Max Planck Society

Max Planck Society

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https://doi.org/10.12688/f1000research.134798.2
Software Tool Article metrics
Revised
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT
[version 2; peer review: 1 approved, 3 approved with reservations]
Maxime Borry, Adrian Forsythe, Aida Andrades Valtueña, Alexander Hübner, Anan Ibrahim, Andrea Quagliariello, Anna E. White, Arthur Kocher, Åshild J. Vågene‬, Bjørn Peare Bartholdy, Diāna Spurīte, Gabriel Yaxal Ponce-Soto, Gunnar Neumann, I-Ting Huang, Ian Light, Irina M. Velsko, Iseult Jackson, Jasmin Frangenberg, Javier G. Serrano, Julien Fumey, Kadir T. Özdoğan, Kelly E. Blevins, Kevin G. Daly, Maria Lopopolo, Markella Moraitou, Megan Michel, Meriam van Os, Miriam J. Bravo-Lopez, Mohamed S. Sarhan, Nihan D. Dagtas, Nikolay Oskolkov, Olivia S. Smith, Ophélie Lebrasseur, Piotr Rozwalak, Raphael Eisenhofer, Sally Wasef, Shreya L. Ramachandran, Valentina Vanghi, Christina Warinner, James A. Fellows Yates
Peer Reviewers Timothy Read and Robert Petit III; Jonas Coelho Kasmanas; Intikhab Alam; Emma Griffiths
  • Funders
  • Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
  • Carlsbergfondet
  • H2020 European Research Council
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek
  • Knut och Alice Wallenbergs Stiftelse
  • National Institutes of Health
  • Carl Tryggers Stiftelse för Vetenskaplig Forskning
  • Deutsche Forschungsgemeinschaft
  • Friedrich-Schiller-Universität Jena
  • Science for Life Laboratory National Sequencing Projects
  • Werner Siemens-Stiftung
  • Max-Planck-Gesellschaft
  • National Science Foundation
  • Leverhulme Trust
  • Svenska Forskningsrådet Formas
  • Science Foundation Ireland-Irish Research Council
  • Science Foundation Ireland Centre for Research Training in Genomics Data Science
  • Università degli Studi di Padova
  • Institut Pasteur
  • H2020 Marie Skłodowska-Curie Actions
LATEST VERSION PUBLISHED 28 May 2024
https://doi.org/10.12688/f1000research.130443.1
Research Article metrics
Assessing structure and disorder prediction tools for de novo emerged proteins in the age of machine learning
[version 1; peer review: 2 approved]
Margaux Aubel, Lars Eicholt, Erich Bornberg-Bauer
Peer Reviewers Caroline Weisman; Isabelle Callebaut
  • Funder
  • Volkswagen Foundation
PUBLISHED 29 Mar 2023
https://doi.org/10.12688/f1000research.126740.1
Research Article metrics
Multidisciplinary digital methodologies for documentation and preservation of immovable Archaeological heritage in the Khovd River Valley, Western Mongolia
[version 1; peer review: 1 approved, 2 approved with reservations]
Michael T. Fisher, Dovydas Jurkenas, Amina Jambajantsan, Bayarsaikhan Jamsranjav, Eredene-Ochir Nasan-Ochir, Eregzen Gelegdorj, Munkhbayar Chuluunbat, Michael Petraglia, Nicole Boivin
Peer Reviewers Georgia Andreou; Cinzia Bettineschi; Fanar Mansour Abed
  • Funder
  • Arcadia, a Charitable Fund of Lisbet Rausing and Peter Baldwin
PUBLISHED 03 Nov 2022
https://doi.org/10.12688/f1000research.110194.1
Software Tool Article metrics
The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms
[version 1; peer review: 1 approved, 3 approved with reservations]
