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• Analysis of the Computational Methods Available for MicroRNA Target Prediction Talayeh Ghezelayagh
• Evaluation of currently available web-servers for 3D-structure based prediction of protein interface regions
• New Editor-in-Chief Named to Lead JAMIA UCSD Professor to Take Reins of Leading Informatics Journal
• Boon Thye Thomas Yeo Biochem 218 Final Project
• T-Tree, a new tool for taxonomy-based phylogenetic co-evolution analysis Term Project for Biochemistry 218 Stanford University Fall 2007
• Vol. 22 no. 17 2006, pages 21582159 doi:10.1093/bioinformatics/btl357BIOINFORMATICS APPLICATIONS NOTE
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• Marina Sirota PROTEIN MULTIPLE ALIGNMENT
• Bioinformatics Approaches to Biomarker Discovery BIOC 218/ BMI 231
• Jinkuk Choi 6/4/2004 BIOCHEM218 Final Project
• Predicting Protein-Protein Interactions with Collaborative Filtering Algorithms
• Dispensability of Mammalian DNA Cory McLean1
• ON THE INVERSE KINEMATICS OF A FRAGMENT OF PROTEIN BACKBONE
• A Slicing Connection Strategy for Constructing PRMs in High-Dimensional Cspaces
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• Kirstin Knox Biochem 218 An Introduction To Motif Based Functional Classification of Large Protein Families
• Transcriptional Regulatory Elements in the Human
• developmental genes Thousands of human mobile element fragments undergo strong purifying selection near
• Motion Planning of Multi-Limbed Robots Subject to Equilibrium Constraints
• Deniable Encryption with Negligible Detection Probability: An Interactive Construction
• An Information Theoretic Quantitative Approach to Natural Selection
• Ideas about the evolutionary significance of non-coding mutations are nearly as old as the discovery of
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• A Survey of Classification Methods for Protein Domain Motions and Flexibility
• Computational Molecular Biology Biochem 218 BioMedical Informatics 231
• Biochem 218 Final Project Hye Young Min (5360242)
• LETTER doi:10.1038/nature09774 Human-specific loss of regulatory DNA and the
• Bioinformatics Analyses of Alternative Splicing Non-EST based Prediction, Influence of
• Kirthi Reddy Biochemistry 218 Final Project
• BIOINFORMATICS APPLICATIONS NOTE Vol. 20 no. 5 2004, pages 788789
• Reducing Shoulder-surfing by Using Gaze-based Password Entry
• An Overview of Protein Structure Prediction: From Homology to Ab Initio
• Trying on Phylogenetic Footprinting Methods Rich Sherwood, Department of Biological Sciences, Stanford University
• A Review of Support Vector Machines in Computational June 6, 2009
• This form is to be submitted by the student to the major department prior to the end of the first quarter of enrollment in the program. Please type or print the application (the pdf can be filled in online and printed for signatures), and retain a copy fo
• Martina Koeva Biochemistry 218 Final Project
• FAST 3D MUSCLE SIMULATIONS USING A NEW QUASISTATIC INVERTIBLE FINITE-ELEMENT ALGORITHM
• Final Project: Computational Molecular Biology BIOC218 Christina Bormann Chung, SCPD student
• BioChem. 218 Computational Molecular Biology December 5th Computational Methods of Discovering Gene Modules and
• Constructing Nature's Building Blocks: An Analysis of Computational Protein Design Today
• David Patariu BIOC218: Computational Molecular Biology
• Analysis of Methods for Predicting Protein Fold and Remote Homologue Recognition
• Developmental Biology PhD Graduation Checklist Decide on your defense date (check with committee), find a location and notify your departmental
• Biological Pathways A pathway to explore diseases mechanism
• Meng How Tan Network Inference from Multiple Data Sources
