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Publications

Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology
Shaffer JR, Orlova E, Lee MK, Leslie EJ, Raffensperger ZD, Heike CL, Weinberg S, et al.. PLoS Genet (Aug 25, 2016)

Using the 3D Facial Norms Database to investigate craniofacial sexual dimorphism in healthy children, adolescents, and adults
Kesterke MJ, Raffensperger ZD, Heike CL, Cunningham ML, Hecht JT, Kau CH, Nidey NL, Moreno LM, Wehby GL, Marazita ML, Weinberg SM.. Biology of Sex Differences (Apr 22, 2016)

The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. (Review)
Van Otterloo E, Williams T, Artinger KB.. Developmental Biology (Jan 22, 2016)

A single nucleotide polymorphism associated with isolated cleft lip and palate, thyroid cancer and hypothyroidism alters the activity of an oral epithelium and thyroid enhancer near FOXE1.
Lidral AC, Liu H, Bullard SA, Bonde G, Machida J, Visel A, Uribe LM, Li X, Amendt B, Cornell RA.. Human Molecular Genetics (Jul 15, 2015)

Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders.
Fairfield H, Srivastava A, Ananda G, Liu R, Kircher M, Lakshminarayana A, Harris BS, Karst SY, Dionne LA, Kane CC, Curtain M, Berry ML, Ward-Bailey PF, Greenstein I, Byers C, Czechanski A, Sharp J, Palmer K, Gudis P, Martin W, Tadenev A, Bogdanik L, Pratt CH, Chang B, Schroeder DG, Cox GA, Cliften P, Milbrandt J, Murray S, Burgess R, Bergstrom DE, Donahue LR, Hamamy H, Masri A, Santoni FA, Makrythanasis P, Antonarakis SE, Shendure J, Reinholdt LG.. Genome Research (Apr 27, 2015)

BMP-SHH signaling network controls epithelial stem cell fate via regulation of its niche in the developing tooth.
Li J, Feng J, Liu Y, Ho TV, Grimes W, Ho HA, Park S, Wang S, Chai Y.. Developmental Cell (Apr 20, 2015)

Integration of comprehensive 3D microCT and signaling analysis reveals differential regulatory mechanisms of craniofacial bone development.
Ho TV, Iwata J, Ho HA, Grimes WC, Park S, Sanchez-Lara PA, Chai Y.. Developmental Biology (Apr 15, 2015)

The suture provides a niche for mesenchymal stem cells of craniofacial bones.
Zhao H, Feng J, Ho TV, Grimes W, Urata M, Chai Y.. Nature Cell Biology (Apr 3, 2015)

A genome-wide study of inherited deletions identified two regions associated with nonsyndromic isolated oral clefts.
Younkin SG, Scharpf RB, Schwender H, Parker MM, Scott AF, Marazita ML, Beaty TH, Ruczinski I.. Birth Defects Research Part A: Clinical and Molecular Teratology (Apr 1, 2015)

A novel allele of Alx4 results in reduced Fgf10 expression and failure of eyelid fusion in mice.
Curtain M, Heffner CS, Maddox DM, Gudis P, Donahue LR, Murray SA.. Mammalian Genome (Apr 1, 2015)

Prenatal sex hormones, digit ratio, and face shape in adult males.
Weinberg SM, Parsons TE, Raffensperger ZD, Marazita ML.. Orthodontics & Craniofacial Research (Feb 1, 2015)

BCL11B expression in intramembranous osteogenesis during murine craniofacial suture development.
Holmes G, van Bakel H, Zhou X, Losic B, Jabs EW.. Gene Expression Patterns (Jan 1, 2015)

HAND2 targets define a network of transcriptional regulators that compartmentalize the early limb bud mesenchyme.
Osterwalder M, Speziale D, Shoukry M, Mohan R, Ivanek R, Kohler M, Beisel C, Wen X, Scales SJ, Christoffels VM, Visel A, Lopez-Rios J, Zeller R.. Developmental Cell (Nov 20, 2014)

Principles of regulatory information conservation between mouse and human.
Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; Mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP.. Nature (Nov 20, 2014)

Airway branching has conserved needs for local parasympathetic innervation but not neurotransmission.
Bower DV, Lee HK, Lansford R, Zinn K, Warburton D, Fraser SE, Jesudason EC.. BMC Biology (Nov 11, 2014)

Functional analysis of SPECC1L in craniofacial development and oblique facial cleft pathogenesis.
Gfrerer L, Shubinets V, Hoyos T, Kong Y, Nguyen C, Pietschmann P, Morton CC, Maas RL, Liao EC.. Plastic Reconstructive Surgery (Oct 1, 2014)

Tissue-specific RNA expression marks distant-acting developmental enhancers.
Wu H, Nord AS, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA, Visel A.. PLOS Genetics (Sep 4, 2014)