Kimberly Walker, Divya Kalra, Rebecca Lowdon, Guangyi Chen, David Molik, Daniela C. Soto, Fawaz Dabbaghie, Ahmad Al Khleifat, Medhat Mahmoud, Luis F Paulin, Muhammad Sohail Raza, Susanne P. Pfeifer, Daniel Paiva Agustinho, Elbay Aliyev, Pavel Avdeyev, Enrico R. Barrozo, Sairam Behera, Kimberley Billingsley, Li Chuin Chong, Deepak Choubey, Wouter De Coster, Yilei Fu, Alejandro R. Gener, Timothy Hefferon, David Morgan Henke, Wolfram Höps, Anastasia Illarionova, Michael D. Jochum, Maria Jose, Rupesh K. Kesharwani, Sree Rohit Raj Kolora, Jędrzej Kubica, Priya Lakra, Damaris Lattimer, Chia-Sin Liew, Bai-Wei Lo, Chunhsuan Lo, Anneri Lötter, Sina Majidian, Suresh Kumar Mendem, Rajarshi Mondal, Hiroko Ohmiya, Nasrin Parvin, Carolina Peralta, Chi-Lam Poon, Ramanandan Prabhakaran, Marie Saitou, Aditi Sammi, Philippe Sanio, Nicolae Sapoval, Najeeb Syed, Todd Treangen, Gaojianyong Wang, Tiancheng Xu, Jianzhi Yang, Shangzhe Zhang, Weiyu Zhou, Fritz J Sedlazeck, Ben Busby
Peer Reviewers Rodolfo Aramayo; Nguyen Quoc Khanh Le; Pedro G. Ferreira; Quan Long
  • Funders
  • National Library of Medicine
  • Swiss National Science Foundation
  • USDA Agricultural Research Service HQ Research Associate program in Big Data
  • Centers for Disease Control and Prevention through the Association of Public Health Laboratories
  • ALS Association Milton Safenowitz Research
  • The Research Council of Norway
  • Large Facilities Office
  • China Scholarship Council PhD scholarship
  • NIHR Maudsley Biomedical Research Centre
  • The Motor Neurone Disease Association
  • FWO
PUBLISHED 16 May 2022
https://doi.org/10.12688/f1000research.54864.2
Research Article metrics
Revised
The need to reassess single-cell RNA sequencing datasets: the importance of biological sample processing
[version 2; peer review: 2 approved]
Alex M. Ascensión, Marcos J. Araúzo-Bravo, Ander Izeta
Peer Reviewers Xiao Long and Zhujun Li; (Jo) Huiqing Zhou
  • Funders
  • Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza
  • Instituto de Salud Carlos III
  • Horizon 2020
  • European Regional Development Fund
LATEST VERSION PUBLISHED 08 Mar 2022
https://doi.org/10.12688/f1000research.51477.2
Software Tool Article metrics
Revised
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
[version 2; peer review: 1 approved, 3 approved with reservations]
Ann M. Mc Cartney, Medhat Mahmoud, Michael Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K Kesharwani, Moritz Smolka, Moez Dawood, Dreycey Albin, Elbay Aliyev, Hakeem Almabrazi, Ahmed Arslan, Advait Balaji, Sairam Behera, Kimberley Billingsley, Daniel L Cameron, Joyjit Daw, Eric T. Dawson, Wouter De Coster, Haowei Du, Christopher Dunn, Rocio Esteban, Angad Jolly, Divya Kalra, Chunxiao Liao, Yunxi Liu, Tsung-Yu Lu, James M Havrilla, Michael M Khayat, Maximillian Marin, Jean Monlong, Stephen Price, Alejandro Rafael Gener, Jingwen Ren, Sagayamary Sagayaradj, Nicolae Sapoval, Claude Sinner, Daniela C. Soto, Arda Soylev, Arun Subramaniyan, Najeeb Syed, Neha Tadimeti, Pamella Tater, Pankaj Vats, Justin Vaughn, Kimberly Walker, Gaojianyong Wang, Qiandong Zeng, Shangzhe Zhang, Tingting Zhao, Bryce Kille, Evan Biederstedt, Mark Chaisson, Adam English, Zev Kronenberg, Todd J. Treangen, Timothy Hefferon, Chen-Shan Chin, Ben Busby, Fritz J Sedlazeck
Peer Reviewers Francois Sabot; Kamil S. Jaron; Ricardo Assunção Vialle; Loren L. Flynn