• Multiple Sequence Alignment: A Critical Comparison of Four Popular Programs
• Computational Molecular Biology Biochem 218 BioMedical Informatics 231
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• Stream Wang Biochemistry 218
• Analysis of The DQ Family of The Human Leukocyte Antigens Computational Mol. Bio
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• Finding genes by computational methods: An analysis of the methods and programs
• Efficient Exact p -Value Computation and Applications to Biosequence Analysis
• SCFGs as Predictors of RNA's Secondary Structure Antonio F. Martnez-Alcntara
• Pair Stochastic Context-Free Grammar Model in Comparative Sequence Analysis
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• Markov Models for Classification of Protein Helices Nancy Ruonan Zhang
• Handling Rearrangements in DNA Sequence Alignment Maneesh Bhand
• Final Project Biochem 218: Computational Molecular Biology
• Final Project Docking Algorithms of Virtual Ligand Screening
• Long-Range Gene Control and Genetic Disease
• COMPUTATIONAL ANALYSIS OF THE MAMMALIAN CIS-REGULATORY LANDSCAPE
• GREAT, a functional enrichment approach and tool for interpretation of genome-wide cis-regulatory datasets
• Dispensability of mammalian DNA Cory McLean1
• 2006 Nature Publishing Group 2006 Nature Publishing Group A distal enhancer and an ultraconserved exon are
• An enhancer near ISL1 and an ultraconserved PCBP2 exon are
• JOURNAL OF COMPUTATIONAL BIOLOGY Volume 11, Number 5, 2004
• 16. L. Shen, K. L. Rock, Proc. Natl. Acad. Sci. U.S.A. 101, 3035 (2004).
• Ultra-conserved elements in the human genome Authors and affiliations
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• BIOINFORMATICS Vol. 17 no. 10 2001 Pages 927934
• University Kiel SNPs in NAGNAG acceptors are highly predictive for variations of
• Chair for Bioinformatics Widespread occurrence of alternative splicing at NAGNAG
• Efficient Exact p -Value Computation and Applications to Biosequence Analysis
• Systematic Literature Search Doug Brutlag
• Computational Molecular Biology Biochem 218 BioMedical Informatics 231
• Doug Brutlag Professor Emeritus
• Computational Molecular Biology Biochem 218 BioMedical Informatics 231
• Computational Molecular Biology Biochem 218 BioMedical Informatics 231
• Structures from Rhiju Das, Departments of
• Computational Molecular Biology! Biochem 218 BioMedical Informatics 231!
• Structural Variation in the Human Genome
• Computational Molecular Biology Biochem 218 BioMedical Informatics 231
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• Change of Dissertation Adviser or Reading Committee Member Stanford University
• Stuart Blair BioC 218 Final Paper Fall 2010 A review of the Gene Ontology: past developments, present roles, and future possibilities.
• A review of recent advances in ab initio protein folding by the Folding@home project
• ChIP-Seq: The new way to `seq' genome wide for transcription factor binding patterns Biochem218: Computational Molecular Biology
• Stacey Shiigi Review: Mathematical models for designing synthetic ribosome binding sites to control protein
• Progress in the Side-Chain Prediction Problem Noah Youngs
• BIOC 218 Autumn 2009 The Phylo-HMM approach to problems
• Eukaryotic Gene Prediction Kelli Davies
• Badreddin Edris | BIOC 218 Final Project (Win-09) Page 1 A comparison of the Oligomap and TargetScan
• P a g e | 1 Protein Multiple Sequence Alignment: Benchmarks and Comparison
• Sequence-and Structure-Based Functional Annotation
• Critical Review of Functional Site Prediction Biochem218 (Spring 2009)
• Protein Structure Prediction by Comparative Modeling: An Analysis of Methodology
• ANALYSIS OF METHODOLOGY IN COPHYLOGENETIC STUDIES Arthur Yang
