The Wall Lab at Stanford University

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Publications


2018

H Kalantarian, P Washington, J Schwartz, J Daniels, N Haber, D Wall (2018). A Gamified Mobile System for Crowdsourcing Video for Autism Research, 2018 IEEE International Conference on Healthcare Informatics (ICHI), 350-352 Full Text

M Duda, H Zhang, HD Li, DP Wall, M Burmeister, Y Guan (2018). Brain-specific functional relationship networks inform autism spectrum disorder gene prediction, Translational psychiatry 8 (1), 56 Full Text

Elizabeth K Ruzzo, Laura Perez-Cano, Jae-Yoon Jung, Lee-kai Wang, Dorna Kashef-Haghighi, Chris Hartl, Jackson Hoekstra, Olivia Leventhal, Michael J Gandal, Kelley Paskov, Nate Stockham, Damon Polioudakis, Jennifer K Lowe, Daniel H Geschwind, Dennis P Wall (2018). Whole genome sequencing in multiplex families reveals novel inherited and de novo genetic risk in autism, bioRxiv, 338855 Full Text

KM Paskov, DP Wall (2018). A Low Rank Model for Phenotype Imputation in Autism Spectrum Disorder, AMIA Summits on Translational Science Proceedings 2017, 178 Full Text

Maude M David, Christine Tataru, Jena Daniels, Jessey Schwartz, Jessica Keating, Jarrad Hampton-Marcell, Neil Gottel, Jack A Gilbert, Dennis P Wall (2018). Crowdsourced study of children with autism and their typically developing siblings identifies differences in taxonomic and predicted function for stool-associated microbes using exact sequence variant analysis., bioRxiv, 319236 Full Text

Jena Daniels, Nick Haber, Catalin Voss, Jessey Schwartz, Serena Tamura, Azar Fazel, Aaron Kline, Peter Washington, Jennifer Phillips, Terry Winograd, Carl Feinstein, Dennis P Wall (2018). Feasibility Testing of a Wearable Behavioral Aid for Social Learning in Children with Autism, Applied clinical informatics 9 (01), 129-140 Full Text

2017

H Abbas, F Garberson, E Glover, DP Wall (2017). Machine learning for early detection of autism (and other conditions) using a parental questionnaire and home video screening, Big Data (Big Data), 2017 IEEE International Conference on, 3558-3561 Full Text

S Levy, M Duda, N Haber, DP Wall (2017). Sparsifying machine learning models identify stable subsets of predictive features for behavioral detection of autism, Molecular autism 8 (1), 65 Full Text

J Daniels, J Schwartz, N Albert, M Du, DP Wall (2017). The GapMap project: a mobile surveillance system to map diagnosed autism cases and gaps in autism services globally, Molecular autism 8 (1), 55 Full Text

L Diaz-Beltran, FJ Esteban, M Varma, A Ortuzk, M David, DP Wall (2017). Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes, BMC genomics 18 (1), 315 Full Text

H Elshazly, Y Souilmi, PJ Tonellato, DP Wall, M Abouelhoda (2017). MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants, BMC bioinformatics 18 (1), 49 Full Text

C Voss, NJ Haber, DP Wall, AS Kline, TA Winograd (2017). Systems and Methods for Using Mobile and Wearable Video Capture and Feedback Plat-Forms for Therapy of Mental Disorders, US Patent App. 15/589,877 Full Text

J Kosmicki, K Samocha, M Lek, D MacArthur, D Wall, E Robinson, M Daly (2017). ONE IN THREE DE NOVO VARIANTS SEEN IN AUTISM SPECTRUM DISORDER PROBANDS ARE PRESENT AS STANDING VARIATION IN A COHORT OF MORE THAN 60,000 NON-ASD INDIVIDUALS, EUROPEAN NEUROPSYCHOPHARMACOLOGY 27, S280-S281 Full Text

Jena Daniels, Jessey Schwartz, Nick Haber, Catalin Voss, Aaron Kline, Azar Fazel, Peter Washington, Titas De, Carl Feinstein, Terry Winograd, Dennis Wall (2017). 5.13 Design and Efficacy of a Wearable Device for Social Affective Learning in Children With Autism, Journal of the American Academy of Child & Adolescent Psychiatry 56 (10), S257 Full Text

