Yu, Tianxiong
first name: Tianxiong
last name: Yu
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selected publications: Authorship 140440
education and training: Tongji University,
research areas: Phascolarctidae
research areas: RNA, Small Interfering
research areas: Endogenous Retroviruses
research areas: Gene Silencing
research areas: Evolution, Molecular
mailing address: Worcester MA 01655
positions: Instructor
positions: https://profiles.umassmed.edu/profile/96021269
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Rotation Projects: Potential Rotation Projects: There are numerous potential rotation project available in the Mello lab: Projects include: Investigation of RNAi and related mechanisms, including Piwi Argonaute pathways and their affects on fertility and epigenetic inheritance; Investigation of germline determination and cell-fate specification during embryogenesis; the exploration of CRISPR mediated genome editing tools for C. elegans and other organisms; and finally the use of CRISPR to generate C. elegans models for human genetic disease.
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webpage: https://profiles.umassmed.edu/profile/28866500

Weng, Zhiping
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Post Docs: The project aims to develop computational algorithms and software programs for analyzing high-throughput sequence data such as ChIP-Seq RNA-Seq small RNA sequencing data. PhD required. A strong background in computational biology especially experience with analyzing high-throughput sequencing data is highly desirable. Excellent communication and writing skills and the ability to work with experimental and computational collaborators are essential. To apply please forward CV cover letter and three references to: Zhiping.Weng@umassmed.edu
Rotation Projects: Please contact Dr. Weng for information on rotations that are available in her lab.
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Luban, Jeremy
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Endowed Chair Honorary Title: David J. Freelander Memorial Professor in AIDS Research
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preferred title: Professor

Theurkauf, William
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Post Docs: A postdoctoral position is available to study in this laboratory. Contact Dr. Theurkauf for additional details.
Rotation Projects: Rotation Projects Proper control of cell division and accurate chromosome segregation are fundamental to cell function and normal development. Chromosome segregation errors lead to birth defects, and abnormal cell division control is associated with essentially all cancers. A major aim of research in the laboratory is to understand cell cycle control and chromosome segregation mechanisms. We use a combination of classical and molecular genetics, high-resolution in vivo imaging, and biochemical techniques to define pathways that control the cell cycle and chromosome segregation in response to environmental insult (DNA damaging agents) and developmental queues. Rotation projects focus on the role of cell cycle checkpoint and tumor suppressor pathways during the earliest stages of embryogenesis, and cell cycle control of actin and microtubule reorganization during mitosis. Through these projects, students gain exposure of the art in vivo imaging and genetic and molecular manipulations of gene function to define pathways controlling cell division and chromosome segregation. Embryonic Patterning Essentially all cells are asymmetric, with structurally distinct surfaces and polarized internal organization. This asymmetry is essential to the specialized functions cells serve within complex multi-cellular organisms . A second area of interest focuses on the mechanisms that establish cellular asymmetry. In Drosophila, the embryonic axes are specified during oogenesis through the asymmetric localization of key morphogenetic molecules within the developing oocyte. We use axis specification in the fly as a model for the processes that establish cellular asymmetry. An intact microtubule network is essential to axis specification in the fly oocyte and to polarization of somatic. We hope to define the molecular functions for microtubules in establishing cellular asymmetry. We are currently using in vivo imaging techniques to directly characterize the microtubule dependent mRNA tran…
preferred title: Professor

