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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Scientific programmer position in neuroimage analysis and machine learning (University of Texas Southwestern,
Dallas, USA)<o:p></o:p></span></b></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> The laboratory of Albert Montillo ( http://www.utsouthwestern.edu/labs/montillo ) in the Bioinformatics Department
of UT Southwestern Medical Center is seeking a full time Scientific Programmer for studies of mental & neurodevelopmental disorders and neurodegenerative diseases. The Scientific Programmer will use multimodal MRI, and MEG/EEG data to study structural and
functional circuit changes, and PET/SPECT, CT to study metabolic and pathophysiological changes associated with diagnosis and prognoses. The main responsibilities of the position include: implementing and optimizing image processing, computational and analyses
pipelines for large-scale multimodal brain imaging data and corresponding clinical data. The lab is an interactive and collaborative team directed by Albert Montillo, Ph.D., conducting cutting-edge research to advance the theory and application of machine
learning for the analysis of medical images. The lab addresses unmet clinical needs by forming predictive models that make diagnoses and prognoses more precise and advance neuroscience by furthering the understanding of mechanisms in disease and intervention.
You will work directly with him and an array of principle investigators, collaborators and trainees.<br>
Medical image analysis software the lab has developed include machine learning-based methods for labeling structures throughout the brain (parcellation), versions of which are used worldwide and FDA approved. The lab has built deep learning methods to
label networks in resting state fMRI and detect artifacts in MEG. The lab has pioneered deep learning decision forests that increase prediction accuracy while reducing prediction time and outcome prediction methods using advanced brain connectomics.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Job responsibilities</span></b><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></p>
<ul type="disc">
<li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Design, implement and optimize image processing, computational and analyses pipelines for large-scale multimodal brain imaging, including resting and task-based fMRI, diffusion MRI, PET/SPECT,
CT, and MEG/EEG data on our high performance compute cluster.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Implement machine learning models to automate preprocessing, quality control, and computational data analysis of imaging, metabolic, genetic, behavioral, and clinical data.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Integrate third party pipelines with tailored in-house pipelines.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Build tools to organize and visualize the growing database of analysis results.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Contribute to writing of journal and conference papers.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Attend lab meetings, stay abreast of developments in image analysis and machine learning.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Coordinate data integration from ongoing studies.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Teach lab members about image processing steps, outputs and to quality control approaches.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">A minimum three-year commitment is strongly encouraged.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Anticipated start date: immediate<o:p></o:p></span></li></ul>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Experience of ideal applicants:</span></b><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></p>
<ul type="disc">
<li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">B.A. or B.S. Degree in Computer Science, Electrical Engineering, Biomedical Engineering or a related field with three (3) years scientific software development; Master's or Ph.D. preferred.
Software development experience on high performance compute clusters or GPU-based machine learning is a strong plus. Will consider record of success in publishing computational results in lieu of experience.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Familiarity with
<u>at least 1</u> image data type: MRI, PET/SPECT, CT, MEG/EEG & format: NIFTI, DICOM.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Experience in <u>
at least 1</u> neuroimage analysis pipeline: NiPype, SPM, FSL, AFNI, FreeSurfer; for diffusion MRI: Camino, DTI-TK, DiPy, TrackVis, DTI/DSI studio, ExploreDTI; for MEG/EEG: Brainstorm, EEGLAB, FieldTrip, MNE, NUTMEG.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Experience developing image processing or image analysis software. Solid understand of standard CS data structures.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">At least 2 years of experience in Linux; Python and 1 other language (Matlab, R, C/C++)<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Practical ML experience applying at least 1 of the following: deep learning neural nets (RNN,CNN,DNN, UNet/VNet), DCGAN, deep reinforcement learning, transfer learning, autoencoders; classical
or shallow machine learning; image/object recognition; time series analysis.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Experience in at least one of these Python libraries: Keras, scikit-learn, TensorFlow, PyTorch, Nilearn.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Experience in brain connectivity, graph theory, and genomic data analyses are significant advantages.<o:p></o:p></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2">
<span style="font-size:12.0pt;font-family:"Times New Roman",serif">Optional but helpful: Experience in C/C++ (ITK library), cMake, software development. Familiarity with XNAT.<o:p></o:p></span></li></ul>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Salary compensation is very competitive and enhanced by the low cost of living in Dallas. Benefits include health
insurance. The candidate will also benefit from membership in vibrant national and international research communities through our on-going collaborations with UCLA, UCSF, UPenn, Stanford, Philips and Siemens Research, as well as a large local neuroscience
communities through UTSW's O’Donnell Brain Institute, and UTD's Centers for Vital Longevity, Brain Health, and Brain Performance.<br>
<br>
<b>Please apply by email to Dr. Montillo [Albert.Montillo@UTSouthwestern.edu] and include your CV and names and addresses of three references. Use the subject line “ScientificProgrammer: <your name>”.</b><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">The Montillo lab is co-located within the Bioinformatics Department on UT Southwestern’s south campus and embedded
in the Radiology Department on north campus. We are an integral part of the Advanced Imaging Research Center, and work closely with research groups within Neuroscience, Neurology, Psychiatry, Radiation Oncology, and Surgery. Montillo lab members have access
to considerable computational resources, including the >6,800-core cluster with >8 Petabyte of storage available through UTSW’s high-performance infrastructure (BioHPC – https://portal.biohpc.swmed.edu ). Future lab members will have the opportunity to work
on a broad range of image analysis, machine learning and modeling on interdisciplinary teams, and participate in all aspects of method development, software implementation, data analysis, and validation with lab collaborators.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Albert Montillo, Ph.D.<br>
Assistant Professor, Director, Deep Learning for Precision Health Laboratory<br>
Departments of Bioinformatics, Radiology and the Advanced Imaging Research Center<br>
University of Texas Southwestern Medical Center<br>
5323 Harry Hines Blvd.<br>
Dallas, TX 75390-8579<br>
Albert.Montillo@UTSouthwestern.edu<br>
http://www.utsouthwestern.edu/labs/montillo<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><i><span style="font-size:12.0pt;font-family:"Times New Roman",serif">UT Southwestern Medical Center is an Affirmative Action/Equal Opportunity Employer. Women, minorities, veterans
and individuals with disabilities are encouraged to apply.</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p align="right" style="text-align:right"><span style="font-size:17pt;letter-spacing:-3px;font-family:"Helvetica","sans-serif";color:#0054A0;font-weight:bolder;">UT</span><span style="font-size:17pt;letter-spacing:-0px;font-family:"Helvetica","sans-serif";color:#0054A0;font-weight:bolder;">
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<p style="text-align:right"><span style="font-size:10pt;font-family:"Helvetica","sans-serif"; color:#666D70;">The future of medicine, today.</span></p>
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