Table of Contents

July 2020; 30 (7)

Research

  • Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

    • Ryne C. Ramaker,
    • Andrew A. Hardigan,
    • Say-Tar Goh,
    • E. Christopher Partridge,
    • Barbara Wold,
    • Sara J. Cooper,
    • and Richard M. Myers
    Genome Res. July 2020 30: 939-950; Published in Advance July 2, 2020, doi:10.1101/gr.260463.119
    OPEN ACCESS ARTICLE

  • Comparative transcriptomics of primary cells in vertebrates

    • Tanvir Alam,
    • Saumya Agrawal,
    • Jessica Severin,
    • Robert S. Young,
    • Robin Andersson,
    • Erik Arner,
    • Akira Hasegawa,
    • Marina Lizio,
    • Jordan A. Ramilowski,
    • Imad Abugessaisa,
    • Yuri Ishizu,
    • Shohei Noma,
    • Hiroshi Tarui,
    • Martin S. Taylor,
    • Timo Lassmann,
    • Masayoshi Itoh,
    • Takeya Kasukawa,
    • Hideya Kawaji,
    • Luigi Marchionni,
    • Guojun Sheng,
    • Alistair R.R. Forrest,
    • Levon M. Khachigian,
    • Yoshihide Hayashizaki,
    • Piero Carninci,
    • and Michiel J.L. de Hoon
    Genome Res. July 2020 30: 951-961; Published in Advance July 27, 2020, doi:10.1101/gr.255679.119
    OPEN ACCESS ARTICLE

  • Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences

    • Arttu Jolma,
    • Jilin Zhang,
    • Estefania Mondragón,
    • Ekaterina Morgunova,
    • Teemu Kivioja,
    • Kaitlin U. Laverty,
    • Yimeng Yin,
    • Fangjie Zhu,
    • Gleb Bourenkov,
    • Quaid Morris,
    • Timothy R. Hughes,
    • Louis James Maher III,
    • and Jussi Taipale
    Genome Res. July 2020 30: 962-973; Published in Advance July 23, 2020, doi:10.1101/gr.258848.119
    OPEN ACCESS ARTICLE

  • Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context

    • Maria S. Benitez-Cantos,
    • Martina M. Yordanova,
    • Patrick B.F. O'Connor,
    • Alexander V. Zhdanov,
    • Sergey I. Kovalchuk,
    • Dmitri B. Papkovsky,
    • Dmitry E. Andreev,
    • and Pavel V. Baranov
    Genome Res. July 2020 30: 974-984; Published in Advance July 15, 2020, doi:10.1101/gr.257352.119
    OPEN ACCESS ARTICLE

  • Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing

    • Alaaddin Bulak Arpat,
    • Angélica Liechti,
    • Mara De Matos,
    • René Dreos,
    • Peggy Janich,
    • and David Gatfield
    Genome Res. July 2020 30: 985-999; Published in Advance July 23, 2020, doi:10.1101/gr.257741.119

  • Independent evolution of transcript abundance and gene regulatory dynamics

    • Gat Krieger,
    • Offir Lupo,
    • Avraham A. Levy,
    • and Naama Barkai
    Genome Res. July 2020 30: 1000-1011; Published in Advance July 22, 2020, doi:10.1101/gr.261537.120

Methods

  • System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organization and function of RNA–protein complexes

    • Cornelia Kilchert,
    • Tea Kecman,
    • Emily Priest,
    • Svenja Hester,
    • Ebru Aydin,
    • Krzysztof Kus,
    • Oliver Rossbach,
    • Alfredo Castello,
    • Shabaz Mohammed,
    • and Lidia Vasiljeva
    Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
    OPEN ACCESS ARTICLE

  • Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility

    • Qiao Rui Xing,
    • Chadi A El Farran,
    • Ying Ying Zeng,
    • Yao Yi,
    • Tushar Warrier,
    • Pradeep Gautam,
    • James J. Collins,
    • Jian Xu,
    • Peter Dröge,
    • Cheng-Gee Koh,
    • Hu Li,
    • Li-Feng Zhang,
    • and Yuin-Han Loh
    Genome Res. July 2020 30: 1027-1039; Published in Advance July 22, 2020, doi:10.1101/gr.257840.119
    OPEN ACCESS ARTICLE

  • TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence

    • Ningxin Ouyang and
    • Alan P. Boyle
    Genome Res. July 2020 30: 1040-1046; Published in Advance July 6, 2020, doi:10.1101/gr.258228.119

Resources

  • A limited set of transcriptional programs define major cell types

    • Alessandra Breschi,
    • Manuel Muñoz-Aguirre,
    • Valentin Wucher,
    • Carrie A. Davis,
    • Diego Garrido-Martín,
    • Sarah Djebali,
    • Jesse Gillis,
    • Dmitri D. Pervouchine,
    • Anna Vlasova,
    • Alexander Dobin,
    • Chris Zaleski,
    • Jorg Drenkow,
    • Cassidy Danyko,
    • Alexandra Scavelli,
    • Ferran Reverter,
    • Michael P. Snyder,
    • Thomas R. Gingeras,
    • and Roderic Guigó
    Genome Res. July 2020 30: 1047-1059; Published in Advance July 29, 2020, doi:10.1101/gr.263186.120
    OPEN ACCESS ARTICLE

