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Bone marrow endosteal stem cells dictate active osteogenesis and aggressive tumorigenesis.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-38034-2
By:
- Matsushita, Yuki;
- Liu, Jialin;
- Chu, Angel Ka Yan;
- Tsutsumi-Arai, Chiaki;
- Nagata, Mizuki;
- Arai, Yuki;
- Ono, Wanida;
- Yamamoto, Kouhei;
- Saunders, Thomas L.;
- Welch, Joshua D.;
- Ono, Noriaki
Publication type:
Article
A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues.
Published in:
Nucleic Acids Research, 2016, v. 44, n. 19, p. 9190, doi. 10.1093/nar/gkw620
By:
- Lyons, Shawn M.;
- Cunningham, Clark H.;
- Welch, Joshua D.;
- Groh, Beezly;
- Guo, Andrew Y.;
- Bruce Wei;
- Whitfield, Michael L.;
- Yue Xiong;
- Marzluff, William F.
Publication type:
Article
Selective single cell isolation for genomics using microraft arrays.
Published in:
Nucleic Acids Research, 2016, v. 44, n. 17, p. 8292, doi. 10.1093/nar/gkw700
By:
- Welch, Joshua D.;
- Williams, Lindsay A.;
- DiSalvo, Matthew;
- Brandt, Alicia T.;
- Marayati, Raoud;
- Sims, Christopher E.;
- Allbritton, Nancy L.;
- Prins, Jan F.;
- Jen Jen Yeh;
- Jones, Corbin D.
Publication type:
Article
Robust detection of alternative splicing in a population of single cells.
Published in:
Nucleic Acids Research, 2016, v. 44, n. 8, p. 1, doi. 10.1093/nar/gkv1525
By:
- Welch, Joshua D.;
- Yin Hu;
- Prins, Jan F.
Publication type:
Article
UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorization.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28431-4
By:
- Kriebel, April R.;
- Welch, Joshua D.
Publication type:
Article
Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction.
Published in:
Nature Biotechnology, 2023, v. 41, n. 3, p. 387, doi. 10.1038/s41587-022-01476-y
By:
- Li, Chen;
- Virgilio, Maria C.;
- Collins, Kathleen L.;
- Welch, Joshua D.
Publication type:
Article
Iterative single-cell multi-omic integration using online learning.
Published in:
Nature Biotechnology, 2021, v. 39, n. 8, p. 1000, doi. 10.1038/s41587-021-00867-x
By:
- Gao, Chao;
- Liu, Jialin;
- Kriebel, April R.;
- Preissl, Sebastian;
- Luo, Chongyuan;
- Castanon, Rosa;
- Sandoval, Justin;
- Rivkin, Angeline;
- Nery, Joseph R.;
- Behrens, Margarita M.;
- Ecker, Joseph R.;
- Ren, Bing;
- Welch, Joshua D.
Publication type:
Article
PyLiger: scalable single-cell multi-omic data integration in Python.
Published in:
Bioinformatics, 2022, v. 38, n. 10, p. 2946, doi. 10.1093/bioinformatics/btac190
By:
- Lu, Lu;
- Welch, Joshua D
Publication type:
Article
SquiggleNet: real-time, direct classification of nanopore signals.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02511-y
By:
- Bao, Yuwei;
- Wadden, Jack;
- Erb-Downward, John R.;
- Ranjan, Piyush;
- Zhou, Weichen;
- McDonald, Torrin L.;
- Mills, Ryan E.;
- Boyle, Alan P.;
- Dickson, Robert P.;
- Blaauw, David;
- Welch, Joshua D.
Publication type:
Article
Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics.
Published in:
2021
By:
- Cao, Kim-Anh Lê;
- Abadi, Al J.;
- Davis-Marcisak, Emily F.;
- Hsu, Lauren;
- Arora, Arshi;
- Coullomb, Alexis;
- Deshpande, Atul;
- Feng, Yuzhou;
- Jeganathan, Pratheepa;
- Loth, Melanie;
- Meng, Chen;
- Mu, Wancen;
- Pancaldi, Vera;
- Sankaran, Kris;
- Righelli, Dario;
- Singh, Amrit;
- Sodicoff, Joshua S.;
- Stein-O'Brien, Genevieve L.;
- Subramanian, Ayshwarya;
- Welch, Joshua D.