Learning to Rank the Severity of Unrepaired Cleft Lip Nasal Deformity on 3D Mesh Data.
Wu J, Tse R, Shapiro LG.. Proceedings from IAPR Int Conf on Pattern Recognition (Aug 2, 2014)

Quantification of skull deformity for craniofacial research.
Lam I, Cunningham M, Birgfeld C, Speltz M, Shapiro L.. Proceedings from IEEE Engineering in Medicine and Biology Society (Aug 2, 2014)

Automated face extraction and normalization of 3D Mesh Data.
Wu J, Tse R, Shapiro LG.. Proceedings from IEEE Engineering in Medicine and Biology Society (Aug 2, 2014)

Identification of novel craniofacial regulatory domains located far upstream of SOX9 and disrupted in Pierre Robin sequence.
Gordon CT, Attanasio C, Bhatia S, Benko S, Ansari M, Tan TY, Munnich A, Pennacchio LA, Abadie V, Temple IK, Goldenberg A, van Heyningen V, Amiel J, FitzPatrick D, Kleinjan DA, Visel A, Lyonnet S.. Human Mutations (Aug 1, 2014)

A gene expression atlas of early craniofacial development.
Brunskill, Eric W, Potter, Andrew S, Distasio, Andrew, Dexheimer, Phillip, Plassard, Andrew, Aronow, Bruce J, Potter, S Steven. Developmental biology (Jul 5, 2014)

Function-based identification of mammalian enhancers using site-specific integration.
Dickel, Diane E; Zhu, Yiwen; Nord, Alex S; Wylie, John N; Akiyama, Jennifer A; Afzal, Veena; Plajzer-Frick, Ingrid; Kirkpatrick, Aileen; Göttgens, Berthold; Bruneau, Benoit G; Visel, Axel; Pennacchio, Len A . Nature methods (May 1, 2014)

Classifying Craniosynostosis with a 3D Projection-Based Feature Extraction System.
Lam I, Cunningham M, Speltz M, Shapiro L.. Proceedings for IEEE International Symposium Computer Based Medical Systems (May 1, 2014)

Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives.
Bureau, Alexandre; Younkin, Samuel; Parker, Margaret M; Bailey-Wilson, Joan E; Marazita, Mary L; Murray, Jeffrey C; Mangold, Elisabeth; Albacha-Hejazi, Hasan; Beaty, Terri H; Ruczinski, Ingo. Bioinformatics (Oxford, England) (Apr 16, 2014)

Evolution of the miR199-214 cluster and vertebrate skeletal development.
Desvignes, Thomas; Contreras, Adam; Postlethwait, John H. RNA biology (Feb 20, 2014)

A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk.
Younkin, Samuel G; Scharpf, Robert B; Schwender, Holger; Parker, Margaret M; Scott, Alan F; Marazita, Mary L; Beaty, Terri H; Ruczinski, Ingo. BMC Genetics (Feb 14, 2014)

Secretion of shh by a neurovascular bundle niche supports mesenchymal stem cell homeostasis in the adult mouse incisor.
Zhao, Hu; Feng, Jifan; Seidel, Kerstin; Shi, Songtao; Klein, Ophir; Sharpe, Paul; Chai, Yang. Cell stem cell (Feb 6, 2014)

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development.
Nord, Alex S; Blow, Matthew J; Attanasio, Catia; Akiyama, Jennifer A; Holt, Amy; Hosseini, Roya; Phouanenavong, Sengthavy; Plajzer-Frick, Ingrid; Shoukry, Malak; Afzal, Veena; Rubenstein, John L R; Rubin, Edward M; Pennacchio, Len A; Visel, Axel . Cell (Dec 19, 2013)

Congenital heart defects in patients with deletions upstream of SOX9.
Sanchez-Castro, Marta; Gordon, Christopher T; Petit, Florence; Nord, Alex S; Callier, Patrick; Andrieux, Joris; Guérin, Patrice; Pichon, Olivier; David, Albert; Abadie, Véronique; Bonnet, Damien; Visel, Axel; Pennacchio, Len A; Amiel, Jeanne; Lyonnet, Stanislas; Le Caignec, Cédric . Human mutation (Dec 1, 2013)

Genetics of cleft lip and cleft palate.
Leslie, Elizabeth J; Marazita, Mary L. American journal of medical genetics. Part C, Seminars in medical genetics (Nov 2, 2013)

Understanding the basis of auriculocondylar syndrome: Insights from human, mouse and zebrafish genetic studies.
Clouthier, David E; Passos-Bueno, Maria Rita; Tavares, Andre L P; Lyonnet, Stanislas; Amiel, Jeanne; Gordon, Christopher T. American journal of medical genetics. Part C, Seminars in medical genetics (Nov 1, 2013)

