Under the Registration Rights Agreement, we have agreed to indemnify the Selling Stockholders and each underwriter of the Securities against certain losses, claims, damages, liabilities, settlement costs and expenses, including liabilities under the Securities Act.

We are registering the shares of common stock previously issued to the Selling Stockholders and issuable upon exercise or exchange of the warrants and upon conversion of the Series A-1 Preferred previously issued to the Selling Stockholders to permit the resale of these shares of common stock by the holders of the common stock, warrants and ~~warrants~~Series A-1 Preferred from time to time after the date of this prospectus. We will not receive any of the proceeds from the sale by the Selling Stockholders of the shares of common stock. We will bear all fees and expenses incident to our obligation to register the shares of common stock.

The Selling Stockholders may sell all or a portion of the shares of common stock beneficially owned by them and offered hereby from time to time directly or through one or more underwriters, broker-dealers or agents. If the shares of common stock are sold through underwriters or broker-dealers, the Selling Stockholders will be responsible for underwriting discounts or commissions or agent’s commissions. The shares of common stock may be sold in one or more transactions at fixed prices, at prevailing market prices at the time of the sale, at varying prices determined at the time of sale, or at negotiated prices. The Selling Stockholders will act independently of us in making decisions with respect to the timing, manner and size of each sale. These sales may be effected in transactions, which may involve crosses or block transactions:

· ~~whereby broker-dealers may agree with the Selling Stockholders to sell a specified number of such shares at a stipulated price per share;~~

If the Selling Stockholders effect such transactions by selling shares of common stock to or through underwriters, broker-dealers or agents, such underwriters, broker-dealers or agents may receive commissions in the form of discounts, concessions or commissions from the Selling Stockholders or commissions from purchasers of the shares of common stock for whom they may act as agent or to whom they may sell as principal (which discounts, concessions or commissions as to particular underwriters, broker-dealers or agents may be in excess of those customary in the types of transactions involved). In connection with sales of the shares of common stock or otherwise, the Selling Stockholders may enter into hedging transactions with broker-dealers, which may in turn engage in short sales of the shares of common stock in the course of hedging in positions they assume. The Selling Stockholders may also sell shares of common stock short and deliver shares of common stock covered by this prospectus to close out short positions and to return borrowed shares in connection with such short sales. The Selling Stockholders may also loan or pledge shares of common stock to broker-dealers that in turn may sell such shares.

The Selling Stockholders may pledge or grant a security interest in some or all of the shares of common stock, warrants or ~~warrants~~Series A-1 Preferred owned by them and, if they default in the performance of their secured obligations, the pledgees or secured parties may offer and sell the shares of common stock from time to time pursuant to this prospectus or any amendment to this prospectus under Rule 424(b)(3) or other applicable provision of the Securities Act amending, if necessary, the list of Selling Stockholders to include the pledgee, transferee or other successors in interest as Selling Stockholders under this prospectus. The Selling Stockholders also may transfer and donate the shares of common stock in other circumstances in which case the transferees, donees, pledgees or other successors in interest will be the selling beneficial owners for purposes of this prospectus.

The Selling Stockholders and any broker-dealer participating in the distribution of the shares of common stock may be deemed to be “underwriters” within the meaning of the Securities Act, and any commission paid, or any discounts or concessions allowed to, any such broker-dealer may be deemed to be underwriting commissions or discounts under the Securities Act. At the time a particular offering of the shares of common stock is made, a prospectus supplement, if required, will be distributed which will set forth the aggregate amount of shares of common stock being offered and the terms of the offering, including the name or names of any broker-dealers or agents, any discounts, commissions and other terms constituting compensation from the Selling Stockholders and any discounts, commissions or concessions allowed or reallowed or paid to broker-dealers. The Selling Stockholders may indemnify any broker-dealer that participates in transactions involving the sale of the shares of common stock against certain liabilities, including liabilities arising under the Securities Act.

Under the securities laws of some states, the shares of common stock may be sold in such states only through registered or licensed brokers or dealers. In addition, in some states the shares of common stock may not be sold unless such shares have been registered or qualified for sale in such state or an exemption from registration or qualification is available and is complied with.

There can be no assurance that any ~~selling stockholder~~Selling Stockholder will sell any or all of the shares of common stock registered pursuant to the registration statement, of which this prospectus forms a part.

The Selling Stockholders and any other person participating in such distribution will be subject to applicable provisions of the Exchange Act and the rules and regulations thereunder, including, without limitation, Regulation M of the Exchange Act, which may limit the timing of purchases and sales of any of the shares of common stock by the Selling Stockholders and any other participating person. Regulation M may also restrict the ability of any person engaged in the distribution of the shares of common stock to engage in market-making activities with respect to the shares of common stock. All of the foregoing may affect the marketability of the shares of common stock and the ability of any person or entity to engage in market-making activities with respect to the shares of common stock.

We will pay all expenses of the registration of the shares of common stock pursuant to the registration rights agreement, estimated to be ~~$60,611~~$35,524 in total, including, without limitation, SEC filing fees and expenses of compliance with state securities or “Blue Sky” laws; provided, however, that a ~~selling stockholder~~Selling Stockholder will pay all underwriting discounts and selling commissions, if any. We will indemnify the Selling Stockholders against liabilities, including some liabilities under the Securities Act, in accordance with the registration rights agreement, or the Selling Stockholders will be entitled to contribution. We may be indemnified by the Selling Stockholders against civil liabilities, including liabilities under the Securities Act, that may arise from any written information furnished to us by the Selling ~~Stockholders~~Stockholder specifically for use in this prospectus, in accordance with the registration rights agreement, or we may be entitled to contribution.

Once sold under the registration statement, of which this prospectus forms a part, the shares of common stock will be freely tradable in the hands of persons other than our affiliates.

Under our Third Amended and Restated Certificate of Incorporation, as amended from time to time, or the Certificate of Incorporation, we are authorized to issue up to 150,000,000 shares of Common Stock, from time to time, as provided in a resolution or resolutions adopted by ~~the~~our Board of Directors.

As of ~~July 7, 2015, 13,802,430~~January 8, 2016, 20,695,870 shares of Common Stock were issued and outstanding, held by approximately 8177 stockholders of record, not including beneficial holders whose shares are held in names other than their own.

Holders of Common Stock are entitled to one vote for each share held of record on all matters submitted to a vote of the stockholders and do not have cumulative voting rights. Holders of Common Stock are entitled to receive ratably such dividends, if any, as may be declared from time to time by our Board of Directors out of funds legally available for dividend payments. All outstanding shares of Common Stock are fully paid and non-assessable. The holders of Common Stock have no preferences or rights of conversion, exchange, pre-emption or other subscription rights. There are no redemption or sinking fund provisions applicable to the Common Stock. In the event of any liquidation, dissolution or winding-up of our affairs, holders of Common Stock will be entitled to share ratably in our assets that are remaining after payment or provision for payment of all of our debts and obligations. The rights, preferences and privileges of the Common Stock are subject to, and may be adversely affected by, the rights of the holders of shares of any series of preferred stock currently outstanding or which we may designate and issue in the future.

Under the Certificate of Incorporation, we have the authority to issue up to 15,000,000 shares of preferred stock, $0.01 par value per share, or the Preferred Stock, issuable in specified series and having specified voting, dividend, conversion, liquidation and other rights and preferences as our Board of Directors may determine, subject to limitations set forth in the Certificate of Incorporation. The Preferred Stock may be issued for any lawful corporate purpose without further action by our stockholders. The issuance of any Preferred Stock having conversion rights might have the effect of diluting the interests of our other stockholders. In addition, shares of Preferred Stock could be issued with rights, privileges and preferences which would deter a tender or exchange offer or discourage the acquisition of control of the Company.

