Author

Shaleen Shrestha

Boston University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Genomics· 1 Molecular Biology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:experimental assay· 2 Organism:human· 2 Assay:proteomics· 2 Organism:C. elegans· 1 Research Focus:cell-cell communication· 1 Research Focus:differential expression· 1 Assay:DNA methylation· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Clarissa Stephanie SantosoiD· 2 shared Jared Allan SewelliD· 2 shared Juan I. Fuxman BassiD· 2 shared Adam FrankishiD· 1 shared Alex M Tamburino· 1 shared Alex S. HolehouseiD· 1 shared Amy D Holdorf· 1 shared Anisa V. PrasadiD· 1 shared

Activity by Year

2016-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersSystems Biology

Clarissa Stephanie SantosoORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

Luke Lambourne, Kaia Mattioli, Clarissa Stephanie Santoso, Gloria Sheynkman, Sachi Inukai, Babita Kaundal, Anna Berenson, Kerstin Spirohn, Anukana Bhattacharjee, Elisabeth Rothman, Shaleen Shrestha, Florent Laval, Brent S. Carroll, Stephen P. Plassmeyer, Ryan J. Emenecker, , Juan I. Fuxman Bass

The paper identifies two categories of transcription factor isoforms with distinct molecular functions and shows they contribute to gene regulatory complexity.

Molecular Cell · Mar 27, 2025Peer-reviewedSystems Biology

Discovering human transcription factor interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays

Shaleen Shrestha, Jared Allan Sewell, Clarissa Stephanie Santoso, Elena J. Forchielli, Sebastian Carrasco Pro, Melissa Martinez, Juan I. Fuxman Bass

The paper develops enhanced yeast one-hybrid assays to study TF binding to repetitive elements, variants, and novel motifs, identifying 75 TFs interacting with Alu elements and changes in TF binding associated with cancer-related mutations.

Genome Research · Sep 1, 2019Peer-reviewedGenomics

PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions

Alex M Tamburino, Ebru Kaymak, Shaleen Shrestha, Amy D Holdorf, Sean P Ryder, Marian (Albertha) Walhout

PRIMA is a method to map RNA-protein interactions by testing RNA baits against multiple RBPs, identifying both known and novel interactions in C. elegans.

bioRxiv · Sep 12, 2016Molecular Biology