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Hi all, <br>
<br>
I've an offer for a PhD student to work on sequence data indexation.
<br>
Starting date is flexible. <br>
<br>
Here is the full announce, do not hesitate to post and to apply :)<br>
<br>
<h2 class="md-end-block md-heading" style="box-sizing: border-box; break-after: avoid-page; break-inside: avoid; orphans: 2; font-size: 1.75em; margin-top: 1rem; margin-bottom: 1rem; position: relative; font-weight: bold; line-height: 1.225; cursor: text; padding-bottom: 0.3em; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: rgb(238, 238, 238); white-space: pre-wrap; caret-color: rgb(51, 51, 51); color: rgb(51, 51, 51); font-family: "Open Sans", "Clear Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; font-style: normal; font-variant-caps: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;"><span class="md-plain md-expand" style="box-sizing: border-box;">PhD offer - Search engine for genomic sequencing data</span></h2>
<p class="md-end-block md-p" style="box-sizing: border-box; line-height: inherit; orphans: 4; margin: 0.8em 0px; white-space: pre-wrap; position: relative; caret-color: rgb(51, 51, 51); color: rgb(51, 51, 51); font-family: "Open Sans", "Clear Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;"><span class="md-plain" style="box-sizing: border-box;">We are currently witnessing a deep knowledge revolution due to the availability of exponentially expanding DNA sequence databases. This is made possible by the continuous acceleration of DNA sequencing throughput. Sequencing data is accumulating faster than Moore’s Law, bringing fundamental new insights, conjecture, and understanding, with impacts in medicine, agronomy and ecology. Today, the </span><span class=" md-link" style="box-sizing: border-box;"><a spellcheck="false" href="https://www.ncbi.nlm.nih.gov/sra" style="box-sizing: border-box; cursor: pointer; color: rgb(65, 131, 196); -webkit-user-drag: none;"><span class="md-plain" style="box-sizing: border-box;">Sequence Read Archive</span></a></span><span class="md-plain" style="box-sizing: border-box;"> raw data archive stores more than </span><span class="md-inline-math math-jax-postprocess" style="box-sizing: border-box; display: inline-block;"><span class="md-math-tex inline-math-svg" style="box-sizing: border-box;"><span class="MathJax_SVG" id="MathJax-Element-1-Frame" tabindex="-1" style="box-sizing: border-box; display: inline-block; font-style: normal; font-weight: normal; line-height: normal; zoom: 0.8999999761581421; text-indent: 0px; text-align: left; text-transform: none; letter-spacing: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; font-size: 16px; vertical-align: 0.2px;"><svg xlink="http://www.w3.org/1999/xlink" width="4.197ex" height="2.461ex" viewBox="0 -956.9 1807.1 1059.4" style="vertical-align: -0.238ex;"><defs><path stroke-width="0" id="E1-MJMAIN-31" d="M213 578L200 573Q186 568 160 563T102 556H83V602H102Q149 604 189 617T245 641T273 663Q275 666 285 666Q294 666 302 660V361L303 61Q310 54 315 52T339 48T401 46H427V0H416Q395 3 257 3Q121 3 100 0H88V46H114Q136 46 152 46T177 47T193 50T201 52T207 57T213 61V578Z"></path><path stroke-width="0" id="E1-MJMAIN-30" d="M96 585Q152 666 249 666Q297 666 345 640T423 548Q460 465 460 320Q460 165 417 83Q397 41 362 16T301 -15T250 -22Q224 -22 198 -16T137 16T82 83Q39 165 39 320Q39 494 96 585ZM321 597Q291 629 250 629Q208 629 178 597Q153 571 145 525T137 333Q137 175 145 125T181 46Q209 16 250 16Q290 16 318 46Q347 76 354 130T362 333Q362 478 354 524T321 597Z"></path><path stroke-width="0" id="E1-MJMAIN-36" d="M42 313Q42 476 123 571T303 666Q372 666 402 630T432 550Q432 525 418 510T379 495Q356 495 341 509T326 548Q326 592 373 601Q351 623 311 626Q240 626 194 566Q147 500 147 364L148 360Q153 366 156 373Q197 433 263 433H267Q313 433 348 414Q372 400 396 374T435 317Q456 268 456 210V192Q456 169 451 149Q440 90 387 34T253 -22Q225 -22 199 -14T143 16T92 75T56 172T42 313ZM257 397Q227 397 205 380T171 335T154 278T148 216Q148 133 160 97T198 39Q222 21 251 21Q302 21 329 59Q342 77 347 104T352 209Q352 289 347 316T329 361Q302 397 257 397Z"></path></defs><g stroke="currentColor" fill="currentColor" stroke-width="0" transform="matrix(1 0 0 -1 0 0)"><use></use><use x="500" y="0"></use><g transform="translate(1000,392)"><use transform="scale(0.707)"></use><use transform="scale(0.707)" x="500" y="0"></use></g></g></svg></span></span><span class="md-math-after-sym" style="box-sizing: border-box;"></span></span><span class="md-plain" style="box-sizing: border-box;"> nucleotides, in the form of short sequences (</span><span class="md-inline-math math-jax-postprocess" style="box-sizing: border-box; display: inline-block;"><span class="md-math-tex inline-math-svg" style="box-sizing: border-box;"><span