Of the number of shares of Preferred Stock authorized by our Certificate of Incorporation, as of ~~July 7, 2015~~January 8, 2016 (i) 3,879,307 shares had been designated Series A Convertible Preferred Stock with such rights, privileges and preferences as set forth in the Certificate of Amendment of Certificate of Designation of Series A Convertible Preferred Stock filed with the Secretary of State of the State of Delaware on March 5, 2014, ~~or the Series A Certificate of Designation, and~~ (ii) 1,443,297 shares had been designated Series B Convertible Preferred Stock with such rights, privileges and preferences as set forth in the Certificate of Designation of Series B Convertible Preferred Stock filed with the Secretary of State of the State of Delaware on March 5, 2014, orand (iii) 2,365,243 shares had been designated Series A-1 Preferred with such rights, privileges and preferences as set forth in the ~~Series B~~ Certificate of ~~Designation.~~Designation of Series A-1 Convertible Preferred Stock filed with the Secretary of State of the State of Delaware on January 8, 2016. As of ~~July 7, 2015, 2,586,205~~January 8, 2016, no shares of the Series A Convertible Preferred Stock or the Series AB Convertible Preferred Stock were outstanding and 2,365,243 shares of Series A-1 Preferred were issued and ~~outstanding and 1,443,297 shares of the Series B Convertible Preferred Stock, or the Series B Preferred, were issued and~~ outstanding. ~~The Series A Preferred and the Series B Preferred are sometimes referred to in this prospectus, together, as the Preferred Shares.~~

Each of the Series A Certificate of Designation and the Series B Certificate of Designation provides that the holders of Preferred Shares shall be entitled, as a separate voting group, at each annual or special election of directors, to elect two directors of the Company.

Certain rights of the holders of the Series BA-1 Preferred are senior ~~to the rights of the holders of the Series A Preferred and~~ to the rights of the holders of our Common Stock. The Series BA-1 Preferred has a liquidation preference equal to its original price per share, plus any accrued and unpaid dividends thereon. The Series B Preferred accrues cumulative dividends at the rate of 6.0% of the original price per share per annum. Additionally, the Series B Certificate of Designation also contains an optional redemption provision whereby the holders of a majority of the then issued and outstanding Series B Preferred, voting together as a separate class, may, after March 5, 2019, the fifth anniversary of the closing of the private placement in which the shares of Series B Preferred were issued, require the Company to redeem all of the then issued and outstanding shares of Series B Preferred at the initial price per share of the Series B Preferred, as adjusted for any stock dividends, combinations or splits, plus all accrued but unpaid dividends.

Certain rights of the holders of the Series A Preferred are senior to the rights of the holders of our Common Stock. Subject to the liquidation preference of the Series B Preferred, the Series A Preferred has a liquidation preference equal to its original price per share, plus any accrued and unpaid dividends thereon. After the payment of dividends to the holders of Series B Preferred, the Series A Preferred accrues cumulative dividends at the rate of 10.0% of the original price per share per annum.

All outstanding shares of Series BA-1 Preferred will be automatically converted into Common Stock, at an initial conversion rate of 1:1, ~~and all outstanding shares of Series A Preferred will be automatically converted into Common Stock, at an initial conversion rate of 4:1,~~ at the election of the holders of a majority of the then-outstanding shares of Series A-1 Preferred, ~~Shares,~~ voting ~~together~~ as a single class on an as-converted ~~to Common Stock~~ basis. The initial conversion rate for ~~each of~~ the Series ~~A Preferred and the Series B~~A-1 Preferred is subject to adjustment in the event of certain stock splits, stock dividends, mergers, reorganizations and reclassifications. ~~After giving effect to the one-for-twelve reverse split of the Common Stock effected in January 2014, the conversion rate for the Series A Preferred was adjusted to 1:3.~~

Generally, the holders of the Series A-1 Preferred ~~Shares~~ are entitled to vote ~~together~~ as a single voting group with the holders of the Common Stock, ~~on an as-converted to Common Stock basis. However, each~~and the holders of the Series ~~A Certificate~~A-1 Preferred are generally entitled to that number of ~~Designation and~~votes as is equal to the product obtained by multiplying: (i) the number of whole shares of Common Stock into which the Series ~~B Certificate ofDesignation~~ ~~provides that we will not perform the following activities, subject to certain exceptions, without the affirmative vote~~A-1 Preferred may be converted as of the ~~holders~~record date of ~~at least two-thirds~~such vote or consent, by (ii) 0.93, rounded down to the nearest whole number. Initially, every 1.075269 shares of ~~the outstanding~~Series A-1 Preferred ~~Shares, voting together as a single class on an as-converted~~will generally be entitled to ~~Common Stock basis:~~one vote.

Anti-Takeover EffectsUnder Section 203 of the General Corporation Law of the State of Delaware

We are subject to Section 203 of the General Corporation Law of the State of Delaware, or the DGCL, which prohibits a Delaware corporation from engaging in any business combination with any interested stockholder for a period of three years after the date that such stockholder became an interested stockholder, with the following exceptions:

In general, Section 203 of the DGCL defines “business combination” to include the following:

In general, Section 203 of the DGCL defines an “interested stockholder” as an entity or a person who, together with the person’s affiliates and associates, beneficially owns, or within three years prior to the time of determination of interested stockholder status did own, 15% or more of the outstanding voting stock of the corporation.

A Delaware corporation may “opt out” of these provisions with an express provision in its original certificate of incorporation or an express provision in its certificate of incorporation or bylaws resulting from a stockholders’ amendment approved by at least a majority of the outstanding voting shares. We have not opted out of these provisions. As a result, mergers or other takeover or change in control attempts of us may be discouraged or prevented.

Anti-Takeover Effects Under Certain Provisions of our Certificate of Incorporation and Bylaws

Our Certificate of Incorporation and our Amended and Restated Bylaws, or the Bylaws, include a number of provisions that may have the effect of deterring hostile takeovers or delaying or preventing changes in control of the management of the Company.

First, our Certificate of Incorporation provides that all stockholder actions must be effected at a duly called meeting of holders and not by a consent in writing.

Second, our Bylaws provide that special meetings of the holders may be called only by the chairman of the Board of Directors, the Chief Executive Officer or our Board of Directors pursuant to a resolution adopted by a majority of the total number of authorized directors.

Third, our Certificate of Incorporation provides that our Board of Directors can issue up to 15,000,000 shares of Preferred Stock without further action by our stockholders, as described under “—Preferred Stock” above.

Fourth, our Certificate of Incorporation and Bylaws provide for a classified Board of Directors in which approximately one-third of the directors are elected each year. Consequently, any potential acquirer would need to successfully complete two proxy contests in order to take control of our Board of Directors. As a result of the provisions of the Certificate of Incorporation and Delaware law, stockholders will not be able to cumulate votes for directors.

Fifth, our Certificate of Incorporation prohibits a business combination with an interested stockholder without the approval of the holders of 75% of all voting shares and the vote of a majority of the voting shares held by disinterested stockholders, unless it has been approved by a majority of the disinterested directors.

Finally, our Bylaws establish procedures, including advance notice procedures, with regard to the nomination of candidates for election as directors and stockholder proposals. These provisions of our Certificate of Incorporation and Bylaws could discourage potential acquisition proposals and could delay or prevent a change in control of the management of our company.

In addition to the shares subject to the Warrants ~~to purchase 1,844,536 of the shares of Common Stock~~that we are registering hereunder, as of ~~July 7, 2015,~~January 8, 2016, warrants to purchase ~~2,947,670~~5,918,004 shares of Common Stock with a weighted-average exercise price of ~~$7.45~~$2.70 per share were outstanding, some of which are subject to a provision that is similar to the Warrant Blocker, and all of the shares subject to the warrants are currently exercisable, except for a warrant to purchase ~~1,293,102~~107,527 shares of ~~Series A Preferred with~~common stock, which will become exercisable on July 8, 2016. Each Placement Warrant (i) has an ~~average~~ exercise price of ~~$2.32~~$1.21 per share ~~were outstanding.~~of Common Stock and became exercisable upon issuance, (ii) became exchangeable pursuant to the Exchange Right upon issuance, subject to receipt of the Placement Warrants Required Approvals to the extent the shares issuable upon exercise of the Exchange Right are greater than the number of shares issuable upon exercise of a Placement Warrant, and (iii) will be exercisable or exchangeable through January 8, 2021. The Amended Warrant (A) has an exercise price of $1.21 per share of Common Stock and provides that no shares of Common Stock may be issued upon exercise or exchange of the Amended Warrant unless the Amended Warrant Required Approvals have been obtained, and (B) subject to obtaining the Amended Warrant Required Approvals, will be exercisable or exchangeable through January 8, 2021. The exercisability or exchangeability of ~~each~~all of the ~~Series A Warrants and the Series B~~ Warrants is subject to the Warrant ~~Blocker. The Warrant~~ Blocker, which will automatically expire 61 calendar days prior to January 7,8, 2021, the expiration date of the Warrants. ~~The Series A~~Each of the Placement Warrants and the Amended Warrant includes both cash and “cashless exercise” features. For any Exchange Right under the Placement Warrants exercised more than 90 days following the issuance of the Placement Warrants, if we have not obtained the Placement Warrants Required Approvals, we will be required to ~~purchase~~pay the Placement Warrant holder an ~~aggregate of 1,177,372~~amount in cash for the shares of Common Stock ~~are not exercisable until January 7, 2016,~~that we cannot issue under the Placement Warrant pursuant to such exercise without the Placement Warrants Required Approvals based on the applicable Exchange Amount. Each Placement Warrant further provides that, to the extent the closing bid price of our Common Stock on the second trading day prior to the date the Placement Warrant is exchanged is less than $0.50, the Exchange Price for the Placement Warrant will be deemed to be equal to $0.50, and, ~~the Series B Warrants~~in addition to ~~purchase an aggregate of 667,164~~issuing shares of Common Stock ~~are currently exercisable, except~~based on this Exchange Price, we will be required to pay to the Placement Warrant holder an amount in cash equal to the product obtained by multiplying (i) $0.50 minus the closing bid price of our Common Stock on the second trading day prior to the date the Placement Warrant is exchanged, by (ii) the aggregate number of shares of Common Stock issued to the Placement Warrant holder by us in such exchange at an Exchange Price equal to $0.50.

