Genome biology

Keyphrases

Publications

volume 25, number 1, 2024

Roberto Vera Alvarez, David Landsman
GTax: improving de novo transcriptome assembly by removing foreign RNA contamination. Genome biology 25 (1) (2024)
Hamid Kian Gaikani, Monika Stolar, Divya Kriti, Corey Nislow, Guri Giaever
From beer to breadboards: yeast as a force for biological innovation. Genome biology 25 (1) (2024)
George Hunt, Roshan Vaid, Sergei Pirogov, Alexander Pfab, Christoph Ziegenhain, Rickard Sandberg, Johan Reimegård, Mattias Mannervik
Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network. Genome biology 25 (1) (2024)
Mengli Zhang, Judith Hyle, Xiaowen Chen, Ye Xin, Yingcai Jin, Jianxiang Zhang, Xue Yang, Xinfeng Chen, Shaela Wright, Zhenling Liu, Wojciech Rosikiewicz, Beisi Xu, Liusheng He, Hong Liu, Nana Ping, Depei Wu, Feiqiu Wen, Chunliang Li, Peng Xu
RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9. Genome biology 25 (1) (2024)
Winston Lau, Aminah Ali, Hannah Maude, Toby Andrew, Dallas M Swallow, Nikolas Maniatis
The hazards of genotype imputation when mapping disease susceptibility variants. Genome biology 25 (1) (2024)
Roberto Vera Alvarez, David Landsman
GTax: improving de novo transcriptome assembly by removing foreign RNA contamination. Genome biology 25 (1) (2024)
Christopher K Tuggle, Jennifer L Clarke, Brenda M Murdoch, Eric Lyons, Nicole M Scott, Bedrich Beneš, Jacqueline D Campbell, Henri Chung, Courtney L Daigle, Sruti Das Choudhury, Jack C M Dekkers, Joao R R Dórea, David S Ertl, Max Feldman, Breno O Fragomeni, Janet E Fulton, Carmela R Guadagno, Darren E Hagen, Andrew S Hess, Luke M Kramer, Carolyn J Lawrence-Dill, Alexander E Lipka, Thomas Lübberstedt, Fiona M McCarthy, Stephanie D McKay, Seth C Murray, Penny K Riggs, Troy N Rowan, Moira J Sheehan, Juan P Steibel, Addie M Thompson, Kara J Thornton, Curtis P Van Tassell, Patrick S Schnable
Current challenges and future of agricultural genomes to phenomes in the USA. Genome biology 25 (1) (2024)
Shujun Ou, Ning Jiang, Candice N Hirsch, Matthew B Hufford
Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome biology 25 (1) (2024)
George Hunt, Roshan Vaid, Sergei Pirogov, Alexander Pfab, Christoph Ziegenhain, Rickard Sandberg, Johan Reimegård, Mattias Mannervik
Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network. Genome biology 25 (1) (2024)
Landen Gozashti, Hopi E Hoekstra
Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome biology 25 (1) (2024)
Haidong Yi, Alec Plotkin, Natalie Stanley
Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets. Genome biology 25 (1) (2024)
Charles E Breeze, Eric Haugen, María Gutierrez-Arcelus, Xiaozheng Yao, Andrew Teschendorff, Stephan Beck, Ian Dunham, John Stamatoyannopoulos, Nora Franceschini, Mitchell J Machiela, Sonja I Berndt
FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases. Genome biology 25 (1) (2024)
Ahmed Abbas, Khyati Chandratre, Yunpeng Gao, Jiapei Yuan, Michael Q Zhang, Ram S Mani
ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features. Genome biology 25 (1) (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Yanying Yu, Sandra Gawlitt, Lisa Barros de Andrade E Sousa, Erinc Merdivan, Marie Piraud, Chase L Beisel, Lars Barquist
Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration. Genome biology 25 (1) (2024)
Hamid Kian Gaikani, Monika Stolar, Divya Kriti, Corey Nislow, Guri Giaever
From beer to breadboards: yeast as a force for biological innovation. Genome biology 25 (1) (2024)
Haidong Yi, Alec Plotkin, Natalie Stanley
Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets. Genome biology 25 (1) (2024)