  • Funders
  • NIH/NICHD
  • C3.ai Digital Transformation Institute COVID-19 award
  • Intramural Research Program of the National Library of Medicine
  • NHMRC
  • Intramural Research Program of NHGRI
  • NIHR Maudsley Biomedical Research Centre
  • NIH
  • The Motor Neurone Disease Association
  • FWO
LATEST VERSION PUBLISHED 03 Sep 2021
https://doi.org/10.12688/f1000research.19630.2
Software Tool Article metrics
Revised
A strategy for building and using a human reference pangenome
[version 2; peer review: 2 approved]
Bastien Llamas, Giuseppe Narzisi, Valerie Schneider, Peter A. Audano, Evan Biederstedt, Lon Blauvelt, Peter Bradbury, Xian Chang, Chen-Shan Chin, Arkarachai Fungtammasan, Wayne E. Clarke, Alan Cleary, Jana Ebler, Jordan Eizenga, Jonas A. Sibbesen, Charles J. Markello, Erik Garrison, Shilpa Garg, Glenn Hickey, Gerard R. Lazo, Michael F. Lin, Medhat Mahmoud, Tobias Marschall, Ilia Minkin, Jean Monlong, Rajeeva L. Musunuri, Sagayamary Sagayaradj, Adam M. Novak, Mikko Rautiainen, Allison Regier, Fritz J. Sedlazeck, Jouni Siren, Yassine Souilmi, Justin Wagner, Travis Wrightsman, Toshiyuki T. Yokoyama, Qiandong Zeng, Justin M. Zook, Benedict Paten, Ben Busby
Peer Reviewers Anna Kuosmanen; Robert A. Beagrie
  • Funders
  • Simons Foundation
  • Carlsbergfondet
  • U.S. National Library of Medicine
  • W. M. Keck Foundation
  • National Institutes of Health
  • Australian Research Council
LATEST VERSION PUBLISHED 29 Jul 2021
https://doi.org/10.12688/f1000research.51164.1
Brief Report metrics
The feasibility of targeted test-trace-isolate for the control of SARS-CoV-2 variants
[version 1; peer review: 2 approved with reservations]
William Bradshaw, Jonathan Huggins, Alun Lloyd, Kevin Esvelt
Peer Reviewers Akira Endo; Tim C. D. Lucas
  • Funders
  • Drexel Endowment
  • Centers for Disease Control and Prevention
  • Open Philanthropy Project
  • Reid Hoffman Foundation
  • COVID-19 HPC consortium
PUBLISHED 16 Apr 2021
https://doi.org/10.12688/f1000research.28250.1
Research Article metrics
Limited containment options of COVID-19 outbreak revealed by regional agent-based simulations for South Africa
[version 1; peer review: 1 approved with reservations, 1 not approved]
Andreas Bossert, Moritz Kersting, Marc Timme, Malte Schröder, Azza Feki, Justin Coetzee, Jan Schlüter
Peer Reviewers Cliff C Kerr; Theresa Marié Rossouw
  • Funders
  • Center for Advancing Electronics Dresden
  • German National Science Foundation
PUBLISHED 11 Feb 2021
https://doi.org/10.12688/f1000research.23224.2
Opinion Article metrics
Revised
An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action
[version 2; peer review: 2 approved]
Hartwig Anzt, Felix Bach, Stephan Druskat, Frank Löffler, Axel Loewe, Bernhard Y. Renard, Gunnar Seemann, Alexander Struck, Elke Achhammer, Piush Aggarwal, Franziska Appel, Michael Bader, Lutz Brusch, Christian Busse, Gerasimos Chourdakis, Piotr Wojciech Dabrowski, Peter Ebert, Bernd Flemisch, Sven Friedl, Bernadette Fritzsch, Maximilian D. Funk, Volker Gast, Florian Goth, Jean-Noël Grad, Jan Hegewald, Sibylle Hermann, Florian Hohmann, Stephan Janosch, Dominik Kutra, Jan Linxweiler, Thilo Muth, Wolfgang Peters-Kottig, Fabian Rack, Fabian H.C. Raters, Stephan Rave, Guido Reina, Malte Reißig, Timo Ropinski, Joerg Schaarschmidt, Heidi Seibold, Jan P. Thiele, Benjamin Uekermann, Stefan Unger, Rudolf Weeber