Pursuant to the terms of the Amended Warrant, in the event the Amended Warrant holder exercises the Exchange Right under the Amended Warrant more than 90 days following the issuance of the Amended Warrant, if we have not obtained the Amended Warrant Required Approvals, we will be required to pay to the Amended Warrant holder an amount in cash for the shares of Common Stock that we cannot issue under the Amended Warrant pursuant to such exercise without the Amended Warrant Required Approvals based on the applicable Exchange Amount. The Amended Warrant also provides that, to the extent the closing bid price of our Common Stock on the second trading day prior to the date the Amended Warrant is exchanged is less than $0.50, the Exchange Price for the Amended Warrant will be deemed to be equal to $0.50, and, in addition to issuing shares of Common Stock based on this Exchange Price (assuming receipt of the Amended Warrant Required Approvals), we will be required to pay to the Amended Warrant holder an amount in cash equal to the product obtained by multiplying (i) $0.50 minus the closing bid price of our Common Stock on the second trading day prior to the date the Amended Warrant is exchanged, by (ii) the aggregate number of shares of Common Stock issued to the Amended Warrant holder by us in such ~~exercise is restricted by the Warrant Blocker, for which we~~exchange at an Exchange Price equal to $0.50.

We are registering all of the underlying shares of Common Stock issuable upon exercise or exchange of the Warrants pursuant to the registration statement of which this prospectus forms a part. All of our other outstanding warrants are currently exercisable, and all outstanding warrants contain provisions for the adjustment of the exercise price in the event of stock dividends, stock splits, reorganizations, reclassifications or mergers. In addition, certain of the warrants contain a “cashless exercise” feature that allows the holders thereof to exercise the warrants without a cash payment to us under certain circumstances.

Pursuant to the terms of an Unsecured Convertible Promissory Note Purchase Agreement, or the Note Purchase Agreement, dated December 31, 2014, by and among ~~the Company~~us and certain accredited investors, ~~the Company~~we issued and sold, in a private placement, unsecured convertible promissory notes, or the Notes, in the aggregate principal amount of $1,675,000. In accordance with the terms of the Notes, the outstanding principal and unpaid interest accrued under each Note is convertible into shares of Common Stock as follows: (i) commencing upon the date of issuance of the Note (but no earlier than January 1, 2015), the investor holding such Note became entitled to convert, on a one-time basis, up to 50% of the outstanding principal and unpaid interest accrued under the Note, into shares of Common Stock at a conversion price equal to the lesser of (a) the average closing price of ~~the~~our Common Stock on the principal securities exchange or securities market on which ~~the~~our Common Stock is then traded, or the Market, for the 20 consecutive trading days immediately preceding the date of conversion, and (b) $2.20 (subject to adjustment for stock splits, stock dividends, other distributions, recapitalizations and the like); and (ii) commencing February 15, 2015, the investor holding such Note became entitled to convert, on a one-time basis, any or all of the remaining outstanding principal and unpaid interest accrued under the Note, into shares of Common Stock at a conversion price equal to 85% of the average closing price of ~~the~~our Common Stock on the Market for the 15 consecutive trading days immediately preceding the date of conversion. As of the date of this prospectus, Notes in an aggregate principal amount of $1,150,000 have been converted into 783,809shares of Common Stock, and Notes in an aggregate principal amount of $525,000 remain outstanding. Craig-Hallum acted as the sole placement agent for the convertible notes offering. In connection with the convertible notes offering, we issued to Craig-Hallum a convertible promissory note on the same terms and conditions as the Notes, in an aggregate principal amount of $46,250, which is outstanding as of the date of this prospectus.

Pursuant to the terms of the Note Purchase Agreement, ~~the Company is~~we are obligated to use ~~its~~our best efforts to file with the SEC by January 31, 2016 a registration statement to register for resale all of the shares of Common Stock issued on or prior to November 30, 2015 pursuant to the conversion of any portion of the Notes, or the Initial Registration Statement, and to use ~~its~~our commercially reasonable efforts to have the Initial Registration Statement declared effective by the SEC by March 31, 2016. In addition, ~~the Company is~~we are obligated to use ~~its~~our best efforts to file with the SEC by January 31, 2017 an additional registration statement to register for resale all of the shares of Common Stock issued pursuant to the conversion of any portion of the Notes that have not previously been registered for resale, or the Additional Registration Statement, and to use ~~its~~our commercially reasonable efforts to have the Additional Registration Statement declared effective by the SEC by March 31, 2017. Under the Note Purchase Agreement, ~~the Company~~we may be required to effect one or more other registrations to register for resale the shares of Common Stock issued or issuable under the Notes in connection with certain “piggy-back” registration rights granted to the investors in the private placement.

~~The Company~~We sold the Notes to “accredited investors”, as that term is defined in the Securities Act and in reliance on the exemption from registration afforded by Section ~~4(2)~~4(a)(2) of the Securities Act and Rule 506 of Regulation D promulgated under the Securities Act and corresponding provisions of state securities or “blue sky” laws. Accordingly, the Notes and the shares of Common Stock issued or issuable under the Notes have not been registered under the Securities Act and such securities may not be offered or sold in the United States absent registration or an exemption from registration under the Securities Act and any applicable state securities laws.

Our commonstock is listed on the NASDAQ Capital Market under the symbol “TBIO”.

The transfer agent and registrar for our ~~common stock~~Common Stock is Wells Fargo Shareowner Services. Its address is 1110 Centre Pointe Curve, Suite 101, Mendota Heights, MN 55120 and its telephone number is 1-855-217-6361.

Unless otherwise indicated in the applicable prospectus supplement, the validity of the Common Stock offered by this prospectus, and any supplement thereto, will be passed upon for us by Paul Hastings LLP, Palo Alto, California.

The consolidated balance sheets of Transgenomic, Inc. and Subsidiary as of December 31, 2014 and 2013, and the related consolidated statements of operations, comprehensive loss, stockholders’ equity and cash flows for each of the two years in the period ended December 31, 2014 ~~included~~appearing in Transgenomic, Inc.’s Annual Report (Form 10-K) for the year ended December 31, 2014, have been audited by Ernst & Young LLP, independent registered public accounting firm, as set forth in their report thereon (which contains an explanatory paragraph that raises substantial doubt about the Company’s ability to continue as a going concern as described in Note 1 to the consolidated financial statements), included therein, and incorporated herein by reference. Such financial statements are incorporated herein in reliance upon ~~the~~such report ~~of Ernst & Young LLP pertaining to such financial statements~~ given on the authority of such firm as experts in accounting and auditing.

The audited consolidated financial statements of Transgenomic, Inc. and subsidiary for the year ended December 31, 2012 included in Transgenomic, Inc.’s Annual Report on Form 10-K for the year ended December 31, 2014 have been audited by ~~McGladrey~~RSM US LLP, independent registered public accounting firm, as set forth in their report dated March 14, 2013, which is incorporated by reference herein. Such financial statements are incorporated herein in reliance upon the report of ~~McGladrey~~RSM US LLP pertaining to such financial statements given on the authority of such firm as experts in accounting and auditing.