Peter Washington, Catalin Voss, Aaron Kline, Nick Haber, Jena Daniels, Azar Fazel, Titas De, Carl Feinstein, Terry Winograd, Dennis Wall (2017). SuperpowerGlass: a wearable aid for the at-home therapy of children with Autism, Proceedings of the ACM on Interactive, Mobile, Wearable and Ubiquitous … Full Text

RL Goldfeder, DP Wall, MJ Khoury, JPA Ioannidis, EA Ashley (2017). Human genome sequencing at the population scale: a primer on high-throughput DNA sequencing and analysis, American journal of epidemiology 186 (8), 1000-1009 Full Text

M Duda, N Haber, J Daniels, DP Wall (2017). Crowdsourced validation of a machine-learning classification system for autism and ADHD, Translational psychiatry 7 (5), e1133 Full Text

N Albert, J Daniels, J Schwartz, M Du, DP Wall (2017). GapMap: Enabling Comprehensive Autism Resource Epidemiology, JMIR public health and surveillance 3 (2) Full Text

Jack A Kosmicki, Kaitlin E Samocha, Daniel P Howrigan, Stephan J Sanders, Kamil Slowikowski, Monkol Lek, Konrad J Karczewski, David J Cutler, Bernie Devlin, Kathryn Roeder, Joseph D Buxbaum, Benjamin M Neale, Daniel G MacArthur, Dennis P Wall, Elise B Robinson, Mark J Daly (2017). Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples, Nature genetics 49 (4), 504 Full Text

H Abbas, F Garberson, E Glover, DP Wall (2017). Machine learning approach for early detection of autism by combining questionnaire and home video screening, Journal of the American Medical Informatics Association Full Text

M Duda, R Ma, N Haber, DP Wall (2017). Use of machine learning for behavioral distinction of autism and ADHD, Translational psychiatry 6 (2), e732 Full Text

A Gupta, MW Sun, KM Paskov, NT Stockham, JY Jung, DP Wall (2017). Coalitional game theory as a promising approach to identify candidate autism genes, Pac Symp Biocomput 23 Full Text

Nick Haber, Catalin Voss, Jena Daniels, Peter Washington, Azar Fazel, Aaron Kline, Titas De, Terry Winograd, Carl Feinstein, Dennis P Wall (2017). A Wearable Social Interaction Aid for Children with Autism (特集 Well-being Computing), 人工知能: 人工知能学会誌: journal of the Japanese Society for Artificial … Full Text

GUHAN RAM VENKATARAMAN, CHLOE O’CONNELL, Fumiko Egawa, DORNA KASHEF-HAGHIGHI, Dennis P Wall (2017). DE NOVO MUTATIONS IN AUTISM IMPLICATE THE SYNAPTIC ELIMINATION NETWORK, PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017, 521-532 Full Text

2016

MM David, BA Babineau, DP Wall (2016). Can we accelerate autism discoveries through crowdsourcing?, Research in Autism Spectrum Disorders 32, 80-83 Full Text

MM David, D Enard, A Ozturk, J Daniels, JY Jung, L Diaz-Beltran, DP Wall (2016). Comorbid Analysis of Genes Associated with Autism Spectrum Disorders Reveals Differential Evolutionary Constraints, PloS one 11 (7), e0157937 Full Text

Russ B Altman, Snehit Prabhu, Arend Sidow, Justin M Zook, Rachel Goldfeder, David Litwack, Euan Ashley, George Asimenos, Carlos D Bustamante, Katherine Donigan, Kathleen M Giacomini, Elaine Johansen, Natalia Khuri, Eunice Lee, Xueying Sharon Liang, Marc Salit, Omar Serang, Zivana Tezak, Dennis P Wall, Elizabeth Mansfield, Taha Kass-Hout (2016). A research roadmap for next-generation sequencing informatics, Science translational medicine 8 (335), 335ps10-335ps10 Full Text

Glenn N Saxe, Alexander Statnikov, David Fenyo, Jiwen Ren, Zhiguo Li, Meera Prasad, Dennis Wall, Nora Bergman, Ernestine C Briggs, Constantin Aliferis (2016). A complex systems approach to causal discovery in psychiatry, PloS one 11 (3), e0151174 Full Text

R Calvo, N Haber, C Voss, M Nova, D Salins, M Snyder, DP Wall (2016). Invited Talks at the AAAI Symposium on Well-Being Computing, 2016 AAAI Spring Symposium Series Full Text

DE Stark, RB Kumar, CA Longhurst, DP Wall (2016). The quantified brain: a framework for mobile device-based assessment of behavior and neurological function, Applied clinical informatics 7 (2), 290 Full Text

Voss, C., Washington, P., Haber, N., Kline, A., Daniels, J., Fazel, A., De, T., McCarthy, B., Feinstein, C., Winograd, T., Wall, D.P. (2016). Superpower Glass: Delivering unobstructive real-time social cues in wearable systems.

