Martin Hemberg

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 59

Top Topics

Endothelial Cells

Network Analysis

Top Venues

Nature communications

bioRxiv : the preprint server for biology

BMC bioinformatics

This page only lists publications with an associated author ORCID identifier.

Publications

Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Author Correction: Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Jae-Won Cho, Jingyi Cao, Martin Hemberg
Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution. Genome biology 25 (1) (2024)
Carina Shiau, Jingyi Cao, Dennis Gong, Mark T Gregory, Nicholas J Caldwell, Xunqin Yin, Jae-Won Cho, Peter L Wang, Jennifer Su, Steven Wang, Jason W Reeves, Tae Kyung Kim, Youngmi Kim, Jimmy A Guo, Nicole A Lester, Jung Woo Bae, Ryan Zhao, Nathan Schurman, Jamie L Barth, Maria L Ganci, Ralph Weissleder, Tyler Jacks, Motaz Qadan, Theodore S Hong, Jennifer Y Wo, Hannah Roberts, Joseph M Beechem, Carlos Fernandez-Del Castillo, Mari A Mino-Kenudson, David Tsai Ting, Martin Hemberg, William L Hwang
Spatially resolved analysis of pancreatic cancer identifies therapy-associated remodeling of the tumor microenvironment. Nature genetics (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Yuyao Song, Guillermo Parada, Jimmy Tsz Hang Lee, Martin Hemberg
Mining alternative splicing patterns in scRNA-seq data using scASfind. Genome biology 25 (1) (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Author Correction: Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Yuyao Song, Guillermo Parada, Jimmy Tsz Hang Lee, Martin Hemberg
Mining alternative splicing patterns in scRNA-seq data using scASfind. Genome biology 25 (1) (2024)
Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Jae-Won Cho, Jingyi Cao, Martin Hemberg
Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution. Genome biology 25 (1) (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Author Correction: Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Yuyao Song, Guillermo Parada, Jimmy Tsz Hang Lee, Martin Hemberg
Mining alternative splicing patterns in scRNA-seq data using scASfind. Genome biology 25 (1) (2024)
Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Timothy Ph Sit, Rachael C Feord, Alexander W E Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline A Lancaster, András Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau
MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv : the preprint server for biology (2024)
Jae-Won Cho, Jingyi Cao, Martin Hemberg
Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution. Genome biology 25 (1) (2024)
Jae-Won Cho, Jingyi Cao, Martin Hemberg
Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution. Genome biology 25 (1) (2024)
Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Wei E Gordon, Seungbyn Baek, Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L Fong, Nayeon Kim, Alexander V Galazyuk, Hoyoung Lee, Melissa R Ingala, Nancy B Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15 (1) (2024)
Ioannis Mouratidis, Candace S Y Chan, Nikol Chantzi, Georgios Christos Tsiatsianis, Martin Hemberg, Nadav Ahituv, Ilias Georgakopoulos-Soares
Quasi-prime peptides: identification of the shortest peptide sequences unique to a species. NAR genomics and bioinformatics 5 (2) (2023)
Jacob Hepkema, Nicholas Keone Lee, Benjamin J Stewart, Siwat Ruangroengkulrith, Varodom Charoensawan, Menna R Clatworthy, Martin Hemberg
Predicting the impact of sequence motifs on gene regulation using single-cell data. Genome biology 24 (1) (2023)
Ioannis Mouratidis, Candace S Y Chan, Nikol Chantzi, Georgios Christos Tsiatsianis, Martin Hemberg, Nadav Ahituv, Ilias Georgakopoulos-Soares
Quasi-prime peptides: identification of the shortest peptide sequences unique to a species. NAR genomics and bioinformatics 5 (2) (2023)
Fu Xiang Quah, Martin Hemberg
SC3s: efficient scaling of single cell consensus clustering to millions of cells. BMC bioinformatics 23 (1) (2022)
Fredrik Salmen, Joachim De Jonghe, Tomasz S Kaminski, Anna Alemany, Guillermo E Parada, Joe Verity-Legg, Ayaka Yanagida, Timo N Kohler, Nicholas Battich, Floris van den Brekel, Anna L Ellermann, Alfonso Martinez Arias, Jennifer Nichols, Martin Hemberg, Florian Hollfelder, Alexander van Oudernaarden