We are a reporting company and file annual, quarterly and current reports, proxy statements and other information with the SEC. We have filed with the SEC a registration statement on Form S-3 under the Securities Act with respect to the Common Stock being offered under this prospectus. This prospectus does not contain all of the information set forth in the registration statement and the exhibits to the registration statement. For further information with respect to us and the shares of Common Stock being offered under this prospectus, we refer you to the registration statement and the exhibits and schedules filed as a part of the registration statement. You may read and copy the registration statement, as well as our reports, proxy statements and other information, at the SEC’s Public Reference Room at 100 F Street, N.E., Washington, D.C. 20549. Please call the SEC at 1-800-SEC-0330 for more information about the operation of the Public Reference Room. The SEC maintains an Internet site that contains reports, proxy and information statements, and other information regarding issuers that file electronically with the SEC, including Transgenomic, Inc. The SEC’s Internet site can be found at http://www.sec.gov.

DISCLOSURE OF COMMISSION POSITION ON INDEMNIFICATION FOR SECURITIES ACT LIABILITIES

Insofar as indemnification for liabilities arising under the Securities Act may be permitted to our directors, officers, and persons controlling us pursuant to the provisions described in Item 15 of the registration statement of which this prospectus is a part or otherwise, we have been advised that in the opinion of the SEC such indemnification is against public policy as expressed in the Securities Act and is therefore unenforceable. In the event that a claim for indemnification against such liabilities (other than our payment of expenses incurred or paid by our directors, officers, or controlling persons in the successful defense of any action, suit, or proceeding) is asserted by our directors, officers, or controlling persons in connection with the common stock being registered, we will, unless in the opinion of our counsel the matter has been settled by controlling precedent, submit to a court of appropriate jurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act and will be governed by the final adjudication of the issue.

The SEC allows us to “incorporate by reference” information into this prospectus, which means that we can disclose important information to you by referring you to another document filed separately with the SEC. The documents incorporated by reference into this prospectus contain important information that you should read about us.

We also incorporate by reference any future filings (other than current reports furnished under Item 2.02 or Item 7.01 of Form 8-K and exhibits filed on such form that are related to such items unless such Form 8-K expressly provides to the contrary) made with the SEC pursuant to Sections 13(a), 13(c), 14 or 15(d) of the Exchange Act, including those made after the date of the initial filing of the registration statement of which this prospectus is a part and prior to effectiveness of such registration statement, until we file a post-effective amendment that indicates the termination of the offering of the Common Stock made by this prospectus and will become a part of this prospectus from the respective dates that such documents are filed with the SEC. Any statement contained herein or in a document incorporated or deemed to be incorporated by reference herein shall be deemed to be modified or superseded for purposes hereof or of the related prospectus supplement to the extent that a statement contained herein or in any other subsequently filed document which is also incorporated or deemed to be incorporated herein modifies or supersedes such statement. Any such statement so modified or superseded shall not be deemed, except as so modified or superseded, to constitute a part of this prospectus.

Documents incorporated by reference are available from us, without charge. You may obtain documents incorporated by reference in this prospectus by requesting them in writing or by telephone at the following address:

Neither we nor the Selling Stockholders have authorized any dealer, salesperson or other person to give any information or to make any representations not contained in this prospectus or any prospectus supplement. You must not rely on any unauthorized information. This prospectus is not an offer to sell these securities in any jurisdiction where an offer or sale is not permitted. The information in this prospectus is current as of the date of this prospectus. You should not assume that this prospectus is accurate as of any other date.

The following table sets forth all expenses payable by the Registrant in connection with the sale of the common stock being registered. The security holders will not bear any portion of such expenses. All the amounts shown are estimates except for the registration fee.

Section 145 of the General Corporation Law of the State of Delaware, or the DGCL, authorizes a court to award, or a corporation to grant, indemnity to directors and officers in terms sufficiently broad to permit such indemnification under certain circumstances for liabilities (including reimbursement of expenses incurred) arising under the Securities Act of 1933, as amended.

As permitted by the DGCL, the Registrant’s Third Amended and Restated Certificate of Incorporation, as amended from time to time, or the Certificate of Incorporation, eliminates the personal liability of its directors for monetary damages for breach of fiduciary duty as a director, except for liability (i) for any breach of the director’s duty of loyalty to the Registrant or its stockholders, (ii) for acts or omissions not in good faith or that involve intentional misconduct or a knowing violation of law, (iii) under Section 174 of the DGCL (regarding unlawful dividends and stock purchases), or (iv) for any transaction from which the director derived an improper personal benefit. If the DGCL is amended to authorize further elimination or limiting of directors’ personal liability, then the Certificate of Incorporation provides that the personal liability of directors will be eliminated or limited to the fullest extent provided under the DGCL.

As permitted by the DGCL, the Certificate of Incorporation and the Registrant’s Amended and Restated Bylaws provide that (i) the Registrant is required to indemnify its directors and officers to the fullest extent permitted by the DGCL, subject to certain very limited exceptions, (ii) the Registrant may indemnify its other employees and agents as set forth in the DGCL, (iii) the Registrant is required to advance expenses, as incurred, to its directors and executive officers in connection with a legal proceeding to the fullest extent permitted by the DGCL, subject to certain conditions, and (iv) the rights conferred by the Certificate of Incorporation and the Registrant’s Amended and Restated Bylaws are not exclusive.

The DGCL authorizes a corporation to indemnify its directors and officers provided that the corporation shall not eliminate or limit the liability of a director as follows:

The DGCL requires a corporation to indemnify a director or officer to the extent that the director or officer has been successful, on the merits or otherwise, in the defense of any action, suit or proceeding for which indemnification is lawful.

Insofar as indemnification for liabilities arising under the Securities Act may be permitted to directors, officers or persons controlling the Registrant pursuant to the foregoing provisions, the Registrant has been informed that in the opinion of the SEC such indemnification is against public policy as expressed in the Securities Act and is therefore unenforceable.

II-1

~~II-1~~

The Registrant maintains a director and officer insurance policy which insures the directors and officers of the Registrant against damages, judgments, settlements and costs incurred by reason of certain wrongful acts committed by such persons in their capacities as directors and officers.

Item 16. Exhibits

Exhibit Number		Description

†2.1		Asset Purchase Agreement among the Registrant, Scoli Acquisition Sub, Inc. and Axial Biotech, Inc. dated August 27, 2012 (incorporated by reference to Exhibit 2.1 to the Registrant’s Quarterly Report on Form 10-Q filed on November 8, 2012).

4.1		Form of Certificate of the Registrant’s Common Stock (incorporated by reference to Exhibit 4 to the Registrant’s Registration Statement on Form S-1 (Registration No. 333-32174) filed on March 10, 2000).

4.2		Form of Series A Convertible Preferred Stock Warrant issued to Third Security Senior Staff 2008 LLC, Third Security Staff 2010 LLC and Third Security Incentive 2010 LLC (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K filed on January 4, 2011).

~~4.3~~		Registration Rights Agreement, dated December 29, 2010, by and among the Registrant, Third Security Senior Staff 2008 LLC, Third Security Staff 2010 LLC and Third Security Incentive 2010 LLC (incorporated by reference to Exhibit 4.3 to the Registrant’s Current Report on Form 8-K filed on January 4, 2011).

~~4.4~~		~~First Amendment to Registration Rights Agreement dated November 8, 2011 (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K filed on November 14, 2011).~~

~~4.5~~		~~Form of~~ Warrant issued by the Registrant to the Third Security Entities on February 7, 2012 (incorporated by reference to Exhibit 10.2 to the Registrant’s Current Report on Form 8-K filed on February 7, 2012).

~~4.6~~4.3		Form of Warrant issued by the Registrant to the Investors on February 7, 2012 (incorporated by reference to Exhibit 10.3 to the Registrant’s Current Report on Form 8-K filed on February 7, 2012).

~~4.7~~4.4		Form of Registration Rights Agreement entered into by and among the Registrant, the Third Security Entities and the Investors dated February 2, 2012 (incorporated by reference to Exhibit 10.4 to the Registrant’s Current Report on Form 8-K filed on February 7, 2012).

~~4.8~~4.5		Registration Rights Agreement, entered into by and among the Registrant and the Investors, dated January 24, 2013 (incorporated by reference to Exhibit 10.3 to the Registrant’s Current Report on Form 8-K/A filed on January 31, 2013).

~~4.9~~4.6		Form of Warrant issued by the Registrant to the Investors on January 30, 2013 (incorporated by reference to Exhibit 10.2 to the Registrant’s Current Report on Form 8-K/A filed on January 31, 2013).

