Preprint

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• Sex chromosome gene expression associated with vocal learning following hormonal manipulation in female zebra finches. Matthew H. Davenport, Ha Na Choe, Hiroaki Matsunami, Erich D. Jarvis. bioRxiv 2021.07.12.452102; doi: https://doi.org/10.1101/2021.07.12.452102

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• Enhancing cortico-motoneuronal projections for vocalization in mice J. Lomax Boyd, Louisa Kuper, Elena Waidmann, Victor Yang, Erich D. Jarvis. bioRxiv 2024.10.14.618267; doi: https://doi.org/10.1101/2024.10.14.618267

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• Complete sequencing of ape genomes. DongAhn Yoo, Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A. Logsdon, Steven J. Solar, Dmitry Antipov, Brandon D. Pickett, Yana Safonova, Francesco Montinaro, Yanting Luo, Joanna Malukiewicz, Jessica M. Storer, Jiadong Lin, Abigail N. Sequeira, Riley J. Mangan, Glenn Hickey, Graciela Monfort Anez, Parithi Balachandran, Anton Bankevich, Christine R. Beck, Arjun Biddanda, Matthew Borchers, Gerard G. Bouffard, Emry Brannan, Shelise Y. Brooks, Lucia Carbone, Laura Carrel, Agnes P. Chan, Juyun Crawford, Mark Diekhans, Eric Engelbrecht, Cedric Feschotte, Giulio Formenti, Gage H. Garcia, Luciana de Gennaro, David Gilbert, Richard E. Green, Andrea Guarracino, Ishaan Gupta, Diana Haddad, Junmin Han, Robert S. Harris, Gabrielle A. Hartley, William T. Harvey, Michael Hiller, Kendra Hoekzema, Marlys L. Houck, Hyeonsoo Jeong, Kaivan Kamali, Manolis Kellis, Bryce Kille, Chul Lee, Youngho Lee, William Lees, Alexandra P. Lewis, Qiuhui Li, Mark Loftus, Yong Hwee Eddie Loh, Hailey Loucks, Jian Ma, Yafei Mao, Juan F. I. Martinez, Patrick Masterson, Rajiv C. McCoy, Barbara McGrath, Sean McKinney, Britta S. Meyer, Karen H. Miga, Saswat K. Mohanty, Katherine M. Munson, Karol Pal, Matt Pennell, Pavel A. Pevzner, David Porubsky, Tamara Potapova, Francisca R. Ringeling, Joana L. Rocha, Oliver A. Ryder, Samuel Sacco, Swati Saha, Takayo Sasaki, Michael C. Schatz, Nicholas J. Schork, Cole Shanks, Linnéa Smeds, Dongmin R. Son, Cynthia Steiner, Alexander P. Sweeten, Michael G. Tassia, Françoise Thibaud-Nissen, Edmundo Torres-González, Mihir Trivedi, Wenjie Wei, Julie Wertz, Muyu Yang, Panpan Zhang, Shilong Zhang, Yang Zhang, Zhenmiao Zhang, Sarah A. Zhao, Yixin Zhu, Erich D. Jarvis, Jennifer L. Gerton, Iker Rivas-González, Benedict Paten, Zachary A. Szpiech, Christian D. Huber, Tobias L. Lenz, Miriam K. Konkel, Soojin V. Yi, Stefan Canzar, Corey T. Watson, Peter H. Sudmant, Erin Molloy, Erik Garrison, Craig B. Lowe, Mario Ventura, Rachel J. O’Neill, Sergey Koren, Kateryna D. Makova, Adam M. Phillippy, Evan E. Eichler. bioRxiv 2024.07.31.605654; doi: https://doi.org/10.1101/2024.07.31.605654

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• Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure. Jun Ishigohoka, Karen Bascón-Cardozo, Andrea Bours, Janina Fuß, Arang Rhie, Jacquelyn Mountcastle, Bettina Haase, William Chow, Joanna Collins, Kerstin Howe, Marcela Uliano-Silva, Olivier Fedrigo, Erich D. Jarvis, Javier Pérez-Tris, Juan Carlos Illera, Miriam Liedvogel. bioRxiv 2021.12.22.473882; doi: https://doi.org/10.1101/2021.12.22.473882

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• A Functional and Non-Homuncular Representation of the Larynx in the Primary Motor Cortex of Mice, a Vocal Non-Learner. César D. M. Vargas, Rajvi K. Agravat, Elena N. Waidmann, Christodoulos Bochalis, Hector Bermudez, Theodoros Giannakopoulos, Erich D. Jarvis. bioRxiv 2024.02.05.579004; doi: https://doi.org/10.1101/2024.02.05.579004