Publication type:
Correction Notice
Community-wide hackathons to identify central themes in single-cell multi-omics.
Published in:
2021
By:
- Lê Cao, Kim-Anh;
- Abadi, Al J.;
- Davis-Marcisak, Emily F.;
- Hsu, Lauren;
- Arora, Arshi;
- Coullomb, Alexis;
- Deshpande, Atul;
- Feng, Yuzhou;
- Jeganathan, Pratheepa;
- Loth, Melanie;
- Meng, Chen;
- Mu, Wancen;
- Pancaldi, Vera;
- Sankaran, Kris;
- Righelli, Dario;
- Singh, Amrit;
- Sodicoff, Joshua S.;
- Stein-O'Brien, Genevieve L.;
- Subramanian, Ayshwarya;
- Welch, Joshua D.
Publication type:
Letter
Community-wide hackathons to identify central themes in single-cell multi-omics.
Published in:
2021
By:
- Lê Cao, Kim-Anh;
- Abadi, Al J.;
- Davis-Marcisak, Emily F.;
- Hsu, Lauren;
- Arora, Arshi;
- Coullomb, Alexis;
- Deshpande, Atul;
- Feng, Yuzhou;
- Jeganathan, Pratheepa;
- Loth, Melanie;
- Meng, Chen;
- Mu, Wancen;
- Pancaldi, Vera;
- Sankaran, Kris;
- Righelli, Dario;
- Singh, Amrit;
- Sodicoff, Joshua S.;
- Stein-O'Brien, Genevieve L.;
- Subramanian, Ayshwarya;
- Welch, Joshua D.
Publication type:
Letter
Community-wide hackathons to identify central themes in single-cell multi-omics.
Published in:
2021
By:
- Lê Cao, Kim-Anh;
- Abadi, Al J.;
- Davis-Marcisak, Emily F.;
- Hsu, Lauren;
- Arora, Arshi;
- Coullomb, Alexis;
- Deshpande, Atul;
- Feng, Yuzhou;
- Jeganathan, Pratheepa;
- Loth, Melanie;
- Meng, Chen;
- Mu, Wancen;
- Pancaldi, Vera;
- Sankaran, Kris;
- Singh, Amrit;
- Sodicoff, Joshua S.;
- Stein-O'Brien, Genevieve L.;
- Subramanian, Ayshwarya;
- Welch, Joshua D.;
- You, Yue
Publication type:
Letter
MichiGAN: sampling from disentangled representations of single-cell data using generative adversarial networks.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02373-4
By:
- Yu, Hengshi;
- Welch, Joshua D.
Publication type:
Article
Functional coordination of non‐myocytes plays a key role in adult zebrafish heart regeneration.
Published in:
EMBO Reports, 2021, v. 22, n. 11, p. 1, doi. 10.15252/embr.202152901
By:
- Ma, Hong;
- Liu, Ziqing;
- Yang, Yuchen;
- Feng, Dong;
- Dong, Yanhan;
- Garbutt, Tiffany A;
- Hu, Zhiyuan;
- Wang, Li;
- Luan, Changfei;
- Cooper, Cynthia D;
- Li, Yun;
- Welch, Joshua D;
- Qian, Li;
- Liu, Jiandong
Publication type:
Article
Word-based characterization of promoters involved in human DNA repair pathways.
Published in:
BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-S1-S18
By:
- Lichtenberg, Jens;
- Jacox, Edwin;
- Welch, Joshua D.;
- Kurz, Kyle;
- Xiaoyu Liang;
- Mary Qu Yang;
- Drews, Frank;
- Ecker, Klaus;
- Lee, Stephen S.;
- Elnitski, Laura;
- Welch, Lonnie R.