~~4.10~~4.7		Registration Rights Agreement, dated as of March 5, 2014, by and among the Registrant, Third Security Senior Staff 2008 LLC, Third Security Staff 2014 LLC and Third Security Incentive 2010 LLC (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K filed on March 6, 2014).

~~4.11~~4.8		Securities Purchase Agreement, dated as of October 22, 2014, by and among Transgenomic, Inc. and the Investors (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K filed on October 22, 2014).

~~4.12~~4.9		Form of Warrant issued by Transgenomic, Inc. to the Investors and the advisor on October 22, 2014 (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K filed on October 22, 2014).

~~4.13~~4.10		Unsecured Convertible Promissory Note Purchase Agreement, dated as of December 31, 2014, by and among Transgenomic, Inc. and the Investors (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K filed on January 7, 2015).

~~4.14~~4.11		Form of Unsecured Convertible Promissory Note issued by Transgenomic, Inc. to the Investor pursuant to the Unsecured Convertible Promissory Note Purchase Agreement, dated as of December 31, 2014 (incorporated by reference to Exhibit 10.2 to the Registrant’s Current Report on Form 8-K filed on January 7, 2015).

~~II-2~~


~~4.15~~4.12		Form of Warrant to Purchase Common Stock (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K filed on February 27, 2015).

~~4.16~~4.13		Registration Rights Agreement, dated June 30, 2015, by and among Transgenomic, Inc. and the Investors (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K/A filed on July 7, 2015).

~~4.17~~4.14		Form of Series A Warrant to Purchase Common Stock issued by Transgenomic, Inc. to the Investors on July 7, 2015 (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K/A filed on July 7, 2015).

II-2


~~4.18~~4.15		Form of Series B Warrant to Purchase Common Stock issued by Transgenomic, Inc. to an Investor on July 7, 2015 (incorporated by reference to Exhibit 4.3 to the Registrant’s Current Report on Form 8-K/A filed on July 7, 2015).

~~4.19~~4.16		Form of Warrant to Purchase Common Stock issued by Transgenomic, Inc. to the Placement Agent on July 7, 2015 (incorporated by reference to Exhibit 4.4 to the Registrant’s Current Report on Form 8-K/A filed on July 7, 2015).

4.17		Registration Rights Agreement, by and among Transgenomic, Inc. and the Investors, dated January 8, 2016 (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K filed on January 11, 2016 (accepted at 7:30 a.m. Eastern Time)).

4.18		Form of Warrant, issued by Transgenomic, Inc. to the Investors on January 8, 2016 (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K filed on January 11, 2016 (accepted at 7:30 a.m. Eastern Time)).

4.19		Form of Amended Warrant, issued by Transgenomic, Inc. to an affiliate of an Investor on January 8, 2016 (incorporated by reference to Exhibit 4.3 to the Registrant’s Current Report on Form 8-K filed on January 11, 2016 (accepted at 7:30 a.m. Eastern Time)).

4.20		Form of Warrant, issued by Transgenomic, Inc. to the Placement Agent on January 8, 2016 (incorporated by reference to Exhibit 4.4 to the Registrant’s Current Report on Form 8-K filed on January 11, 2016 (accepted at 7:30 a.m. Eastern Time)).

5.1		Opinion of Paul Hastings LLP.

23.1		Consent of Ernst & Young LLP, Independent Registered Public Accounting Firm.

23.2		Consent of ~~McGladrey~~RSM US LLP, Independent Registered Public Accounting Firm.

23.3		Consent of Paul Hastings LLP is contained in Exhibit 5.1 to this Registration Statement.

24.1		Power of Attorney is contained on the signature page.

†	Pursuant to Item 601(b)(2) of Regulation S-K, the schedules to this agreement have been omitted. The Registrant agrees to furnish supplementally a copy of any omitted schedule to the Securities and Exchange Commission upon request.

Item 17. Undertakings

The undersigned Registrant hereby undertakes:

(1) To file, during any period in which offers or sales are being made, a post-effective amendment to this registration statement:

(i) To include any prospectus required by section 10(a)(3) of the Securities Act of 1933;

(ii) To reflect in the prospectus any facts or events arising after the effective date of the registration statement (or the most recent post-effective amendment thereof) which, individually or in the aggregate, represent a fundamental change in the information set forth in the registration statement. Notwithstanding the foregoing, any increase or decrease in volume of securities offered (if the total dollar value of securities offered would not exceed that which was registered) and any deviation from the low or high end of the estimated maximum offering range may be reflected in the form of prospectus filed with the Commission pursuant to Rule 424(b) if, in the aggregate, the changes in volume and price represent no more than a 20 percent change in the maximum aggregate offering price set forth in the “Calculation of Registration Fee” table in the effective registration statement.

(iii) To include any material information with respect to the plan of distribution not previously disclosed in the registration statement or any material change to such information in the registration statement;

Provided, however, that:

Paragraphs (1)(i), (1)(ii) and (1)(iii) of this section do not apply if the information required to be included in a post-effective amendment by those paragraphs is contained in reports filed with or furnished to the Commission by the registrant pursuant to section 13 or section 15(d) of the Securities Exchange Act of 1934 that are incorporated by reference in the registration statement, or is contained in a form of prospectus filed pursuant to Rule 424(b) that is part of the registration statement.

~~II-3~~

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(2) That, for the purpose of determining any liability under the Securities Act of 1933, each such post-effective amendment shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

(3) To remove from registration by means of a post-effective amendment any of the securities being registered which remain unsold at the termination of the offering.

(4) That, for the purpose of determining liability under the Securities Act of 1933 to any purchaser:

(i) Each prospectus filed by the registrant pursuant to Rule 424(b)(3) shall be deemed to be part of the registration statement as of the date the filed prospectus was deemed part of and included in the registration statement; and

(ii) Each prospectus required to be filed pursuant to Rule 424(b)(2), (b)(5), or (b)(7) as part of a registration statement in reliance on Rule 430B relating to an offering made pursuant to Rule 415(a)(1)(i), (vii), or (x) for the purpose of providing the information required by section 10(a) of the Securities Act of 1933 shall be deemed to be part of and included in the registration statement as of the earlier of the date such form of prospectus is first used after effectiveness or the date of the first contract of sale of securities in the offering described in the prospectus. As provided in Rule 430B, for liability purposes of the issuer and any person that is at that date an underwriter, such date shall be deemed to be a new effective date of the registration statement relating to the securities in the registration statement to which that prospectus relates, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof. Provided, however, that no statement made in a registration statement or prospectus that is part of the registration statement or made in a document incorporated or deemed incorporated by reference into the registration statement or prospectus that is part of the registration statement will, as to a purchaser with a time of contract of sale prior to such effective date, supersede or modify any statement that was made in the registration statement or prospectus that was part of the registration statement or made in any such document immediately prior to such effective date.

(6) That, for purposes of determining any liability under the Securities Act of 1933, each filing of the registrant’s annual report pursuant to Section 13(a) or 15(d) of the Securities Exchange Act of 1934 (and, where applicable, each filing of an employee benefit plan’s annual report pursuant to Section 15(d) of the Securities Exchange Act of 1934) that is incorporated by reference in the registration statement shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

(7) Insofar as indemnification for liabilities arising under the Securities Act of 1933 may be permitted to directors, officers and controlling persons of the registrant pursuant to the foregoing provisions, or otherwise, the registrant has been advised that in the opinion of the Securities and Exchange Commission such indemnification is against public policy as expressed in the Securities Act of 1933 and is, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than the payment by the registrant of expenses incurred or paid by a director, officer or controlling person of the registrant in the successful defense of any action, suit or proceeding) is asserted by such director, officer or controlling person in connection with the securities being registered, the registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of appropriate jurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act of 1933 and will be governed by the final adjudication of such issue.

II-4

~~II-4~~

SIGNATURES

Pursuant to the requirements of the Securities Act of 1933, as amended, the Registrant certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-3 and has duly caused this Registration Statement to be signed on its behalf by the undersigned, thereunto duly authorized, in the City of Omaha, State of Nebraska, on ~~July 22, 2015.~~January 25, 2016.

	TRANSGENOMIC, INC.

	By:	/s/ Paul Kinnon
		Paul Kinnon President, Chief Executive Officer and Interim Chief Financial Officer

POWER OF ATTORNEY

Know All Persons By These Presents, that each person whose signature appears below constitutes and appoints Paul Kinnon and Leon Richards, and each or any one of them, his true and lawful attorney-in-fact and agent, with full power of substitution and resubstitution, for him and in his name, place and stead, in any and all capacities, to sign any and all amendments (including post-effective amendments) to this Registration Statement, and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite and necessary to be done in connection therewith, as fully to all intents and purposes as he might or could do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents, or any of them, or their or his substitutes or substitute, may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Act of 1933, this Registration Statement has been signed by the following persons in the capacities and on the dates indicated.