Jizeng Jia, Yilin Xie, Jingfei Cheng, Chuizheng Kong, Meiyue Wang, Lifeng Gao, Fei Zhao, Jingyu Guo, Kai Wang, Guangwei Li, Dangqun Cui, Tiezhu Hu, Guangyao Zhao, Daowen Wang, Zhengang Ru, Yijing Zhang
Author Correction: Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression. Genome biology 25 (1) (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Charles E Breeze, Eric Haugen, María Gutierrez-Arcelus, Xiaozheng Yao, Andrew Teschendorff, Stephan Beck, Ian Dunham, John Stamatoyannopoulos, Nora Franceschini, Mitchell J Machiela, Sonja I Berndt
FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases. Genome biology 25 (1) (2024)
Christopher K Tuggle, Jennifer L Clarke, Brenda M Murdoch, Eric Lyons, Nicole M Scott, Bedrich Beneš, Jacqueline D Campbell, Henri Chung, Courtney L Daigle, Sruti Das Choudhury, Jack C M Dekkers, Joao R R Dórea, David S Ertl, Max Feldman, Breno O Fragomeni, Janet E Fulton, Carmela R Guadagno, Darren E Hagen, Andrew S Hess, Luke M Kramer, Carolyn J Lawrence-Dill, Alexander E Lipka, Thomas Lübberstedt, Fiona M McCarthy, Stephanie D McKay, Seth C Murray, Penny K Riggs, Troy N Rowan, Moira J Sheehan, Juan P Steibel, Addie M Thompson, Kara J Thornton, Curtis P Van Tassell, Patrick S Schnable
Current challenges and future of agricultural genomes to phenomes in the USA. Genome biology 25 (1) (2024)
Haidong Yi, Alec Plotkin, Natalie Stanley
Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets. Genome biology 25 (1) (2024)
Winston Lau, Aminah Ali, Hannah Maude, Toby Andrew, Dallas M Swallow, Nikolas Maniatis
The hazards of genotype imputation when mapping disease susceptibility variants. Genome biology 25 (1) (2024)
Xiang Zhu, Shining Ma, Wing Hung Wong
Genetic effects of sequence-conserved enhancer-like elements on human complex traits. Genome biology 25 (1) (2024)
Shujun Ou, Ning Jiang, Candice N Hirsch, Matthew B Hufford
Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome biology 25 (1) (2024)
Mengli Zhang, Judith Hyle, Xiaowen Chen, Ye Xin, Yingcai Jin, Jianxiang Zhang, Xue Yang, Xinfeng Chen, Shaela Wright, Zhenling Liu, Wojciech Rosikiewicz, Beisi Xu, Liusheng He, Hong Liu, Nana Ping, Depei Wu, Feiqiu Wen, Chunliang Li, Peng Xu
RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9. Genome biology 25 (1) (2024)
George Hunt, Roshan Vaid, Sergei Pirogov, Alexander Pfab, Christoph Ziegenhain, Rickard Sandberg, Johan Reimegård, Mattias Mannervik
Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network. Genome biology 25 (1) (2024)
Kaishu Mason, Anuja Sathe, Paul R Hess, Jiazhen Rong, Chi-Yun Wu, Emma Furth, Katalin Susztak, Jonathan Levinsohn, Hanlee P Ji, Nancy Zhang
Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions. Genome biology 25 (1) (2024)
Kaishu Mason, Anuja Sathe, Paul R Hess, Jiazhen Rong, Chi-Yun Wu, Emma Furth, Katalin Susztak, Jonathan Levinsohn, Hanlee P Ji, Nancy Zhang
Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions. Genome biology 25 (1) (2024)
Ahmed Abbas, Khyati Chandratre, Yunpeng Gao, Jiapei Yuan, Michael Q Zhang, Ram S Mani
ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features. Genome biology 25 (1) (2024)
Yanying Yu, Sandra Gawlitt, Lisa Barros de Andrade E Sousa, Erinc Merdivan, Marie Piraud, Chase L Beisel, Lars Barquist
Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration. Genome biology 25 (1) (2024)
Yanying Yu, Sandra Gawlitt, Lisa Barros de Andrade E Sousa, Erinc Merdivan, Marie Piraud, Chase L Beisel, Lars Barquist
Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration. Genome biology 25 (1) (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Hongyu Luo, Linjiang Lao, Kit Sing Au, Hope Northrup, Xiao He, Diane Forget, Marie-Soleil Gauthier, Benoit Coulombe, Isabelle Bourdeau, Wei Shi, Lucia Gagliardi, Maria Candida Barisson Villares Fragoso, Junzheng Peng, Jiangping Wu
