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Publications and Data

AmpliDrop™ Publications

Single-Molecule Barcoding Technology for Single-Cell Genomics (2024) (UST)

Single-Molecule Barcoding Technology for Single-Cell Genomics (2024) PDF

Ivan Garcia-Bassets, Guoya Mo, Yu Xia, Tsai-Chin Wu, Immanuel Mekuria, Veronika Mikhaylova, Madison Rzepka, Tetsuya Kawamura, Peter L. Chang, Amber Paasch, Long Pham, Surya Shiv Venugopal, Sandra Sanchez, Janaina S. de Souza, Likun Yao, Sifeng Gu, Zsolt Bodai, Alexis C. Komor, Alysson R. Muotri, Joy Wang, Yong Wang, Ming Lei, Angels Almenar-Queralt, and Zhoutao Chen

View in: BioRxiv

TREX1 is required for microglial cholesterol homeostasis and oligodendrocyte terminal differentiation in human neural assembloids (2024) (UST)

TREX1 is required for microglial cholesterol homeostasis and oligodendrocyte terminal differentiation in human neural assembloids (2024) PDF

Gabriela Goldberg, Luisa Coelho, Guoya Mo, Laura A. Adang, Meenakshi Patne, Zhoutao Chen, Ivan Garcia-Bassets,
Pinar Mesci, Alysson R. Muotri

View: PubMed

TELL-Seq™ Publications

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera) (2024)

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera) (PDF)

Kimberly K. O. Walden, Yanghui Cao, Christopher J. Fields, Alvaro G. Hernandez, Gloria A. Rendon, Gene E. Robinson, Rachel K. Skinner, Jeffrey A. Stein, Christopher H. Dietrich

View in: Molecular Ecology Resources

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes byTELL-Seq (2024)

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes by TELL-Seq PDF

Zhuoying Wu, Ting Zhang, Sheng Li, Lingzhu Shen, Zhangnv Yang,Yunfeng
Yang, Xuanheng Chen, Bolin Li, Shicong Zhou, Xintian Zhou, Beibei Wu, Jianmin
Jiang, Xiao Li

View in: bioRxiv

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method (2024) (UST)

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method (PDF)

Veronika Mikhaylova, Madison Rzepka, Tetsuya Kawamura, Yu Xia, Peter L. Chang, Shiguo Zhou, Amber Paasch, Long Pham, Naisarg Modi, Likun Yao,
Adrian Perez‑Agustin, Sara Pagans, T. Christian Boles, Ming Lei, Yong Wang, Ivan Garcia‑Bassets, Zhoutao Chen

View in: Nature

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert (2024)

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert (PDF)

Rosalina Stancheva, Arun Sethuraman, Hossein Khadivar,
Jenna Archambeau, Ella Caughran, Ashley Chang, Brad Hunter, Christian Ihenyen, Marvin Onwukwe, Dariana Palacios, Chloe La Prairie, Nicole Read, Julianna Tsang, Brianna Vega, Cristina Velasquez, Xiaoyu Zhang, Elinne Becket, Betsy Read

View in: Genome Sequences

TELL-Seq™ Publications

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera) (2024)

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera) (PDF)

Kimberly K. O. Walden, Yanghui Cao, Christopher J. Fields, Alvaro G. Hernandez, Gloria A. Rendon, Gene E. Robinson, Rachel K. Skinner, Jeffrey A. Stein, Christopher H. Dietrich

View in: Molecular Ecology Resources

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes byTELL-Seq (2024)

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes by TELL-Seq PDF

Zhuoying Wu, Ting Zhang, Sheng Li, Lingzhu Shen, Zhangnv Yang,Yunfeng
Yang, Xuanheng Chen, Bolin Li, Shicong Zhou, Xintian Zhou, Beibei Wu, Jianmin
Jiang, Xiao Li

View in: bioRxiv

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method (2024) (UST)

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method (PDF)

Veronika Mikhaylova, Madison Rzepka, Tetsuya Kawamura, Yu Xia, Peter L. Chang, Shiguo Zhou, Amber Paasch, Long Pham, Naisarg Modi, Likun Yao,
Adrian Perez‑Agustin, Sara Pagans, T. Christian Boles, Ming Lei, Yong Wang, Ivan Garcia‑Bassets, Zhoutao Chen