Diaz-Beltran, L., F. Esteban, F. &and D.P. Wall, D.P. (2016). A common molecular signature in ASD gene expression: following Root 66 to Autism. Nature Translational Psychiatry. 2016 Jan 9, 6(732). Doi: 10.1038/tp.2015.112. Full Text

Kumar, R.B., Goren, N.D., Stark, D.E., Wall, D.P*., Longhurst, C.A. (2016). Automated integration of continuous glucose monitor data in the electronic health record using consumer technology. Journal of the American Medical Informatics Association, doi: 10.1093/jamia/ocv206.

Duda, M., Daniels, J., & Wall, D.P. (2016). Clinical evaluation of a novel and mobile autism risk assessment. Journal of Autism and Developmental Disorders, 1-9. Published online 12 February 2016. Abstract

Duda, M., Ma, R., Haber, N., & Wall, D.P. (2016). Use of machine learning for behavioral distinction of autism and ADHD. Translational Psychiatry, 6(732), doi: 10.1038/tp2015.221. Published online 9 February 2016. Full Text

Washington, P., Voss, C., Haber, N., Tanaka, S., Daniels, J.,Feinstein, C., Winograd, T., & Wall, D.P. (2016). A wearable social interaction aid for children with autism. To appear in ACM annual conference on Human Factors in Computing Systems (CHI) Late-Breaking Work.

Nick Haber, N., Catalin Voss, C., Wall, D.P., Azar Fazel, A., & Terry Winograd, T. (2016). A practical approach to real-time neutral subtraction for facial expression recognition. Accepted to IEEE Winter Conference on Applications of Computer Vision.

2015

Li, J., Ma, Z., Shi, M., Malty, R.H., Aoki, H., Minic, Z., Phanse, S., Jin, K., Wasll, D.P., Zhang, Z., Urban, A.E., Hallmayer, J., Babu, M., & Snyder, M. (2015). Identification of human neuronal protein complexes reveals biochemical activities and convergent mechanisms of action in Autism Spectrum Disorders. Cell Syst. 2015 Nov 25, 1(5), 361-74.

J.A. Kosmicki, V. Sochat, M. Duda, and D.P. Wall. Searching for a minimal set of behaviors for autism detection through feature selection-based machine learning. Translational Psychiatry. February 2015; doi:10.1038/tp.2015.7. Full Text

Duda, M. & D.P. Wall, D.P. (2015). Rising interdisciplinary collaborations refine our understanding of autisms and give hope to more personalized solutions. Personalized Medicine, 12, : 359-69. Full Text

Fulga, T. A., McNeill, E. M., Binari, R., Yelick, J., Blanche, A., Booker, M., Streinkraus, B., Schnall-Levin, M., Zhao, Y., DeLucca, T., Bejarano, F., Han, Z., Lai, E. C., Wall, D. P., Perrimon, N., & Van Vactor, D. ( 2015). Unbiased screening by conditional competitive inhibition reveals novel functions of conserved Drosophila miRNAs during development and adult behavior. Nature Communications, 6(7279). Full Text

Souilmi, Y., Lancaster, A.K., Jung, J., Rizzo, E., Hawkins, J.B., Powles, R., Amzazi, S., Ghazal, H., Tonellato, P.J., & Wall, D.P. (2015). Scalable and Cost-effective NGS Genotyping in the Cloud. BMC Med Genomics. 8(1), 64. Full Text

2014

Duda, M., Kosmicki, J., & Wall, D. P. Testing the accuracy of an observation-based classifier for rapid detection of autism risk. Translational Psychiatry. August 2014; doi:10.1038/tp.2014.65. Full Text

Gafni, E., Luquette L. J., Lancaster, A. K., Hawkins, J. B., Jung, J-Y., Souilmi, Y., Wall, D. P. & Tonellato, P. J. COSMOS: a Python library for massively parallel workflows. Bioinformatics. 2014; doi:10.1093/bioinformatics/btu385. Full Text

Fusaro, V. A., Daniels, J., Duda, M., DeLuca, T. F., D’Angelo, O., Tamburello, J., … & Wall, D. P. (2014). The Potential of Accelerating Early Detection of Autism through Content Analysis of YouTube Videos. PloS one, 9(4), e93533. Full Text, html.

