Preprint

The following preprint publications are research papers made accessible to the public while they are in preparation or under review.

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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

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

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

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

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

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

Pronounced early differentiation underlies zebra finch gonadal germ cell development. Matthew T. Biegler, Kirubel Belay, Wei Wang, Christina Szi, Paul Collier, Ji-Dung Luo, Bettina Haase, Gregory L. Gedman, Asha V. Sidhu, Elijah Harter, Carlos Rivera-López, Kwame Amoako-Boadu, Olivier Fedrigo, Hagen U. Tilgner, Thomas Carroll, Erich D. Jarvis, Anna L. Keyte. bioRxiv 2023.12.30.572255; doi: https://doi.org/10.1101/2023.12.30.572255

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

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

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

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

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

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

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

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

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

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

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

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
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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development. Anoushka Joglekar, Andrey Prjibelski, Ahmed Mahfouz, Paul Collier, Susan Lin, Anna Katharina Schlusche, Jordan Marrocco, Stephen R. Williams, Bettina Haase, Ashley Hayes, Jennifer G. Chew, Neil I Weisenfeld, Man Ying Wong, Alexander N. Stein, Simon Hardwick, Toby Hunt, Zachary Bent, Olivier Fedrigo, Steven A. Sloan, Davide Risso, Erich D. Jarvis, Paul Flicek, Wenjie Luo, Geoffrey S. Pitt, Adam Frankish, August B. Smit, M. Elizabeth Ross, Hagen U. Tilgner. bioRxiv 2020.08.27.268730; doi: https://doi.org/10.1101/2020.08.27.268730

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats. Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Capodiferro, Farooq O. Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge, Jale Dolucan, Craig Corton, Iliana Bista, James Torrance, Alan Tracey, Jonathan Wood, Marcela Uliano-Silva, Kerstin Howe, Shane McCarthy, Sylke Winkler, Woori Kwak, Jonas Korlach, Arkarachai Fungtammasan, Daniel Fordham, Vania Costa, Simon Mayes, Matteo Chiara, David S. Horner, Eugene Myers, Richard Durbin, Alessandro Achilli, Edward L. Braun, Adam M. Phillippy, Erich D. Jarvis, The Vertebrate Genomes Project Consortium. bioRxiv 2020.06.30.177956; doi: https://doi.org/10.1101/2020.06.30.177956

Reference genome and demographic history of the most endangered marine mammal, the vaquita. Phillip A. Morin, Frederick I. Archer, Catherine D. Avila, Jennifer R. Balacco, Yury V. Bukhman, William Chow, Olivier Fedrigo, Giulio Formenti, Julie A. Fronczek, Arkarachai Fungtammasan, Frances M.D. Gulland, Bettina Haase, Mads Peter Heide-Jorgensen, Marlys L. Houck, Kerstin Howe, Ann C. Misuraca, Jacquelyn Mountcastle, Whitney Musser, Sadye Paez, Sarah Pelan, Adam Phillippy, Arang Rhie, Jacqueline Robinson, Lorenzo Rojas-Bracho, Teri K. Rowles, Oliver A. Ryder, Cynthia R. Smith, Sacha Stevenson, Barbara L. Taylor, Jonas Teilmann, James Torrance, Randall S. Wells, Andrew Westgate, Erich D. Jarvis. bioRxiv 2020.05.27.098582; doi: https://doi.org/10.1101/2020.05.27.098582

Towards complete and error-free genome assemblies of all vertebrate species. Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Chul Lee, Byung June Ko, Juwan Kim, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher Balakrishnan, Dave Burt, Julia M. George, Mathew Biegler, David Iorns, Andrew Digby, Daryl Eason, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H William Detrich III, Hannes Svardal, Maximilian Wagner, Gavin J.P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Jonas Korlach, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Dengfeng Guan, Sarah E. London, David F. Clayton, Claudio V. Mello, Samantha R. Friedrich, Peter V. Lovell, Ekaterina Osipova, Farooq O. Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H.S. Kraus, Harris Lewin, Andrew J. Crawford, M. Thomas P. Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Di Palma, Tomas Margues-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A. Ryder, David Hausler, Stephen J. O’Brien, Kerstin Howe, Eugene W. Myers, Richard Durbin, Adam M. Phillippy, Erich D. Jarvis. bioRxiv 2020.05.22.110833; doi: https://doi.org/10.1101/2020.05.22.110833

Estrogen and sex-dependent loss of the vocal learning system in female zebra finches. Ha Na Choe, Jeevan Tewari, Kevin W. Zhu, Matthew Davenport, Hiroaki Matsunami, Erich D. Jarvis. bioRxiv 2020.03.28.011932; doi: https://doi.org/10.1101/2020.03.28.011932

Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations. David Jebb, Zixia Huang, Martin Pippel, Graham M. Hughes, Ksenia Lavrichenko, Paolo Devanna, Sylke Winkler, Lars S. Jermiin, Emilia C. Skirmuntt, Aris Katzourakis, Lucy Burkitt-Gray, David A. Ray, Kevin A. M. Sullivan, Juliana G. Roscito, Bogdan M. Kirilenko, Liliana M. Dávalos, Angelique P. Corthals, Megan L. Power, Gareth Jones, Roger D. Ransome, Dina Dechmann, Andrea G. Locatelli, Sebastien J. Puechmaille, Olivier Fedrigo, Erich D. Jarvis, Mark S. Springer, Michael Hiller, Sonja C. Vernes, Eugene W. Myers, Emma C. Teeling. bioRxiv 836874; doi: https://doi.org/10.1101/836874

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

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

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