Peer Reviewers Wilhelm Hasselbring; Radovan Bast
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Karlsruher Institut für Technologie
LATEST VERSION PUBLISHED 26 Jan 2021
https://doi.org/10.12688/f1000research.20244.2
Opinion Article metrics
Revised
The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
[version 2; peer review: 2 approved]
Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan, Andreas Tauch, Ulrike Trojahn, Björn Usadel, Oliver Kohlbacher
Peer Reviewers Roland Krause; Loredana Le Pera and Allegra Via
  • Funders
  • Bundesministerium für Bildung und Forschung
  • Ministerium für Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen
LATEST VERSION PUBLISHED 11 Sep 2020
https://doi.org/10.12688/f1000research.20408.1
Editorial metrics NOT PEER REVIEWED
Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers
[version 1; peer review: not peer reviewed]
Sayane Shome, R. Gonzalo Parra, Nazeefa Fatima, Alexander Miguel Monzon, Bart Cuypers, Yumna Moosa, Nilson Da Rocha Coimbra, Juliana Assis, Carla Giner-Delgado, Handan Melike Dönertaş, Yesid Cuesta-Astroz, Geetha Saarunya, Imane Allali, Shruti Gupta, Ambuj Srivastava, Manisha Kalsan, Catalina Valdivia, Gabriel J. Olguin-Orellana, Sofia Papadimitriou, Daniele Parisi, Nikolaj Pagh Kristensen, Leonor Rib, Marouen Ben Guebila, Eugen Bauer, Gaia Zaffaroni, Amel Bekkar, Efejiro Ashano, Lisanna Paladin, Marco Necci, Nicolás N. Moreyra, Martin Rydén, Jordan Villalobos-Solís, Nikolaos Papadopoulos, Candice Rafael, Tülay Karakulak, Yasin Kaya, Yvonne Gladbach, Sandeep Kumar Dhanda, Nikolina Šoštarić, Aishwarya Alex, Dan DeBlasio, Farzana Rahman
  • Funder
  • International Society for Computational Biology
PUBLISHED 02 Sep 2019
https://doi.org/10.12688/f1000research.16200.2
Research Article metrics
Revised
Predicting transcription factor binding using ensemble random forest models
[version 2; peer review: 2 approved]
Fatemeh Behjati Ardakani, Florian Schmidt, Marcel H. Schulz
Peer Reviewers Jan Grau; Gary D Stormo
  • Funder
  • Cluster of Excellence on Multimodal Computing and Interaction (DFG)
LATEST VERSION PUBLISHED 02 Sep 2019
https://doi.org/10.12688/f1000research.17739.1
Editorial metrics NOT PEER REVIEWED
Nurturing tomorrow’s leaders: The ISCB Student Council Symposia in 2018
[version 1; peer review: not peer reviewed]
Daniele Parisi, Gabriel J. Olguín-Orellana, Eli J. Draizen, Nilson Da Rocha Coimbra, Nikolaos Papadopoulos, Susanne Kirchen, Yvonne Saara Gladbach, Numrah Fadra, Nazeefa Fatima, Aishwarya Alex Namasivayam, Sayane Shome, Dan DeBlasio, Alexander M. Monzon, Farzana Rahman, R. Gonzalo Parra
  • Funder
  • International Society for Computational Biology
PUBLISHED 09 Jan 2019
https://doi.org/10.12688/f1000research.16905.1
Software Tool Article metrics
ProbeSpec: batch specificity testing and visualization of oligonucleotide probe sets implemented in ARB
[version 1; peer review: 2 approved with reservations]
Tim Kahlke, Paavo Jumppanen, Ralf Westram, Guy C.G. Abell, Levente Bodrossy
Peer Reviewers Michael Dondrup; Jizhong Zhou and Naijia Xiao
  • Funder
  • Commonwealth Scientific and Industrial Research Organisation
PUBLISHED 06 Dec 2018
https://doi.org/10.12688/f1000research.13588.1