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• Mountable miniature microphones to identify and assign mouse ultrasonic vocalizations. Elena N. Waidmann, Victor H.Y. Yang, William C. Doyle, Erich D. Jarvis. bioRxiv 2024.02.05.579003; doi: https://doi.org/10.1101/2024.02.05.579003

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• A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): building genomic resources to study evolution in cave environments. Carlos Daniel Cadena, Laura Pabón, Carlos DoNascimiento, Linelle Abueg, Tatiana Tiley, Brian O-Toole, Dominic Absolon, Ying Sims, Giulio Formenti, Olivier Fedrigo, Erich D. Jarvis, Mauricio Torres. bioRxiv 2023.11.11.566715; doi: https://doi.org/10.1101/2023.11.11.566715

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• Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy. Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjorn Grüning, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D. Pickett, Keon Rabbani, Jennifer R. Balacco, Mark Chaisson, Haoyu Cheng, Joanna Collins, Alexandra Denisova, Olivier Fedrigo, Guido Roberto Gallo, Alice Maria Giani, Grenville MacDonald Gooder, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O’Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert M. Waterhouse, Adam M. Phillippy, Erich D. Jarvis, Michael C. Schatz, Anton Nekrutenko, Giulio Formenti. bioRxiv 2023.06.28.546576; doi: https://doi.org/10.1101/2023.06.28.546576

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• Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development. Anoushka Joglekar, Wen Hu, Bei Zhang, Oleksandr Narykov, Mark Diekhans, Jennifer Balacco, Lishomwa C Ndhlovu, Teresa A Milner, Olivier Fedrigo, Erich D Jarvis, Gloria Sheynkman, Dmitry Korkin, M. Elizabeth Ross, Hagen U. Tilgner. bioRxiv 2023.04.02.535281; doi: https://doi.org/10.1101/2023.04.02.535281

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• Genomic, genetic and phylogenetic evidence for a new falcon species using chromosome-level genome assembly of the gyrfalcon and population genomics. Farooq Omar Al-Ajli, Giulio Formenti, Olivier Fedrigo, Alan Tracey, Ying Sims, Kerstin Howe, Ikdam M. Al-Karkhi, Asmaa Ali Althani, Erich D. Jarvis, Sadequr Rahman, Qasim Ayub. bioRxiv 2023.02.12.525808; doi: https://doi.org/10.1101/2023.02.12.525808

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• A Chromosome-Level Genome Assembly for the Rock Ptarmigan (Lagopus muta). Theodore E. Squires, Patrik Rödin-Mörch, Giulio Formenti, Alan Tracey, Linelle Abueg, Nadolina Brajuka, Erich Jarvis, Eva C. Halapi, Páll Melsted, Jacob Höglund, Kristinn Pétur Magnússon. bioRxiv 2023.01.31.526508; doi: https://doi.org/10.1101/2023.01.31.526508

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• Species-wide genomics of kākāpō provides transformational tools to accelerate recovery. Joseph Guhlin, Marissa F. Le Lec, Jana Wold, Emily Koot, David Winter, Patrick Biggs, Stephanie J. Galla, Lara Urban, Yasmin Foster, Murray P. Cox, Andrew Digby, Lydia Uddstrom, Daryl Eason, Deidre Vercoe, Tāne Davis, Kākāpō Recovery Team, Jason T Howard, Erich Jarvis, Fiona E. Robertson, Bruce C. Robertson, Neil Gemmell, Tammy E. Steeves, Anna W. Santure, Peter K. Dearden. bioRxiv 2022.10.22.513130; doi: https://doi.org/10.1101/2022.10.22.513130

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• A Draft Human Pangenome Reference. Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Human Pangenome Reference Consortium, Guillaume Bourque, Mark JP Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Erich D. Jarvis, Karen H. Miga, Ting Wang, Erik Garrison, Tobias Marschall, Ira Hall, Heng Li, Benedict Paten. bioRxiv 2022.07.09.499321; doi: https://doi.org/10.1101/2022.07.09.499321

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• Convergent gene expression highlights shared vocal motor microcircuitry in songbirds and humans. Gregory L Gedman, Matthew T. Biegler, Bettina Haase, Morgan E. Wirthlin, Olivier Fedrigo, Andreas R. Pfenning, Erich D. Jarvis. bioRxiv 2022.07.01.498177; doi: https://doi.org/10.1101/2022.07.01.498177

