Genome research

Keyphrases

Publications

volume 34, number 6, 2024

Lee H Wong, Kate H Brettingham-Moore, Lyn Chan, Julie M Quach, Melissa A Anderson, Emma L Northrop, Ross Hannan, Richard Saffery, Margaret L Shaw, Evan Williams, K H Andy Choo
Corrigendum: Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere. Genome research 34 (6) (2024)
Shuangshuang Feng, Maitena Tellaetxe-Abete, Yujie Zhang, Yan Peng, Han Zhou, Mingjie Dong, Erika Larrea, Liang Xue, Li Zhang, Magdalena J Koziol
Single-cell discovery of m 6 A RNA modifications in the hippocampus. Genome research 34 (6) (2024)
Aarthi Venkat, Maximillian J Carlino, Betty R Lawton, Manju L Prasad, Matthew Amodio, Courtney E Gibson, Caroline J Zeiss, Scott E Youlten, Smita Krishnaswamy, Diane S Krause
Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue. Genome research 34 (6) (2024)
Alexis Morrissey, Jeffrey Shi, Daniela Q James, Shaun Mahony
Accurate allocation of multimapped reads enables regulatory element analysis at repeats. Genome research 34 (6) (2024)
Nikolaos Vakirlis, Anne Kupczok
Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins. Genome research 34 (6) (2024)
Reuben M Buckley, Elaine A Ostrander
Large-scale genomic analysis of the domestic dog informs biological discovery. Genome research 34 (6) (2024)
Sunjae Lee, Theo Portlock, Emmanuelle Le Chatelier, Fernando Garcia-Guevara, Frederick Clasen, Florian Plaza Oñate, Nicolas Pons, Neelu Begum, Azadeh Harzandi, Ceri Proffitt, Dorines Rosario, Stefania Vaga, Junseok Park, Kalle von Feilitzen, Fredric Johansson, Cheng Zhang, Lindsey A Edwards, Vincent Lombard, Franck Gauthier, Claire J Steves, David-Gómez Cabrero, Bernard Henrissat, Doheon Lee, Lars Engstrand, Debbie L Shawcross, Gordon Proctor, Mathieu Almeida, Jens Nielsen, Adil Mardinoglu, David L Moyes, Stanislav Dusko Ehrlich, Mathias Uhlen, Saeed Shoaie
Global compositional and functional states of the human gut microbiome in health and disease. Genome research 34 (6) (2024)
Sunjae Lee, Theo Portlock, Emmanuelle Le Chatelier, Fernando Garcia-Guevara, Frederick Clasen, Florian Plaza Oñate, Nicolas Pons, Neelu Begum, Azadeh Harzandi, Ceri Proffitt, Dorines Rosario, Stefania Vaga, Junseok Park, Kalle von Feilitzen, Fredric Johansson, Cheng Zhang, Lindsey A Edwards, Vincent Lombard, Franck Gauthier, Claire J Steves, David-Gómez Cabrero, Bernard Henrissat, Doheon Lee, Lars Engstrand, Debbie L Shawcross, Gordon Proctor, Mathieu Almeida, Jens Nielsen, Adil Mardinoglu, David L Moyes, Stanislav Dusko Ehrlich, Mathias Uhlen, Saeed Shoaie
Global compositional and functional states of the human gut microbiome in health and disease. Genome research 34 (6) (2024)
Shuangshuang Feng, Maitena Tellaetxe-Abete, Yujie Zhang, Yan Peng, Han Zhou, Mingjie Dong, Erika Larrea, Liang Xue, Li Zhang, Magdalena J Koziol
Single-cell discovery of m 6 A RNA modifications in the hippocampus. Genome research 34 (6) (2024)
Alexander Hirth, Edoardo Fatti, Eugen Netz, Sergio P Acebron, Dimitris Papageorgiou, Andrea Švorinić, Cristina-Maria Cruciat, Emil Karaulanov, Alexandr Gopanenko, Tianheng Zhu, Irmgard Sinning, Jeroen Krijgsveld, Oliver Kohlbacher, Christof Niehrs
DEAD box RNA helicases are pervasive protein kinase interactors and activators. Genome research 34 (6) (2024)
Daniel Davis, Avishai Wizel, Yotam Drier
