PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation

by Medhat Mahmoud, Harshavardhan Doddapaneni, Winston Timp, Fritz J. Sedlazeck
Published 2021-09-01

A multi-task convolutional deep neural network for variant calling in single molecule sequencing

by Ruibang Luo, Fritz J. Sedlazeck, Tak-Wah Lam, Michael C. Schatz
Published 2019-03-01

LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning

by Ruibang Luo, Fritz J. Sedlazeck, Charlotte A. Darby, Stephen M. Kelly, Michael C. Schatz
Published 2017-01-01

Structural variant calling: the long and the short of it

by Medhat Mahmoud, Nastassia Gobet, Diana Ivette Cruz-Dávalos, Ninon Mounier, Christophe Dessimoz, Fritz J. Sedlazeck
Published 2019-11-01

Tools for annotation and comparison of structural variation [version 1; referees: 1 approved, 2 approved with reservations]

by Fritz J. Sedlazeck, Andi Dhroso, Dale L. Bodian, Justin Paschall, Farrah Hermes, Justin M. Zook
Published 2017-10-01

Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis.

by Huy Q Dinh, Manu Dubin, Fritz J Sedlazeck, Nicole Lettner, Ortrun Mittelsten Scheid, Arndt von Haeseler
Published 2012-01-01

RaGOO: fast and accurate reference-guided scaffolding of draft genomes

by Michael Alonge, Sebastian Soyk, Srividya Ramakrishnan, Xingang Wang, Sara Goodwin, Fritz J. Sedlazeck, Zachary B. Lippman, Michael C. Schatz
Published 2019-10-01

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

by Daniel C. Jeffares, Clemency Jolly, Mimoza Hoti, Doug Speed, Liam Shaw, Charalampos Rallis, Francois Balloux, Christophe Dessimoz, Jürg Bähler, Fritz J. Sedlazeck
Published 2017-01-01

The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways.

by Michael Tscherner, Florian Zwolanek, Sabrina Jenull, Fritz J Sedlazeck, Andriy Petryshyn, Ingrid E Frohner, John Mavrianos, Neeraj Chauhan, Arndt von Haeseler, Karl Kuchler
Published 2015-10-01

Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase

by Sven Schenk, Stephanie C Bannister, Fritz J Sedlazeck, Dorothea Anrather, Bui Quang Minh, Andrea Bileck, Markus Hartl, Arndt von Haeseler, Christopher Gerner, Florian Raible, Kristin Tessmar-Raible
Published 2019-02-01

Paragraph: a graph-based structural variant genotyper for short-read sequence data

by Sai Chen, Peter Krusche, Egor Dolzhenko, Rachel M. Sherman, Roman Petrovski, Felix Schlesinger, Melanie Kirsche, David R. Bentley, Michael C. Schatz, Fritz J. Sedlazeck, Michael A. Eberle
Published 2019-12-01

Discovery and population genomics of structural variation in a songbird genus

by Matthias H. Weissensteiner, Ignas Bunikis, Ana Catalán, Kees-Jan Francoijs, Ulrich Knief, Wieland Heim, Valentina Peona, Saurabh D. Pophaly, Fritz J. Sedlazeck, Alexander Suh, Vera M. Warmuth, Jochen B. W. Wolf
Published 2020-07-01

Author Correction: Discovery and population genomics of structural variation in a songbird genus

by Matthias H. Weissensteiner, Ignas Bunikis, Ana Catalán, Kees-Jan Francoijs, Ulrich Knief, Wieland Heim, Valentina Peona, Saurabh D. Pophaly, Fritz J. Sedlazeck, Alexander Suh, Vera M. Warmuth, Jochen B. W. Wolf
Published 2021-05-01

