a person in the record
Bonnie Berger
American mathematician and computer scientist
Supervised 36 doctoral students and 25 master's students at Massachusetts Institute of Technology between 1996 and 2026; Wikidata names Silvio Micali as doctoral advisor, lists 22 doctoral students, and lists 1 person they taught. Linked to Wikidata, ORCID, and 8 other registers.

How to read the markscited by a repository's recordstated by Wikidata or indexed by OpenAlexclaimed on an ORCID list, or inferred
Students61
- cited by a thesis record2026 · Massachusetts Institute of Technology · doctoral
- cited by a thesis record
Tony Ao Cui“Graph Representation Learning for Structural Variation Discovery”
2026 · Massachusetts Institute of Technology · master's - cited by a thesis record2025 · Massachusetts Institute of Technology · doctoral
- cited by a thesis record
Ragulan Sivakumar“Automated Finetuning via Sparse Autoencoders”
2025 · Massachusetts Institute of Technology · master's - cited by a thesis record
Adrina Tang“Integrating Functional Knowledge into Protein Design: A Novel Approach to Tokenization and Noise Injection for Function-Aware Protein Language Models”
2025 · Massachusetts Institute of Technology · master's - cited by a thesis record
Matthew M. Hong“Secure Discovery of Genetic Relatives across Large-Scale and Distributed Genomic Datasets”
2024 · Massachusetts Institute of Technology · master's - cited by a thesis record
Shuvom Sadhuka“A More Holistic Analysis of Privacy Risks in Transcriptomic Datasets”
2024 · Massachusetts Institute of Technology · master's - cited by a thesis record
Derek Jia-Wen Yen“Private Random Variate Sampling for Secure and Federated Polygenic Risk Scores”
2024 · Massachusetts Institute of Technology · master's - cited by a thesis record
Adam U. Yaari“Untangling the complexity of nature: Machine-learning for accelerated life-sciences”
2023 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Younhun Kim“Algorithms for Reconstructing Biological History from Genomic Data”
2023 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Chiho Im“Learning the Language of Antibody Hypervariability Through Biological Property Prediction”
2023 · Massachusetts Institute of Technology · master's - cited by a thesis record
Maxwell A. Sherman“From genetics to disease: Algorithms to decode somatic mutations”
2023 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Ashwin Narayan“Similarity Metrics for Biological Data: Algorithmic developments for high-dimensional datasets”
2022 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Jeffrey Chen“SafeGENIE: Secure and federated linear mixed model association tests”
2022 · Massachusetts Institute of Technology · master's - cited by a thesis record
Sarah Kate Nyquist“Differential analysis of scRNA-Seq data to characterize epithelial cells in health and disease”
2022 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Ellen D. Zhong“Machine Learning for Reconstructing Dynamic Protein Structures from Cryo-EM Images”
2022 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Samuel Sledzieski“Structurally Motivated Deep Learning for Genome Scale Protein Interaction Prediction”
2021 · Massachusetts Institute of Technology · master's - cited by a thesis record2021 · Massachusetts Institute of Technology · doctoral
- cited by a thesis record
Andy Tso“Language Models Predict Drug Resistance from Complex Sequence Variation”
2021 · Massachusetts Institute of Technology · master's - cited by a thesis record
Adam Uri Yaari“Multi-resolution modeling of a discrete stochastic process identifies causes of cancer”
2021 · Massachusetts Institute of Technology · master's - cited by a thesis record
Tristan Bepler“Machine learning for understanding protein sequence and structure”
2020 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Shreyan Jain“Developing a cloud-based secure computation platform for genomics research”
2020 · Massachusetts Institute of Technology · master's - cited by a thesis record
Timothy F. Jr Truong“Interpretable deep learning framework for binding affinity prediction”
2020 · Massachusetts Institute of Technology · master's - cited by a thesis record
Hyunghoon Cho“Biomedical data sharing and analysis at scale : privacy, compaction, and integration”
2019 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Brian Hie“Stitching and sketching large-scale single-cell transcriptomic data”
2019 · Massachusetts Institute of Technology · master's - cited by a thesis record
Sumaiya Nazeen“Computational methods for functional interpretation of diverse omics data”
2019 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Ryan Kyong-doc Chung“Deep learning approach to metagenomic binning”
2018 · Massachusetts Institute of Technology · master's - cited by a thesis record
Deniz Yorukoglu“Scalable methods for storage, processing and analysis of sequencing datasets”
2017 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Yun William Yu“Compressive algorithms for search and storage in biological data”
2017 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Larson J Hogstrom“Return on investment and library complexity analysis for DNA sequencing”
2016 · Massachusetts Institute of Technology · master's - cited by a thesis record
Yuhao Wang“Predicting Substrates of [gamma]-secretase in Drosophila/”
2016 · Massachusetts Institute of Technology · master's - cited by a thesis record
Sean Kenneth Simmons“Preserving patient privacy in biomedical data analysis”
2015 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Mark Lipson“New statistical genetic methods for elucidating the history and evolution of human populations”