Signature	Title	Date

/s/ Paul Kinnon	President, Chief Executive Officer, Interim Chief Financial Officer and Director	~~July 22, 2015~~January 25, 2016
Paul Kinnon	(Principal Executive Officer and Principal Financial Officer)

/s/ Leon Richards	Chief Accounting Officer	~~July 22, 2015~~January 25, 2016
Leon Richards	(Principal Accounting Officer)

/s/ Robert M. Patzig	Director	~~July 22, 2015~~January 25, 2016
Robert M. Patzig

/s/ Doit L. Koppler II	Director	~~July 22, 2015~~January 25, 2016
Doit L. Koppler II

/s/ Michael A. Luther	Director	~~July 22, 2015~~January 25, 2016
Michael A. Luther

~~/s/ Mya Thomae~~	Director	~~July 22, 2015~~
Mya Thomae

~~/s/ John D. Thompson~~	~~Director~~	~~July 22, 2015~~
~~John D. Thompson~~

~~II-5~~

II-5

INDEX TO EXHIBITS

Exhibit Number		Description

†2.1		Asset Purchase Agreement among the Registrant, Scoli Acquisition Sub, Inc. and Axial Biotech, Inc. dated August 27, 2012 (incorporated by reference to Exhibit 2.1 to the Registrant’s Quarterly Report on Form 10-Q filed on November 8, 2012).

4.1		Form of Certificate of the Registrant’s Common Stock (incorporated by reference to Exhibit 4 to the Registrant’s Registration Statement on Form S-1 (Registration No. 333-32174) filed on March 10, 2000).

4.2		Form of Series A Convertible Preferred Stock Warrant issued to Third Security Senior Staff 2008 LLC, Third Security Staff 2010 LLC and Third Security Incentive 2010 LLC (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K filed on January 4, 2011).

~~4.3~~		Registration Rights Agreement, dated December 29, 2010, by and among the Registrant, Third Security Senior Staff 2008 LLC, Third Security Staff 2010 LLC and Third Security Incentive 2010 LLC (incorporated by reference to Exhibit 4.3 to the Registrant’s Current Report on Form 8-K filed on January 4, 2011).

~~4.4~~		~~First Amendment to Registration Rights Agreement dated November 8, 2011 (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K filed on November 14, 2011).~~

~~4.5~~		~~Form of~~ Warrant issued by the Registrant to the Third Security Entities on February 7, 2012 (incorporated by reference to Exhibit 10.2 to the Registrant’s Current Report on Form 8-K filed on February 7, 2012).

~~4.6~~4.3		Form of Warrant issued by the Registrant to the Investors on February 7, 2012 (incorporated by reference to Exhibit 10.3 to the Registrant’s Current Report on Form 8-K filed on February 7, 2012).

~~4.7~~4.4		Form of Registration Rights Agreement entered into by and among the Registrant, the Third Security Entities and the Investors dated February 2, 2012 (incorporated by reference to Exhibit 10.4 to the Registrant’s Current Report on Form 8-K filed on February 7, 2012).

~~4.8~~4.5		Registration Rights Agreement, entered into by and among the Registrant and the Investors, dated January 24, 2013 (incorporated by reference to Exhibit 10.3 to the Registrant’s Current Report on Form 8-K/A filed on January 31, 2013).

~~4.9~~4.6		Form of Warrant issued by the Registrant to the Investors on January 30, 2013 (incorporated by reference to Exhibit 10.2 to the Registrant’s Current Report on Form 8-K/A filed on January 31, 2013).

~~4.10~~4.7		Registration Rights Agreement, dated as of March 5, 2014, by and among the Registrant, Third Security Senior Staff 2008 LLC, Third Security Staff 2014 LLC and Third Security Incentive 2010 LLC (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K filed on March 6, 2014).

~~4.11~~4.8		Securities Purchase Agreement, dated as of October 22, 2014, by and among Transgenomic, Inc. and the Investors (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K filed on October 22, 2014).

~~4.12~~4.9		Form of Warrant issued by Transgenomic, Inc. to the Investors and the advisor on October 22, 2014 (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K filed on October 22, 2014).

~~4.13~~4.10		Unsecured Convertible Promissory Note Purchase Agreement, dated as of December 31, 2014, by and among Transgenomic, Inc. and the Investors (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K filed on January 7, 2015).

~~4.14~~4.11		Form of Unsecured Convertible Promissory Note issued by Transgenomic, Inc. to the Investor pursuant to the Unsecured Convertible Promissory Note Purchase Agreement, dated as of December 31, 2014 (incorporated by reference to Exhibit 10.2 to the Registrant’s Current Report on Form 8-K filed on January 7, 2015).

~~4.15~~4.12		Form of Warrant to Purchase Common Stock (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K filed on February 27, 2015).

~~II-6~~


~~4.16~~4.13		Registration Rights Agreement, dated June 30, 2015, by and among Transgenomic, Inc. and the Investors (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K/A filed on July 7, 2015).

~~4.17~~4.14		Form of Series A Warrant to Purchase Common Stock issued by Transgenomic, Inc. to the Investors on July 7, 2015 (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K/A filed on July 7, 2015).

~~4.18~~4.15		Form of Series B Warrant to Purchase Common Stock issued by Transgenomic, Inc. to an Investor on July 7, 2015 (incorporated by reference to Exhibit 4.3 to the Registrant’s Current Report on Form 8-K/A filed on July 7, 2015).

II-6


~~4.19~~4.16		Form of Warrant to Purchase Common Stock issued by Transgenomic, Inc. to the Placement Agent on July 7, 2015 (incorporated by reference to Exhibit 4.4 to the Registrant’s Current Report on Form 8-K/A filed on July 7, 2015).

4.17		Registration Rights Agreement, by and among Transgenomic, Inc. and the Investors, dated January 8, 2016 (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K filed on January 11, 2016 (accepted at 7:30 a.m. Eastern Time)).

4.18		Form of Warrant, issued by Transgenomic, Inc. to the Investors on January 8, 2016 (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K filed on January 11, 2016 (accepted at 7:30 a.m. Eastern Time)).

4.19		Form of Amended Warrant, issued by Transgenomic, Inc. to an affiliate of an Investor on January 8, 2016 (incorporated by reference to Exhibit 4.3 to the Registrant’s Current Report on Form 8-K filed on January 11, 2016 (accepted at 7:30 a.m. Eastern Time)).

4.20		Form of Warrant, issued by Transgenomic, Inc. to the Placement Agent on January 8, 2016 (incorporated by reference to Exhibit 4.4 to the Registrant’s Current Report on Form 8-K filed on January 11, 2016 (accepted at 7:30 a.m. Eastern Time)).

5.1		Opinion of Paul Hastings LLP.

23.1		Consent of Ernst & Young LLP, Independent Registered Public Accounting Firm.

23.2		Consent of ~~McGladrey~~RSM US LLP, Independent Registered Public Accounting Firm.

23.3		Consent of Paul Hastings LLP is contained in Exhibit 5.1 to this Registration Statement.

24.1		Power of Attorney is contained on the signature page.

†	Pursuant to Item 601(b)(2) of Regulation S-K, the schedules to this agreement have been omitted. The Registrant agrees to furnish supplementally a copy of any omitted schedule to the Securities and Exchange Commission upon request.