2013

Vardarajan BN, Eran A, Jung JY, Kunkel LM, Wall DP. Haplotype structure enables prioritization of common markers and candidate genes in autism spectrum disorder. Nature, Translational Psychiatry e262. Full Text

Jung, J. Y., DeLuca, T. F., Nelson, T. H., & Wall, D. P. (2013). A literature search tool for intelligent extraction of disease-associated genes. Journal of the American Medical Informatics Association, amiajnl-2012. Full Text, html.

Wall DP, Tonellato PJ. Genomics-informed pathology. The Scientist. 2013. Full Text

Diaz-Beltran L, Cano C, Wall DP, and Esteban, FJ. Systems biology as a comparative approach to understand complex gene expression in neurological diseases. Behavioral Sciences 3: 253-272. Abstract

Issa S A, Kienzler R, El-Kalioby M, Tonellato P J, Wall D, Bruggmann R & Abouelhoda M. Streaming support for data intensive cloud-based sequence analysis. BioMed Research International 2013, 791051, doi:10.1155/2013/791051 (2013). Abstract

2012

Nelson TH, Jung JY, Deluca TF, Hinebaugh BK, St Gabriel KC, Wall DP. Autworks: a cross-disease network biology application for Autism and related disorders. BMC Med Genomics. 2012 Nov 28;5(1):56. Full Text

Marlena Duda, Tristan Nelson and Dennis P Wall. Cross-pollination of research findings, although uncommon, may accelerate discovery of human disease genes. BMC Medical Genetics 2012, 13:114. Abstract

Insik Kim, Jung JY, DeLuca TF, Nelson TH, Wall DP. Cloud Computing for Comparative Genomics with Windows Azure Platform. Evolutionary Bioinformatics. 2012 Aug 30. Full Text

DP Wall, Dally R, Luyster R, Jung JY, DeLuca TF. Use of Artificial Intelligence to Shorten the Behavioral Diagnosis of Autism. PLoS ONE. 2012 Aug 27. Full-text link.

DP Wall, Tonellato PJ. The future of genomics in pathology. F1000 Med Rep. 2012 Jul 2. Full-text link.

DP Wall, Kosmicki J, DeLuca TF, Harstad E, Fusaro VA. Use of machine learning to shorten observation-based screening and diagnosis of autism. Transl Psychiatry. 2012 Apr 10. Full-text link. PDF.

Satoru Suzuki, Takako Takai-Igarashi, Yutaka Fukuoka, DP Wall, Hiroshi Tanaka, Peter J Tonellato. Systems analysis of inflammatory bowel disease based on comprehensive gene information. BMC Med Genet. 2012; 13: 25. Full-text link.

DeLuca TF, Cui J, Jung JY, St. Gabriel KC, Wall DP. Roundup 2.0: Enabling comparative genomics for over 1800 genomes. Bioinformatics. 2012 Jan 13.

2011

Cui J, Deluca TF, Jung JY, Wall DP. Phylogenetically informed logic relationships improve detection of biological network organization. BMC Bioinformatics. 2011 Dec 15;12(1):476. Jung JY, Kohane IS, Wall DP. Identification of autoimmune gene signatures in autism. Transl Psychiatry. 2011 Dec 13. Full-text link

Fusaro VA, Patil P, Gafni E, Wall DP, Tonellato PJ. Biomedical cloud computing with Amazon Web Services. PLoS Comput Biol. 2011 Aug. Cui J, DeLuca TF, Jung JY, Wall DP. Detecting biological network organization and functional gene orthologs. Bioinformatics. 2011 Oct 15;27(20):2919-20.