  • Functional annotation of human long noncoding RNAs via molecular phenotyping

    • Jordan A. Ramilowski,
    • Chi Wai Yip,
    • Saumya Agrawal,
    • Jen-Chien Chang,
    • Yari Ciani,
    • Ivan V. Kulakovskiy,
    • Mickaël Mendez,
    • Jasmine Li Ching Ooi,
    • John F. Ouyang,
    • Nick Parkinson,
    • Andreas Petri,
    • Leonie Roos,
    • Jessica Severin,
    • Kayoko Yasuzawa,
    • Imad Abugessaisa,
    • Altuna Akalin,
    • Ivan V. Antonov,
    • Erik Arner,
    • Alessandro Bonetti,
    • Hidemasa Bono,
    • Beatrice Borsari,
    • Frank Brombacher,
    • Christopher J.F. Cameron,
    • Carlo Vittorio Cannistraci,
    • Ryan Cardenas,
    • Melissa Cardon,
    • Howard Chang,
    • Josée Dostie,
    • Luca Ducoli,
    • Alexander Favorov,
    • Alexandre Fort,
    • Diego Garrido,
    • Noa Gil,
    • Juliette Gimenez,
    • Reto Guler,
    • Lusy Handoko,
    • Jayson Harshbarger,
    • Akira Hasegawa,
    • Yuki Hasegawa,
    • Kosuke Hashimoto,
    • Norihito Hayatsu,
    • Peter Heutink,
    • Tetsuro Hirose,
    • Eddie L. Imada,
    • Masayoshi Itoh,
    • Bogumil Kaczkowski,
    • Aditi Kanhere,
    • Emily Kawabata,
    • Hideya Kawaji,
    • Tsugumi Kawashima,
    • S. Thomas Kelly,
    • Miki Kojima,
    • Naoto Kondo,
    • Haruhiko Koseki,
    • Tsukasa Kouno,
    • Anton Kratz,
    • Mariola Kurowska-Stolarska,
    • Andrew Tae Jun Kwon,
    • Jeffrey Leek,
    • Andreas Lennartsson,
    • Marina Lizio,
    • Fernando López-Redondo,
    • Joachim Luginbühl,
    • Shiori Maeda,
    • Vsevolod J. Makeev,
    • Luigi Marchionni,
    • Yulia A. Medvedeva,
    • Aki Minoda,
    • Ferenc Müller,
    • Manuel Muñoz-Aguirre,
    • Mitsuyoshi Murata,
    • Hiromi Nishiyori,
    • Kazuhiro R. Nitta,
    • Shuhei Noguchi,
    • Yukihiko Noro,
    • Ramil Nurtdinov,
    • Yasushi Okazaki,
    • Valerio Orlando,
    • Denis Paquette,
    • Callum J.C. Parr,
    • Owen J.L. Rackham,
    • Patrizia Rizzu,
    • Diego Fernando Sánchez Martinez,
    • Albin Sandelin,
    • Pillay Sanjana,
    • Colin A.M. Semple,
    • Youtaro Shibayama,
    • Divya M. Sivaraman,
    • Takahiro Suzuki,
    • Suzannah C. Szumowski,
    • Michihira Tagami,
    • Martin S. Taylor,
    • Chikashi Terao,
    • Malte Thodberg,
    • Supat Thongjuea,
    • Vidisha Tripathi,
    • Igor Ulitsky,
    • Roberto Verardo,
    • Ilya E. Vorontsov,
    • Chinatsu Yamamoto,
    • Robert S. Young,
    • J. Kenneth Baillie,
    • Alistair R.R. Forrest,
    • Roderic Guigó,
    • Michael M. Hoffman,
    • Chung Chau Hon,
    • Takeya Kasukawa,
    • Sakari Kauppinen,
    • Juha Kere,
    • Boris Lenhard,
    • Claudio Schneider,
    • Harukazu Suzuki,
    • Ken Yagi,
    • Michiel J.L. de Hoon,
    • Jay W. Shin,
    • and Piero Carninci
    Genome Res. July 2020 30: 1060-1072; Published in Advance July 27, 2020, doi:10.1101/gr.254219.119
    OPEN ACCESS ARTICLE

  • Recounting the FANTOM CAGE-Associated Transcriptome

    • Eddie Luidy Imada,
    • Diego Fernando Sanchez,
    • Leonardo Collado-Torres,
    • Christopher Wilks,
    • Tejasvi Matam,
    • Wikum Dinalankara,
    • Aleksey Stupnikov,
    • Francisco Lobo-Pereira,
    • Chi-Wai Yip,
    • Kayoko Yasuzawa,
    • Naoto Kondo,
    • Masayoshi Itoh,
    • Harukazu Suzuki,
    • Takeya Kasukawa,
    • Chung-Chau Hon,
    • Michiel J.L. de Hoon,
    • Jay W. Shin,
    • Piero Carninci,
    • Andrew E. Jaffe,
    • Jeffrey T. Leek,
    • Alexander Favorov,
    • Gloria R. Franco,
    • Ben Langmead,
    • and Luigi Marchionni
    Genome Res. July 2020 30: 1073-1081; Published in Advance February 20, 2020, doi:10.1101/gr.254656.119
    OPEN ACCESS ARTICLE
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This Issue

July 2020; 30 (7)
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