Fine tuning of craniofacial morphology by distant-acting enhancers.
Attanasio, Catia; Nord, Alex S; Zhu, Yiwen; Blow, Matthew J; Li, Zirong; Liberton, Denise K; Morrison, Harris; Plajzer-Frick, Ingrid; Holt, Amy; Hosseini, Roya; Phouanenavong, Sengthavy; Akiyama, Jennifer A; Shoukry, Malak; Afzal, Veena; Rubin, Edward M; FitzPatrick, David R; Ren, Bing; Hallgrímsson, Benedikt; Pennacchio, Len A; Visel, Axel.. Science (New York, N.Y.) (Oct 25, 2013)

Search for genetic modifiers of IRF6 and genotype-phenotype correlations in Van der Woude and popliteal pterygium syndromes.
Leslie, Elizabeth J; Mancuso, Jennifer L; Schutte, Brian C; Cooper, Margaret E; Durda, Kate M; L'heureux, Jamie; Zucchero, Theresa M; Marazita, Mary L; Murray, Jeffrey C.. American journal of medical genetics. Part A (Oct 2, 2013)

SP8 regulates signaling centers during craniofacial development.
Kasberg, Abigail D; Brunskill, Eric W; Steven Potter, S.. Developmental biology (Sep 15, 2013)

The Use of Pseudo-landmarks for Craniofacial Analysis: A Comparative Study with L1-Regularized Logistic Regression.
Mercan E, Shapiro LG, Weinberg SM, Lee SI.. Proceedings from IEEE Engineering in Medicine and Biology Society Annual Conference (Jul 2, 2013)

Improved Detection of Landmarks on 3D Human Face Data.
Liang S, Wu J, Weinberg SM, Shapiro LG.. Proceedings from IEEE Engineering in Medicine and Biology Society Annual Conference (Jul 1, 2013)

A New Tool for Quantifying and Characterizing Asymmetry in Bilaterally Paired Structures.
Rolfe SM, Camci ED, Mercan E, Shapiro LG, Cox TC.. Proceedings from IEEE Engineering in Medicine and Biology Society Annual Conference (Jul 1, 2013)

Skull Retrieval for Craniosynostosis Using Sparse Logistic Regression Models.
Yang S, Shapiro L, Cunningham M, Speltz M, Birgfeld C, Atmosukarto I, Lee SI.. Medical Image Computing and Computer-Assisted Intervention (Jun 13, 2013)

3D object retrieval using salient views.
Atmosukarto, Indriyati; Shapiro, Linda G.. International journal of multimedia information retrieval (Jun 2, 2013)

3D object retrieval using salient views.
Atmosukarto I, Shapiro LG.. International Journal of Multimedia Information Retrieval (Jun 1, 2013)

Comparative analysis of IRF6 variants in families with Van der Woude syndrome and popliteal pterygium syndrome using public whole-exome databases.
Leslie, Elizabeth J; Standley, Jennifer; Compton, John; Bale, Sherri; Schutte, Brian C; Murray, Jeffrey C.. Genetics in medicine : official journal of the American College of Medical Genetics (May 1, 2013)

Transgenic quail as a model for research in the avian nervous system: a comparative study of the auditory brainstem.
Seidl, Armin H; Sanchez, Jason Tait; Schecterson, Leslayann; Tabor, Kathryn M; Wang, Yuan; Kashima, Daniel T; Poynter, Greg; Huss, David; Fraser, Scott E; Lansford, Rusty; Rubel, Edwin W.. The Journal of comparative neurology (Jan 1, 2013)

Functional anatomy of distant-acting mammalian enhancers.
Dickel, D E; Visel, A; Pennacchio, L A.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences (Jan 1, 2013)

3D shape isometric correspondence by spectral assignment.
Pan X, Shapiro L.. Proceedings of International Conference on Pattern Recognition (Nov 12, 2012)

fras1 shapes endodermal pouch 1 and stabilizes zebrafish pharyngeal skeletal development.
Talbot, Jared Coffin; Walker, Macie B; Carney, Thomas J; Huycke, Tyler R; Yan, Yi-Lin; BreMiller, Ruth A; Gai, Linda; Delaurier, April; Postlethwait, John H; Hammerschmidt, Matthias; Kimmel, Charles B.. Development (Cambridge, England) (Aug 1, 2012)

Shape-based classification of 3D facial data to support 22q11.2DS craniofacial research.
Wilamowska K, Wu J, Heike C, Shapiro L. Journal of Digital Imaging (Jun 25, 2012)

The evolution of human genetic studies of cleft lip and cleft palate.
Marazita ML. Annual Review of Genomics and Human Genetics (Jun 6, 2012)

Advances in multiphoton microscopy for imaging embryos.
Supatto, Willy; Truong, Thai V; Débarre, Delphine; Beaurepaire, Emmanuel.. Current opinion in genetics & development (Oct 15, 2011)