class="MathJax_SVG" id="MathJax-Element-2-Frame" tabindex="-1" style="box-sizing: border-box; display: inline-block; font-style: normal; font-weight: normal; line-height: normal; zoom: 0.8999999761581421; text-indent: 0px; text-align: left; text-transform: none; letter-spacing: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; font-size: 16px; vertical-align: 0.2px;"><svg xlink="http://www.w3.org/1999/xlink" width="7.097ex" height="2.227ex" viewBox="0 -755.9 3055.8 958.9" style="vertical-align: -0.472ex;"><defs><path stroke-width="0" id="E2-MJMAIN-2264" d="M674 636Q682 636 688 630T694 615T687 601Q686 600 417 472L151 346L399 228Q687 92 691 87Q694 81 694 76Q694 58 676 56H670L382 192Q92 329 90 331Q83 336 83 348Q84 359 96 365Q104 369 382 500T665 634Q669 636 674 636ZM84 -118Q84 -108 99 -98H678Q694 -104 694 -118Q694 -130 679 -138H98Q84 -131 84 -118Z"></path><path stroke-width="0" id="E2-MJMAIN-31" d="M213 578L200 573Q186 568 160 563T102 556H83V602H102Q149 604 189 617T245 641T273 663Q275 666 285 666Q294 666 302 660V361L303 61Q310 54 315 52T339 48T401 46H427V0H416Q395 3 257 3Q121 3 100 0H88V46H114Q136 46 152 46T177 47T193 50T201 52T207 57T213 61V578Z"></path><path stroke-width="0" id="E2-MJMAIN-30" d="M96 585Q152 666 249 666Q297 666 345 640T423 548Q460 465 460 320Q460 165 417 83Q397 41 362 16T301 -15T250 -22Q224 -22 198 -16T137 16T82 83Q39 165 39 320Q39 494 96 585ZM321 597Q291 629 250 629Q208 629 178 597Q153 571 145 525T137 333Q137 175 145 125T181 46Q209 16 250 16Q290 16 318 46Q347 76 354 130T362 333Q362 478 354 524T321 597Z"></path></defs><g stroke="currentColor" fill="currentColor" stroke-width="0" transform="matrix(1 0 0 -1 0 0)"><use x="0" y="0"></use><g transform="translate(1055,0)"><use></use><use x="500" y="0"></use><use x="1000" y="0"></use><use x="1500" y="0"></use></g></g></svg></span></span><span class="md-math-after-sym" style="box-sizing: border-box;"></span></span><span class="md-plain" style="box-sizing: border-box;"> bp) which represent fragments from generally unknown genomic location (the “reads”). </span></p>
<p class="md-end-block md-p" style="box-sizing: border-box; line-height: inherit; orphans: 4; margin: 0.8em 0px; white-space: pre-wrap; position: relative; caret-color: rgb(51, 51, 51); color: rgb(51, 51, 51); font-family: "Open Sans", "Clear Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;"><span class="md-plain" style="box-sizing: border-box;">Currently there exists no way to query this treasure of information. Today, it would be unthinkable to access the Internet without powerful search engines. However, this is precisely the current situation for raw read archives, where precious data sleep undisturbed in rarely-opened drawers. In this project we propose to develop a new scaling breakthrough, allowing users to directly query sequencing data on the fly in order to tap into the largest underexploited resource in life sciences. </span></p>
<p class="md-end-block md-p" style="box-sizing: border-box; line-height: inherit; orphans: 4; margin: 0.8em 0px; white-space: pre-wrap; position: relative; caret-color: rgb(51, 51, 51); color: rgb(51, 51, 51); font-family: "Open Sans", "Clear Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;"><span class="md-plain" style="box-sizing: border-box;">In the framework of the broader </span><span class=" md-link" style="box-sizing: border-box;"><a spellcheck="false" href="https://www.cesgo.org/seqdigger/" style="box-sizing: border-box; cursor: pointer; color: rgb(65, 131, 196); -webkit-user-drag: none;"><span class="md-plain" style="box-sizing: border-box;">SeqDigger ANR project</span></a></span><span class="md-plain" style="box-sizing: border-box;">, we propose to design and propose new indexing schemes, scaling up very large DNA collection (assembled or not), and offering a way to query in real time input sequences of interest. The recruited PhD student will explore existing methods, mainly based on Bloom Filters, and will propose new algorithmic solutions.</span></p>
<h3 class="md-end-block md-heading" style="box-sizing: border-box; break-after: avoid-page; break-inside: avoid; orphans: 2; font-size: 1.5em; margin-top: 1rem; margin-bottom: 1rem; position: relative; font-weight: bold; line-height: 1.43; cursor: text; white-space: pre-wrap; caret-color: rgb(51, 51, 51); color: rgb(51, 51, 51); font-family: "Open Sans", "Clear Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; font-style: normal; font-variant-caps: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;"><span class="md-plain" style="box-sizing: border-box;">Required skills </span></h3>