Khvorova, Anastasia
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last name: Khvorova
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Person ID: 3413
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Endowed Chair Honorary Title: Remondi Family Chair in Biomedical Research
Post Docs: POSTDOCTORAL POSITION: RNAI PRECLINICAL DEVELOPMENT Excellent training opportunity for a person considering industrial carrier in drug development Oligonucleotides represent a new class of drugs, which have the promise to become a major class of future therapeutics. There are several classes of oligonucleotides which can efficiently silence genes in various tissues with acceptable level of toxicity. There are also new chemistries being developed to further improve oligonucleotide tissue distribution and cellular uptake. The successful candidate will be a key part of an intra-disciplinary team working with biologists and chemists to develop novel types of therapeutics for treatment of neurological disease, liver disease and orphan indications. The work will include compounds identification, screening, characterization, in vivo efficacy and PK/PD studies, novel assays development etc. In addition exposure and training in nucleic acid pre-clinical development, project management etc will be provided. QUALIFICATIONS: Applicants must have (or expect to obtain shortly) a Ph.D. in Chemistry, Organic Chemistry Biochemistry, Cell Biology, Molecular Biology or a related field , be bright, ambitious, independent and collaborative and ideally, have research experience in nucleic acid molecular cell biology or pharmacology.
Post Docs: RNAI MEDICINAL CHEMISTRY/ RNA OLIGONUCLEOTIDE CHEMISTRY Develop and characterize novel RNA chemistries to promote efficient oligonucleotide internalization and tissue distribution. Oligonucleotides represent a new class of drugs, which have the promise to become a major class of future therapeutics. There are several chemistries and formulations developed by us and others that effectively support oligo internalization and favorable PK/PD. In most cases in vivo efficacy is limited by (1) poor PK (2) inefficient tissue distribution (3) compound entrapment in biologically inactive intracellular compartments. The objective of future studies will be development of novel chemistries, which promote receptor mediated cellular internalization and/ or endosomal escape. The successful candidate will be responsible for the design and synthesis of novel RNA precursors, optimization of RNA synthesis and conjugation protocols and interface with the biology part of the lab. In addition, exposure to pre-clinical development programs and oligonucleotide manufacturing will be available. QUALIFICATIONS: Applicants must have (or expect to obtain shortly) a Ph.D. in Chemistry, Organic Chemistry Biochemistry, Cell Biology, Molecular Biology or a related field , be bright, ambitious, independent and collaborative and have previous experience in nucleic acid / oligonucleotide chemistry.
Post Docs: SMALL RNA TRAFFICKING Discover, characterize and adapt mechanisms of small RNA extracellular and intracellular trafficking for development of novel classes of oligonucleotide drugs. A serious limitation in realizing the potential of oligonucleotide based therapies has been the exceedingly inefficient transit of oligonucleotides from outside cells to the intracellular compartments where the biologically relevant activity happens. On the other hand, there are multiple lines of evidence supporting the notion that nature has implemented evolutionarily conserved mechanisms and pathways for efficiently trafficking small RNAs across cellular boundaries. The objective of future studies will be the systematic evaluation of mechanisms of cellular uptake of different classes of oligonucleotides and their comparison to mechanisms of native RNA trafficking using a combination of experimental approaches, including advanced RNA chemistry and high temporal and spatial resolution microscopy in living cells, Mass spectrometry, cell biology and others. The successful candidate will work closely with Victor Ambros and Silvia Corvera labs and the UMASS imaging group and receive training in RNA chemistry, biochemistry, cell biology and pre-clinical development. QUALIFICATIONS:Applicants must have (or expect to obtain shortly) a Ph.D. in Chemistry, Organic Chemistry Biochemistry, Cell Biology, Molecular Biology or a related field , be bright, ambitious, independent and collaborative and ideally, have research experience in nucleic acid molecular and cell biology
Rotation Projects: Our laboratory uses a combination of nucleic acid and oligonucleotide chemistry, biochemistry, cell biology, and pharmacology and develops and evaluate novel technologies for development of oligonucleotide therapeutics. A rotation project is available to develop and identify chemically modified self-delivering RNAi compounds for treatment of Huntington and other diseases.
preferred title: Professor

Zamore, Phillip
first name: Phillip
last name: Zamore
full name: Phillip D Zamore PhD
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latitude: 42.27587600000000
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Person ID: 418
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Endowed Chair Honorary Title: Gretchen Stone Cook Chair in Biomedical Sciences
Post Docs: A postdoctoral position is available to study in this laboratory. Contact Dr. Zamore for additional details
Rotation Projects: Potential Rotation Projects Our laboratory uses a combination of biochemistry, cell biology, and genetics to dissect the RNAi pathway. A rotation project is available to explore the mechanisms that underlie the RNAi phenomenon or the biological pathways in which RNAi enzymes participate in flies, mice and humans.
preferred title: Chair and Professor
webpage: https://profiles.umassmed.edu/profile/28866555
webpage: https://profiles.umassmed.edu/profile/28866537
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Tongji University,
educational organization: Tongji University
training location: Zha Bei Qu, 31, China
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Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin.
PubMed Identifier: 30257203
author list: Zhang G, Tu S, Yu T, Zhang XO, Parhad SS, Weng Z, Theurkauf WE
published in: Cell reports
information resource reference: Zhang G, Tu S, Yu T, Zhang XO, Parhad SS, Weng Z, Theurkauf WE. Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin. Cell Rep. 2018 09 25; 24(13):3413-3422.e4.
journal title abbreviation: Cell Rep
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Lodato, Michael
first name: Michael
last name: Lodato
Twitter: https://profiles.umassmed.edu/profile/28867077
full name: Michael Anthony Lodato PhD
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Post Docs: Wet-lab and Bioinformatic postdoctoral fellow positions are available for candidates with recent Ph.D. or M.D./Ph.D. degrees in Molecular Biology, Neuroscience, Genetics, Genomics, Cell Biology, or related fields. They should be highly motivated, have a strong desire to learn, and excellent communication skills. Applicants should send their CV, summary of previous research and the name of three references to Dr. Michael Lodato.
Rotation Projects: Rotations will revolve around studying somatic mutations in the normal brain, in the diseased brain, and outside of the brain using single-cell genomics. Please contact Dr. Lodato for details.
preferred title: Associate Professor
webpage: https://profiles.umassmed.edu/profile/28866604