Accurate estimation of pathway activity in single cells for clustering and differential analysis. Genome research 34 (6) (2024)
Alexander Hirth, Edoardo Fatti, Eugen Netz, Sergio P Acebron, Dimitris Papageorgiou, Andrea Švorinić, Cristina-Maria Cruciat, Emil Karaulanov, Alexandr Gopanenko, Tianheng Zhu, Irmgard Sinning, Jeroen Krijgsveld, Oliver Kohlbacher, Christof Niehrs
DEAD box RNA helicases are pervasive protein kinase interactors and activators. Genome research 34 (6) (2024)
Greta Bellinzona, Tiago Nardi, Michele Castelli, Gherard Batisti Biffignandi, Karim Adjou, Martha Betson, Yannick Blanchard, Ioana Bujila, Rachel Chalmers, Rebecca Davidson, Nicoletta D'Avino, Tuulia Enbom, Jacinto Gomes, Gregory Karadjian, Christian Klotz, Emma Östlund, Judith Plutzer, Ruska Rimhanen-Finne, Guy Robinson, Anna Rosa Sannella, Jacek Sroka, Christen Rune Stensvold, Karin Troell, Paolo Vatta, Barbora Zalewska, Claudio Bandi, Davide Sassera, Simone M Cacciò
Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States. Genome research 34 (6) (2024)
Mohammed Errbii, Juergen Gadau, Kerstin Becker, Lukas Schrader, Jan Oettler
Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior . Genome research 34 (6) (2024)
Bo Yan, Duan Wang, Laurence M Ettwiller
Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine. Genome research 34 (6) (2024)
Alexis Morrissey, Jeffrey Shi, Daniela Q James, Shaun Mahony
Accurate allocation of multimapped reads enables regulatory element analysis at repeats. Genome research 34 (6) (2024)
Jens-Uwe Ulrich, Bernhard Y Renard
Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters. Genome research 34 (6) (2024)
Aarthi Venkat, Maximillian J Carlino, Betty R Lawton, Manju L Prasad, Matthew Amodio, Courtney E Gibson, Caroline J Zeiss, Scott E Youlten, Smita Krishnaswamy, Diane S Krause
Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue. Genome research 34 (6) (2024)
Nikolaos Vakirlis, Anne Kupczok
Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins. Genome research 34 (6) (2024)
Greta Bellinzona, Tiago Nardi, Michele Castelli, Gherard Batisti Biffignandi, Karim Adjou, Martha Betson, Yannick Blanchard, Ioana Bujila, Rachel Chalmers, Rebecca Davidson, Nicoletta D'Avino, Tuulia Enbom, Jacinto Gomes, Gregory Karadjian, Christian Klotz, Emma Östlund, Judith Plutzer, Ruska Rimhanen-Finne, Guy Robinson, Anna Rosa Sannella, Jacek Sroka, Christen Rune Stensvold, Karin Troell, Paolo Vatta, Barbora Zalewska, Claudio Bandi, Davide Sassera, Simone M Cacciò
Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States. Genome research 34 (6) (2024)
Reuben M Buckley, Elaine A Ostrander
Large-scale genomic analysis of the domestic dog informs biological discovery. Genome research 34 (6) (2024)
Xuejing Wang, Gerald Heckel
Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles. Genome research 34 (6) (2024)
Daniel Davis, Avishai Wizel, Yotam Drier
Accurate estimation of pathway activity in single cells for clustering and differential analysis. Genome research 34 (6) (2024)
Xuejing Wang, Gerald Heckel
Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles. Genome research 34 (6) (2024)
Jens-Uwe Ulrich, Bernhard Y Renard
Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters. Genome research 34 (6) (2024)