Large accelerated filer¨	Accelerated filer£¨	Non-accelerated filer¨	Smaller reporting companyx
		(Do not check if a smaller reporting company)

Title of Each Class of Securities to be Registered	Amount to be Registered⁽¹⁾			Proposed Maximum Offering Price Per Share⁽⁴⁾		Proposed Maximum Aggregate Offering Price		Amount of Registration Fee		Amount to be Registered⁽¹⁾			Proposed Maximum Offering Price Per Share⁽⁴⁾			Proposed Maximum Aggregate Offering Price		Amount of Registration Fee
Common Stock, par value $0.01 per share		1,473,512	⁽²⁾	$	1.585	$	2,335,516.52	$	271.39
Common Stock, par value $0.01 per share, issuable upon conversion of shares of Series A-1 Convertible Preferred Stock											2,365,243	⁽²⁾		$	0.73	$	1,726,627.39	$	173.87
Common Stock, par value $0.01 per share, issuable upon exercise of Warrants		1,844,536	⁽³⁾	$	1.585	$	2,923,589.56	$	339.72		4,756,160	⁽³⁾		$	0.73	$	3,471,996.80	$	349.63
Total:		3,318,048				$	5,259,106.08	$	611.11		7,121,403					$	5,198,624.19	$	523.50

	Page
Summary	1
Risk Factors	21
Disclosure Regarding Forward-Looking Statements	32
Use of Proceeds	43
Selling Stockholders	54
Plan of Distribution	78
Description of Capital Stock	910
Legal Matters	14
Experts	14
Where You Can Find More Information	14
Disclosure of Commission Position on Indemnification for Securities Act Liabilities	14
Important Information Incorporated by Reference	15

	Shares BeneficiallyOwned Prior to the Offering⁽¹⁾							Maximum Number of Shares of Common Stock to be Offered Pursuant to this Prospectus			SharesBeneficiallyOwned After theOffering⁽²⁾
Name		Number			Percentage				Number			Number		Percentage
Crede CG III, Ltd.			3,274,648	⁽³⁾		21.0	%			3,274,648			--		--
David J. Wambeke			169,922	⁽⁴⁾		1.2	%			43,400			126,522		*
TOTAL			3,476,263			22.2	%			3,318,048			126,522		*

	Shares Beneficially Owned Prior to the Offering⁽¹⁾						Maximum Number of Shares of Common Stock to be Offered Pursuant to this Prospectus		Shares Beneficially Owned After the Offering⁽²⁾
Name	Number			Percentage			Number		Number		Percentage
Crede CG III, Ltd.		8,758,512	⁽³⁾		31.3	%		6,645,836		2,112,676		7.5	%
Third Security Senior Staff 2008 LLC		3,481,329	⁽⁴⁾		16.5	%		190,228		3,291,101		15.6	%
Third Security Staff 2010 LLC		2,491,601	⁽⁵⁾		11.8	%		95,113		2,396,488		11.4	%
Third Security Incentive 2010 LLC		1,740,662	⁽⁶⁾		8.3	%		95,113		1,645,549		7.9	%
Third Security Staff 2014 LLC		989,726	⁽⁷⁾		4.8	%		95,113		894,613		4.3	%
TOTAL		17,461,830			—			7,121,403		10,340,427		—

(1)	Pursuant to Rule 416(a) under the Securities Act of 1933, as amended, this Registration Statement shall also cover any additional shares of the Registrant’s Common Stock that become issuable by reason of any stock dividend, stock split, recapitalization or other similar transaction effected without receipt of consideration.
(2)	All ~~1,473,512~~2,365,243 shares of Common Stock issuable upon conversion of the shares of Series A-1 Convertible Preferred Stock are to be offered by the selling stockholders named herein, ~~all~~which such shares of ~~which~~Series A-1 Convertible Preferred Stock were acquired by the selling stockholders in a private placement.
(3)	All ~~1,844,536~~4,756,160 shares of Common Stock issuable upon exercise or exchange of the Warrants are to be offered by the selling stockholders named herein, ~~all of~~ which such Warrants were acquired by the selling stockholders in a private placement.
(4)	Estimated solely for the purpose of calculating the amount of the registration fee pursuant to Rule 457(c) under the Securities Act of 1933, as amended. The offering price per share and aggregate offering price are based upon the average of the high and low prices for the Registrant’s Common Stock as reported on the NASDAQ Capital Market on ~~July~~January 21, ~~2015,~~2016, a date within five business days prior to the filing of this Registration Statement.

(1)	Beneficial ownership is determined in accordance with Rule 13d-3 under the Exchange Act. In computing the number of shares beneficially owned by a person and the percentage ownership of that person, shares of common stock subject to warrants, options and other convertible securities held by that person that are currently exercisable or exercisable within 60 days (of ~~July 7, 2015)~~January 8, 2016) are deemed outstanding. Shares subject to warrants, options and other convertible securities, however, are not deemed outstanding for the purpose of computing the percentage ownership of any other person.
(2)	Assumes that the Selling Stockholders dispose of all of the shares of Common Stock covered by this prospectus and do not acquire beneficial ownership of any additional shares. The registration of these shares does not necessarily mean that the Selling Stockholders will sell all or any portion of the shares covered by this prospectus.
(3)	The number of shares consists of (i) 1,445,512 shares of Common Stock, (ii) ~~1,161,972~~2,150,538 shares of Common Stock issuable upon conversion of 2,150,538 shares of Series A-1 Preferred, which such shares of Common Stock are covered by this prospectus, (iii) 1,612,903 shares of Common Stock issuable upon exercise or exchange of ~~Series A Warrants~~a Placement Warrant that ~~will become exercisable beginning January 7, 2016, except to the extent such exercise~~ is ~~restricted by the Warrant Blocker, and are covered by this prospectus, and (iii) 667,164 shares of Common Stock issuable upon exercise of Series B Warrants that are~~ currently exercisable, except to the extent such exercise is restricted by the Warrant ~~Blocker, and~~Blocker; however, if the Placement Warrants Required Approvals have been obtained, the Placement Warrant holder may receive an additional 1,000,000 shares of Common Stock upon exercise of the Exchange Right under the Placement Warrant for an aggregate of up to 2,612,903 shares of Common Stock issuable upon exchange of the Placement Warrant, all of which such Warrant Shares are covered by this ~~prospectus.~~prospectus, (iv) subject to receipt of the Amended Warrant Required Approvals, 1,161,972 shares of Common Stock issuable upon exercise or exchange of the Amended Warrant that is currently exercisable, except to the extent such exercise is restricted by the Warrant Blocker; however, if the Amended Warrant Required Approvals have been obtained, the Amended Warrant holder may receive an additional 720,423 shares of Common Stock upon exercise of the Exchange Right under the Amended Warrant for an aggregate of up to 1,882,395 shares of Common Stock issuable upon exchange of the Amended Warrant, all of which such Warrant Shares are covered by this prospectus, and (v) 667,164 shares of Common Stock issuable upon exercise of Series B Warrant to purchase shares of Common Stock that is currently exercisable, except to the extent such exercise is restricted by a blocker provision in the Series B Warrant similar to the Warrant Blocker. The Warrant Blocker will automatically expire 61 calendar days prior to the expiration date of the Warrants. The table above includes Warrants that are not currently exercisable because of the Warrant Blocker, the Placement Warrants Required Approvals and the Amended Warrant Required Approvals and which are not deemed to be beneficially owned by Crede CG III, Ltd. The sole stockholder of Crede CG III, Ltd. is Crede Capital Group, LLC. Acuitas Financial Group, LLC holds all of the membership interests of Crede Capital Group, LLC and Terren Peizer holds all of the membership interests of Acuitas Financial Group, LLC. Voting and dispositive power with respect to the shares held by Crede CG III, Ltd. is exercised by Terren Peizer, the sole and Managing Member of Acuitas Financial Group, LLC and Crede Capital Group, LLC and Managing Director of Crede CG III, Ltd., who acts as investment advisor to these entities. Terren Peizer, Acuitas Financial Group, LLC and Crede Capital Group, LLC disclaim beneficial ownership with respect to the shares held by Crede CG III, Ltd. The business address of Crede Capital Group, LLC is 11601 Wilshire Blvd., Suite 1100, Los Angeles, CA 90025.