High-throughput total RNA sequencing in single cells using VASA-seq. Nature biotechnology (2022)
Fu Xiang Quah, Martin Hemberg
SC3s: efficient scaling of single cell consensus clustering to millions of cells. BMC bioinformatics 23 (1) (2022)
Kevin Riehl, Cristian Riccio, Eric A Miska, Martin Hemberg
TransposonUltimate: software for transposon classification, annotation and detection. Nucleic acids research 50 (11) (2022)
Fu Xiang Quah, Martin Hemberg
SC3s: efficient scaling of single cell consensus clustering to millions of cells. BMC bioinformatics 23 (1) (2022)
Ilias Georgakopoulos-Soares, Guillermo E Parada, Hei Yuen Wong, Ragini Medhi, Giulia Furlan, Roberto Munita, Eric A Miska, Chun Kit Kwok, Martin Hemberg
Alternative splicing modulation by G-quadruplexes. Nature communications 13 (1) (2022)
Fu Xiang Quah, Martin Hemberg
SC3s: efficient scaling of single cell consensus clustering to millions of cells. BMC bioinformatics 23 (1) (2022)
Ilias Georgakopoulos-Soares, Candace S Y Chan, Nadav Ahituv, Martin Hemberg
High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation. Genome biology 23 (1) (2022)
Kathryn J Gray Guseh, Martin Hemberg, S Ananth Karumanchi
Cell-Free RNA Transcriptome and Prediction of Adverse Pregnancy Outcomes. Clinical chemistry 68 (11) (2022)
Junha Cha, Jiwon Yu, Jae-Won Cho, Martin Hemberg, Hoyoung Lee
scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes. Nucleic acids research (2022)
Guste Urbonaite, Jimmy Tsz Hang Lee, Ping Liu, Guillermo E Parada, Martin Hemberg, Murat Acar
Author Correction: A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels. Communications biology 4 (1) (2021)
Guillermo E Parada, Roberto Munita, Ilias Georgakopoulos-Soares, Hugo J R Fernandes, Veronika R Kedlian, Emmanouil Metzakopian, Maria Estela Andres, Eric A Miska, Martin Hemberg
MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development. Genome biology 22 (1) (2021)
Guste Urbonaite, Jimmy Tsz Hang Lee, Ping Liu, Guillermo E Parada, Martin Hemberg, Murat Acar
A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels. Communications biology 4 (1) (2021)
Jimmy Tsz Hang Lee, Nikolaos Patikas, Vladimir Yu Kiselev, Martin Hemberg
Fast searches of large collections of single-cell data using scfind. Nature methods 18 (3) (2021)
Haynes Heaton, Arthur M Talman, Andrew J Knights, Maria Imaz, Daniel J Gaffney, Richard Durbin, Martin Hemberg, Mara N K Lawniczak
Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Nature methods 17 (6) (2020)
Virginia M Howick, Andrew J C Russell, Tallulah S Andrews, Haynes Heaton, Adam J Reid, Kedar Nath Natrajan, Hellen Butungi, Tom Metcalf, Lisa H Verzier, Julian C Rayner, Matthew Berriman, Jeremy Keith Herren, Oliver Billker, Martin Hemberg, Arthur M Talman, Mara N K Lawniczak
The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle. Science (New York, N.Y.) 365 (6455) (2020)
Tallulah S Andrews, Vladimir Yu Kiselev, Davis J McCarthy, Martin Hemberg
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data. Nature protocols 16 (1) (2020)
Ilias Georgakopoulos-Soares, Gene Ching Chiek Koh, Sophie E Momen, Josef Jiricny, Martin Hemberg, Serena Nik-Zainal
Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts. Nature communications 11 (1) (2020)
Omer Ali Bayraktar, Theresa Bartels, Staffan Holmqvist, Vitalii Kleshchevnikov, Araks Martirosyan, Damon Polioudakis, Lucile Ben Haim, Adam M H Young, Mykhailo Y Batiuk, Kirti Prakash, Alexander Brown, Kenny Roberts, Mercedes F Paredes, Riki Kawaguchi, John H Stockley, Khalida Sabeur, Sandra M Chang, Eric J Huang, Peter Hutchinson, Erik M Ullian, Martin Hemberg, Giovanni Coppola, Matthew G Holt, Daniel H Geschwind, David H Rowitch
Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map. Nature neuroscience 23 (4) (2020)
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg
Challenges in unsupervised clustering of single-cell RNA-seq data. Nature reviews. Genetics 20 (5) (2019)
Jennifer Westoby, Marcela Sjöberg Herrera, Anne C Ferguson-Smith, Martin Hemberg
Simulation-based benchmarking of isoform quantification in single-cell RNA-seq. Genome biology 19 (1) (2018)
Vladimir Yu Kiselev, Andrew Yiu, Martin Hemberg
scmap: projection of single-cell RNA-seq data across data sets. Nature methods 15 (5) (2018)