View in: Nature

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert (2024)

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert (PDF)

Rosalina Stancheva, Arun Sethuraman, Hossein Khadivar,
Jenna Archambeau, Ella Caughran, Ashley Chang, Brad Hunter, Christian Ihenyen, Marvin Onwukwe, Dariana Palacios, Chloe La Prairie, Nicole Read, Julianna Tsang, Brianna Vega, Cristina Velasquez, Xiaoyu Zhang, Elinne Becket, Betsy Read

View in: Genome Sequences

TELL-Seq™ Publications

Microbial Isolate and Other Small Genome De Novo Sequencing

"Low-cost and highly efficient generation of near-complete bacterial pathogen genomes by TELL-Seq" (2024) bioRxiv DOI: 608388

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes by TELL-Seq (PDF)

Large Genome De Novo Sequencing and Scaffolding

"High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera)" (2024) PMID: 39155537

"High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera)" (2024) PMID: 39155537

"High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera)" (2024) PMID: 39155537

TELL-Seq™ Publications

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera) (2024)

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera) (PDF)

Kimberly K. O. Walden, Yanghui Cao, Christopher J. Fields, Alvaro G. Hernandez, Gloria A. Rendon, Gene E. Robinson, Rachel K. Skinner, Jeffrey A. Stein, Christopher H. Dietrich

View in: Molecular Ecology Resources

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes byTELL-Seq (2024)

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes by TELL-Seq PDF

Zhuoying Wu, Ting Zhang, Sheng Li, Lingzhu Shen, Zhangnv Yang,Yunfeng
Yang, Xuanheng Chen, Bolin Li, Shicong Zhou, Xintian Zhou, Beibei Wu, Jianmin
Jiang, Xiao Li

View in: bioRxiv

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method (2024) (UST)

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method (PDF)

Veronika Mikhaylova, Madison Rzepka, Tetsuya Kawamura, Yu Xia, Peter L. Chang, Shiguo Zhou, Amber Paasch, Long Pham, Naisarg Modi, Likun Yao,
Adrian Perez‑Agustin, Sara Pagans, T. Christian Boles, Ming Lei, Yong Wang, Ivan Garcia‑Bassets, Zhoutao Chen

View in: Nature

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert (2024)

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert (PDF)

Rosalina Stancheva, Arun Sethuraman, Hossein Khadivar,
Jenna Archambeau, Ella Caughran, Ashley Chang, Brad Hunter, Christian Ihenyen, Marvin Onwukwe, Dariana Palacios, Chloe La Prairie, Nicole Read, Julianna Tsang, Brianna Vega, Cristina Velasquez, Xiaoyu Zhang, Elinne Becket, Betsy Read

View in: Genome Sequences

LRTK a platform agnostic toolkit for linked-read analysis of both human genome and metagenome (2024)

LRTK a platform agnostic toolkit for linked-read analysis of both human genome and metagenome (PDF)

Chao Yang, Zhenmiao Zhang, Yufen Huang, Xuefeng Xie,
Herui Liao, Jin Xiao, Werner Pieter Veldsman, Kejing Yin,
Xiaodong Fang, Lu Zhang

View: GigaScience

Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre (2024)

Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre (PDF)

J. M. Tsuji, N. A. Shaw, S. Nagashima, J. J. Venkiteswaran, S. L. Schiff, T. Watanabe,
M. Fukui, S. Hanada, M. Tank & J. D. Neufeld

View in: Nature

Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity (2024)

Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity (PDF)

Zhenmiao Zhang, Jin Xiao, Hongbo Wang, Chao Yang, Yufen Huang, Zhen Yue, Yang Chen, Lijuan Han, Kejing Yin, Aiping Lyu, Xiaodong Fang & Lu Zhang

View: Nature

Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease (2023)

Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease (PDF)

Faith M. Anderson, Noelle D. Visser, Kevin R. Amses, Andrea Hodgins-Davis, Alexandra M. Weber, Katura M. Metzner, Michael J. McFadden, Ryan E. Mills, Matthew J. O’Meara, Timothy Y. James, Teresa R. O’Meara

View in: PLOS Biology

Understanding the impact of radical changes in diet and the gut microbiota on brain function and structure rationale and design of the EMBRACE study (2023)