Publication type:
Article
The word landscape of the non-coding segments of the Arabidopsis thaliana genome.
Published in:
BMC Genomics, 2009, v. 10, p. 463, doi. 10.1186/1471-2164-10-463
By:
- Lichtenberg, Jens;
- Yilmaz, Alper;
- Welch, Joshua D.;
- Kurz, Kyle;
- Xiaoyu Liang;
- Drews, Frank;
- Ecker, Klaus;
- Lee, Stephen S.;
- Geisler, Matt;
- Grotewold, Erich;
- Welch, Lonnie R.
Publication type:
Article
WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures.
Published in:
BMC Bioinformatics, 2010, v. 11, p. 1, doi. 10.1186/1471-2105-11-S12-S6
By:
- Lichtenberg, Jens;
- Kurz, Kyle;
- Xiaoyu Liang;
- Al-ouran, Rami;
- Neiman, Lev;
- Nau, Lee J.;
- Welch, Joshua D.;
- Jacox, Edwin;
- Bitterman, Thomas;
- Ecker, Klaus;
- Elnitski, Laura;
- Drews, Frank;
- Lee, Stephen Sauchi;
- Welch, Lonnie R.
Publication type:
Article
SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data.
Published in:
Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-0975-3
By:
- Welch, Joshua D.;
- Hartemink, Alexander J.;
- Prins, Jan F.
Publication type:
Article
MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics.
Published in:
Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1269-0
By:
- Welch, Joshua D.;
- Hartemink, Alexander J.;
- Prins, Jan F.
Publication type:
Article
HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49635-w
By:
- Virgilio, Maria C.;
- Ramnani, Barkha;
- Chen, Thomas;
- Disbennett, W. Miguel;
- Lubow, Jay;
- Welch, Joshua D.;
- Collins, Kathleen L.
Publication type:
Article
Endosteal stem cells at the bone‐blood interface: A double‐edged sword for rapid bone formation: Bone marrow endosteal stem cells provide a robust source of bone‐making osteoblasts both in normal and abnormal bone formation.
Published in:
BioEssays, 2024, v. 46, n. 3, p. 1, doi. 10.1002/bies.202300173
By:
- Matsushita, Yuki;
- Liu, Jialin;
- Chu, Angel Ka Yan;
- Ono, Wanida;
- Welch, Joshua D.;
- Ono, Noriaki
Publication type:
Article
Jointly defining cell types from multiple single-cell datasets using LIGER.
Published in:
Nature Protocols, 2020, v. 15, n. 11, p. 3632, doi. 10.1038/s41596-020-0391-8
By:
- Liu, Jialin;
- Gao, Chao;
- Sodicoff, Joshua;
- Kozareva, Velina;
- Macosko, Evan Z.;
- Welch, Joshua D.
Publication type:
Article
Intercellular Interactions of an Adipogenic CXCL12‐Expressing Stromal Cell Subset in Murine Bone Marrow.
Published in:
Journal of Bone & Mineral Research, 2021, v. 36, n. 6, p. 1145, doi. 10.1002/jbmr.4282
By:
- Matsushita, Yuki;
- Chu, Angel Ka Yan;
- Ono, Wanida;
- Welch, Joshua D;
- Ono, Noriaki
Publication type:
Article
Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential.
Published in:
BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1227-8
By:
- Welch, Joshua D.;
- Baran-Gale, Jeanette;
- Perou, Charles M.;
- Sethupathy, Praveen;
- Prins, Jan F.
Publication type:
Article
A Wnt-mediated transformation of the bone marrow stromal cell identity orchestrates skeletal regeneration.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-019-14029-w
By:
- Matsushita, Yuki;
- Nagata, Mizuki;
- Kozloff, Kenneth M.;
- Welch, Joshua D.;
- Mizuhashi, Koji;
- Tokavanich, Nicha;
- Hallett, Shawn A.;
- Link, Daniel C.;
- Nagasawa, Takashi;
- Ono, Wanida;
- Ono, Noriaki
Publication type:
Article

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