The piRNA Response to Retroviral Invasion of the Koala Genome.
PubMed Identifier: 31607510
author list: Yu T, Koppetsch BS, Pagliarani S, Johnston S, Silverstein NJ, Luban J, Chappell K, Weng Z, Theurkauf WE
published in: Cell
information resource reference: Yu T, Koppetsch BS, Pagliarani S, Johnston S, Silverstein NJ, Luban J, Chappell K, Weng Z, Theurkauf WE. The piRNA Response to Retroviral Invasion of the Koala Genome. Cell. 2019 10 17; 179(3):632-643.e12.
journal title abbreviation: Cell
publication date: 2019-10-10T00:00:00
year: 2019
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Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans.
PubMed Identifier: 31900453
author list: ?zata DM, Yu T, Mou H, Gainetdinov I, Colpan C, Cecchini K, Kaymaz Y, Wu PH, Fan K, Kucukural A, Weng Z, Zamore PD
published in: Nature ecology & evolution
information resource reference: ?zata DM, Yu T, Mou H, Gainetdinov I, Colpan C, Cecchini K, Kaymaz Y, Wu PH, Fan K, Kucukural A, Weng Z, Zamore PD. Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans. Nat Ecol Evol. 2020 01; 4(1):156-168.
journal title abbreviation: Nat Ecol Evol
publication date: 2019-12-23T00:00:00
year: 2019
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Adaptive Evolution Targets a piRNA Precursor Transcription Network.
PubMed Identifier: 32101744
author list: Parhad SS, Yu T, Zhang G, Rice NP, Weng Z, Theurkauf WE
published in: Cell reports
information resource reference: Parhad SS, Yu T, Zhang G, Rice NP, Weng Z, Theurkauf WE. Adaptive Evolution Targets a piRNA Precursor Transcription Network. Cell Rep. 2020 02 25; 30(8):2672-2685.e5.
journal title abbreviation: Cell Rep
publication date: 2020-02-25T00:00:00
year: 2020
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YAP1 Withdrawal in Hepatoblastoma Drives Therapeutic Differentiation of Tumor Cells to Functional Hepatocyte-Like Cells.
PubMed Identifier: 32452550
author list: Smith JL, Rodr?guez TC, Mou H, Kwan SY, Pratt H, Zhang XO, Cao Y, Liang S, Ozata DM, Yu T, Yin Q, Hazeltine M, Weng Z, Sontheimer EJ, Xue W
published in: Hepatology (Baltimore, Md.)
information resource reference: Smith JL, Rodr?guez TC, Mou H, Kwan SY, Pratt H, Zhang XO, Cao Y, Liang S, Ozata DM, Yu T, Yin Q, Hazeltine M, Weng Z, Sontheimer EJ, Xue W. YAP1 Withdrawal in Hepatoblastoma Drives Therapeutic Differentiation of Tumor Cells to Functional Hepatocyte-Like Cells. Hepatology. 2021 03; 73(3):1011-1027.
journal title abbreviation: Hepatology
publication date: 2021-02-08T00:00:00
year: 2021
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The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility.
PubMed Identifier: 32601478
author list: Wu PH, Fu Y, Cecchini K, ?zata DM, Arif A, Yu T, Colpan C, Gainetdinov I, Weng Z, Zamore PD
published in: Nature genetics
information resource reference: Wu PH, Fu Y, Cecchini K, ?zata DM, Arif A, Yu T, Colpan C, Gainetdinov I, Weng Z, Zamore PD. The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility. Nat Genet. 2020 07; 52(7):728-739.
journal title abbreviation: Nat Genet
publication date: 2020-06-29T00:00:00
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piRNA-independent transposon silencing by the Drosophila THO complex.
PubMed Identifier: 34547226
author list: Zhang G, Yu T, Parhad SS, Ho S, Weng Z, Theurkauf WE