Understanding the impact of radical changes in diet and the gut microbiota on brain function and structure rationale and design of the EMBRACE study (PDF)

Tair Ben-Porat, Angela Alberga, Marie-Claude Audet, Sylvie Belleville, Tamara R. Cohen, Pierre Y. Garneau, Kim L. Lavoie, Patrick Marion, Samira Mellah, Radu Pescarus, Elham Rahme, Sylvia Santosa, Anne-Sophie Studer, Dajana Vuckovic, Robbie Woods,
Reyhaneh Yousefi, Simon L. Bacon

View in: Surgery for Obesity and Related Diseases

Benchmarking genome assembly methods on metagenomic sequencing data (2023)

Zhenmiao Zhang, Chao Yang, Werner Pieter Veldsman, Xiaodong Fang and Lu Zhang

View in: Briefings in Bioinformatics

SpLitteR: Diploid genome assembly using TELL-Seq linked-reads and assembly graphs (2023)

SpLitteR: Diploid genome assembly using TELL-Seq linked-reads and assembly graphs (PDF)

IVAN TOLSTOGANOV, ZHOUTAO CHEN, PAVEL A. PEVZNER, ANTON KOROBEYNIKOV

View: BioRxiv (2023)

Genome Sequence of Lichtheimia ornata, an Emerging Opportunistic Mucorales Pathogen (2023)

Genome Sequence of Lichtheimia ornata, an Emerging Opportunistic Mucorales Pathogen (PDF)

TERRANCE SHEA, JASON T. MOHABIR, TANIA
KURBESSOIAN, BRITTANY BERDY, JAMES FONTAINE, ANDREAS GNIRKE, JONATHAN LIVNY,
JASON E. STAJICH, CHRISTINA A. CUOMO

View: Genome Sequences

Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen (2023)

Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen (PDF)

ANDREW D SWEET, DANIEL R BROWNE, ALVARO G HERNANDEZ, KEVIN P JOHNSON, STEPHEN L CAMERON AUTHOR NOTES

View: Oxford Academic (2023)

Genome of a novel Sediminibacterium discovered in association with two species of freshwater cyanobacteria from streams in Southern California (2022)

Genome of a novel Sediminibacterium discovered in association with two species of freshwater cyanobacteria from streams in Southern California (PDF)

ARUN SETHURAMAN, ET AL.

View: G3 Genes | Genomes | Genetics, jkac123, May 2022

Whole-genome risk prediction of common diseases in human preimplantation embryos (2022)

Whole-genome risk prediction of common diseases in human preimplantation embryos (PDF)

AKASH KUMAR, ET AL.

View: Nat Med., March 2022; 28(3): 513–516

Linked‑read sequencing for detecting short tandem repeat expansions (2022)

Linked‑read sequencing for detecting short tandem repeat expansions (PDF)

READMAN CHIU, INDHU-SHREE RAJAN-BABU, INANC BIROL & JAN M. FRIEDMAN

View: Nature, Sci Rep 12, 9352 (2022)

Ultra-low input single tube linked-read library method enables short-read second-generation sequencing systems to generate highly accurate and economical long-range sequencing information routinely (2000) (UST)

Ultra-low input single tube linked-read library method enables short-read second-generation sequencing systems to generate highly accurate and economical long-range sequencing (PDF)

Zhoutao Chen, Long Pham, Tsai-Chin Wu, Guoya Mo, Yu Xia, Peter L. Chang,
Devin Porter, Tan Phan, Huu Che, Hao Tran, Vikas Bansal, Justin Shaffer, Pedro Belda-Ferre, Greg Humphrey, Rob Knight, Pavel Pevzner, Son Pham, Yong Wang, and Ming Lei

View in: Genome Research

cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs (2019)

cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs (PDF)

IVAN TOLSTOGANOV, ANTON BANKEVICH, ZHOUTAO CHEN, PAVEL A PEVZNER

View: Bioinformatics, Volume 35, Issue 14, July 2019, Pages i61–i70

Public Data Set

Ultra-low input single tube linked read library method enables short read NGS systems to generate highly accurate and economical long-range sequencing information...