Epigenetic integration of the developing brain and face.
Parsons, Trish E; Schmidt, Eric J; Boughner, Julia C; Jamniczky, Heather A; Marcucio, Ralph S; Hallgrímsson, Benedikt.. Developmental dynamics : an official publication of the American Association of Anatomists (Oct 15, 2011)

miR-196 regulates axial patterning and pectoral appendage initiation.
He, Xinjun; Yan, Yi-Lin; Eberhart, Johann K; Herpin, Amaury; Wagner, Toni U; Schartl, Manfred; Postlethwait, John H.. Developmental biology (Sep 15, 2011)

A Landmark-free Framework for the Detection and Description of Shape Differences in Embryos
Shapiro, Linda. International IEEE EMBS Conference (Sep 3, 2011)

Learning to Compute the Plane of Symmetry for Human Faces
Shapiro, Linda. ACM-BCB '11 (Aug 2, 2011)

Classification and Feature Selection for Craniosynostosis
Shapiro, Linda; Cunningham, Michael L.. ACM-BCB '11 (Aug 1, 2011)

Dynamic lineage analysis of embryonic morphogenesis using transgenic quail and 4D multispectral imaging.
Bower, Danielle V; Sato, Yuki; Lansford, Rusty.. Genesis (New York, N.Y. : 2000 (Jul 2, 2011)

SMAD4-mediated WNT signaling controls the fate of cranial neural crest cells during tooth morphogenesis.
Li, Jingyuan; Huang, Xiaofeng; Xu, Xun; Mayo, Julie; Bringas, Pablo; Jiang, Rulang; Wang, Songling; Chai, Yang.. Development (Cambridge, England) (May 2, 2011)

Observation of miRNA gene expression in zebrafish embryos by in situ hybridization to microRNA primary transcripts.
He, Xinjun; Yan, Yi-Lin; DeLaurier, April; Postlethwait, John H.. Zebrafish (Mar 8, 2011)

Wwp2 is essential for palatogenesis mediated by the interaction between Sox9 and mediator subunit 25.
Nakamura, Yukio; Yamamoto, Koji; He, Xinjun; Otsuki, Bungo; Kim, Youngwoo; Murao, Hiroki; Soeda, Tsunemitsu; Tsumaki, Noriyuki; Deng, Jian Min; Zhang, Zhaoping; Behringer, Richard R; Crombrugghe, Benoit de; Postlethwait, John H; Warman, Matthew L; Nakamura, Takashi; Akiyama, Haruhiko.. Nature communications (Jan 2, 2011)

Groupwise Pose Normalization for Craniofacial Applications
Chen JH Shapiro LG.. IEEE Workshop on Applications of Computer Vision (Jan 1, 2011)

A landmark-free framework for the detection and description of shape differences in embryos.
Rolfe, S M; Shapiro, L G; Cox, T C; Maga, A M; Cox, L L.. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference (Jan 1, 2011)

3D digital stereophotogrammetry: a practical guide to facial image acquisition.
Heike, Carrie L; Upson, Kristen; Stuhaug, Erik; Weinberg, Seth M.. Head & face medicine (Jul 28, 2010)

Limits of sequence and functional conservation.
Pennacchio, Len A; Visel, Axel.. Nature genetics (Jul 2, 2010)

PhenoHM: human-mouse comparative phenome-genome server.
Sardana, Divya; Vasa, Suresh; Vepachedu, Nishanth; Chen, Jing; Gudivada, Ranga Chandra; Aronow, Bruce J; Jegga, Anil G.. Nucleic acids research (Jul 1, 2010)

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems.
Kaimal, Vivek; Bardes, Eric E; Tabar, Scott C; Jegga, Anil G; Aronow, Bruce J.. Nucleic acids research (Jul 1, 2010)

Transforming growth factor-beta regulates basal transcriptional regulatory machinery to control cell proliferation and differentiation in cranial neural crest-derived osteoprogenitor cells.
Iwata, Jun-ichi; Hosokawa, Ryoichi; Sanchez-Lara, Pedro A; Urata, Mark; Slavkin, Harold; Chai, Yang.. The Journal of biological chemistry (Feb 12, 2010)

The Use of Genetic Programming for Learning 3D Craniofacial Shape Quantifications.
Chen JH, Zheng KC, Shapiro LG.. European Conference on Computer Vision (Jan 2, 2010)

The Use of Genetic Programming for Learning 3D Craniofacial Shape Quantifications.
Atmosukarto I, Shapiro LG, Heike C. Proc IAPR International Conference on Pattern Recognition (Jan 1, 2010)

Shape-Based Classification of 3D Head Data.
Shapiro L, Wilamowska K, Atmosukarto I, Wu J, Heike C, Speltz M, Cunningham M.. Proc International Conference Image Analysis Processing (Jan 1, 2009)