<p class="md-end-block md-p" style="box-sizing: border-box; line-height: inherit; orphans: 4; margin: 0.8em 0px; white-space: pre-wrap; position: relative; caret-color: rgb(51, 51, 51); color: rgb(51, 51, 51); font-family: "Open Sans", "Clear Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;"><span class="md-plain" style="box-sizing: border-box;">Candidates must have strong interest and expertise in algorithmics, data structures and C++ implementation. </span></p>
<p class="md-end-block md-p" style="box-sizing: border-box; line-height: inherit; orphans: 4; margin: 0.8em 0px; white-space: pre-wrap; position: relative; caret-color: rgb(51, 51, 51); color: rgb(51, 51, 51); font-family: "Open Sans", "Clear Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;"><span class="md-plain" style="box-sizing: border-box;">Knowledge in genomics and biology will be highly appreciated but is not a prerequisite. </span></p>
<h3 class="md-end-block md-heading" style="box-sizing: border-box; break-after: avoid-page; break-inside: avoid; orphans: 2; font-size: 1.5em; margin-top: 1rem; margin-bottom: 1rem; position: relative; font-weight: bold; line-height: 1.43; cursor: text; white-space: pre-wrap; caret-color: rgb(51, 51, 51); color: rgb(51, 51, 51); font-family: "Open Sans", "Clear Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; font-style: normal; font-variant-caps: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;"><span class="md-plain" style="box-sizing: border-box;">Practical information </span></h3>
<p class="md-end-block md-p" style="box-sizing: border-box; line-height: inherit; orphans: 4; margin: 0.8em 0px; white-space: pre-wrap; position: relative; caret-color: rgb(51, 51, 51); color: rgb(51, 51, 51); font-family: "Open Sans", "Clear Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;"><span class="md-plain" style="box-sizing: border-box;">The recruited PhD student will work in the </span><span class=" md-link" style="box-sizing: border-box;"><a spellcheck="false" href="https://team.inria.fr/genscale/" style="box-sizing: border-box; cursor: pointer; color: rgb(65, 131, 196); -webkit-user-drag: none;"><span class="md-plain" style="box-sizing: border-box;">GenScale</span></a></span><span class="md-plain" style="box-sizing: border-box;"> team at Inria Rennes, France. She/he will work in close collaboration with the SeqDigger partners (Pasteur Institute Paris, CEA Genoscope, MIO) and external collaborators (</span><span class=" md-link" style="box-sizing: border-box;"><a spellcheck="false" href="https://www.ebi.ac.uk/" style="box-sizing: border-box; cursor: pointer; color: rgb(65, 131, 196); -webkit-user-drag: none;"><span class="md-plain" style="box-sizing: border-box;">EBI</span></a></span><span class="md-plain" style="box-sizing: border-box;">, </span><span class=" md-link" style="box-sizing: border-box;"><a spellcheck="false" href="https://www.techfak.uni-bielefeld.de/~stoye/" style="box-sizing: border-box; cursor: pointer; color: rgb(65, 131, 196); -webkit-user-drag: none;"><span class="md-plain" style="box-sizing: border-box;">Bielefeld University</span></a></span><span class="md-plain" style="box-sizing: border-box;">, ...). Short stays at EBI, Cambridge, are expected. </span></p>
<p class="md-end-block md-p" style="box-sizing: border-box; line-height: inherit; orphans: 4; margin: 0.8em 0px; white-space: pre-wrap; position: relative; caret-color: rgb(51, 51, 51); color: rgb(51, 51, 51); font-family: "Open Sans", "Clear Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;"><span class="md-plain" style="box-sizing: border-box;">Starting date is flexible. PhD could start as early as October 2019.</span></p>
<p class="md-end-block md-p" style="box-sizing: border-box; line-height: inherit; orphans: 4; margin: 0.8em 0px; white-space: pre-wrap; position: relative; caret-color: rgb(51, 51, 51); color: rgb(51, 51, 51); font-family: "Open Sans", "Clear Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;"><span class="md-plain" style="box-sizing: border-box;">Informal enquiries are encouraged. Please contact </span><span class=" md-link" style="box-sizing: border-box;"><a spellcheck="false" style="box-sizing: border-box; cursor: pointer; color: rgb(65, 131, 196); -webkit-user-drag: none;"><span class="md-plain" style="box-sizing: border-box;">pierre.peterlongo@inria.fr</span></a></span></p>
<p class="md-end-block md-p md-focus" style="box-sizing: border-box; line-height: inherit; orphans: 4; margin: 0.8em 0px; white-space: pre-wrap; position: relative; caret-color: rgb(51, 51, 51); color: rgb(51, 51, 51); font-family: "Open Sans", "Clear Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;"><span class="md-plain" style="box-sizing: border-box;">Applicants should send a full CV, a cover letter explaining their motivation, experience, and achievements, at least 2 references with contact information, and their date of availability.</span></p>
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