Ultra-low input single tube linked read library method enables short read NGS systems to generate highly accurate and economical long-range sequencing information for de novo assembly and haplotype phasing

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA591637

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Publications and Data

AmpliDrop™ Publications

Single-Molecule Barcoding Technology for Single-Cell Genomics (2024) (UST)

TREX1 is required for microglial cholesterol homeostasis and oligodendrocyte terminal differentiation in human neural assembloids (2024) (UST)

TELL-Seq™ Publications

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera) (2024)

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes byTELL-Seq (2024)

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method (2024) (UST)

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert (2024)

TELL-Seq™ Publications

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera) (2024)

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes byTELL-Seq (2024)

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method (2024) (UST)

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert (2024)

TELL-Seq™ Publications

Microbial Isolate and Other Small Genome De Novo Sequencing

Large Genome De Novo Sequencing and Scaffolding

TELL-Seq™ Publications

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera) (2024)

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes byTELL-Seq (2024)

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method (2024) (UST)

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert (2024)

LRTK a platform agnostic toolkit for linked-read analysis of both human genome and metagenome (2024)

Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre (2024)

Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity (2024)

Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease (2023)

Understanding the impact of radical changes in diet and the gut microbiota on brain function and structure rationale and design of the EMBRACE study (2023)

Benchmarking genome assembly methods on metagenomic sequencing data (2023)

SpLitteR: Diploid genome assembly using TELL-Seq linked-reads and assembly graphs (2023)

Genome Sequence of Lichtheimia ornata, an Emerging Opportunistic Mucorales Pathogen (2023)

Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen (2023)

Genome of a novel Sediminibacterium discovered in association with two species of freshwater cyanobacteria from streams in Southern California (2022)

Whole-genome risk prediction of common diseases in human preimplantation embryos (2022)

Linked‑read sequencing for detecting short tandem repeat expansions (2022)

Ultra-low input single tube linked-read library method enables short-read second-generation sequencing systems to generate highly accurate and economical long-range sequencing information routinely (2000) (UST)

cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs (2019)

Public Data Set

Ultra-low input single tube linked read library method enables short read NGS systems to generate highly accurate and economical long-range sequencing information...

Posters

Publications and Data

AmpliDrop™ Publications

Single-Molecule Barcoding Technology for Single-Cell Genomics (2024) (UST)

TREX1 is required for microglial cholesterol homeostasis and oligodendrocyte terminal differentiation in human neural assembloids (2024) (UST)

TELL-Seq™ Publications

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera) (2024)

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes byTELL-Seq (2024)

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method (2024) (UST)

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert (2024)

TELL-Seq™ Publications

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera) (2024)

Collapsible content

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes byTELL-Seq (2024)

Collapsible content

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method (2024) (UST)

Collapsible content

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert (2024)

TELL-Seq™ Publications

Microbial Isolate and Other Small Genome De Novo Sequencing

Collapsible content

Large Genome De Novo Sequencing and Scaffolding

TELL-Seq™ Publications

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera) (2024)

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes byTELL-Seq (2024)

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method (2024) (UST)

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert (2024)

LRTK a platform agnostic toolkit for linked-read analysis of both human genome and metagenome (2024)

Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre (2024)

Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity (2024)

Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease (2023)

Understanding the impact of radical changes in diet and the gut microbiota on brain function and structure rationale and design of the EMBRACE study (2023)

Benchmarking genome assembly methods on metagenomic sequencing data (2023)

Collapsible content

SpLitteR: Diploid genome assembly using TELL-Seq linked-reads and assembly graphs (2023)

Genome Sequence of Lichtheimia ornata, an Emerging Opportunistic Mucorales Pathogen (2023)

Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen (2023)

Genome of a novel Sediminibacterium discovered in association with two species of freshwater cyanobacteria from streams in Southern California (2022)

Whole-genome risk prediction of common diseases in human preimplantation embryos (2022)

Linked‑read sequencing for detecting short tandem repeat expansions (2022)

Ultra-low input single tube linked-read library method enables short-read second-generation sequencing systems to generate highly accurate and economical long-range sequencing information routinely (2000) (UST)

cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs (2019)

Public Data Set

Ultra-low input single tube linked read library method enables short read NGS systems to generate highly accurate and economical long-range sequencing information...

Posters