published in: Developmental cell
information resource reference: Zhang G, Yu T, Parhad SS, Ho S, Weng Z, Theurkauf WE. piRNA-independent transposon silencing by the Drosophila THO complex. Dev Cell. 2021 09 27; 56(18):2623-2635.e5.
journal title abbreviation: Dev Cell
publication date: 2021-09-20T00:00:00
year: 2021
type: Academic Article
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The transcription factor TCFL5 responds to A-MYB to elaborate the male meiotic program in mice.
PubMed Identifier: 36395073
author list: Cecchini K, Biasini A, Yu T, S?flund M, Mou H, Arif A, Eghbali A, Colpan C, Gainetdinov I, de Rooij DG, Weng Z, Zamore PD, ?zata DM
published in: Reproduction (Cambridge, England)
information resource reference: Cecchini K, Biasini A, Yu T, S?flund M, Mou H, Arif A, Eghbali A, Colpan C, Gainetdinov I, de Rooij DG, Weng Z, Zamore PD, ?zata DM. The transcription factor TCFL5 responds to A-MYB to elaborate the male meiotic program in mice. Reproduction. 2023 02 01; 165(2):183-196.
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Aub, Vasa and Armi localization to phase separated nuage is dispensable for piRNA biogenesis and transposon silencing in Drosophila.
PubMed Identifier: 37546958
author list: Ho S, Rice NP, Yu T, Weng Z, Theurkauf WE
published in: bioRxiv : the preprint server for biology
information resource reference: Ho S, Rice NP, Yu T, Weng Z, Theurkauf WE. Aub, Vasa and Armi localization to phase separated nuage is dispensable for piRNA biogenesis and transposon silencing in Drosophila. bioRxiv. 2023 Jul 26.
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Single-cell transcriptomic and genomic changes in the aging human brain.
PubMed Identifier: 37986960
author list: Jeffries AM, Yu T, Ziegenfuss JS, Tolles AK, Kim Y, Weng Z, Lodato MA
published in: bioRxiv : the preprint server for biology
information resource reference: Jeffries AM, Yu T, Ziegenfuss JS, Tolles AK, Kim Y, Weng Z, Lodato MA. Single-cell transcriptomic and genomic changes in the aging human brain. bioRxiv. 2023 Nov 07.
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The Trajectory of KoRV-A Evolution Indicates Initial Integration into the Koala Germline Genome Near Coffs Harbour.
PubMed Identifier: 39764129
author list: Yu T, Blyton MBJ, Koppetsch BS, Abajorga M, Luban J, Chappell K, Theurkauf WE, Weng Z
published in: Research square
information resource reference: Yu T, Blyton MBJ, Koppetsch BS, Abajorga M, Luban J, Chappell K, Theurkauf WE, Weng Z. The Trajectory of KoRV-A Evolution Indicates Initial Integration into the Koala Germline Genome Near Coffs Harbour. Res Sq. 2024 Dec 23.
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Evolution of KoRV-A transcriptional silencing in wild koalas.
PubMed Identifier: 40056902
author list: Yu T, Blyton MBJ, Abajorga M, Koppetsch BS, Ho S, Xu B, Hu Z, Luban J, Chappell K, Weng Z, Theurkauf WE
published in: Cell
information resource reference: Yu T, Blyton MBJ, Abajorga M, Koppetsch BS, Ho S, Xu B, Hu Z, Luban J, Chappell K, Weng Z, Theurkauf WE. Evolution of KoRV-A transcriptional silencing in wild koalas. Cell. 2025 Apr 17; 188(8):2081-2093.e16.
journal title abbreviation: Cell
publication date: 2025-03-07T00:00:00
year: 2025
type: Academic Article
type: Article
type: Document
type: Information Resource

Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR.
PubMed Identifier: 40277192
author list: Gustafsson HT, Ferguson L, Galan C, Yu T, Upton H, Kaymak E, Weng Z, Collins K, Rando OJ
published in: eLife
information resource reference: Gustafsson HT, Ferguson L, Galan C, Yu T, Upton H, Kaymak E, Weng Z, Collins K, Rando OJ. Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR. Elife. 2025 Apr 25; 14.
journal title abbreviation: Elife
publication date: 2025-04-25T00:00:00
year: 2025
type: Academic Article
type: Article
type: Document
type: Information Resource

Chair and Professor
is primary position: true
position in department: RNA Therapeutics Institute
position in division: https://profiles.umassmed.edu/profile/15590085
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Distinguished Professor
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position in department: RNA Therapeutics Institute
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Professor
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position in department: RNA Therapeutics Institute
position in division: https://profiles.umassmed.edu/profile/15590085
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HR job title: Professor
position in organization: UMass Chan Medical School

Single-cell transcriptomic and genomic changes in the ageing human brain.
PubMed Identifier: 40903571
author list: Jeffries AM, Yu T, Ziegenfuss JS, Tolles AK, Baer CE, Sotelo CB, Kim Y, Weng Z, Lodato MA
published in: Nature
information resource reference: Jeffries AM, Yu T, Ziegenfuss JS, Tolles AK, Baer CE, Sotelo CB, Kim Y, Weng Z, Lodato MA. Single-cell transcriptomic and genomic changes in the ageing human brain. Nature. 2025 Oct; 646(8085):657-666.
journal title abbreviation: Nature
publication date: 2025-09-03T00:00:00
year: 2025
type: Academic Article
type: Article
type: Document
type: Information Resource

Worcester MA 01655
type: Address
address line 1: UMass Chan Medical School
address line 2: 55 Lake Avenue North
address line 3: Worcester MA 01655

https://profiles.umassmed.edu/profile/96021269
position in department: Genomics and Computational Biology
position in division: https://profiles.umassmed.edu/profile/15590085
sort order: 2
type: Position
position in organization: T.H. Chan School of Medicine

Instructor
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position in department: Genomics and Computational Biology
position in division: https://profiles.umassmed.edu/profile/15590085
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HR job title: Instructor
position in organization: UMass Chan Medical School

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selected publications
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Authorship 140440
type: Authorship
author rank in publication: 3
linked author: Yu, Tianxiong
linked information resource: Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin.

Authorship 140441
type: Authorship
author rank in publication: 6
linked author: Yu, Tianxiong
linked information resource: The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility.

Authorship 140444
type: Authorship
author rank in publication: 2
linked author: Yu, Tianxiong
linked information resource: Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans.

Authorship 140446
type: Authorship
author rank in publication: 2
linked author: Yu, Tianxiong
linked information resource: piRNA-independent transposon silencing by the Drosophila THO complex.

Authorship 140447
type: Authorship
author rank in publication: 10
linked author: Yu, Tianxiong
linked information resource: YAP1 Withdrawal in Hepatoblastoma Drives Therapeutic Differentiation of Tumor Cells to Functional Hepatocyte-Like Cells.

Authorship 140448
type: Authorship
author rank in publication: 2
linked author: Yu, Tianxiong
linked information resource: Single-cell transcriptomic and genomic changes in the aging human brain.

Authorship 140449
type: Authorship
author rank in publication: 4
linked author: Yu, Tianxiong
linked information resource: Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR.

Authorship 140450
type: Authorship
author rank in publication: 3
linked author: Yu, Tianxiong
linked information resource: The transcription factor TCFL5 responds to A-MYB to elaborate the male meiotic program in mice.

Authorship 140451
type: Authorship
author rank in publication: 1
linked author: Yu, Tianxiong
linked information resource: Evolution of KoRV-A transcriptional silencing in wild koalas.

Authorship 140452
type: Authorship
author rank in publication: 3
linked author: Yu, Tianxiong
linked information resource: Aub, Vasa and Armi localization to phase separated nuage is dispensable for piRNA biogenesis and transposon silencing in Drosophila.

Authorship 140453
type: Authorship
author rank in publication: 1
linked author: Yu, Tianxiong
linked information resource: The Trajectory of KoRV-A Evolution Indicates Initial Integration into the Koala Germline Genome Near Coffs Harbour.

Authorship 140454
type: Authorship
author rank in publication: 2
linked author: Yu, Tianxiong
linked information resource: Single-cell transcriptomic and genomic changes in the ageing human brain.

Authorship 140457
type: Authorship
author rank in publication: 1
linked author: Yu, Tianxiong
linked information resource: The piRNA Response to Retroviral Invasion of the Koala Genome.

Authorship 140458
type: Authorship
author rank in publication: 2
linked author: Yu, Tianxiong
linked information resource: Adaptive Evolution Targets a piRNA Precursor Transcription Network.