• A Review on Common Applications Designed to Optimize the SEQUEST Search Algorithm With Respect to Limiting False Positive Identification
• Anant Vinjamoori Biochem 218 Final Project
• Simulating chromatin: Gene prediction at the structural level? Steve Dennis
• A Critical Review of Gene Prediction Software
• Inexact Pattern Matching Algorithms via Automata1 Chung W. Ng
• DISTANCE BASED METHODS IN PHYLOGENTIC TREE CONSTRUCTION CHUANG PENG
• Review of immunoinformatic approaches to in-silico B-cell epitope prediction
• Sequence Motifs are Necessary but not Sufficient for Predicting
• Proc. BIOC 218 Vol. 1, pp. 1-20, March 2005
• BIOCHEM218: Computational Molecular Biology Professor Douglas Brutlag
• Critical Review of Methods available for Microarray Data Analysis Krithika Ramamoorthy
• An Analysis of Pairwise Sequence Alignment Algorithm Complexities: Needleman-Wunsch, Smith-Waterman, FASTA, BLAST and Gapped BLAST
• Detecting motifs with EMOTIF-MAKER and MASIA: A critical comparison of two tools for finding protein motifs
• BIOC218 Computational Molecular Biology Course Project, Brad Mills
• Predicting Phosphorylation: A critique of the NetPhos program and potential alternatives
• Protein Structure Prediction Jayanthi Sourirajan
• Proteomics for the Discovery of Biomarkers and Diagnosis of Diseases Shanti Gunawardena
• Chris Moore Biochem 218
• Will You Find Me? A Critical Evaluation of Motif Finding
• Improved Methods for Inferring Regulatory Networks from Temporal Expression Data
• Data Analysis Methods for DNA Microarrays: A Critical Review of Applications to Breast Cancer Research
• Eric Bennett Computational Molecular Biology
• Critical Analysis of Secondary Structure Prediction Elizabeth D. Chao
• john.edwards@acm.org BIOCHEM218, Autumn 2001, Project
• Stacy Evans Computational Molecular Biology
• Margaret Gentile Computational Methods for the Design of PCR Primers
• COMPUTATIONAL METHODS FOR PREDICTING TRANSMEMBRANE ALPHA HELICES
• Microarray Data Analysis Methods Comparison : A Review Biochemistry 218 Project
• Data Analysis of Villin Headpiece Subdomain Folding Simulations.
• eMOTIF Maker: Nodally Awesome: Comparing Results of eMOTIF Maker with
• A Review of DNA Microarray Data Analysis Background
• A Comparative Analysis of Position Specific Scoring Matrixes for the Identification of Related Proteins
• Thomas Vigdal Biochem 218
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• Comparative Analysis of Methods for Multiple Sequence Alignment
• A sequence based analysis of the structure of SNARE family N terminal domains Yuanyuan Hua
• New Secondary Structure Prediction software package using automatically trained Bayesian Networks
• BIOC218 Project Paul Segars
• Jamie Schroeder Biochemistry 218 Final Project
• MECHANICAL FORCE REVIEW & CRITICAL ANALYSIS OF MODERN
• Hirofumi Sawada M.D., Ph.D. November 2009
• Motif Finding in Upstream Regions of Chaperone Genes Downregulated in Response to
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• Final Paper: Large-Scale Alignment of Encyclopedic Metabolic Networks
• Can HMMgene Net a Gene Too? : Analysis of
• Automata Learning and Stochastic Modeling for Biosequence Analysis
• Efficiency and Accuracy of Phylogenetic Trees for Large Sequence Datasets
• In Silico Transfer of Ligand Binding Function between Structurally Analogous Proteins
• BioC 218/BMI 231 Jessie Tenenbaum 12/6/02 Page 1
• Randal C. Cevallos Final Project
• Recent Developments in RNA Secondary Structure Adelene Sim
• bmi231 Fall 2002 Final Project A Go Model of proteins and RNA
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• 10.1101/gr.6761107Access the most recent version at doi: published online Nov 5, 2007;Genome Res.