2014 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
George Jay Tucker“Statistical methods to infer biological interactions”
2014 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Alex Levin“Graphs, matrices, and populations : linear algebraic techniques in theoretical computer science and population genetics”
2013 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Po-Ru Loh“Algorithms for genomics and genetics : compression-accelerated search and admixture analysis”
2013 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Daniel K. Park“Web servers, databases, and algorithms for the analysis of protein interaction networks”
2013 · Massachusetts Institute of Technology · master's - cited by a thesis record
Raghavendra Hosur“Structure-based algorithms for protein-protein interaction prediction”
2012 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Rohit Singh“Algorithms for the analysis of protein interaction networks”
2012 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Eric David Eisner“Incorporating diverse data to improve genetic network alignment with IsoRank”
2011 · Massachusetts Institute of Technology · master's - cited by a thesis record
Charles William O'Donnell“Ensemble modeling of [beta]-sheet proteins”
2011 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Nathan Patrick Palmer“Data mining techniques for large-scale gene expression analysis”
2011 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Michael Schnall-Levin“RNA : algorithms, evolution and design”
2011 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Michael Ku Yu“Structure-based realignment of non-coding RNAs in multiple whole genome alignments”
2011 · Massachusetts Institute of Technology · master's - cited by a thesis record
Leonid Alexandrovich Chindelevitch“Extracting information from biological networks”
2010 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Oaz Nir“Single-cell morphological data reveals signaling network architecture”
2010 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Jason Trigg“Multicoil-HMM : improved prediction of coiled-coil oligomer state from sequence”
2010 · Massachusetts Institute of Technology · master's - cited by a thesis record
Michael Hartmann Baym“Large, noisy, and incomplete : mathematics for modern biology”
2009 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Allen Wayne Bryan“Prediction of parallel in-register amyloidogenic beta-structures In highly beta-rich protein sequences by pairwise propensity analysis”
2009 · Massachusetts Institute of Technology · doctoral - cited by a thesis record2008 · Massachusetts Institute of Technology · master's
- cited by a thesis record
Shannon Christine Wieland“Computational, statistical and graph-theoretical methods for disease mapping and cluster detection”
2007 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Yu-An Dong“Statistical analysis of protein interaction network topology”
2005 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Matthew Ewald Menke“Predicting the beta-trefoil fold from protein sequence data”
2004 · Massachusetts Institute of Technology · master's - cited by a thesis record
Alex Coventry“Detection of non-coding RNA with comparative genomics and the sequential closure of smooth graphs in Cartesian currents”
2003 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Philip H. Bradley“Mathematical methods for protein structural motif recognition”
2001 · Massachusetts Institute of Technology · doctoral - cited by a thesis record2000 · Massachusetts Institute of Technology · master's
- cited by a thesis record
Serafim Batzoglou“Computational genomics : mapping, comparison, and annotation of genomes”
2000 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Russell S. Schwartz“The local rules dynamics model for self-assembly simulation”
2000 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Vinay Pulim“A simulator for the topological modeling of ceramic structures using local rules”
1999 · Massachusetts Institute of Technology · master's - cited by a thesis record
Caroline Esther Jesurum“Local-rules based topological modeling of tetrahedral ceramic network structures”
1998 · Massachusetts Institute of Technology · doctoral - cited by a thesis record
Ethan Wolf“Statistical prediction schemes for the coiled-coil motif”
1996 · Massachusetts Institute of Technology · doctoral
Advisors on Wikidata1
From Wikidata, shown separately from the thesis records.
- stated by Wikidata
Students on Wikidata22
From Wikidata, shown separately from the thesis records.
- stated by Wikidataborn 1973
- stated by Wikidataborn 1977
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
- stated by Wikidata
Taught1
Wikidata's "student of" and "student" statements: a line of training beside the lineage, never a thesis supervision and never counted with one.
- a teacher or mentor, stated by Wikidata: not a thesis supervisionborn 1977
The line above and below4 steps
The advisors of their advisors, four steps up at most, in the thesis records and on Wikidata, each kind marked; a person in both is listed once.
- 1 step up
stated by WikidataSilvio Micali
- 2 steps up
stated by WikidataManuel Blum
- 3 steps up
stated by WikidataMarvin Minsky
- 4 steps up
stated by WikidataAlbert W. Tucker
Below them, within 3 steps, the record reaches 109 people: 36 cited by thesis records, 73 stated by Wikidata.
Education and career3
From Wikidata, shown separately from the thesis records. Each place opens its Wikidata item.
- undated
- undatedstudied
- undated