural Network Approaches for DNA Methylation
10.1101/2020.08.14.251306
[ "Levy Joshua J.", "Chen Youdinghuan", "Azizgolshani Nasim", "Peterson Curtis L.", "Titus Alexander J.", "Moen Erika L.", "Vaickus Louis J.", "Salas Lucas A.", "Christensen Brock C." ]
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