A diploid assembly-based benchmark for variants in the major histocompatibility complex

by Chen-Shan Chin, Justin Wagner, Qiandong Zeng, Erik Garrison, Shilpa Garg, Arkarachai Fungtammasan, Mikko Rautiainen, Sergey Aganezov, Melanie Kirsche, Samantha Zarate, Michael C. Schatz, Chunlin Xiao, William J. Rowell, Charles Markello, Jesse Farek, Fritz J. Sedlazeck, Vikas Bansal, Byunggil Yoo, Neil Miller, Xin Zhou, Andrew Carroll, Alvaro Martinez Barrio, Marc Salit, Tobias Marschall, Alexander T. Dilthey, Justin M. Zook
Published 2020-09-01

A strategy for building and using a human reference pangenome [version 2; peer review: 2 approved]

by 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
Published 2021-07-01

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.

by Shubha Vij, Heiner Kuhl, Inna S Kuznetsova, Aleksey Komissarov, Andrey A Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha M Thevasagayam, Sai Rama Sridatta Prakki, Kathiresan Purushothaman, Jolly M Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Hin Yan Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S Hon, James P Drake, Matthew Boitano, Richard Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J Sedlazeck, Gregory W Vurture, Gopikrishna Gopalapillai, Vinaya Kumar Katneni, Tansyn H Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R Jerry, Stephen J O'Brien, Michael C Schatz, Tamás Dalmay, Stephen W Turner, Si Lok, Alan Christoffels, László Orbán
Published 2016-04-01

Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.

by Shubha Vij, Heiner Kuhl, Inna S Kuznetsova, Aleksey Komissarov, Andrey A Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha M Thevasagayam, Sai Rama Sridatta Prakki, Kathiresan Purushothaman, Jolly M Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Hin Yan Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S Hon, James P Drake, Matthew Boitano, Richard Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J Sedlazeck, Gregory W Vurture, Gopikrishna Gopalapillai, Vinaya Kumar Katneni, Tansyn H Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R Jerry, Stephen J O'Brien, Michael C Schatz, Tamás Dalmay, Stephen W Turner, Si Lok, Alan Christoffels, László Orbán
Published 2016-12-01

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 approv...

by 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
Published 2021-09-01

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

by Daniel Butler, Christopher Mozsary, Cem Meydan, Jonathan Foox, Joel Rosiene, Alon Shaiber, David Danko, Ebrahim Afshinnekoo, Matthew MacKay, Fritz J. Sedlazeck, Nikolay A. Ivanov, Maria Sierra, Diana Pohle, Michael Zietz, Undina Gisladottir, Vijendra Ramlall, Evan T. Sholle, Edward J. Schenck, Craig D. Westover, Ciaran Hassan, Krista Ryon, Benjamin Young, Chandrima Bhattacharya, Dianna L. Ng, Andrea C. Granados, Yale A. Santos, Venice Servellita, Scot Federman, Phyllis Ruggiero, Arkarachai Fungtammasan, Chen-Shan Chin, Nathaniel M. Pearson, Bradley W. Langhorst, Nathan A. Tanner, Youngmi Kim, Jason W. Reeves, Tyler D. Hether, Sarah E. Warren, Michael Bailey, Justyna Gawrys, Dmitry Meleshko, Dong Xu, Mara Couto-Rodriguez, Dorottya Nagy-Szakal, Joseph Barrows, Heather Wells, Niamh B. O’Hara, Jeffrey A. Rosenfeld, Ying Chen, Peter A. D. Steel, Amos J. Shemesh, Jenny Xiang, Jean Thierry-Mieg, Danielle Thierry-Mieg, Angelika Iftner, Daniela Bezdan, Elizabeth Sanchez, Thomas R. Campion, John Sipley, Lin Cong, Arryn Craney, Priya Velu, Ari M. Melnick, Sagi Shapira, Iman Hajirasouliha, Alain Borczuk, Thomas Iftner, Mirella Salvatore, Massimo Loda, Lars F. Westblade, Melissa Cushing, Shixiu Wu, Shawn Levy, Charles Chiu, Robert E. Schwartz, Nicholas Tatonetti, Hanna Rennert, Marcin Imielinski, Christopher E. Mason
Published 2021-03-01