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• The swan genome and transcriptome: its not all black and white. Anjana C. Karawita, Yuanyuan Cheng, Keng Yih Chew, Arjun Challgula, Robert Kraus, Ralf C. Mueller, Marcus Z. W. Tong, Katina D. Hulme, Helle Beielefeldt-Ohmann, Lauren E. Steele, Melanie Wu, Julian Sng, Ellesandra Noye, Timothy J. Bruxner, Gough G. Au, Suzanne Lowther, Julie Blommaert, Alexander Suh, Alexander J. McCauley, Parwinder Kaur, Olga Dudchenko, Erez Aiden, Olivier Fedrigo, Giulio Formenti, Jacquelyn Mountcastle, William Chow, Fergal J. Martin, Denye N. Ogeh, Françoise Thiaud-Nissen, Kerstin Howe, Joanna Collins, Alan Tracey, Jacqueline Smith, Richard I. Kuo, Marilyn B. Renfree, Takashi Kimura, Yoshihiro Sakoda, Mathew McDougall, Hamish G. Spencer, Michael Pyne, Conny Tolf, Jonas Waldenström, Erich D. Jarvis, Michelle L. Baker, David W. Burt, Kirsty R. Short. bioRxiv 2022.05.02.490350; doi: https://doi.org/10.1101/2022.05.02.490350

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• Pangenomics provides insights into the role of synanthropy in barn swallow evolution. Simona Secomandi, Guido Roberto Gallo, Marcella Sozzoni, Alessio Iannucci, Elena Galati, Linelle Abueg, Jennifer Balacco, Manuela Caprioli, William Chow, Claudio Ciofi, Joanna Collins, Olivier Fedrigo, Luca Ferretti, Arkarachai Fungtammasan, Bettina Haase, Kerstin Howe, Woori Kwak, Gianluca Lombardo, Patrick Masterson, Graziella Messina, Anders Pape Møller, Jacquelyn Mountcastle, Timothy A. Mousseau, Joan Ferrer-Obiol, Anna Olivieri, Arang Rhie, Diego Rubolini, Marielle Saclier, Roscoe Stanyon, David Stucki, Françoise Thibaud-Nissen, James Torrance, Antonio Torroni, Kristina Weber, Roberto Ambrosini, Andrea Bonisoli-Alquati, Erich D. Jarvis, Luca Gianfranceschi, Giulio Formenti. bioRxiv 2022.03.28.486082; doi: https://doi.org/10.1101/2022.03.28.486082

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• Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. Giulio Formenti, Linelle Abueg, Angelo Brajuka, Nadolina Brajuka, Cristo Gallardo, Alice Giani, Olivier Fedrigo, Erich D. Jarvis. bioRxiv 2022.03.24.485682; doi: https://doi.org/10.1101/2022.03.24.485682

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• Automated assembly of high-quality diploid human reference genomes. Erich D. Jarvis, Giulio Formenti, Arang Rhie, Andrea Guarracino, Chentao Yang, Jonathan Wood, Alan Tracey, Francoise Thibaud-Nissen, Mitchell R. Vollger, David Porubsky, Haoyu Cheng, Mobin Asri, Glennis A. Logsdon, Paolo Carnevali, Mark J.P. Chaisson, Chen-Shan Chin, Sarah Cody, Joanna Collins, Peter Ebert, Merly Escalona, Olivier Fedrigo, Robert S. Fulton, Lucinda L. Fulton, Shilpa Garg, Jay Ghurye, Ana Granat, Edward Green, Ira Hall, William Harvey, Patrick Hasenfeld, Alex Hastie, Marina Haukness, Erich B. Jaeger, Miten Jain, Melanie Kirsche, Mikhail Kolmogorov, Jan O. Korbel, Sergey Koren, Jonas Korlach, Joyce Lee, Daofeng Li, Tina Lindsay, Julian Lucas, Feng Luo, Tobias Marschall, Jennifer McDaniel, Fan Nie, Hugh E. Olsen, Nathan D. Olson, Trevor Pesout, Daniela Puiu, Allison Regier, Jue Ruan, Steven L. Salzberg, Ashley D. Sanders, Michael C. Schatz, Anthony Schmitt, Valerie A. Schneider, Siddarth Selvaraj, Kishwar Shafin, Alaina Shumate, Catherine Stober, James Torrance, Justin Wagner, Jianxin Wang, Aaron Wenger, Chuanle Xiao, Aleksey V. Zimin, Guojie Zhang, Ting Wang, Heng Li, Erik Garrison, David Haussler, Justin M. Zook, Evan E. Eichler, Adam M. Phillippy, Benedict Paten, Kerstin Howe, Karen H. Miga, Human Pangenome Reference Consortium. bioRxiv 2022.03.06.483034; doi: https://doi.org/10.1101/2022.03.06.483034