Sunjae Lee, Theo Portlock, Emmanuelle Le Chatelier, Fernando Garcia-Guevara, Frederick Clasen, Florian Plaza Oñate, Nicolas Pons, Neelu Begum, Azadeh Harzandi, Ceri Proffitt, Dorines Rosario, Stefania Vaga, Junseok Park, Kalle von Feilitzen, Fredric Johansson, Cheng Zhang, Lindsey A Edwards, Vincent Lombard, Franck Gauthier, Claire J Steves, David-Gómez Cabrero, Bernard Henrissat, Doheon Lee, Lars Engstrand, Debbie L Shawcross, Gordon Proctor, Mathieu Almeida, Jens Nielsen, Adil Mardinoglu, David L Moyes, Stanislav Dusko Ehrlich, Mathias Uhlen, Saeed Shoaie
Global compositional and functional states of the human gut microbiome in health and disease. Genome research 34 (6) (2024)
Lee H Wong, Kate H Brettingham-Moore, Lyn Chan, Julie M Quach, Melissa A Anderson, Emma L Northrop, Ross Hannan, Richard Saffery, Margaret L Shaw, Evan Williams, K H Andy Choo
Corrigendum: Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere. Genome research 34 (6) (2024)
Shuangshuang Feng, Maitena Tellaetxe-Abete, Yujie Zhang, Yan Peng, Han Zhou, Mingjie Dong, Erika Larrea, Liang Xue, Li Zhang, Magdalena J Koziol
Single-cell discovery of m 6 A RNA modifications in the hippocampus. Genome research 34 (6) (2024)
Shuangshuang Feng, Maitena Tellaetxe-Abete, Yujie Zhang, Yan Peng, Han Zhou, Mingjie Dong, Erika Larrea, Liang Xue, Li Zhang, Magdalena J Koziol
Single-cell discovery of m 6 A RNA modifications in the hippocampus. Genome research 34 (6) (2024)

volume 34, number 7, 2024

Emily Kunce Stroup, Zhe Ji
Delineating yeast cleavage and polyadenylation signals using deep learning. Genome research 34 (7) (2024)
Chencheng Xu, Suying Bao, Ye Wang, Wenxing Li, Hao Chen, Yufeng Shen, Tao Jiang, Chaolin Zhang
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome research 34 (7) (2024)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Isaac, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David M Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome research 34 (7) (2024)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Isaac, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David M Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome research 34 (7) (2024)
Sizhen Li, Saeed Moayedpour, Ruijiang Li, Michael Bailey, Saleh Riahi, Lorenzo Kogler-Anele, Milad Miladi, Jacob Miner, Fabien Pertuy, Dinghai Zheng, Jun Wang, Akshay Balsubramani, Khang Tran, Minnie Zacharia, Monica Wu, Xiaobo Gu, Ryan Clinton, Carla Asquith, Joseph Skaleski, Lianne Boeglin, Sudha Chivukula, Anusha Dias, Tod Strugnell, Fernando Ulloa Montoya, Vikram Agarwal, Ziv Bar-Joseph, Sven Jager
CodonBERT large language model for mRNA vaccines. Genome research 34 (7) (2024)
Juri Kuronen, Samuel T Horsfield, Anna Kaarina Pöntinen, Sudaraka Mallawaarachchi, Sergio Arredondo-Alonso, Harry A Thorpe, Rebecca A Gladstone, Rob J L Willems, Stephen D Bentley, Nicholas J Croucher, Johan Pensar, John A Lees, Gerry Q Tonkin-Hill, Jukka Corander
Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs. Genome research 34 (7) (2024)
Sizhen Li, Saeed Moayedpour, Ruijiang Li, Michael Bailey, Saleh Riahi, Lorenzo Kogler-Anele, Milad Miladi, Jacob Miner, Fabien Pertuy, Dinghai Zheng, Jun Wang, Akshay Balsubramani, Khang Tran, Minnie Zacharia, Monica Wu, Xiaobo Gu, Ryan Clinton, Carla Asquith, Joseph Skaleski, Lianne Boeglin, Sudha Chivukula, Anusha Dias, Tod Strugnell, Fernando Ulloa Montoya, Vikram Agarwal, Ziv Bar-Joseph, Sven Jager