Review metrics
Progress and challenges in TB vaccine development
[version 1; peer review: 2 approved]
Gerald Voss, Danilo Casimiro, Olivier Neyrolles, Ann Williams, Stefan H.E. Kaufmann, Helen McShane, Mark Hatherill, Helen A Fletcher
Peer Reviewers Rhea Coler; Ashley Birkett
  • Funder
  • Tuberculosis Vaccine Initiative
PUBLISHED 16 Feb 2018
https://doi.org/10.12688/f1000research.12342.2
Opinion Article metrics
Revised
The future of metabolomics in ELIXIR
[version 2; peer review: 3 approved]
Merlijn van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra Gonzalez-Beltran, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-Garcia, Rafael C. Jimenez, Fabien Jourdan, Namrata Kale, Maria I. Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Pablo Moreno, Nicholas K. Moschonas, Steffen Neumann, Claire O’Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M. Salek, Susanna-Assunta Sansone, Venkata Satagopam, Daniel Schober, Ruth Shimmo, Rachel A. Spicer, Ola Spjuth, Etienne A. Thévenot, Mark R. Viant, Ralf J. M. Weber, Egon L. Willighagen, Gianluigi Zanetti, Christoph Steinbeck
Peer Reviewers Charles F. Burant; Carl Brunius; Emmanuel Mikros
  • Funder
  • Horizon 2020 Framework Programme
LATEST VERSION PUBLISHED 30 Oct 2017
https://doi.org/10.12688/f1000research.12321.1
Editorial metrics NOT PEER REVIEWED
Second ISCB Latin American Student Council Symposium (LA-SCS) 2016
[version 1; peer review: not peer reviewed]
Alexander Miguel Monzon, Marcia A. Hasenahuer, Estefanía Mancini, Nilson Coimbra, Fiorella Cravero, Javier Cáceres-Molina, César A. Ramírez-Sarmiento, Nicolas Palopoli, Pieter Meysman, R. Gonzalo Parra
  • Funders
  • European Molecular Biology Organization
  • uBiome
  • Universidad Nacional de San Martin
  • Consejo Nacional de Investigaciones Científicas y Técnicas
  • Asociación Argentina de Bioinformática y Biología Computacional
PUBLISHED 16 Aug 2017
https://doi.org/10.12688/f1000research.11751.1
Opinion Article metrics
A community proposal to integrate proteomics activities in ELIXIR
[version 1; peer review: 2 approved]
Juan Antonio Vizcaíno, Mathias Walzer, Rafael C. Jiménez, Wout Bittremieux, David Bouyssié, Christine Carapito, Fernando Corrales, Myriam Ferro, Albert J.R. Heck, Peter Horvatovich, Martin Hubalek, Lydie Lane, Kris Laukens, Fredrik Levander, Frederique Lisacek, Petr Novak, Magnus Palmblad, Damiano Piovesan, Alfred Pühler, Veit Schwämmle, Dirk Valkenborg, Merlijn van Rijswijk, Jiri Vondrasek, Martin Eisenacher, Lennart Martens, Oliver Kohlbacher
Peer Reviewers Felix Elortza; Chuming Chen
  • Funder
  • Horizon 2020
PUBLISHED 13 Jun 2017
https://doi.org/10.12688/f1000research.10509.1
Research Article metrics
Inducible targeting of CNS astrocytes in Aldh1l1-CreERT2 BAC transgenic mice
[version 1; peer review: 3 approved]
Jan Winchenbach, Tim Düking, Stefan A. Berghoff, Sina K. Stumpf, Swen Hülsmann, Klaus-Armin Nave, Gesine Saher
Peer Reviewers David H. Rowitch; Andrea Volterra and Iaroslav Savtchouk; Jeffrey D. Rothstein and Sean Miller
  • Funders
  • Deutsche Forschungsgemeinschaft
  • European Research Council
  • Cluster of Excellence “Nanoscale Microscopy and Molecular Physiology of the Brain"
PUBLISHED 30 Dec 2016
1-20 of 28 ARTICLES
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