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• Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. Blair P. Bentley, Tomás Carrasco-Valenzuela, Elisa K. S. Ramos, Harvinder Pawar, Larissa Souza Arantes, Alana Alexander, Shreya M. Banerjee, Patrick Masterson, Martin Kuhlwilm, Martin Pippel, Jacquelyn Mountcastle, Bettina Haase, Marcela Uliano-Silva, Giulio Formenti, Kerstin Howe, William Chow, Alan Tracey, Ying Sims, Sarah Pelan, Jonathan Wood, Kelsey Yetsko, Justin R. Perrault, Kelly Stewart, Scott R. Benson, Yaniv Levy, Erica V. Todd, H. Bradley Shaffer, Peter Scott, Brian T. Henen, Robert W. Murphy, David W. Mohr, Alan F. Scott, David J. Duffy, Neil J. Gemmell, Alexander Suh, Sylke Winkler, Françoise Thibaud-Nissen, Mariana F. Nery, Tomas Marques-Bonet, Agostinho Antunes, Yaron Tikochinski, Peter H. Dutton, Olivier Fedrigo, Eugene W. Myers, Erich D. Jarvis, Camila J. Mazzoni, Lisa M. Komoroske. bioRxiv 2022.01.10.475373; doi: https://doi.org/10.1101/2022.01.10.475373

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• Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. Zhen Huang, Luohao Xu, Cheng Cai, Yitao Zhou, Jing Liu, Zexian Zhu, Wen Kang, Duo Chen, Surui Pei, Ting Xue, Wan Cen, Chenggang Shi, Xiaotong Wu, Yongji Huang, Chaohua Xu, Yanan Yan, Ying Yang, Wenjing He, Xuefeng Hu, Yanding Zhang, Youqiang Chen, Changwei Bi, Chunpeng He, Lingzhan Xue, Shijun Xiao, Zhicao Yue, Yu Jiang, Jr-Kai Yu, Erich D. Jarvis, Guang Li, Gang Lin, Qiujin Zhang, Qi Zhou. bioRxiv 2022.01.04.475009; doi: https://doi.org/10.1101/2022.01.04.475009

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• Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types. Simon A Hardwick, Wen Hu, Anoushka Joglekar, Li Fan, Paul G Collier, Careen Foord, Jennifer Balacco, Natan Belchikov, Julien Jarroux, Andrey Prjibelski, Alla Mikheenko, Wenjie Luo, Teresa A Milner, Lishomwa C Ndhlovu, John Q Trojanowski, Virginia MY Lee, Olivier Fedrigo, Dóra Tombácz, M Elizabeth Ross, Erich Jarvis, Zsolt Boldogkői, Li Gan, Hagen U Tilgner. bioRxiv 2021.12.29.474385; doi: https://doi.org/10.1101/2021.12.29.474385

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• A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes. H. Toh, C. Yang, G. Formenti, K. Raja, L. Yan, A. Tracey, W. Chow, K. Howe, L.A. Bergeron, G. Zhang, B. Haase, J. Mountcastle, O. Fedrigo, J. Fogg, B. Kirilenko, C. Munegowda, M. Hiller, A. Jain, D. Kihara, A. Rhie, A.M. Phillippy, S. Swanson, P. Jiang, D.O. Clegg, E.D. Jarvis, J.A. Thomson, R. Stewart, M.J.P. Chaisson, Y.V. Bukhman. bioRxiv 2021.12.08.471837; doi: https://doi.org/10.1101/2021.12.08.471837

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• Analysis of Mouse Vocal Communication (AMVOC): A deep, unsupervised method for rapid detection, analysis, and classification of ultrasonic vocalizations. Vasiliki Stoumpou, César D. M. Vargas, Peter F. Schade, Theodoros Giannakopoulos, Erich D. Jarvis. bioRxiv 2021.08.13.456283; doi: https://doi.org/10.1101/2021.08.13.456283