• December 15, 2009 Page 1 of 6 Administrative Guide Memo 23.3 Stanford University
• Self-Inspections: Why Do It and Where to Find Info?
• Department of Biology STANFORD UNIVERSITY 2010-2011 Approved Out-Of-Department Electives
• Analysis of Ebola Glycoprotein Sequences from Strains of Varying Lethality
• June 15, 2009 Page 1 of 3 Administrative Guide Memo 63 Stanford University
• March 15, 2006 Page 1 of 4 Administrative Guide Memo 64 Stanford University
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• Singular Value Decomposition applied to the building of class
• Applying Near-Optimal Alignments to Protein Structure Prediction
• Doug Brutlag Professor Emeritus
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• Genomic Identification of Regulatory Elements by
• Improving Structural Superpositions for Complex Protein Structures by Limiting
• Determination of Common Motifs in Proteins Found to Interact with TriC/CCT Subunits During Large-Scale
• Por Sae-Seaw Final Paper Bioc218
• Seeking Solutions, Educating Leaders Pioneering Solutions for Depression
• Conditional Random Fields for Classification of Protein Families: An Alternative to Hidden Markov Models
• Using Blocks in Pairwise Sequence Alignment December 6, 2002
• Combinatorial Relationships in Transcription Factors Jack Middleton
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• Tara Watkins Biochem 218
• Computational Molecular Biology Biochem 218 BioMedical Informatics 231
• Hi-C: Genome-wide Chromosome Conformation Capture Biochem 218
• Supplement: Thousands of human mobile element
• EURASIP Journal on Applied Signal Processing 2003:2, 93102 c 2003 Hindawi Publishing Corporation
• Katie M. Shelef Biochemistry 218, Fall 2007
• Jenny Radosevich Biochemistry 218 Final Project
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• David Lalush Page 1 08/08/01 Clique Scoring for Enhancing Protein Family Classification of Hidden Markov Models
• Final Project Biochemistry 218 Computational Molecular Biology
• Methods of Phylogenetic Analysis: New Improvements on Old Methods.
• Erin Davies 3/10/03 BIOCHEM218 Final Project
• Investigations into a Genetic Algorithm for Protein Sequences Selwyn-Lloyd McPherson
• Daniel Van de Mark Biochem 218
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• Examining the Current Problems of Whole Genome Comparison: A Review
• June 15, 2009 Page 1 of 4 Administrative Guide Memo 67 Stanford University
• B.S. Handbook 2010 2011
• Huntzicker2003.doc 6/12/2003 Erik G. Huntzicker Page 1 of 21
• Critical Analysis of the Computational Methods used to Discover Biomarkers to assist in the
• Protein-Ligand Docking: A Critical Review of Molecular Dynamics, Robotics, and Rotamer Library Methods
• Investigating the Mechanism of Follistatin Function with Bioinformatics Heather L. Stickney
• Ross Metzger June 4, 2004
• Uses of the Singular Value Decompositions in Biology The Singular Value Decomposition is a very useful tool deeply rooted in linear
• A Critical Evaluation of Multiple Sequence Alignment Programs in Aligning Domains of the Bcl-2 Family
• December 15, 2009 Page 1 of 4 Administrative Guide Memo 15.1 Stanford University
• Stronger Password Authentication Using Browser Extensions
• The Use of Computational Methods to Describe and Establish Utility of a DNA Sequence
• Supplementary Figure 1 Sagittal sections of the E11.5 brain of BAF53a BAC reporter near the 4th
• Jennifer A. Chen Biochem 218 Final Project
• Organization of Conserved Elements Near Key
• Available online at www.sciencedirect.com Finding distal regulatory elements in the human genome
• Anne Hilgendorff, MD, Curriculum Vitae 1 CURRICULUM VITAE
• William Chen wcchen@stanford.edu
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• BIOINFORMATICS Vol. 20 Suppl. 1 2004, pages i40i48
