# Tatsunori Hashimoto

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Note: I have graduated and moved to stanford university as a post-doc for Percy Liang and John Duchi.
I was a fifth-year graduate student in computer science at MIT.
Co-advised by Tommi Jaakkola and David Gifford.

Before MIT, I graduated from Harvard University with an A.B. in statistics and mathematics and was advised by Edoardo Airoldi

## Writings

### Computational biology research

##### Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(w/ R. Sherwood, C. O'Donnell, T. Jaakkola and D. Gifford), Nature biotechnology **32** (2014),
171-178. (journal)

Method for transcription factor binding estimates via analysis of DNAse-I seq data .

##### Universal Count Correction for High-Throughput Sequencing

(w/ M. Edwards and D. Gifford), PLOS Comp. Bio. **10** (2014),
(journal)

Method for controlling marginal overdispersion fo high-throughtput sequending data .

##### Lineage based identification of cellular states and expression programs.

(w/ T. Jaakkola, D. Gifford), Proceedings of 20th ISMB (2012), (proceedings)

Technique for analyzing lineage-structured gene expression datasets using trace norm penalties

##### Finding drug discovery rules of thumb with bump hunting

(w/ M. Segall), Proceedings of the ACS (2010)
Technique for constructing human-memorizable decision rules based on drug discoery data.

##### BFL: a node and edge betweenness based fast layout algorithm for large scale networks

(w/ M. Nagasaki, K. Kojima, S. Miyano), BMC Bioinformatics **10** (2009), (journal)

### Statistics research

##### Word, graph, and manifold embedding from Markov processes

(w/ D. Avarez-Melis, T. Jaakkola), Preprint (arXiv)(supplemental data and code)

##### From random walks to distances on unweighted graphs

(w/ Y.Sun, T. Jaakkola), NIPS 2015, to appear. (preprint)(supplement)

##### Metric recovery from directed unweighted graphs

(w/ Y. Sun, T. Jaakkola), NIPS workshop on networks (2014, Best student poster), AISTATS (2015), (preprint)

A method to recover both the distance and density on a graph using unweighted edges; shows an equivalence between the random walk and its continuum limit on a geometric graph.

##### Tree preserving embedding

(w/ A.D Shieh, E.M Airoldi), Proc. Natl. Acad. Sciences (2011), (journal)

Nonlinear dimensionality reduction by preserving cluster constraints defined by clustering

### Other research (not primary author)

##### Long-term persistence and development of induced pancreatic beta cells generated by lineage conversion of acinar cells

(w/ W. Li, D. Gifford, Q. Zhou et al), Nature biotechnology **32** (2014), 1223-1230. (journal)

##### Quantifying Condition-Dependent Intracellular Protein Levels Enables High-Precision Fitness Estimates

(w/ K.A. Samerotte, E.M. Airoldi), PLOS one. **8** (2013),
( journal )

## Code

**Universal Count Correction for High-Throughput Sequencing** bitbucket

**Discovery of directional and nondirectional pioneer transcription factors** bitbucket

###### Website format originally from Jonathan Wang.

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