2010

Wall DP, Pivovarov R, Tong M, Jung JY, Fusaro VA, DeLuca TF, Tonellato PJ. Genotator: a disease-agnostic tool for genetic annotation of disease. BMC Med Genomics. 2010 pdf

Wall D, Kudtarkar P, Fusaro V, Pivovarov R, Patil P, Tonellato P. Cloud computing for comparative genomics. BMC Bioinformatics 2010;11:259. pdf

2009

Esteban FJ and Wall DP. Using game theory to detect genes involved in Autism Spectrum Disorder. TOP. 2009. pdf

Abu-Elneel K, Liu T, Gazzaniga FS, Nishimura Y, Wall DP, Geschwind DH, Lao K, Kosik KS. Reply to the “Letter to the Editors” by Steven Buyske. Neurogenetics. 2009 Feb 24. pdf

Cano C, Monaghan T, Blanco A, Wall DP, Peshkin L. Collaborative text-annotation resource for disease-centered relation extraction from biomedical text. J Biomed Inform. 2009 Feb 14. pdf

Wall DP, Esteban FJ, Deluca TF, Huyck M, Monaghan T, Velez de Mendizabal N, Goñí J, Kohane IS. Comparative analysis of neurological disorders focuses genome-wide search for autism genes. Genomics. 2009 Feb;93(2):120-9. pdf

2008

Abu-Elneel K, Liu T, Gazzaniga FS, Nishimura Y, Wall DP, Geschwind DH, Lao K, Kosik KS. Heterogeneous dysregulation of microRNAs across the autism spectrum. Neurogenetics. 2008 Jul;9(3):153-61. pdf

Singh S, Wall DP. Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function. Evol Bioinform Online. 2008;4:217-23. pdf

2007

Wall DP, Deluca T. Ortholog detection using the reciprocal smallest distance algorithm. Methods Mol Biol. 2007;396:95-110. pdf

2006

Deluca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP. Roundup: a multi-genome repository of orthologs and evolutionary distances. Bioinformatics. 2006 Aug 15;22(16):2044-6. pdf

Van Vactor D, Wall DP, Johnson KG. Heparan sulfate proteoglycans and the emergence of neuronal connectivity. Curr Opin Neurobiol. 2006 Feb;16(1):40-51. pdf

Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K, Passarino G, Underhill PA, Scharfe C, Torroni A, Scozzari R, Modiano D, Coppa A, de Knijff P, Feldman M, Cavalli-Sforza LL, Oefner PJ. The role of selection in the evolution of human mitochondrial genomes. Genetics. 2006 Jan;172(1):373-87. pdf

2005

Herbeck JT, Wall DP. Converging on a general model of protein evolution. Trends Biotechnol. 2005 Oct;23(10):485-7. pdf

Wall DP. Origin and rapid diversification of a tropical moss. Evolution. 2005 Jul;59(7):1413-24. pdf

Sivakumaran TA, Shen P, Wall DP, Do BH, Kucheria K, Oefner PJ. Conservation of the RB1 gene in human and primates. Hum Mutat. 2005 Apr;25(4):396-409. pdf

Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, Eisen MB, Feldman MW. Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5483-8. pdf

Hirsh AE, Fraser HB, Wall DP. Adjusting for selection on synonymous sites in estimates of evolutionary distance. Mol Biol Evol. 2005 Jan;22(1):174-7. pdf

2004

Fraser HB, Hirsh AE, Wall DP, Eisen MB. Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):9033-8. pdf

2003

Herbeck JT, Wall DP, Wernegreen JJ. Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia. Microbiology. 2003 Sep;149(Pt 9):2585-96. pdf

Wall DP, Fraser HB, Hirsh AE. Detecting putative orthologs. Bioinformatics. 2003 Sep 1;19(13):1710-1. pdf

Wall DP, Herbeck JT. Evolutionary patterns of codon usage in the chloroplast gene rbcL. J Mol Evol. 2003 Jun;56(6):673-88; discussion 689-90. pdf

Fraser HB, Wall DP, Hirsh AE. A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol Biol. 2003 May 23;3:11. pdf

2002

Wall DP. Use of the nuclear gene glyceraldehyde 3-phosphate dehydrogenase for phylogeny reconstruction of recently diverged lineages in Mitthyridium (Musci: Calymperaceae). Mol Phylogenet Evol. 2002 Oct;25(1):10-26. pdf