• Gene clustering methods for time series microarray data Laney Kuenzel
• Analysis of Fundamental Exact and Inexact Pattern Matching Algorithms
• ACLS Rhythms for the ACLS Algorithms A p p e n d i x 3
• Department of Linguistics Ph.D. Handbook
• Biomedical Informatics (Rev. 9/09) Biomedical Informatics (Rev. 9/09)
• Artificial Neural Networks and Hidden Markov Models for Predicting the Protein Structures: The Secondary Structure
• A Critical Review of Computational Methods for RNA Secondary Structure Prediction
• Biochemistry 218 -BioMedical Informatics 231 Computational Molecular Biology
• JOURNAL OF COMPUTATIONAL BIOLOGY Volume 7, Numbers 3/4, 2000
• Biochemistry 218 A critical review of PCR primer design algorithms and cross-
• Computational Molecular Biology Biochem 218 BioMedical Informatics 231
• Secondary Structure Prediction of Proposed RNAi
• CURRICULUM VITAE Tero-Pekka Alastalo
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• Biochem 218 -2010 Gavin Sherlock
• R You Out There?: Computational Strategies for Identifying Resistance
• Lifeasweknowit To understand the human genome, researchers must spread their wings to all branches of life.
• June 15, 2009 Page 1 of 4 Administrative Guide Memo 61 Stanford University
• Elyn C. Tan SUID: 4862645
• nature biotechnology VOLUME 28 NUMBER 5 MAY 2010 495 A n A ly s i s
• Frederick Lo Biochemistry 218
• Genomics and Bioinformatics Doug Brutlag
• Final Project Biochemistry 218 Computational Molecular Biology
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• 10.1101/gr.080184.108Access the most recent version at doi: published online Oct 2, 2008;Genome Res.
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• 10.1101/gr.114587.110Access the most recent version at doi: 2011 21: 245-254 originally published online December 22, 2010Genome Res.
• Obituary of Darlene P. Vian Darlene LeMay Pearson Vian, 78, a resident of Palo Alto, CA, for over 51 years, passed away on 9 February
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• Bejerano Lab http://bejerano.stanford.edu As of 3/2/11
• Bejerano Lab http://bejerano.stanford.edu (10/10/11)
• Bejerano Lab http://bejerano.stanford.edu Chromatin preparation from small cell populations
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• Material and methods Six genome assemblies were used throughout this study: Human NCBI Build 36.1 (UCSC
• Bejerano Lab http://bejerano.stanford.edu As of 1/10/11
• Biomedical Informatics (Rev. 9/11) http://bmi.stanford.edu/biomedical-informatics-students/handbook.html Biomedical Informatics (Rev. 9/11) http://bmi.stanford.edu/biomedical-informatics-students/handbook.html
• The nematode worm Caenorhabditis elegans has many features that make it an attractive model organism,
• Bejerano Lab http://bejerano.stanford.edu Electrophoretic mobility shift assay (EMSA) Protocol
• RNA-Seq: Current Methods and Potential Applications Philip Pauerstein
• Predicting Protein Complex Structures: A Review of the Docking Process BIOC218 Final Project
• Winter 2011 Evaluating Protein-Protein Docking Web Servers
• Using MotifScan to Discover Transcription Factor Binding Sites in Nonhuman Genomes
• Degenerate Primer Design using Computational Tools Computational Molecular Biology
• Template-Based Modeling of Protein Structure David Constant
• A Critical Review of Strategies for Selecting Haplotype Tag SNPs Ruby Lee
• Considerations and Recent Advances in Molecular Dynamics Introduction
• Multiple Sequence Alignments BIOC 218 Final Project
• Nikhil Gopal BIOC 218 Final Project
• Hunting the Monsters in the Database A critical review of computational tools for detecting chimeric 16S
• Bejerano Lab http://bejerano.stanford.edu SDSPAGE and Western Blot Protocol