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• Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. Hollis A. Dahn, Jacquelyn Mountcastle, Jennifer Balacco, Sylke Winkler, Iliana Bista, Anthony D. Schmitt, Olga Vinnere Pettersson, Giulio Formenti, Karen Oliver, Michelle Smith, Wenhua Tan, Anne Kraus, Stephen Mac, Lisa M. Komoroske, Tanya Lama, Andrew J. Crawford, Robert W. Murphy, Samara Brown, Alan F. Scott, Phillip A. Morin, Erich D. Jarvis, Olivier Fedrigo. bioRxiv 2021.07.13.451380; doi: https://doi.org/10.1101/2021.07.13.451380

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• Merfin: improved variant filtering and polishing via k-mer validation. Giulio Formenti, Arang Rhie, Brian P. Walenz, Françoise Thibaud-Nissen, Kishwar Shafin, Sergey Koren, Eugene W. Myers, Erich D. Jarvis, Adam M. Phillippy. bioRxiv 2021.07.16.452324; doi: https://doi.org/10.1101/2021.07.16.452324

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• Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9. Matthew T. Biegler, Olivier Fedrigo, Paul Collier, Jacquelyn Mountcastle, Bettina Haase, Hagen U. Tilgner, Erich D. Jarvis. bioRxiv 2021.05.27.445896; doi: https://doi.org/10.1101/2021.05.27.445896

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• The complete sequence of a human genome. Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J. Hoyt, Mark Diekhans, Glennis A. Logsdon, Michael Alonge, Stylianos E. Antonarakis, Matthew Borchers, Gerard G. Bouffard, Shelise Y. Brooks, Gina V. Caldas, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G. de Lima, Philip C. Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T. Fiddes, Giulio Formenti, Robert S. Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G.S. Grady, Tina A. Graves-Lindsay, Ira M. Hall, Nancy F. Hansen, Gabrielle A. Hartley, Marina Haukness, Kerstin Howe, Michael W. Hunkapiller, Chirag Jain, Miten Jain, Erich D. Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V. Maduro, Tobias Marschall, Ann M. McCartney, Jennifer McDaniel, Danny E. Miller, James C. Mullikin, Eugene W. Myers, Nathan D. Olson, Benedict Paten, Paul Peluso, Pavel A. Pevzner, David Porubsky, Tamara Potapova, Evgeny I. Rogaev, Jeffrey A. Rosenfeld, Steven L. Salzberg, Valerie A. Schneider, Fritz J. Sedlazeck, Kishwar Shafin, Colin J. Shew, Alaina Shumate, Yumi Sims, Arian F. A. Smit, Daniela C. Soto, Ivan Sović, Jessica M. Storer, Aaron Streets, Beth A. Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P. Walenz, Aaron Wenger, Jonathan M. D. Wood, Chunlin Xiao, Stephanie M. Yan, Alice C. Young, Samantha Zarate, Urvashi Surti, Rajiv C. McCoy, Megan Y. Dennis, Ivan A. Alexandrov, Jennifer L. Gerton, Rachel J. O’Neill, Winston Timp, Justin M. Zook, Michael C. Schatz, Evan E. Eichler, Karen H. Miga, Adam M. Phillippy.bioRxiv 2021.05.26.445798; doi: https://doi.org/10.1101/2021.05.26.445798

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• Widespread false gene gains caused by duplication errors in genome assemblies. Byung June Ko, Chul Lee, Juwan Kim, Arang Rhie, DongAhn Yoo, Kerstin Howe, Jonathan Wood, Seoae Cho, Samara Brown, Giulio Formenti, Erich D. Jarvis, Heebal Kim. bioRxiv 2021.04.09.438957; doi: https://doi.org/10.1101/2021.04.09.438957

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• False gene and chromosome losses affected by assembly and sequence errors. Juwan Kim, Chul Lee, Byung June Ko, DongAhn Yoo, Sohyoung Won, Adam Phillippy, Olivier Fedrigo, Guojie Zhang, Kerstin Howe, Jonathan Wood, Richard Durbin, Giulio Formenti, Samara Brown, Lindsey Cantin, Claudio V. Mello, Seoae Cho, Arang Rhie, Heebal Kim, Erich D. Jarvis. bioRxiv 2021.04.09.438906; doi: https://doi.org/10.1101/2021.04.09.438906