ARMC5 controls the degradation of most Pol II subunits, and ARMC5 mutation increases neural tube defect risks in mice and humans. Genome biology 25 (1) (2024)
Hamid Kian Gaikani, Monika Stolar, Divya Kriti, Corey Nislow, Guri Giaever
From beer to breadboards: yeast as a force for biological innovation. Genome biology 25 (1) (2024)
Haidong Yi, Alec Plotkin, Natalie Stanley
Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets. Genome biology 25 (1) (2024)
Winston Lau, Aminah Ali, Hannah Maude, Toby Andrew, Dallas M Swallow, Nikolas Maniatis
The hazards of genotype imputation when mapping disease susceptibility variants. Genome biology 25 (1) (2024)
Roberto Vera Alvarez, David Landsman
GTax: improving de novo transcriptome assembly by removing foreign RNA contamination. Genome biology 25 (1) (2024)
Charles E Breeze, Eric Haugen, María Gutierrez-Arcelus, Xiaozheng Yao, Andrew Teschendorff, Stephan Beck, Ian Dunham, John Stamatoyannopoulos, Nora Franceschini, Mitchell J Machiela, Sonja I Berndt
FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases. Genome biology 25 (1) (2024)
Xiang Zhu, Shining Ma, Wing Hung Wong
Genetic effects of sequence-conserved enhancer-like elements on human complex traits. Genome biology 25 (1) (2024)
Landen Gozashti, Hopi E Hoekstra
Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome biology 25 (1) (2024)
Sarah E Cooper, Matthew A Coelho, Magdalena E Strauss, Aleksander M Gontarczyk, Qianxin Wu, Mathew J Garnett, John C Marioni, Andrew R Bassett
scSNV-seq: high-throughput phenotyping of single nucleotide variants by coupled single-cell genotyping and transcriptomics. Genome biology 25 (1) (2024)
Xiang Zhu, Shining Ma, Wing Hung Wong
Genetic effects of sequence-conserved enhancer-like elements on human complex traits. Genome biology 25 (1) (2024)
Shujun Ou, Ning Jiang, Candice N Hirsch, Matthew B Hufford
Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome biology 25 (1) (2024)
Liang Yang, Jiali Lyu, Xi Li, Gaigai Guo, Xueya Zhou, Taoyu Chen, Yi Lin, Tingting Li
Phase separation as a possible mechanism for dosage sensitivity. Genome biology 25 (1) (2024)
Kade P Pettie, Maxwell Mumbach, Amanda J Lea, Julien Ayroles, Howard Y Chang, Maya Kasowski, Hunter B Fraser
Chromatin activity identifies differential gene regulation across human ancestries. Genome biology 25 (1) (2024)
Haidong Yi, Alec Plotkin, Natalie Stanley
Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets. Genome biology 25 (1) (2024)
Christopher K Tuggle, Jennifer L Clarke, Brenda M Murdoch, Eric Lyons, Nicole M Scott, Bedrich Beneš, Jacqueline D Campbell, Henri Chung, Courtney L Daigle, Sruti Das Choudhury, Jack C M Dekkers, Joao R R Dórea, David S Ertl, Max Feldman, Breno O Fragomeni, Janet E Fulton, Carmela R Guadagno, Darren E Hagen, Andrew S Hess, Luke M Kramer, Carolyn J Lawrence-Dill, Alexander E Lipka, Thomas Lübberstedt, Fiona M McCarthy, Stephanie D McKay, Seth C Murray, Penny K Riggs, Troy N Rowan, Moira J Sheehan, Juan P Steibel, Addie M Thompson, Kara J Thornton, Curtis P Van Tassell, Patrick S Schnable
Current challenges and future of agricultural genomes to phenomes in the USA. Genome biology 25 (1) (2024)
Jizeng Jia, Yilin Xie, Jingfei Cheng, Chuizheng Kong, Meiyue Wang, Lifeng Gao, Fei Zhao, Jingyu Guo, Kai Wang, Guangwei Li, Dangqun Cui, Tiezhu Hu, Guangyao Zhao, Daowen Wang, Zhengang Ru, Yijing Zhang
Author Correction: Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression. Genome biology 25 (1) (2024)
Landen Gozashti, Hopi E Hoekstra
Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome biology 25 (1) (2024)