CodonBERT large language model for mRNA vaccines. Genome research 34 (7) (2024)
Caitlin A Loh, Danielle A Shields, Adam Schwing, Gilad D Evrony
High-fidelity, large-scale targeted profiling of microsatellites. Genome research 34 (7) (2024)
Chencheng Xu, Suying Bao, Ye Wang, Wenxing Li, Hao Chen, Yufeng Shen, Tao Jiang, Chaolin Zhang
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome research 34 (7) (2024)
Caitlin A Loh, Danielle A Shields, Adam Schwing, Gilad D Evrony
High-fidelity, large-scale targeted profiling of microsatellites. Genome research 34 (7) (2024)
Emily Kunce Stroup, Zhe Ji
Delineating yeast cleavage and polyadenylation signals using deep learning. Genome research 34 (7) (2024)
Mengyuan Zhao, Jiawei Li, Xiaoyi Liu, Ke Ma, Jijun Tang, Fei Guo
A gene regulatory network-aware graph learning method for cell identity annotation in single-cell RNA-seq data. Genome research 34 (7) (2024)
Mengyuan Zhao, Jiawei Li, Xiaoyi Liu, Ke Ma, Jijun Tang, Fei Guo
A gene regulatory network-aware graph learning method for cell identity annotation in single-cell RNA-seq data. Genome research 34 (7) (2024)
Mengyuan Zhao, Jiawei Li, Xiaoyi Liu, Ke Ma, Jijun Tang, Fei Guo
A gene regulatory network-aware graph learning method for cell identity annotation in single-cell RNA-seq data. Genome research 34 (7) (2024)
Xinghua Li, Judith E Mank, Liping Ban
The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution. Genome research 34 (7) (2024)
Tom Denyer, Pin-Jou Wu, Kelly Colt, Bradley W Abramson, Zhili Pang, Pavel Solansky, Allen Mamerto, Tatsuya Nobori, Joseph R Ecker, Eric Lam, Todd P Michael, Marja C P Timmermans
Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana . Genome research 34 (7) (2024)
Yulong Liu, Gang Zhai, Jingzhi Su, Yulong Gong, Bingyuan Yang, Qisheng Lu, Longwei Xi, Yutong Zheng, Jingyue Cao, Haokun Liu, Junyan Jin, Zhimin Zhang, Yunxia Yang, Xiaoming Zhu, Zhongwei Wang, Gaorui Gong, Jie Mei, Zhan Yin, Rodolphe E Gozlan, Shouqi Xie, Dong Han
The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores. Genome research 34 (7) (2024)
Yulong Liu, Gang Zhai, Jingzhi Su, Yulong Gong, Bingyuan Yang, Qisheng Lu, Longwei Xi, Yutong Zheng, Jingyue Cao, Haokun Liu, Junyan Jin, Zhimin Zhang, Yunxia Yang, Xiaoming Zhu, Zhongwei Wang, Gaorui Gong, Jie Mei, Zhan Yin, Rodolphe E Gozlan, Shouqi Xie, Dong Han
The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores. Genome research 34 (7) (2024)
Tom Denyer, Pin-Jou Wu, Kelly Colt, Bradley W Abramson, Zhili Pang, Pavel Solansky, Allen Mamerto, Tatsuya Nobori, Joseph R Ecker, Eric Lam, Todd P Michael, Marja C P Timmermans
Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana . Genome research 34 (7) (2024)
Juri Kuronen, Samuel T Horsfield, Anna Kaarina Pöntinen, Sudaraka Mallawaarachchi, Sergio Arredondo-Alonso, Harry A Thorpe, Rebecca A Gladstone, Rob J L Willems, Stephen D Bentley, Nicholas J Croucher, Johan Pensar, John A Lees, Gerry Q Tonkin-Hill, Jukka Corander
Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs. Genome research 34 (7) (2024)
Xinghua Li, Judith E Mank, Liping Ban
The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution. Genome research 34 (7) (2024)