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• Decreased synthesis and variable gene transcripts of oxytocin in a domesticated avian species. Yasuko Tobari, Constantina Theofanopoulou, Chihiro Mori, Yoshimi Sato, Momoka Marutani, Sayaka Fujioka, Norifumi Konno, Kenta Suzuki, Akari Furutani, Shiomi Hakataya, Cheng-Te Yao, En-Yun Yang, Chia-Ren Tsai, Pin-Chi Tang, Chih-Feng Chen, Cedric Boeckx, Erich D. Jarvis, Kazuo Okanoya. bioRxiv 2021.03.17.435911; doi: https://doi.org/10.1101/2021.03.17.435911

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• A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck Aythya fuligula (Tufted Duck). Ralf C Mueller, Patrik Ellström, Kerstin Howe, Marcela Uliano-Silva, Richard I Kuo, Katarzyna Miedzinska, Amanda Warr, Olivier Fedrigo, Bettina Haase, Jacquelyn Mountcastle, William Chow, James Torrance, Jonathan Wood, Josef D Järhult, Mahmoud M Naguib, Björn Olsen, Erich D Jarvis, Jacqueline Smith, Lél Eöry, Robert HS Kraus. bioRxiv 2021.02.24.432697; doi: https://doi.org/10.1101/2021.02.24.432697

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• Variation in predicted COVID-19 risk among lemurs and lorises. Amanda D. Melin, Joseph D. Orkin, Mareike C. Janiak, Alejandro Valenzuela, Lukas Kuderna, Frank Marrone III, Hasinala Ramangason, Julie E. Horvath, Christian Roos, Andrew C. Kitchener, Chiea Chuen Khor, Weng Khong Lim, Jessica G. H. Lee, Patrick Tan, Govindhaswamy Umapathy, Muthuswamy Raveendran, R. Alan Harris, Ivo Gut, Marta Gut, Esther Lizano, Tilo Nadler, Dietmar Zinner, Steig E. Johnson, Erich D. Jarvis, Olivier Fedrigo, Dongdong Wu, Guojie Zhang, Kyle Kai-How Farh, Jeffrey Rogers, Tomas Marques-Bonet, Arcadi Navarro, David Juan, Paramjit S. Arora, James P. Higham. bioRxiv 2021.02.03.429540; doi: https://doi.org/10.1101/2021.02.03.429540

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• As above, so below: Whole transcriptome profiling supports the continuum hypothesis of avian dorsal and ventral pallium organization. Gregory Gedman, Bettina Haase, Gillian Durieux, Matthew Biegler, Olivier Fedrigo, Erich D. Jarvis. bioRxiv 2020.11.13.375055; doi: https://doi.org/10.1101/2020.11.13.375055

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• A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. Jing Li, Jilin Zhang, Jing Liu, Yang Zhou, Cheng Cai, Luohao Xu, Xuelei Dai, Shaohong Feng, Chunxue Guo, Jinpeng Rao, Kai Wei, Erich D. Jarvis, Yu Jiang, Zhengkui Zhou, Guojie Zhang, Qi Zhou. bioRxiv 2020.11.04.368910; doi: https://doi.org/10.1101/2020.11.04.368910​​​​​​​​​​​

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• Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era. Joel Armstrong, Glenn Hickey, Mark Diekhans, Alden Deran, Qi Fang, Duo Xie, Shaohong Feng, Josefin Stiller, Diane Genereux, Jeremy Johnson, Voichita Dana Marinescu, David Haussler, Jessica Alföldi, Kerstin Lindblad-Toh, Elinor Karlsson, Erich D. Jarvis, Guojie Zhang, Benedict Paten. bioRxiv 730531; doi: https://doi.org/10.1101/730531

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• Extended haplotype phasing of de novo genome assemblies with FALCON-Phase. Zev N. Kronenberg, Arang Rhie, Sergey Koren, Gregory T. Concepcion, Paul Peluso, Katherine M. Munson, Stefan Hiendleder, Olivier Fedrigo, Erich D. Jarvis, Adam M. Phillippy, Evan E. Eichler, John L. Williams, Tim P.L. Smith, Richard J. Hall, Shawn T. Sullivan, Sarah B. Kingan. bioRxiv 327064; doi: https://doi.org/10.1101/327064

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• De Novo PacBio long-read and phased avian genome assemblies correct and add to genes important in neuroscience research. Jonas Korlach, Gregory Gedman, Sarah B. Kingan, Chen-Shan Chin, Jason Howard, Lindsey Cantin, Erich D. Jarvis. bioRxiv 103911; doi: https://doi.org/10.1101/103911