(4)	The number of shares consists of (i) ~~77,770~~3,020,267 shares of Common Stock, (ii) ~~61,367~~85,882 shares of Common Stock issuable upon conversion of 85,882 shares of Series A-1 Preferred, which such shares of Common Stock are covered by this prospectus, (iii) 64,411 shares of Common Stock issuable upon exercise or exchange of a ~~convertible promissory note~~Placement Warrant that is currently exercisable, ~~(assuming conversion as~~except to the extent such exercise is restricted by the Warrant Blocker; however, if the Placement Warrants Required Approvals have been obtained, Third Security Senior Staff 2008 LLC may receive an additional 39,935 shares of ~~July 7, 2015), (iii) 15,385~~Common Stock upon exercise of the Exchange Right under the Placement Warrant for an aggregate of up to 104,346 shares of Common Stock issuable upon exchange of the Placement Warrant, all of which such Warrant Shares are covered by this prospectus, and (iv) 270,834 shares of Common Stock issuable upon exercise of warrants to purchase Common Stock that are not Placement Warrants and are currently exercisable. The Warrant Blocker will automatically expire 61 calendar days prior to the expiration date of the Placement Warrant. The table above includes a Placement Warrant that is not currently exercisable because of the Warrant Blocker and the Placement Warrants Required Approvals and which is not deemed to be beneficially owned by Third Security Senior Staff 2008 LLC. Third Security Senior Staff 2008 LLC is managed by Third Security, LLC (“Third Security”), which is managed by Mr. Randal J. Kirk. Mr. Randal J. Kirk could be deemed to have indirect beneficial ownership of these shares. The business address of Third Security Senior Staff 2008 LLC is 1881 Grove Avenue, Radford, Virginia 24141. We are party to that certain Loan and Security Agreement (Term Loan and Revolving Loan), dated as of March 13, 2013, as amended (the “Loan and Security Agreement”), with affiliates of Third Security. Additionally, Doit L. Koppler II, a director of the Company, is an employee of Third Security and Robert Patzig, a director of the Company, is a former employee of Third Security.
(5)	The number of shares consists of (i) 2,125,654 shares of Common Stock, (ii) 42,941 shares of Common Stock issuable upon conversion of 42,941 shares of Series A-1 Preferred, which such shares of Common Stock are covered by this prospectus, (iii) 32,205 shares of Common Stock issuable upon exercise or exchange of a Placement Warrant that is currently exercisable, except to the extent such exercise is restricted by the Warrant Blocker; however, if the Placement Warrants Required Approvals have been obtained, Third Security Staff 2010 LLC may receive an additional 19,967 shares of Common Stock upon exercise of the Exchange Right under the Placement Warrant for an aggregate of up to 52,172 shares of Common Stock issuable upon exchange of the Placement Warrant, all of which such Warrant Shares are covered by this prospectus, and (iv) ~~15,400~~270,834 shares of Common Stock issuable upon exercise of warrants to purchase Common Stock that are not Placement Warrants and are currently exercisable. The Warrant Blocker will automatically expire 61 calendar days prior to the expiration date of the Placement Warrant. The table above includes a Placement Warrant that is not currently exercisable because of the Warrant Blocker and the Placement Warrants Required Approvals and which is not deemed to be beneficially owned by Third Security Staff 2010 LLC. Third Security Staff 2010 LLC is managed by Third Security, which is managed by Mr. Randal J. Kirk. Mr. Randal J. Kirk could be deemed to have indirect beneficial ownership of these shares. The business address of Third Security Staff 2010 LLC is 1881 Grove Avenue, Radford, Virginia 24141. We are party to the Loan and Security Agreement with affiliates of Third Security. Additionally, Doit L. Koppler II, a director of the Company, is an employee of Third Security and Robert Patzig, a director of the Company, is a former employee of Third Security.
(6)	The number of shares consists of (i) 1,510,135 shares of Common Stock, (ii) 42,941 shares of Common Stock issuable upon conversion of 42,941 shares of Series AA-1 Preferred, which such shares of Common Stock are covered by this prospectus, (iii) 32,205 shares of Common Stock issuable upon exercise or exchange of a Placement Warrant that is currently exercisable, except to the extent such exercise is restricted by the Warrant Blocker; however, if the Placement Warrants Required Approvals have been obtained, Third Security Incentive 2010 LLC may receive an additional 19,967 shares of Common Stock upon exercise of the Exchange Right under the Placement Warrant for an aggregate of up to 52,172 shares of Common Stock issuable upon exchange of the Placement Warrant, all of which such Warrant Shares are covered by this prospectus, and (iv) 135,414 shares of Common Stock issuable upon exercise of warrants to purchase Common Stock that are not Placement Warrants and are currently exercisable. The Warrant Blocker will ~~become~~automatically expire 61 calendar days prior to the expiration date of the Placement Warrant. The table above includes a Placement Warrant that is not currently exercisable ~~beginning January 7, 2016~~because of the Warrant Blocker and the Placement Warrants Required Approvals and which is not deemed to be beneficially owned by Third Security Incentive 2010 LLC. Third Security Incentive 2010 LLC is managed by Third Security, which is managed by Mr. Randal J. Kirk. Mr. Randal J. Kirk could be deemed to have indirect beneficial ownership of these shares. The business address of Third Security Incentive 2010 LLC is 1881 Grove Avenue, Radford, Virginia 24141. We are party to the Loan and Security Agreement with affiliates of Third Security. Additionally, Doit L. Koppler II, a director of the Company, is an employee of Third Security and Robert Patzig, a director of the Company, is a former employee of Third Security.
(7)	The number of shares consists of (i) 894,613 shares of Common Stock, (ii) 42,941 shares of Common Stock issuable upon conversion of 42,941 shares of Series A-1 Preferred, which such shares of Common Stock are covered by this prospectus, and (iii) 32,205 shares of Common Stock issuable upon exercise or exchange of a Placement Warrant that is currently exercisable, except to the extent such exercise is restricted by the Warrant Blocker; however, if the Placement Warrants Required Approvals have been obtained, Third Security Staff 2014 LLC may receive an additional 19,967 shares of Common Stock upon exercise of the Exchange Right under the Placement Warrant for an aggregate of up to 52,172 shares of Common Stock issuable upon exchange of the Placement Warrant, all of which such Warrant Shares are covered by this prospectus. The ~~Selling Stockholder indicated~~Warrant Blocker will automatically expire 61 calendar days prior to the expiration date of the Placement Warrant. The table above includes a Placement Warrant that ~~he may~~is not currently exercisable because of the Warrant Blocker and the Placement Warrants Required Approvals and which is not deemed to be beneficially owned by Third Security Staff 2014 LLC. Third Security Staff 2014 LLC is managed by Third Security, which is managed by Mr. Randal J. Kirk. Mr. Randal J. Kirk could be deemed to ~~be an affiliate~~have indirect beneficial ownership of ~~Craig-Hallum Capital Group~~these shares. The business address of Third Security Staff 2014 LLC is 1881 Grove Avenue, Radford, Virginia 24141. We are party to the Loan and Security Agreement with affiliates of Third Security. Additionally, Doit L. Koppler II, a ~~registered broker-dealer. The Selling Stockholder represented that he acquired the Securities in the ordinary course of business and, at the time~~director of the ~~acquisition~~Company, is an employee of Third Security and Robert Patzig, a director of the ~~Securities, had no agreements or understandings, directly or indirectly, with any person to distribute the Securities.~~Company, is a former employee of Third Security.

	(a)	The Registrant’s Annual Report on Form 10-K for the fiscal year ended December 31, 2014, filed with the SEC on April 15, 2015, as amended pursuant to that Amendment No. 1 filed with the SEC on August 14, 2015 and Amendment No. 2 filed with the SEC on August 21, 2015;
	(b)	The Registrant’s Definitive Proxy Statement on Schedule 14A filed with the SEC on April 30, 2015;
	(c)	The Registrant’s Quarterly Report on Form 10-Q for the quarter ended March 31, 2015, filed with the SEC on May 14, 2015;
	(d)	The Registrant’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2015, filed with the SEC on August 14, 2015;
	(e)	The Registrant’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2015, filed with the SEC on November 16, 2015;
	(f)	The Registrant’s Current Reports on Form 8-K filed with the SEC on (i) January 7, 2015, (ii) January 14, 2015, (iii) January 20, 2015, (iv) February 19, 2015, (v) February 27, 2015, (vi) April 2, 2015, (vii) June 3, 2015, (viii) June 9, 2015, (ix) June 22, 2015, ~~and~~ (x) July 1, ~~2015;~~2015, (xi) September 9, 2015, (xii) September 17, 2015, (xiii) September 30, 2015, (xiv) December 1, 2015, (xv) January 11, 2016, filed at 7:30 a.m. Eastern Time, (xvi) January 11, 2016, filed at 7:33 a.m. Eastern Time, and (xvii) January 20, 2016;
	~~(e)~~(g)	The Registrant’s Current Report on Form 8-K/A filed with the SEC on July 7, 2015; and
	~~(f)~~(h)	The description of the Registrant’s common stock set forth in the Registrant’s Registration Statement on Form 8-A (File No. 001-36439), filed with the SEC on May 5, 2014, including any amendments or reports filed for the purpose of updating such description.

SEC registration fee	$	611	$	524
Legal fees and expenses		50,000		25,000
Accounting fees and expenses		5,000		5,000
Printing, transfer agent fees and miscellaneous expenses		5,000		5,000
Total	$	60,611	$	35,524